diff --git a/__init__.py b/__init__.py
index 4b0132c45f452626a336edf603e4ddbd57f34b16..0c594765f9422837b35eabfa5fa5aa4226beda80 100644
--- a/__init__.py
+++ b/__init__.py
@@ -57,6 +57,52 @@ with app.app_context():
if db is not None:
app.config['postgreSQL_pool'].putconn(db)
+
+# Main homepage route
+@app.route('/home_page')
+def home():
+ return render_template('home.html')
+
+# Research page route
+@app.route('/research')
+def research():
+ return render_template('research.html')
+
+# Data sheet page - displays detailed information for individual oligosaccharides
+@app.route('/sheet')
+def sheet():
+ return render_template('sheet.html')
+
+#to upload an oligo structure
+@app.route('/upload_structure', methods=['POST'])
+def upload_structure():
+ if 'file' not in request.files:
+ return jsonify({'error': 'No file part'}), 400
+ file = request.files['file']
+ if file.filename == '':
+ return jsonify({'error': 'No selected file'}), 400
+ if file and allowed_file(file.filename):
+ filename = secure_filename(file.filename)
+ file.save(os.path.join(app.config['UPLOAD_FOLDER'], filename))
+ return jsonify({'success': True, 'filename': filename})
+
+#to save the modifications in the sheet
+@app.route('/save_field', methods=['POST'])
+def save_field():
+ data = request.json
+ field_id = data.get('field_id')
+ value = data.get('value')
+ # Update your database here
+ return jsonify({'success': True})
+
+#to download the sheet
+@app.route('/download_fiche', methods=['POST'])
+def download_fiche():
+ filename = 'fiche_modified.pdf'
+ return jsonify({'success': True, 'filename': filename})
+
+
+
# Home page
@app.route('/index')
def index():
@@ -92,75 +138,154 @@ def demo():
def contact():
return render_template('contact.html')
-# Search by Taxon page (habitat)
+
+
+
+
+##### TEST #####
+# Search by Taxon page (oligo name)
+@app.route('/searchByTaxonForOligosaccharideName/')
+@app.route('/searchByTaxonForOligosaccharideName')
+def searchByTaxonForOligosaccharideName():
+ taxon = request.args.get('taxon', None)
+ oligoname = request.args.get('oligoname', None)
+ return render_template('searchByTaxonForOligosaccharideName.html', taxon=taxon,
+ oligoname=oligoname,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+# Search by Oligo name page
+@app.route('/searchByOligosaccharideName/')
+@app.route('/searchByOligosaccharideName')
+def searchByOligosaccharideName():
+ oligoname = request.args.get('oligoname', None)
+ taxon = request.args.get('taxon', None)
+ return render_template('searchByOligosaccharideName.html', oligoname=oligoname,
+ taxon=taxon,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+
+# Search by Taxon page (oligo type)
+@app.route('/searchByTaxonForOligosaccharideType/')
+@app.route('/searchByTaxonForOligosaccharideType')
+def searchByTaxonForOligosaccharideType():
+ taxon = request.args.get('taxon', None)
+ oligotype = request.args.get('oligotype', None)
+ return render_template('searchByTaxonForOligosaccharideType.html', taxon=taxon,
+ oligotype=oligotype,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+# Search by Oligo type page
+@app.route('/searchByOligosaccharideType/')
+@app.route('/searchByOligosaccharideType')
+def searchByOligosaccharideType():
+ oligotype = request.args.get('oligotype', None)
+ taxon = request.args.get('taxon', None)
+ return render_template('searchByOligosaccharideType.html', oligotype=oligotype,
+ taxon=taxon,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+
+##### FIN TEST #####
+
+# Search by Taxon page (stage)
@app.route('/searchByTaxon/')
@app.route('/searchByTaxon')
def searchByTaxon():
taxon = request.args.get('taxon', None)
- habitat = request.args.get('habitat', None)
- qps = request.args.get('qps', None)
- sources = request.args.getlist("source", None)
+ stage = request.args.get('stage', None)
+ # qps = request.args.get('qps', None)
+ # sources = request.args.getlist("source", None)
return render_template('searchByTaxon.html', taxon=taxon,
- habitat=habitat,
- qps=qps,
- sources=sources,
+ stage=stage,
+ # qps=qps,
+ # sources=sources,
version=VERSION,
alvisir=URL_ALVISIR)
-# Search by Habitat page
-@app.route('/searchByHabitat/')
-@app.route('/searchByHabitat')
-def searchByHabitat():
- habitat = request.args.get('habitat', None)
+# Search by Stage page
+@app.route('/searchByPhysiologicalStage/')
+@app.route('/searchByPhysiologicalStage')
+def searchByPhysiologicalStage():
+ stage = request.args.get('stage', None)
taxon = request.args.get('taxon', None)
- qps = request.args.get('qps', None)
- sources = request.args.getlist("source", None)
- return render_template('searchByHabitat.html', habitat=habitat,
+ # qps = request.args.get('qps', None)
+ # sources = request.args.getlist("source", None)
+ return render_template('searchByPhysiologicalStage.html', stage=stage,
taxon=taxon,
- qps=qps,
- sources=sources,
+ # qps=qps,
+ # sources=sources,
version=VERSION,
alvisir=URL_ALVISIR)
-# Search by Taxon page (phenotype)
-@app.route('/searchByTaxonForPhenotype/')
-@app.route('/searchByTaxonForPhenotype')
-def searchByTaxonForPhenotype():
+
+# Search by Taxon page (postpartum)
+@app.route('/searchByTaxonForPostpartum/')
+@app.route('/searchByTaxonForPostpartum')
+def searchByTaxonForPostpartum():
taxon = request.args.get('taxon', None)
- phenotype = request.args.get('phenotype', None)
- qps = request.args.get('qps', None)
- return render_template('searchByTaxonForPhenotype.html', taxon=taxon,
- phenotype=phenotype,
- qps=qps,
+ postpartum = request.args.get('postpartum', None)
+ # qps = request.args.get('qps', None)
+ return render_template('searchByTaxonForPostpartum.html', taxon=taxon,
+ postpartum=postpartum,
+ # qps=qps,
version=VERSION,
alvisir=URL_ALVISIR)
# Search by Phenotype page
-@app.route('/searchByPhenotype/')
-@app.route('/searchByPhenotype')
-def searchByPhenotype():
- phenotype = request.args.get('phenotype', None)
+@app.route('/searchByPostpartum/')
+@app.route('/searchByPostpartum')
+def searchByPostpartum():
+ postpartum = request.args.get('postpartum', None)
taxon = request.args.get('taxon', None)
- qps = request.args.get('qps', None)
- return render_template('searchByPhenotype.html', phenotype=phenotype,
- taxon=taxon, qps=qps,
+ # qps = request.args.get('qps', None)
+ return render_template('searchByPostpartum.html', postpartum=postpartum,
+ taxon=taxon,
+ # qps=qps,
version=VERSION,
alvisir=URL_ALVISIR)
+
# Search by Taxon page (use)
-@app.route('/searchByTaxonForUse/')
-@app.route('/searchByTaxonForUse')
-def searchByTaxonForUse():
+@app.route('/searchByTaxonForSampleType/')
+@app.route('/searchByTaxonForSampleType')
+def searchByTaxonForSampleType():
taxon = request.args.get('taxon', None)
- use = request.args.get('use', None)
- qps = request.args.get('qps', None)
- return render_template('searchByTaxonForUse.html', taxon=taxon, use=use,
- qps=qps, version=VERSION,
- alvisir=URL_ALVISIR)
-# Search by Use page
-@app.route('/searchByUse/')
-@app.route('/searchByUse')
-def searchByUse():
- use = request.args.get('use', None)
+ sample = request.args.get('sample', None)
+ # qps = request.args.get('qps', None)
+ return render_template('searchByTaxonForSampleType.html', taxon=taxon,
+ sample=sample,
+ # qps=qps,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+# Search by Sample page
+@app.route('/searchBySampleType/')
+@app.route('/searchBySampleType')
+def searchBySampleType():
+ sample = request.args.get('sample', None)
taxon = request.args.get('taxon', None)
- qps = request.args.get('qps', None)
- return render_template('searchByUse.html', use=use, taxon=taxon, qps=qps,
+ # qps = request.args.get('qps', None)
+ return render_template('searchBySampleType.html', sample=sample, taxon=taxon,
+ # qps=qps,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+
+# Search by Taxon page (lactation)
+@app.route('/searchByTaxonForLactation/')
+@app.route('/searchByTaxonForLactation')
+def searchByTaxonForLactation():
+ taxon = request.args.get('taxon', None)
+ lactation = request.args.get('lactation', None)
+ # qps = request.args.get('qps', None)
+ return render_template('searchByTaxonForLactation.html', taxon=taxon,
+ lactation=lactation,
+ # qps=qps,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+# Search by Lactation page
+@app.route('/searchByLactation/')
+@app.route('/searchByLactation')
+def searchByLactation():
+ lactation = request.args.get('lactation', None)
+ taxon = request.args.get('taxon', None)
+ # qps = request.args.get('qps', None)
+ return render_template('searchByLactationStage.html', lactation=lactation, taxon=taxon,
+ # qps=qps,
version=VERSION,
alvisir=URL_ALVISIR)
@@ -293,6 +418,37 @@ def get_taxid():
qps = request.args.get('qps', None)
return(jsonify(list_taxid(app, conn, path, qps)))
+# Database queries (V2)
+@app.route('/_get_stat_entity')
+def get_stat_entity():
+ return(jsonify(stat_entity(app, conn)))
+
+@app.route('/_get/stat_occurrence')
+def get_stat_occurrence():
+ return(jsonify(stat_occurrence(app, conn)))
+
+# @app.route('/_get/nb_occ_by_concept')
+# def get_nb_occ_by_concept():
+# concept = request.args.get('concept', None) # concept = 'Species' or 'Oligosaccharide_type'
+# return(jsonify(fetch_nb_occ_by_concept(app, conn, concept)))
+@app.route('/_get/nb_occ_by_concept')
+def get_nb_occ_by_concept():
+ concept = request.args.get('concept', None) # Exemple : 'Species' ou 'Oligosaccharide_type'
+ if not concept:
+ return jsonify({"error": "Concept parameter is missing"}), 400
+
+ # Appeler la fonction pour récupérer les données
+ results = fetch_nb_occ_by_concept(app, conn, concept)
+ if "error" in results:
+ return jsonify({"error": "Failed to fetch data", "details": results}), 500
+
+ # Formatage des données pour Chart.js
+ labels = list(results.keys())
+ data = list(results.values())
+
+ return jsonify({"labels": labels, "data": data})
+
+
# API
source_choices = ["pubmed", "CIRM-BIA", "CIRM-CFBP", "CIRM-Levures", "dsmz", "genbank"]
qps_choices = ["yes", "no", "true", "false"]
diff --git a/database.py b/database.py
index d409d6cde4410124173790660642e349c8abf5be..dceb3a2e5dc41cbf0c408e55e95816fae08f2a63 100644
--- a/database.py
+++ b/database.py
@@ -18,6 +18,7 @@ import psycopg2
from psycopg2 import pool
import re
from omnicrobe_web.config import *
+import json
# Get Database connection
def get_db(app):
@@ -59,6 +60,67 @@ def get_version(app, conn):
return dict(zip(columns, cursor.fetchall()[0]))
cursor.close()
+# Get statistics: /get/stat*
+def stat_occurrence(app, conn):
+ conn = get_db(app)
+ if conn != None:
+ cursor = conn.cursor()
+ try:
+ cursor.execute("SELECT co_type, count(relation_occurrence.ro_id) \
+ FROM relation_occurrence, concept_occurrence \
+ WHERE relation_occurrence.ro_fk_concept_occurrence_id = concept_occurrence.co_id \
+ GROUP BY concept_occurrence.co_type")
+ except Exception as err:
+ print_psycopg2_exception(err)
+ results = dict()
+ for row in cursor.fetchall():
+ results[row[0]] = row[1]
+ cursor.close()
+ return results
+
+def stat_entity(app, conn):
+ conn = get_db(app)
+ if conn != None:
+ cursor = conn.cursor()
+ try:
+ cursor.execute("SELECT c, sum(n) \
+ FROM ( \
+ SELECT co_type c, count(distinct co_fk_concept_id) n \
+ FROM concept_occurrence GROUP BY co_type \
+ UNION \
+ SELECT co_type, count(distinct co_form_concept) \
+ FROM concept_occurrence WHERE co_fk_concept_id ISNULL \
+ GROUP BY co_type) \
+ GROUP BY c")
+ except Exception as err:
+ print_psycopg2_exception(err)
+ results = dict()
+ for row in cursor.fetchall():
+ results[row[0]] = row[1]
+ cursor.close()
+ return results
+
+# Get occurrence number by concept:
+def fetch_nb_occ_by_concept(app, conn, concept):
+ conn = get_db(app)
+ if conn != None:
+ cursor = conn.cursor()
+ try:
+ cursor.execute("SELECT cn_name, count(distinct co_id) \
+ FROM concept_occurrence, concept, concept_name \
+ WHERE co_type = %s \
+ AND concept_occurrence.co_fk_concept_id = concept.c_id \
+ AND concept.c_id = concept_name.cn_fk_concept_id \
+ GROUP BY concept_name.cn_name", (concept,))
+ except Exception as err:
+ print_psycopg2_exception(err)
+ results = dict()
+ for row in cursor.fetchall():
+ results[row[0]] = row[1]
+ cursor.close()
+ return results
+
+
# Get taxon: /get/taxon
def get_taxon(app, conn, id):
conn = get_db(app)
@@ -605,7 +667,8 @@ def list_relations(app, conn, source, taxonid, qps, ontobiotopeid, types):
if conn != None:
cursor = conn.cursor()
query = "SELECT DISTINCT r.form_taxon, r.form_element, r.id_source, \
- r.type, r.source, e.identifier, t.taxonid, t.qps, e.path, t.path, t.diffusion "
+ r.type, r.source, e.identifier, t.taxonid, t.qps, e.path, t.path, t.diffusion, \
+ e.name, t.name"
query += " FROM relation r, taxon t, element e"
query += " WHERE r.id_element = e.id AND t.id = r.id_taxon"
if source != None and source != []:
@@ -628,6 +691,7 @@ def list_relations(app, conn, source, taxonid, qps, ontobiotopeid, types):
if ontobiotopeid != None and ontobiotopeid != '':
query += " AND r.id_element in (SELECT id FROM element e WHERE e.path like '%/" + ontobiotopeid + "/%' OR e.identifier = '" + ontobiotopeid + "')"
try:
+ print(query)
cursor.execute(query)
except Exception as err:
print_psycopg2_exception(err)
@@ -640,6 +704,18 @@ def list_relations(app, conn, source, taxonid, qps, ontobiotopeid, types):
str_taxforms = clean_form(row[0])
elements.append(str_taxforms)
# relation type
+ if row[3] == 'have_produced_tmp_1':
+ elements.append('Have produced tmp 1')
+ if row[3] == 'have_produced_tmp_2':
+ elements.append('Have produced tmp 2')
+ if row[3] == 'have_produced_1':
+ elements.append('Have produced 1')
+ if row[3] == 'have_produced_2':
+ elements.append('Have produced 2')
+ if row[3] == 'has_given_birth_since':
+ elements.append('Has given birth since')
+ if row[3] == 'has_a_physiological_stage':
+ elements.append('Has a physiological stage')
if row[3] == 'habitat':
if taxonid != None:
elements.append('Lives in')
@@ -671,8 +747,10 @@ def list_relations(app, conn, source, taxonid, qps, ontobiotopeid, types):
elements.append(row[5])
elements.append(row[6])
elements.append(row[10])
- elements.append("")
- elements.append("")
+ # elements.append("")
+ # elements.append("")
+ elements.append(row[11])
+ elements.append(row[12])
results.append(elements)
cursor.close()
return results
diff --git a/static/css/home.css b/static/css/home.css
new file mode 100644
index 0000000000000000000000000000000000000000..fae9b5cef46a92c210d2d570633be3379d46be89
--- /dev/null
+++ b/static/css/home.css
@@ -0,0 +1,143 @@
+body {
+ font-family: 'Roboto', sans-serif;
+ color: #333;
+ background-color: #f8f9fa;
+}
+
+/* Hero Section */
+.hero-section {
+ background: linear-gradient(145deg, #274757, #0077cc);
+ padding: 4rem 0;
+ border-radius: 0 0 2rem 2rem;
+ color: white;
+ margin-top: 40px;
+}
+
+.hero-section h1 {
+ color: black;
+ font-size: 2.8rem;
+ margin-bottom: 1.5rem;
+}
+
+.hero-section .description {
+ max-width: 800px;
+ margin: 0 auto;
+ font-size: 1.2rem;
+ line-height: 1.6;
+ color :black;
+ opacity: 0.95;
+}
+
+.btn-info {
+ background-color: #274757;
+ border: none;
+ padding: 0.8rem 2rem;
+ border-radius: 2rem;
+ font-weight: 500;
+ transition: transform 0.2s;
+}
+
+.btn-info:hover {
+ transform: translateY(-2px);
+ background-color: #274757;
+}
+
+/* Data Overview Section */
+.section-title {
+ font-size: 2.2rem;
+ color: #274757;
+ font-weight: 600;
+}
+
+.visualization-row {
+ margin: 0 -15px;
+}
+
+.viz-card1 {
+ background: white;
+ border-radius: 1rem;
+ padding: 1.5rem;
+ height: 400px;
+ box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
+ transition: transform 0.2s;
+ align-items: center;
+}
+
+
+/* Data Visualization Section */
+.viz-card {
+ background: white;
+ border-radius: 1rem;
+ padding: 1.5rem;
+ height: 400px;
+ box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
+ transition: transform 0.2s;
+ align-items: center;
+ display: flex;
+ flex-direction: column;
+ justify-content: center;
+}
+
+.viz-card canvas {
+ max-width: 100%;
+ margin: 0 auto;
+}
+
+
+#taxonsChart {
+ width: auto;
+ height: auto;
+}
+
+
+.viz-card:hover {
+ transform: translateY(-5px);
+}
+
+.viz-card h3 {
+ color: #274757;
+ font-size: 1.3rem;
+ margin-bottom: 1.5rem;
+ text-align: center;
+}
+
+.table-wrapper {
+ max-height: 300px;
+ overflow-y: auto;
+}
+
+.table {
+ margin-bottom: 0;
+}
+
+.table th {
+ background-color: #274757;
+ color: white;
+ position: sticky;
+ top: 0;
+}
+
+.coming-soon {
+ height: 100%;
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ justify-content: center;
+ color: #888;
+}
+
+.coming-soon i {
+ font-size: 3rem;
+ margin-bottom: 1rem;
+}
+
+@media (max-width: 768px) {
+ .visualization-row {
+ flex-direction: column;
+ }
+
+ .viz-card {
+ margin-bottom: 2rem;
+ }
+}
+
diff --git a/static/css/research.css b/static/css/research.css
new file mode 100644
index 0000000000000000000000000000000000000000..4511e6621bdca39c16ddb33beb9fda9f84474d11
--- /dev/null
+++ b/static/css/research.css
@@ -0,0 +1,273 @@
+
+* {
+ margin: 0;
+ padding: 0;
+ box-sizing: border-box;
+}
+
+body {
+ font-family: 'Arial', sans-serif;
+ line-height: 1.6;
+ background: linear-gradient(180deg, #ffffff, #f0f0f5);
+ color: #333;
+ margin: 0;
+ display: flex;
+ flex-direction: column;
+ min-height: 100vh;
+}
+
+.container2 {
+ flex: 1;
+ display: flex;
+ flex-direction: column;
+ padding: 2rem;
+ gap: 2rem;
+ width: 100%;
+ max-width: 95%;
+ margin-top: 30px;
+ overflow-x: auto;
+}
+
+.main-content2 {
+ padding: 2rem;
+ background: #ffffff;
+ /* border-radius: 10px; */
+ /* box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1); */
+ /* overflow-y: auto; */
+ /* width: 100%;
+ height: 100%; */
+ margin-top: 100px;
+}
+
+/* Search Bar */
+.search-bar2 {
+ display: flex;
+ align-items: center;
+ gap: 1rem;
+ padding: 1.5rem;
+ background: #8eb1b5;
+ border-radius: 10px;
+ box-shadow: 0 2px 8px rgba(0, 0, 0, 0.05);
+ position: relative;
+}
+
+.search-bar2 span {
+ color: #21517A;
+ font-weight: 500;
+ white-space: nowrap;
+}
+
+.search-bar2 select {
+ padding: 0.75rem 1rem;
+ border: 1px solid #ddd;
+ border-radius: 6px;
+ background: #fff;
+ color: #333;
+ font-size: 1rem;
+ cursor: pointer;
+ min-width: 180px;
+ transition: all 0.3s ease;
+}
+
+.search-bar2 select:hover,
+.search-bar2 select:focus {
+ border-color: #3498db;
+ box-shadow: 0 0 0 2px rgba(52, 152, 219, 0.1);
+}
+
+.search-bar2 input {
+ flex: 1;
+ padding: 0.75rem 1rem;
+ border: 1px solid #ddd;
+ border-radius: 6px;
+ font-size: 1rem;
+ transition: all 0.3s ease;
+}
+
+.search-bar2 input:focus {
+ outline: none;
+ border-color: #3498db;
+ box-shadow: 0 0 0 2px rgba(52, 152, 219, 0.1);
+}
+
+/* Autocomplete */
+.autocomplete-box {
+ position: absolute;
+ top: calc(100% - 10px);
+ left: 250px;
+ right: 100px;
+ background: white;
+ border: 1px solid #ddd;
+ border-radius: 0 0 8px 8px;
+ max-height: 200px;
+ overflow-y: auto;
+ z-index: 1000;
+ /* box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1); */
+}
+
+.autocomplete-box div {
+ padding: 0.75rem 1rem;
+ cursor: pointer;
+ transition: all 0.2s ease;
+}
+
+.autocomplete-box div:hover {
+ background-color: #f0f7ff;
+ color: #21517A;
+}
+
+
+/* Table Styles for Large Data */
+.results-section {
+ background: #ffffff;
+ padding: 20px;
+ border-radius: 10px;
+ box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);
+ width: 100%;
+ overflow-x: auto;
+ display: none;
+ /* margin-top: 100px; */
+}
+
+.results-table {
+ width: 100%;
+ border-collapse: collapse;
+ margin-top: 20px;
+ font-size: 1rem;
+ table-layout: fixed;
+}
+
+.results-table th,
+.results-table td {
+ text-align: left;
+ padding: 15px;
+ border: 1px solid #ddd;
+ word-wrap: break-word;
+}
+
+.results-table th {
+ background: #274757;
+ color: white;
+ font-size: 1.1rem;
+ text-transform: uppercase;
+}
+
+.results-table tr:nth-child(even) {
+ background-color: #f9f9f9;
+}
+
+.results-table tr:hover {
+ background-color: #f1f1f1;
+ transition: background-color 0.3s ease;
+}
+
+/* Pagination Styles */
+#pagination {
+ margin-top: 20px;
+ text-align: center;
+}
+
+#pagination button {
+ background: linear-gradient(45deg, #3498db, #2980b9);
+ color: white;
+ border: none;
+ padding: 10px 15px;
+ margin: 0 5px;
+ border-radius: 8px;
+ cursor: pointer;
+ font-size: 1rem;
+ transition: transform 0.3s ease, box-shadow 0.3s ease;
+}
+
+#pagination button.active {
+ background: #2980b9;
+ font-weight: bold;
+}
+
+#pagination button:hover {
+ transform: scale(1.1);
+ box-shadow: 0 4px 8px rgba(0, 0, 0, 0.2);
+}
+
+/* Large Data Adjustments */
+.results-table td {
+ max-width: 300px;
+ white-space: nowrap;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+
+.results-table th:first-child,
+.results-table td:first-child {
+ width: 25%;
+}
+
+.results-table td:hover {
+ overflow: visible;
+ white-space: normal;
+}
+
+
+/* Responsive */
+@media (min-width: 1200px) {
+ .container {
+ max-width: 90%;
+ }
+
+ .main-content {
+ padding: 4rem;
+ }
+}
+
+.info-section {
+ background-color: #f0f7f6;
+ border-radius: 10px;
+ box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);
+ padding: 20px;
+ text-align: center;
+ margin-bottom: 20px;
+}
+
+.info-section {
+ margin-bottom: 10px;
+}
+
+.info-section h2 {
+ font-size: 2rem;
+ color: #21517A;
+}
+
+.info-section p {
+ font-size: 1.1rem;
+ color: #333;
+}
+
+/* Section Getting Started */
+.getting-started {
+ background-color: #f0f7f6;
+ border-radius: 10px;
+ box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);
+ padding: 20px;
+ margin-bottom: 20px;
+}
+
+.getting-started h3 {
+ color: #21517A;
+ font-size: 1.5rem;
+}
+
+.getting-started ul {
+ font-size: 1.1rem;
+ color: #333;
+ text-align: left;
+ margin-top: 10px;
+ padding-left: 20px;
+}
+
+.getting-started ul li {
+ margin-bottom: 10px;
+}
+
+.search-icon i {
+ font-size: 40px;
+}
diff --git a/static/css/sheet.css b/static/css/sheet.css
new file mode 100644
index 0000000000000000000000000000000000000000..eefd291e10aeb544d39b4be8bab250c69775a63b
--- /dev/null
+++ b/static/css/sheet.css
@@ -0,0 +1,186 @@
+* {
+ margin: 0;
+ padding: 0;
+ box-sizing: border-box;
+}
+
+body {
+ font-family: 'Arial', sans-serif;
+ line-height: 1.6;
+ color: #333;
+ background-color: #f5f7fa;
+}
+
+/* Main Layout */
+.main-container {
+ display: flex;
+ min-height: 100vh;
+ background-color: #f5f7fa;
+ margin-top: 40px;
+}
+
+/* Sidebar Navigation */
+.sidebar {
+ width: 250px;
+ background-color: #2c3e50;
+ padding: 2rem 0;
+ flex-shrink: 0;
+ height: 100vh;
+ position: sticky;
+ top: 0;
+}
+
+.nav-menu {
+ list-style: none;
+ padding: 0;
+ margin: 0;
+}
+
+.nav-btn {
+ width: 100%;
+ padding: 1rem 2rem;
+ text-align: left;
+ background: none;
+ border: none;
+ color: #ecf0f1;
+ font-size: 1rem;
+ cursor: pointer;
+ transition: background-color 0.3s;
+}
+
+.nav-btn:hover {
+ background-color: #34495e;
+}
+
+/* Content Area */
+.content {
+ flex-grow: 1;
+ padding: 2rem;
+ max-width: calc(100vw - 250px);
+}
+
+.section {
+ max-width: 1200px;
+ margin: 0 auto;
+}
+
+.section.hidden {
+ display: none;
+}
+
+/* Information Cards */
+.info-card {
+ background-color: #ffffff;
+ border-radius: 8px;
+ box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1);
+ margin-bottom: 2rem;
+ overflow: hidden;
+}
+
+.card-header {
+ padding: 1.5rem;
+ margin: 0;
+ background-color: #f8f9fa;
+ border-bottom: 1px solid #e1e8ed;
+ font-size: 1.25rem;
+ color: #2c3e50;
+ font-weight: 600;
+}
+
+.info-grid {
+ display: grid;
+ grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
+ gap: 1.5rem;
+ padding: 1.5rem;
+}
+
+.info-item {
+ display: flex;
+ flex-direction: column;
+ gap: 0.5rem;
+}
+
+.info-label {
+ font-size: 0.875rem;
+ color: #7f8c8d;
+ font-weight: 500;
+}
+
+.info-value {
+ font-size: 1rem;
+ color: #2c3e50;
+ padding: 0.5rem;
+ background-color: #f8f9fa;
+ border-radius: 4px;
+ min-height: 2.5rem;
+ display: flex;
+ align-items: center;
+}
+
+/* Structure Viewer */
+.structure-viewer {
+ padding: 1.5rem;
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ background-color: #f8f9fa;
+}
+
+.structure-image {
+ max-width: 100%;
+ height: auto;
+ border-radius: 4px;
+ max-height: 400px;
+ object-fit: contain;
+}
+
+/* Action Bar */
+.action-bar {
+ display: flex;
+ justify-content: flex-end;
+ padding: 1rem;
+ background-color: #f8f9fa;
+ border-top: 1px solid #e1e8ed;
+}
+
+.download-btn {
+ padding: 0.75rem 1.5rem;
+ background-color: #3498db;
+ color: white;
+ border: none;
+ border-radius: 4px;
+ cursor: pointer;
+ transition: background-color 0.3s;
+ font-weight: 500;
+}
+
+.download-btn:hover {
+ background-color: #2980b9;
+}
+
+/* Responsive Design */
+@media (max-width: 768px) {
+ .main-container {
+ flex-direction: column;
+ }
+
+ .sidebar {
+ width: 100%;
+ height: auto;
+ position: static;
+ padding: 1rem 0;
+ }
+
+ .content {
+ max-width: 100%;
+ padding: 1rem;
+ }
+
+ .info-grid {
+ grid-template-columns: 1fr;
+ }
+
+ .info-item {
+ padding: 0.5rem;
+ }
+}
\ No newline at end of file
diff --git a/static/img/2'-Fucosyllactose.png b/static/img/2'-Fucosyllactose.png
new file mode 100644
index 0000000000000000000000000000000000000000..3852c228aa130ce91312576f70ce6ec6db51c325
Binary files /dev/null and b/static/img/2'-Fucosyllactose.png differ
diff --git a/static/js/advancedSearch.js b/static/js/advancedSearch.js
index a158cc1b53473b0ea36bef0f6b9cc41bec9728a2..5af855fe9868c38bd6fea6fdc8aa297fdbc3f70d 100644
--- a/static/js/advancedSearch.js
+++ b/static/js/advancedSearch.js
@@ -14,216 +14,226 @@
# limitations under the License.
**/
-import { format_docs } from './utils.js';
+import { format_docs } from "./utils.js";
// Spinner
-$('#spinner_advanced').show();
-$('#spinner_advanced2').show();
+$("#spinner_advanced").show();
+$("#spinner_advanced2").show();
// Fix size input for Selectize
-$('#builder').on('afterCreateRuleInput.queryBuilder', function(e, rule) {
- if (rule.filter.plugin == 'selectize') {
- rule.$el.find('.rule-value-container').css('min-width', '200px')
- .find('.selectize-control').removeClass('form-control');
+$("#builder").on("afterCreateRuleInput.queryBuilder", function (e, rule) {
+ if (rule.filter.plugin == "selectize") {
+ rule.$el
+ .find(".rule-value-container")
+ .css("min-width", "200px")
+ .find(".selectize-control")
+ .removeClass("form-control");
}
});
// Default display
var rules_basic = {
- condition: 'AND',
- rules: [{
- id: 'taxon'
- }
-]
+ condition: "AND",
+ rules: [
+ {
+ id: "taxon",
+ },
+ ],
};
// Options for Selectize
var options = {
allow_empty: false,
// plugins: ['bt-tooltip-errors'],
+ conditions: ["AND", "OR", "NOT"], // Added NOT operator
filters: [
- {
- id: 'taxon',
- label: 'Taxon',
- type: 'string',
- placeholder: 'Bacillus subtilis',
- plugin: 'selectize',
- operators: ['equal'],
- plugin_config: {
- valueField: 'path',
- labelField: 'name',
- searchField: 'name',
- sortField: 'name',
- create: false,
- maxItems: 1,
- onInitialize: function() {
- var that = this;
-
- $.getJSON($SCRIPT_ROOT + '/_get_list_taxon_name',
- function(data) {
- data.forEach(function(item) {
- that.addOption(item);
- });
- $('#spinner_advanced').hide();
- $('#spinner_advanced2').hide();
- });
- }
+ {
+ id: "taxon",
+ label: "Taxon",
+ type: "string",
+ placeholder: "Bacillus subtilis",
+ plugin: "selectize",
+ operators: ["equal", "not_equal"],
+ plugin_config: {
+ valueField: "path",
+ labelField: "name",
+ searchField: "name",
+ sortField: "name",
+ create: false,
+ maxItems: 1,
+ onInitialize: async function () {
+ try {
+ const response = await fetch(
+ `${$SCRIPT_ROOT}/_get_list_taxon_name`
+ );
+ const data = await response.json();
+ data.forEach((item) => this.addOption(item));
+ $("#spinner_advanced, #spinner_advanced2").hide();
+ } catch (error) {
+ console.error("Error loading taxon data:", error);
+ }
+ },
+ },
},
- valueSetter: function(rule, value) {
- rule.$el.find('.rule-value-container input')[0].selectize.setValue(value);
- }
- },
- {
- id: 'habitat',
- label: 'Habitat',
- type: 'string',
- placeholder: 'milk product',
- plugin: 'selectize',
- operators: ['equal'],
- plugin_config: {
- valueField: 'path',
- labelField: 'name',
- searchField: 'name',
- sortField: 'name',
- create: false,
- maxItems: 1,
- onInitialize: function() {
- var that = this;
-
- if (localStorage.ontoHabitat === undefined) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
- { table: 'list_habitat' },
- function(data) {
+ {
+ id: "habitat",
+ label: "Habitat",
+ type: "string",
+ placeholder: "milk product",
+ plugin: "selectize",
+ operators: ["equal", "not_equal"],
+ plugin_config: {
+ valueField: "path",
+ labelField: "name",
+ searchField: "name",
+ sortField: "name",
+ create: false,
+ maxItems: 1,
+ onInitialize: async function () {
+ try {
+ if (!localStorage.ontoHabitat) {
+ const response = await fetch(
+ `${$SCRIPT_ROOT}/_get_list_obt_class`,
+ {
+ method: "POST",
+ headers: { "Content-Type": "application/json" },
+ body: JSON.stringify({ table: "list_habitat" }),
+ }
+ );
+ const data = await response.json();
localStorage.ontoHabitat = JSON.stringify(data);
- data.forEach(function(item) {
- that.addOption(item);
- });
+ data.forEach((item) => this.addOption(item));
+ } else {
+ JSON.parse(localStorage.ontoHabitat).forEach((item) =>
+ this.addOption(item)
+ );
}
- );
- }
- else {
- JSON.parse(localStorage.ontoHabitat).forEach(function(item) {
- that.addOption(item);
- });
- }
- }
+ } catch (error) {
+ console.error("Error loading habitat data:", error);
+ }
+ },
+ },
},
- valueSetter: function(rule, value) {
- rule.$el.find('.rule-value-container input')[0].selectize.setValue(value);
- }
- },
- {
- id: 'phenotype',
- label: 'Phenotype',
- placeholder: 'adherent',
- type: 'string',
- plugin: 'selectize',
- operators: ['equal'],
- plugin_config: {
- valueField: 'path',
- labelField: 'name',
- searchField: 'name',
- sortField: 'name',
- create: false,
- maxItems: 1,
- onInitialize: function() {
- var that = this;
-
- if (localStorage.ontoPhenotype === undefined) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
- { table: 'list_phenotype_taxon' },
- function(data) {
+ {
+ id: "phenotype",
+ label: "Phenotype",
+ placeholder: "adherent",
+ type: "string",
+ plugin: "selectize",
+ operators: ["equal", "not_equal"],
+ plugin_config: {
+ valueField: "path",
+ labelField: "name",
+ searchField: "name",
+ sortField: "name",
+ create: false,
+ maxItems: 1,
+ onInitialize: async function () {
+ try {
+ if (!localStorage.ontoPhenotype) {
+ const response = await fetch(
+ `${$SCRIPT_ROOT}/_get_list_obt_class`,
+ {
+ method: "POST",
+ headers: { "Content-Type": "application/json" },
+ body: JSON.stringify({ table: "list_phenotype_taxon" }),
+ }
+ );
+ const data = await response.json();
localStorage.ontoPhenotype = JSON.stringify(data);
- data.forEach(function(item) {
- that.addOption(item);
- });
+ data.forEach((item) => this.addOption(item));
+ } else {
+ JSON.parse(localStorage.ontoPhenotype).forEach((item) =>
+ this.addOption(item)
+ );
}
- );
- }
- else {
- JSON.parse(localStorage.ontoPhenotype).forEach(function(item) {
- that.addOption(item);
- });
- }
- }
+ } catch (error) {
+ console.error("Error loading phenotype data:", error);
+ }
+ },
+ },
},
- valueSetter: function(rule, value) {
- rule.$el.find('.rule-value-container input')[0].selectize.setValue(value);
- }
- },
- {
- id: 'use',
- label: 'Use',
- placeholder: 'acidification activity',
- type: 'string',
- plugin: 'selectize',
- operators: ['equal'],
- plugin_config: {
- valueField: 'path',
- labelField: 'name',
- searchField: 'name',
- sortField: 'name',
- create: false,
- maxItems: 1,
- onInitialize: function() {
- var that = this;
-
- if (localStorage.ontoUse === undefined) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
- { table: 'list_use_taxon' },
- function(data) {
+ {
+ id: "use",
+ label: "Use",
+ placeholder: "acidification activity",
+ type: "string",
+ plugin: "selectize",
+ operators: ["equal", "not_equal"],
+ plugin_config: {
+ valueField: "path",
+ labelField: "name",
+ searchField: "name",
+ sortField: "name",
+ create: false,
+ maxItems: 1,
+ onInitialize: async function () {
+ try {
+ if (!localStorage.ontoUse) {
+ const response = await fetch(
+ `${$SCRIPT_ROOT}/_get_list_obt_class`,
+ {
+ method: "POST",
+ headers: { "Content-Type": "application/json" },
+ body: JSON.stringify({ table: "list_use_taxon" }),
+ }
+ );
+ const data = await response.json();
localStorage.ontoUse = JSON.stringify(data);
- data.forEach(function(item) {
- that.addOption(item);
- });
+ data.forEach((item) => this.addOption(item));
+ } else {
+ JSON.parse(localStorage.ontoUse).forEach((item) =>
+ this.addOption(item)
+ );
}
- );
- }
- else {
- JSON.parse(localStorage.ontoUse).forEach(function(item) {
- that.addOption(item);
- });
- }
- }
+ } catch (error) {
+ console.error("Error loading use data:", error);
+ }
+ },
+ },
},
- valueSetter: function(rule, value) {
- rule.$el.find('.rule-value-container input')[0].selectize.setValue(value);
- }
- },
- {
- id: 'source',
- label: 'Source',
- type: 'string',
- input: 'checkbox',
- values: {
- 'PubMed': 'PubMed',
- 'GenBank': 'GenBank',
- 'DSMZ': 'DSMZ',
- 'CIRM-BIA': 'CIRM-BIA',
- 'CIRM-CFBP': 'CIRM-CFBP',
- 'CIRM-Levures': 'CIRM-Levures'
+ {
+ id: "source",
+ label: "Source",
+ type: "string",
+ input: "checkbox",
+ operators: ["in", "not_in"],
+ values: {
+ PubMed: "PubMed",
+ GenBank: "GenBank",
+ DSMZ: "DSMZ",
+ "CIRM-BIA": "CIRM-BIA",
+ "CIRM-CFBP": "CIRM-CFBP",
+ "CIRM-Levures": "CIRM-Levures",
+ },
+ default_value: [
+ "PubMed",
+ "GenBank",
+ "DSMZ",
+ "CIRM-BIA",
+ "CIRM-CFBP",
+ "CIRM-Levures",
+ ],
+ operators: ["in"],
},
- default_value: ['PubMed', 'GenBank', 'DSMZ', 'CIRM-BIA', 'CIRM-CFBP', 'CIRM-Levures'],
- operators: ['in'],
- },
- {
- id: 'qps',
- label: 'QPS',
- type: 'string',
- input: 'radio',
- vertical: true,
- values: {
- 'yes': 'only QPS (<i>Qualified presumption of safety</i>)',
- 'no': 'all'
+ {
+ id: "qps",
+ label: "QPS",
+ type: "string",
+ input: "radio",
+ vertical: true,
+ values: {
+ yes: "only QPS (<i>Qualified presumption of safety</i>)",
+ no: "all",
+ },
+ operators: ["equal", "not_equal"],
},
- operators: ['equal']
- }
],
- rules: rules_basic
+ rules: rules_basic,
};
// Query Builder
-var $qb = $("#builder").queryBuilder(options);
+// var $qb = $("#builder").queryBuilder(options);
// function format(d, alvisir) {
//
@@ -249,153 +259,315 @@ var $qb = $("#builder").queryBuilder(options);
// '</table>';
// }
-var thtable = $('#results_advanced').DataTable();
+// var thtable = $('#results_advanced').DataTable();
+
+// Initialize QueryBuilder
+const $qb = $("#builder").queryBuilder(options);
+
+// Initialize DataTable with modern configuration
+let thtable = $("#results_advanced").DataTable({
+ dom: "Bfrtip",
+ responsive: true,
+ buttons: [
+ {
+ extend: "collection",
+ text: "Export",
+ buttons: ["copy", "csv", "excel", "pdf"],
+ },
+ "colvis",
+ ],
+ language: {
+ searchBuilder: {
+ button: "Advanced Search",
+ title: "Advanced Search",
+ data: "Column",
+ condition: "Condition",
+ value: "Value",
+ },
+ },
+});
+
+// Parse query and execute search
+$(".parse-json").on("click", async function () {
+ $("#spinner_advanced, #spinner_advanced2").show();
+
+ try {
+ const queryData = $("#builder").queryBuilder("getSQL");
+ const sql = JSON.parse(JSON.stringify(queryData)).sql;
+
+ // Process NOT conditions
+ const processedSql = processNotConditions(sql);
+
+ const response = await fetch(
+ `${$SCRIPT_ROOT}/_get_list_advanced_relations`,
+ {
+ method: "POST",
+ headers: { "Content-Type": "application/json" },
+ body: JSON.stringify({ query: processedSql }),
+ }
+ );
+
+ const data = await response.json();
+ updateResultsTable(data);
+ } catch (error) {
+ console.error("Error executing search:", error);
+ alert("An error occurred while searching. Please try again.");
+ } finally {
+ $("#spinner_advanced, #spinner_advanced2").hide();
+ }
+});
+
+// Helper function to process NOT conditions
+function processNotConditions(sql) {
+ // Handle NOT operator in SQL query
+ return sql.replace(/NOT\s+([^=]+=[^AND|OR]+)/g, (match, p1) => {
+ return `NOT EXISTS (SELECT 1 WHERE ${p1})`;
+ });
+}
+
+// Update results table with new data
+function updateResultsTable(data) {
+ thtable.clear();
+ thtable.rows.add(data);
+ thtable.draw();
+}
// Create results table
function createTableTest(relations) {
-
- $('#hide').css( 'display', 'block' );
- $('#results_advanced').DataTable().destroy();
- thtable = $('#results_advanced').DataTable(
+ $("#hide").css("display", "block");
+ $("#results_advanced").DataTable().destroy();
+ thtable = $("#results_advanced").DataTable({
+ dom: "lifrtBp",
+ data: relations,
+ buttons: [
+ {
+ extend: "copyHtml5",
+ exportOptions: {
+ columns: function (idx, data, node) {
+ var table_id = node.getAttribute("aria-controls");
+ if (idx == 0) {
+ return false;
+ } // Never Source Text
+ else if (idx == 6) {
+ return true;
+ } // Always Full Source Text
+ return $("#" + table_id)
+ .DataTable()
+ .column(idx)
+ .visible();
+ },
+ },
+ title: "Omnicrobe_V_" + version,
+ },
+ {
+ extend: "csvHtml5",
+ exportOptions: {
+ columns: function (idx, data, node) {
+ var table_id = node.getAttribute("aria-controls");
+ if (idx == 0) {
+ return false;
+ } // Never Source Text
+ else if (idx == 6) {
+ return true;
+ } // Always Full Source Text
+ return $("#" + table_id)
+ .DataTable()
+ .column(idx)
+ .visible();
+ },
+ },
+ title: "Omnicrobe_V_" + version,
+ },
{
- dom: 'lifrtBp',
- data: relations,
- buttons: [
- {
- extend: 'copyHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'csvHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'excelHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'pdfHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- 'colvis'
- ],
- columns: [
- {"render": function(data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- let docs = "";
- if ( data.includes(', ') ) { docs = data.split(', '); }
- else { docs = data.split(','); }
- let docs_f = "";
- if ( docs.length > 2 ) { // 3
- docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
- }
- else {
- docs_f = docids;
- }
- return docs_f;
- }},
- {"render": function ( data, type, row, meta ) {
- let taxa = row[1].split(', ');
- let taxon = taxa[0];
- if ( row[9].includes("ncbi") ) {
- taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ extend: "excelHtml5",
+ exportOptions: {
+ columns: function (idx, data, node) {
+ var table_id = node.getAttribute("aria-controls");
+ if (idx == 0) {
+ return false;
+ } // Never Source Text
+ else if (idx == 6) {
+ return true;
+ } // Always Full Source Text
+ else {
+ return $("#" + table_id)
+ .DataTable()
+ .column(idx)
+ .visible();
}
- else if ( row[9].includes("bd") ) {
- taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ },
+ },
+ title: "Omnicrobe_V_" + version,
+ },
+ {
+ extend: "pdfHtml5",
+ exportOptions: {
+ columns: function (idx, data, node) {
+ var table_id = node.getAttribute("aria-controls");
+ if (idx == 0) {
+ return false;
+ } // Never Source Text
+ else if (idx == 6) {
+ return true;
+ } // Always Full Source Text
+ return $("#" + table_id)
+ .DataTable()
+ .column(idx)
+ .visible();
+ },
+ },
+ title: "Omnicrobe_V_" + version,
+ },
+ "colvis",
+ ],
+ columns: [
+ {
+ render: function (data, type, row, meta) {
+ let rtype = "";
+ if (row[2] == "Lives in" || row[2] == "Contains") {
+ rtype = "habitat";
+ } else if (row[2] == "Studied for" || row[2] == "Involves") {
+ rtype = "use";
+ } else if (row[2] == "Exhibits" || row[2] == "Is exhibited by") {
+ rtype = "phenotype";
+ }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if (data.includes(", ")) {
+ docs = data.split(", ");
+ } else {
+ docs = data.split(",");
+ }
+ let docs_f = "";
+ if (docs.length > 2) {
+ // 3
+ docs_f = docids.split(", ").slice(0, 2).join(", ") + ", ..."; // 0,3
+ } else {
+ docs_f = docids;
+ }
+ return docs_f;
+ },
+ },
+ {
+ render: function (data, type, row, meta) {
+ let taxa = row[1].split(", ");
+ let taxon = taxa[0];
+ if (row[9].includes("ncbi")) {
+ taxon =
+ "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" +
+ row[9].replace(/.+:/gi, "") +
+ "'>" +
+ taxa[0] +
+ "</a>";
+ } else if (row[9].includes("bd")) {
+ taxon =
+ "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/" +
+ row[9].replace(/.+:/gi, "") +
+ "'>" +
+ taxa[0] +
+ "</a>";
+ }
+ return taxon;
+ },
+ },
+ {
+ render: function (data, type, row, meta) {
+ return row[2];
+ },
+ },
+ {
+ render: function (data, type, row, meta) {
+ return row[3].split(",")[0];
+ },
+ },
+ {
+ orderable: false,
+ render: function (data, type, row, meta) {
+ return row[4];
+ },
+ },
+ {
+ render: function (data, type, row, meta) {
+ return row[5];
+ },
+ },
+ {
+ render: function (data, type, row, meta) {
+ let taxs = row[1].split(", ");
+ let forms = "";
+ for (let i = 1; i < taxs.length; i++) {
+ forms += taxs[i];
+ if (i != taxs.length - 1) {
+ forms += ", ";
}
- return taxon;
- }},
- {"render": function (data, type, row, meta) {
- return row[2];
- }},
- {"render": function (data, type, row, meta) {
- return row[3].split(',')[0];
- }},
- {"orderable": false, "render": function (data, type, row, meta) {
- return row[4];
- }},
- {"render": function (data, type, row, meta) {
- return row[5];
- }},
- {"render": function (data, type, row, meta) {
- let taxs = row[1].split(', ');
- let forms = "";
- for ( let i = 1; i < taxs.length ; i++ ) {
- forms += taxs[i]
- if ( i != taxs.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let elts = row[3].split(', ');
- let forms = "";
- for ( let i = 1; i < elts.length ; i++ ) {
- forms += elts[i]
- if ( i != elts.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- return docids;
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[9];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[7];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[8];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[6];
- }}
- ]
- });
+ }
+ return forms;
+ },
+ },
+ {
+ render: function (data, type, row, meta) {
+ let elts = row[3].split(", ");
+ let forms = "";
+ for (let i = 1; i < elts.length; i++) {
+ forms += elts[i];
+ if (i != elts.length - 1) {
+ forms += ", ";
+ }
+ }
+ return forms;
+ },
+ },
+ {
+ render: function (data, type, row, meta) {
+ let rtype = "";
+ if (row[2] == "Lives in" || row[2] == "Contains") {
+ rtype = "habitat";
+ } else if (row[2] == "Studied for" || row[2] == "Involves") {
+ rtype = "use";
+ } else if (row[2] == "Exhibits" || row[2] == "Is exhibited by") {
+ rtype = "phenotype";
+ }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ },
+ },
+ {
+ visible: false,
+ render: function (data, type, row, meta) {
+ return row[9];
+ },
+ },
+ {
+ visible: false,
+ render: function (data, type, row, meta) {
+ return row[7];
+ },
+ },
+ {
+ visible: false,
+ render: function (data, type, row, meta) {
+ return row[8];
+ },
+ },
+ {
+ visible: false,
+ render: function (data, type, row, meta) {
+ return row[6];
+ },
+ },
+ ],
+ });
- $('#spinner_advanced').hide();
- $('#spinner_advanced2').hide();
+ $("#spinner_advanced").hide();
+ $("#spinner_advanced2").hide();
}
-$('.parse-json').on('click', function() {
+$(".parse-json").on("click", function () {
// console.log(JSON.stringify($('#builder').queryBuilder('getSQL'), undefined, 2));
- $('#spinner_advanced').show();
- $('#spinner_advanced2').show();
+ $("#spinner_advanced").show();
+ $("#spinner_advanced2").show();
- var sql = JSON.stringify($('#builder').queryBuilder('getSQL'), undefined, 2);
+ var sql = JSON.stringify($("#builder").queryBuilder("getSQL"), undefined, 2);
sql = JSON.parse(sql).sql;
var sql_f = sql;
@@ -403,22 +575,24 @@ $('.parse-json').on('click', function() {
var regex_s = /source\s(IN\(.+\))/g;
var found_s = sql.match(regex_s);
var list_sources = [];
- if ( found_s != null ) {
+ if (found_s != null) {
var l_source = "";
- for ( let i = 0 ; i < found_s.length ; i++ ) {
- var sources = found_s[i].replace(regex_s, '$1');
- sources = sources.replace('IN(', '');
- sources = sources.replace(')', '');
+ for (let i = 0; i < found_s.length; i++) {
+ var sources = found_s[i].replace(regex_s, "$1");
+ sources = sources.replace("IN(", "");
+ sources = sources.replace(")", "");
l_source = sources.replaceAll("'", "");
}
- if ( l_source != "" ) { list_sources = l_source.split(', '); }
+ if (l_source != "") {
+ list_sources = l_source.split(", ");
+ }
}
// qps
var regex_q = /qps\s=\s'([a-z]+)'/g;
var found_q = sql.match(regex_q);
- if ( found_q != null ) {
- var qps = found_q[0].replace(regex_q, '$1');
+ if (found_q != null) {
+ var qps = found_q[0].replace(regex_q, "$1");
}
// taxon
@@ -427,60 +601,102 @@ $('.parse-json').on('click', function() {
var list_taxid = [];
var list_op_tax = [];
var op_tax = "";
- if ( found_t != null ) {
+ if (found_t != null) {
var l_taxid = "";
- for ( let i = 0 ; i < found_t.length ; i++ ) {
- var op_tax = found_t[i].replace(regex_t, '$1');
- var par_tax_s = found_t[i].replace(regex_t, '$2');
- var path_t = found_t[i].replace(regex_t, '$3'); // $2
- var par_tax_e = found_t[i].replace(regex_t, '$4');
- var id_t = path_t.split('/'); id_t = id_t[id_t.length - 1];
- if ( l_taxid == "" ) { l_taxid = id_t; }
- else { l_taxid += ", " + id_t; }
+ for (let i = 0; i < found_t.length; i++) {
+ var op_tax = found_t[i].replace(regex_t, "$1");
+ var par_tax_s = found_t[i].replace(regex_t, "$2");
+ var path_t = found_t[i].replace(regex_t, "$3"); // $2
+ var par_tax_e = found_t[i].replace(regex_t, "$4");
+ var id_t = path_t.split("/");
+ id_t = id_t[id_t.length - 1];
+ if (l_taxid == "") {
+ l_taxid = id_t;
+ } else {
+ l_taxid += ", " + id_t;
+ }
list_taxid.push(id_t);
- if ( op_tax != "" ) { list_op_tax.push(op_tax); }
- sql_f = sql_f.replace(found_t[i], "r.id_taxon in (SELECT id FROM taxon t WHERE t.path like '%/"+id_t+"/%' OR t.taxonid = '"+id_t+"')");
+ if (op_tax != "") {
+ list_op_tax.push(op_tax);
+ }
+ sql_f = sql_f.replace(
+ found_t[i],
+ "r.id_taxon in (SELECT id FROM taxon t WHERE t.path like '%/" +
+ id_t +
+ "/%' OR t.taxonid = '" +
+ id_t +
+ "')"
+ );
}
}
// habitat | phenotype | use
- var regex_h = /(AND|OR)?\s?(\(?)\s?\b(habitat|phenotype|use)\b\s=\s'([\/A-Z0-9:,]+)'\s?(\)?)/g;
+ var regex_h =
+ /(AND|OR)?\s?(\(?)\s?\b(habitat|phenotype|use)\b\s=\s'([\/A-Z0-9:,]+)'\s?(\)?)/g;
var found_h = sql.match(regex_h);
var list_obtid = [];
var list_op_obt = [];
var op_obt = "";
- if ( found_h != null ) {
+ if (found_h != null) {
var type_obt = "";
var l_obtid = "";
var test = "";
- for ( let i = 0 ; i < found_h.length ; i++ ) {
- var op_obt = found_h[i].replace(regex_h, '$1');
- var par_obt_s = found_h[i].replace(regex_h, '$2');
- var type_obt = found_h[i].replace(regex_h, '$3'); // $2
- var path_h = found_h[i].replace(regex_h, '$4'); // $3
- var par_obt_e = found_h[i].replace(regex_h, '$5');
- var id_h = path_h.split('/'); id_h = id_h[id_h.length - 1];
- if ( op_obt == "AND" && i > 0 ) { test += "INTERSECT "; }
- else if ( op_obt == "OR" && i > 0 ) { test += "UNION "; }
- if ( par_obt_s == "(" ) { test += "("; }
- test += "select distinct(t.taxonid) from taxon t, relation r, element e where r.id_taxon = t.id and r.id_element = e.id ";
- test += "and (e.identifier = '"+id_h+"' or e.path like '%/"+id_h+"/%') ";
- if ( list_taxid[0] != undefined ) {
- test += "and (t.taxonid = '"+list_taxid[0]+"' or t.path like '%/"+list_taxid[0]+"/%') "; }
- if ( qps == "yes" ) { test += "and t.qps = 'yes' "; }
- if ( list_sources.length > 0 ) {
+ for (let i = 0; i < found_h.length; i++) {
+ var op_obt = found_h[i].replace(regex_h, "$1");
+ var par_obt_s = found_h[i].replace(regex_h, "$2");
+ var type_obt = found_h[i].replace(regex_h, "$3"); // $2
+ var path_h = found_h[i].replace(regex_h, "$4"); // $3
+ var par_obt_e = found_h[i].replace(regex_h, "$5");
+ var id_h = path_h.split("/");
+ id_h = id_h[id_h.length - 1];
+ if (op_obt == "AND" && i > 0) {
+ test += "INTERSECT ";
+ } else if (op_obt == "OR" && i > 0) {
+ test += "UNION ";
+ }
+ if (par_obt_s == "(") {
+ test += "(";
+ }
+ test +=
+ "select distinct(t.taxonid) from taxon t, relation r, element e where r.id_taxon = t.id and r.id_element = e.id ";
+ test +=
+ "and (e.identifier = '" +
+ id_h +
+ "' or e.path like '%/" +
+ id_h +
+ "/%') ";
+ if (list_taxid[0] != undefined) {
+ test +=
+ "and (t.taxonid = '" +
+ list_taxid[0] +
+ "' or t.path like '%/" +
+ list_taxid[0] +
+ "/%') ";
+ }
+ if (qps == "yes") {
+ test += "and t.qps = 'yes' ";
+ }
+ if (list_sources.length > 0) {
test += "and r.source in (";
- for ( var k = 0 ; k < list_sources.length ; k++ ) {
+ for (var k = 0; k < list_sources.length; k++) {
test += "'" + list_sources[k] + "'";
}
test += ") ";
}
- if ( par_obt_e == ")" ) { test += ")"; }
- var id_h = path_h.split('/'); id_h = id_h[id_h.length - 1];
- if ( l_obtid == "" ) { l_obtid = id_h; }
- else { l_obtid += ", " + id_h; }
+ if (par_obt_e == ")") {
+ test += ")";
+ }
+ var id_h = path_h.split("/");
+ id_h = id_h[id_h.length - 1];
+ if (l_obtid == "") {
+ l_obtid = id_h;
+ } else {
+ l_obtid += ", " + id_h;
+ }
list_obtid.push(id_h);
- if ( op_obt != "" ) { list_op_obt.push(op_obt); }
+ if (op_obt != "") {
+ list_op_obt.push(op_obt);
+ }
}
}
@@ -488,91 +704,142 @@ $('.parse-json').on('click', function() {
// 1.b. Taxon = subtilis OR taxon = cereus
// 1.c. Taxon = subtilis AND OBT = abdomen
if (
- (list_taxid.length > 1 && list_obtid.length == 0 && op_obt == '' && op_tax == 'OR') ||
- (list_taxid.length == 0 && list_obtid.length > 1 && op_obt == 'OR' && op_tax == '' && (list_op_obt.includes("OR") || list_op_obt.includes("AND"))) ||
- (list_taxid.length == 1 && list_obtid.length == 1 && op_obt != 'OR' && op_tax != 'OR') ||
- (list_taxid.length == 1 && list_obtid.length == 0) ||
- (list_taxid.length == 0 && list_obtid.length == 1)) {
-
- $.getJSON($SCRIPT_ROOT + '/_get_list_advanced_relations',
+ (list_taxid.length > 1 &&
+ list_obtid.length == 0 &&
+ op_obt == "" &&
+ op_tax == "OR") ||
+ (list_taxid.length == 0 &&
+ list_obtid.length > 1 &&
+ op_obt == "OR" &&
+ op_tax == "" &&
+ (list_op_obt.includes("OR") || list_op_obt.includes("AND"))) ||
+ (list_taxid.length == 1 &&
+ list_obtid.length == 1 &&
+ op_obt != "OR" &&
+ op_tax != "OR") ||
+ (list_taxid.length == 1 && list_obtid.length == 0) ||
+ (list_taxid.length == 0 && list_obtid.length == 1)
+ ) {
+ $.getJSON(
+ $SCRIPT_ROOT + "/_get_list_advanced_relations",
{
source: l_source,
taxonid: l_taxid,
qps: qps,
ontobiotopeid: l_obtid,
- type: type_obt
+ type: type_obt,
},
function success(relations) {
createTableTest(relations);
- });
+ }
+ );
}
// 4. Taxon = subtilis OR taxon = cereus AND OBT = abdomen
// 4. OBT = abdomen OR OBT = salt AND taxon = Bacillus_subtilis
- else if ( (list_taxid.length > 1 && list_obtid.length == 1 && ((op_tax == 'OR' && op_obt == 'AND') || (list_op_tax.indexOf('OR') !== -1 && list_op_tax.indexOf('AND') !== -1 && list_op_obt.length == 0))) ) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_advanced_relations',
+ else if (
+ list_taxid.length > 1 &&
+ list_obtid.length == 1 &&
+ ((op_tax == "OR" && op_obt == "AND") ||
+ (list_op_tax.indexOf("OR") !== -1 &&
+ list_op_tax.indexOf("AND") !== -1 &&
+ list_op_obt.length == 0))
+ ) {
+ $.getJSON(
+ $SCRIPT_ROOT + "/_get_list_advanced_relations",
{
source: l_source,
taxonid: l_taxid,
qps: qps,
ontobiotopeid: l_obtid,
- type: type_obt
+ type: type_obt,
},
function success(relations) {
createTableTest(relations);
- });
+ }
+ );
}
// 2.a. Taxon = subtilis OR OBT = abdomen
// 2.b. Taxon = subtilis OR taxon = cereus OR OBT = abdomen
- else if ( (list_taxid.length > 1 && list_obtid.length == 1 && op_tax != 'AND' && op_obt != 'AND' && par_tax_e == "") ||
- (list_taxid.length == 1 && list_obtid.length > 1 && op_tax != 'AND' && op_obt != 'AND' && par_obt_e == "") ||
- (list_taxid.length >= 1 && list_obtid.length >= 1 && (op_tax == 'OR' || op_obt == 'OR') && list_op_obt.indexOf('AND') == -1 && list_op_tax.indexOf('AND') == -1)) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_advanced_relations_2',
+ else if (
+ (list_taxid.length > 1 &&
+ list_obtid.length == 1 &&
+ op_tax != "AND" &&
+ op_obt != "AND" &&
+ par_tax_e == "") ||
+ (list_taxid.length == 1 &&
+ list_obtid.length > 1 &&
+ op_tax != "AND" &&
+ op_obt != "AND" &&
+ par_obt_e == "") ||
+ (list_taxid.length >= 1 &&
+ list_obtid.length >= 1 &&
+ (op_tax == "OR" || op_obt == "OR") &&
+ list_op_obt.indexOf("AND") == -1 &&
+ list_op_tax.indexOf("AND") == -1)
+ ) {
+ $.getJSON(
+ $SCRIPT_ROOT + "/_get_list_advanced_relations_2",
{
source: l_source,
taxonid: l_taxid,
qps: qps,
ontobiotopeid: l_obtid,
- type: type_obt
+ type: type_obt,
},
function success(relations) {
createTableTest(relations);
- });
+ }
+ );
}
// 3.a. Taxon = subtilis AND taxon = cereus / OBT = abdomen AND OBT = salt
// 3.b. Taxon = subtilis AND taxon = cereus AND OBT = abdomen / OBT = abdomen AND OBT = salt AND taxon = subtilis
- else if ( (list_taxid.length > 1 && list_obtid.length == 0 && op_tax == 'AND' && op_obt == '') ||
- (list_taxid.length == 0 && list_obtid.length > 1 && op_tax == '' && op_obt == 'AND') ||
- (list_taxid.length > 1 && list_obtid.length == 1 && op_tax == 'AND' && op_obt != 'OR') ||
- (list_taxid.length == 1 && list_obtid.length > 1 && op_tax != 'OR' && ["AND","OR"].includes(op_obt)) ) {
-
- if ( test != null ) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_advanced_relations_4',
+ else if (
+ (list_taxid.length > 1 &&
+ list_obtid.length == 0 &&
+ op_tax == "AND" &&
+ op_obt == "") ||
+ (list_taxid.length == 0 &&
+ list_obtid.length > 1 &&
+ op_tax == "" &&
+ op_obt == "AND") ||
+ (list_taxid.length > 1 &&
+ list_obtid.length == 1 &&
+ op_tax == "AND" &&
+ op_obt != "OR") ||
+ (list_taxid.length == 1 &&
+ list_obtid.length > 1 &&
+ op_tax != "OR" &&
+ ["AND", "OR"].includes(op_obt))
+ ) {
+ if (test != null) {
+ $.getJSON(
+ $SCRIPT_ROOT + "/_get_list_advanced_relations_4",
{
test: test,
source: l_source,
taxonid: l_taxid,
- ontobiotopeid: l_obtid
+ ontobiotopeid: l_obtid,
},
function success(relations) {
createTableTest(relations);
- });
- }
- else {
+ }
+ );
+ } else {
alert("Not implemented ! In progress ...");
createTableTest([]);
}
- }
-
- else {
+ } else {
alert("Not implemented ! In progress ...");
createTableTest([]);
}
- $('#divQuery').show();
- $('#queryDisabled').val(JSON.stringify($('#builder').queryBuilder('getSQL'), undefined, 2));
+ $("#divQuery").show();
+ $("#queryDisabled").val(
+ JSON.stringify($("#builder").queryBuilder("getSQL"), undefined, 2)
+ );
});
// $('#results_advanced tbody').on('click', 'td.details-control', function () {
diff --git a/static/js/home.js b/static/js/home.js
new file mode 100644
index 0000000000000000000000000000000000000000..ea3cfe4283a70e74d887361ceeda40c6d0b7f464
--- /dev/null
+++ b/static/js/home.js
@@ -0,0 +1,110 @@
+//table displaying statistics for each entity
+document.addEventListener("DOMContentLoaded", function () {
+ // The API URL from which we are fetching the JSON data
+ const apiUrl = '/_get/stat_occurrence';
+
+ // Fetching the JSON data from the API
+ fetch(apiUrl)
+ .then((response) => response.json()) // Convert the API response to JSON
+ .then((data) => {
+
+ // Log the received data to the console for verification
+ console.log("Data received from the API:", data);
+
+ // Check if the data is empty or null
+ if (!data || Object.keys(data).length === 0) {
+ throw new Error("The data from the API is empty or invalid.");
+ }
+
+ // Initialize an object to store role statistics
+ const rolesStats = {};
+
+ // Iterate over the data and populate the rolesStats object
+ Object.keys(data).forEach((key) => {
+ rolesStats[key] = data[key];
+ });
+
+ // Get the table body element where we will display the data
+ const entitiesTableBody = document.getElementById("entitiesTableBody");
+
+ // Iterate over the rolesStats object and create table rows for each entity
+ Object.keys(rolesStats).forEach((entity) => {
+ const row = document.createElement("tr");
+ const cell1 = document.createElement("td");
+ const cell2 = document.createElement("td");
+
+ // Set the content of the cells
+ cell1.textContent = entity;
+ cell2.textContent = rolesStats[entity];
+
+ // Append the cells to the row
+ row.appendChild(cell1);
+ row.appendChild(cell2);
+
+ // Append the row to the table body
+ entitiesTableBody.appendChild(row);
+ });
+ })
+ .catch((error) => {
+ console.error("Error fetching the JSON data:", error);
+ });})
+
+
+ // Event listener that triggers when the DOM is fully loaded
+ document.addEventListener("DOMContentLoaded", function () {
+ // Get the context of the canvas where the chart will be drawn
+ const taxonsCtx = document.getElementById("taxonsChart").getContext("2d");
+ // Function to fetch taxon data from the API
+ function fetchTaxonData() {
+ const apiUrl = "/_get/nb_occ_by_concept?concept=Oligosaccharide_type";
+ fetch(apiUrl)
+ .then((response) => {
+ if (!response.ok) {
+ throw new Error(`HTTP error! status: ${response.status}`);
+ }
+ return response.json();
+ })
+ .then((data) => {
+ if (!data.labels || !data.data || data.labels.length !== data.data.length) {
+ throw new Error("The structure of fetched data is invalid.");
+ }
+ // Create the chart with the fetched data
+ const taxonsChart = new Chart(taxonsCtx, {
+ type: "pie",
+ data: {
+ labels: data.labels,
+ datasets: [
+ {
+ label: "Number of occurrences",
+ data: data.data,
+ backgroundColor: [
+ "#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F"
+ ],
+ borderColor: "#ffffff",
+ borderWidth: 2,
+ },
+ ],
+ },
+ options: {
+ responsive: true,
+ plugins: {
+ legend: {
+ position: "top",
+ labels: {
+ font: {
+ size: 14,
+ },
+ },
+ },
+ },
+ },
+ });
+ })
+ .catch((error) => {
+ console.error("Error while fetching the data :", error);
+ alert("An error occurred while loading the data. Please try again later.");
+ });
+ }
+
+ fetchTaxonData();
+ });
\ No newline at end of file
diff --git a/static/js/research.js b/static/js/research.js
new file mode 100644
index 0000000000000000000000000000000000000000..2e540c7d3383a6861b2d0549b01207d8cca1b3b6
--- /dev/null
+++ b/static/js/research.js
@@ -0,0 +1,386 @@
+// ========================= Mock Data =========================
+// Sample data used for demonstrating search and pagination functionality
+const dummyData = [
+ {
+ oligosaccharide: {
+ name: "2'-Fucosyllactose",
+ url: "https://pubmed.ncbi.nlm.nih.gov/30149573/"
+ },
+ oligosaccharide_type: "Fucosylated" ,
+ sample: "Milk Sample A-123 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",
+ species: "Human",
+ descendants: ["Homo sapiens sapiens", "Homo erectus"],
+ lactationStage: "Early",
+ },
+ {
+ oligosaccharide: {
+ name: "3'-Sialyllactose (3'-SL)",
+ url : null
+ },
+ oligosaccharide_type: "Sialylated",
+ sample: "Milk Sample B-456",
+ species: "Cow",
+ descendants: null,
+ lactationStage: "Mid",
+ },
+
+
+ {
+ oligosaccharide: {
+ name: "3'-Sialyllactose (3'-SL)",
+ url : null
+ },
+ oligosaccharide_type: "Sialylated",
+ sample: "Milk Sample B-456",
+ species: "homo sapiens",
+ descendants: null,
+ lactationStage: "Mid",
+ },
+
+
+ {
+ oligosaccharide: {
+ name: "6'-Sialyllactose (6'-SL)",
+ url : null,
+ },
+ oligosaccharide_type: "Sialylated" ,
+ sample: "Milk Sample C-789",
+ species: "Goat",
+ descendants: null,
+ lactationStage: "Late",
+ },
+ {
+ oligosaccharide: {
+ name : "Lacto-N-tetraose (LNT)",
+ url : null
+ },
+ oligosaccharide_type: "Lacto-N",
+ sample: "Milk Sample D-101",
+ species: "Human",
+ lactationStage: "Early",
+ },
+ {
+ oligosaccharide: {
+ name : "Lacto-N-neotetraose (LNnT)",
+ url : null
+ },
+ oligosaccharide_type: "Lacto-N",
+ sample: "Milk Sample E-112",
+ species: "Human",
+ lactationStage: "Mid",
+ },
+ {
+ oligosaccharide: {
+ name : "Lacto-N-fucopentaose I (LNFP-I)",
+ url : null
+ },
+ oligosaccharide_type: "Lacto-N",
+ sample: "Milk Sample F-131",
+ species: "Human",
+ lactationStage: "Late",
+ },
+ {
+ oligosaccharide: {
+ name : "3'-Galactosyllactose (3'-GL)",
+ url : null,
+ },
+ oligosaccharide_type: "Galactosylated",
+ sample: "Milk Sample G-415",
+ species: "Rabbit",
+ descendants: null,
+ lactationStage: "Early",
+ },
+ {
+ oligosaccharide: {
+ name : "4'-Galactosyllactose (4'-GL)",
+ url : null
+ },
+ oligosaccharide_type: "Galactosylated",
+ sample: "Milk Sample H-521",
+ species: "Rabbit",
+ descendants: null,
+ lactationStage: "Mid",
+ },
+ {
+ oligosaccharide: {
+ name : "Sialyl-lacto-N-tetraose a (LSTa)",
+ url : null,
+ },
+ oligosaccharide_type: "Sialylated",
+ sample: "Milk Sample I-634",
+ species: "Sheep",
+ descendants: null,
+ lactationStage: "Early",
+ },
+ {
+ oligosaccharide: {
+ name : "Sialyl-lacto-N-tetraose b (LSTb)",
+ url : null,
+
+ },
+ oligosaccharide_type: "Sialylated",
+ sample: "Milk Sample J-747",
+ species: "Sheep",
+ lactationStage: "Mid",
+ },
+ {
+ oligosaccharide: {
+ name : "Sialyl-lacto-N-tetraose c (LSTc)",
+ url : null,
+ },
+ oligosaccharide_type : "Sialylated",
+ sample: "Milk Sample K-858",
+ species: "Horse",
+ descendants: null,
+ lactationStage: "Late",
+ }
+];
+
+// ========================= Global Variables =========================
+// Global variables to store the current dataset and manage pagination
+let currentData = [...dummyData];
+let currentPage = 1;
+const resultsPerPage = 5;
+
+// ========================= Simple Search =========================
+// Initialize DOM elements for simple search functionality
+const searchInput = document.getElementById('simple-search');
+const searchButton = document.querySelector('#simple-search-section .search-btn');
+const suggestionBox = document.getElementById('suggestion-box');
+let activeIndex = -1; // Active index for navigating through suggestions
+
+// Main function to perform a simple search
+function performSimpleSearch() {
+ const searchType = document.getElementById('simple-search-type').value; // Type of search (e.g., name, species)
+ const searchQuery = searchInput.value.toLowerCase().trim();
+ if (!searchQuery) {
+ // If no keyword, reset results to the full dataset
+ currentData = [...dummyData];
+ populateResults(currentData);
+ return;
+ }
+
+ // Filter the data based on the search type and query
+ const filteredData = dummyData.filter(item => {
+ switch (searchType) {
+ case 'oligosaccharide_name':
+ return item.oligosaccharide.name.toLowerCase().includes(searchQuery);
+ case 'species':
+ return (item.species.toLowerCase().includes(searchQuery) ||
+ (item.descendants && item.descendants.some(desc => desc.toLowerCase().includes(searchQuery)))
+ );
+ case 'samples':
+ return item.sample.toLowerCase().includes(searchQuery);
+ case 'lactation-stage':
+ return item.lactationStage.toLowerCase().includes(searchQuery);
+ case 'oligosaccharide_type':
+ return item.oligosaccharide_type.toLowerCase().includes(searchQuery);
+ default:
+ return true;
+ }
+ });
+
+ // Update the current data and refresh the results table
+ currentData = filteredData;
+ populateResults(filteredData);
+}
+
+// ========================= Autocomplete =========================
+// Function to provide suggestions for simple search input
+function autocompleteSearch(query) {
+ if (!query) {
+ // Clear suggestions if query is empty
+ document.getElementById('autocomplete-suggestions').innerHTML = '';
+ return;
+ }
+
+ const searchType = document.getElementById('simple-search-type').value;
+ const suggestions = new Set();
+ const queryLower = query.toLowerCase();
+
+ // Generate suggestions based on search type
+ dummyData.forEach(item => {
+ let value = '';
+ switch (searchType) {
+ case 'oligosaccharide_name':
+ value = item.oligosaccharide.name;
+ break;
+ case 'oligosaccharide_type':
+ value = item.oligosaccharide_type;
+ break;
+ case 'species':
+ // Include both species and descendants in suggestions
+ value = item.species;
+ if (value.toLowerCase().includes(queryLower)) suggestions.add(value);
+ if (item.descendants) {
+ item.descendants.forEach(desc => {
+ if (desc.toLowerCase().includes(queryLower)) suggestions.add(desc);
+ });
+ }
+ break;
+ case 'samples':
+ value = item.sample;
+ break;
+ case 'lactation-stage':
+ value = item.lactationStage;
+ break;
+ }
+ if (value.toLowerCase().includes(queryLower)) {
+ suggestions.add(value);
+ }
+ });
+
+ // Update the suggestions box with the filtered suggestions
+ const suggestionBox = document.getElementById('autocomplete-suggestions');
+ suggestionBox.innerHTML = '';
+ activeIndex = -1;
+
+ if (suggestions.size > 0) {
+ Array.from(suggestions)
+ .slice(0, 5)
+ .forEach(item => {
+ const div = document.createElement('div');
+ div.textContent = item;
+ div.onclick = () => {
+ searchInput.value = item;
+ suggestionBox.innerHTML = '';
+ performSimpleSearch();
+ };
+ suggestionBox.appendChild(div);
+ });
+ }
+
+}
+
+// ========================= Pagination =========================
+// Function to paginate results based on the current page and results per page
+function paginateResults(data) {
+ const start = (currentPage - 1) * resultsPerPage;
+ const end = start + resultsPerPage;
+ return data.slice(start, end);
+}
+
+// Function to render pagination buttons
+function renderPagination(totalItems) {
+ const paginationElement = document.getElementById('pagination');
+ paginationElement.innerHTML = '';
+
+ const totalPages = Math.ceil(totalItems / resultsPerPage);
+ for (let i = 1; i <= totalPages; i++) {
+ const button = document.createElement('button');
+ button.textContent = i;
+ button.className = i === currentPage ? 'active' : '';
+ button.onclick = () => {
+ currentPage = i;
+ populateResults(currentData);
+ };
+ paginationElement.appendChild(button);
+ }
+}
+
+// ========================= Results Table =========================
+// Function to populate the results table with the given data
+function populateResults(data) {
+ const resultsBody = document.getElementById("results-body");
+ const paginatedData = paginateResults(data);
+ resultsBody.innerHTML = "";
+
+ if (data.length === 0) {
+ const row = document.createElement("tr");
+ row.innerHTML = `
+ <td colspan="5" style="text-align: center; padding: 20px;">
+ No results found. Please try a different search.
+ </td>
+ `;
+ resultsBody.appendChild(row);
+ return;
+ }
+
+ // Create table rows for each item in the paginated data
+ paginatedData.forEach((item) => {
+ const oligosaccharideContent = item.oligosaccharide.url
+ ? `<a href="${item.oligosaccharide.url}" target="_blank">${item.oligosaccharide.name}</a>`
+ : item.oligosaccharide.name;
+
+ const row = document.createElement("tr");
+ row.innerHTML = `
+ <td>${oligosaccharideContent}</td>
+ <td>${item.oligosaccharide_type}</td>
+ <td>${item.sample}</td>
+ <td>${item.species}</td>
+ <td>${item.lactationStage}</td>
+ <td><button class="details-btn" onclick="showDetails('${item.oligosaccharide.name}')">Details</button></td>
+ `;
+ resultsBody.appendChild(row);
+ });
+
+ // Render pagination buttons
+ renderPagination(data.length);
+}
+
+// ========================= Additional Features =========================
+// Redirect to a details page with the selected oligosaccharide
+function showDetails(oligosaccharideName) {
+ window.location.href = `sheet?oligosaccharide=${encodeURIComponent(oligosaccharideName)}`;
+}
+
+// Toggle visibility of extra information
+function toggleExtraInfo(button) {
+ const extraInfo = button.nextElementSibling;
+ if (extraInfo.style.display === "none") {
+ extraInfo.style.display = "block";
+ button.textContent = "-";
+ } else {
+ extraInfo.style.display = "none";
+ button.textContent = "+";
+ }
+}
+
+// Sort table data by the selected column
+function sortTable(columnIndex) {
+ const sortedData = [...currentData].sort((a, b) => {
+ const valueA = Object.values(a)[columnIndex]?.toString().toLowerCase() || '';
+ const valueB = Object.values(b)[columnIndex]?.toString().toLowerCase() || '';
+ return valueA.localeCompare(valueB);
+ });
+ populateResults(sortedData);
+}
+
+// ========================= Initialization =========================
+// Initialize the page and set up event listeners on page load
+window.onload = function() {
+ currentData = [...dummyData];
+ populateResults(currentData);
+};
+
+function showSimpleSearchResults() {
+ const searchType = document.getElementById('simple-search-type').value;
+ const searchKeyword = document.getElementById('simple-search').value;
+
+ if (searchKeyword.trim() === '') {
+ alert('Please enter a keyword!');
+ return;
+ }
+
+ const resultsSection = document.getElementById('results-section');
+ resultsSection.style.display = 'block';
+
+ console.log(`Search by ${searchType} with keyword "${searchKeyword}"`);
+ }
+
+// This script toggles the visibility of table columns based on checkbox selections.
+ document.querySelectorAll('#column-toggles input[type="checkbox"]').forEach((checkbox) => {
+ checkbox.addEventListener('change', function () {
+ const column = this.dataset.column;
+ const table = document.querySelector('.results-table');
+ const rows = table.querySelectorAll('tr');
+
+ rows.forEach((row) => {
+ const cells = row.querySelectorAll('th, td');
+ if (cells[column]) {
+ cells[column].style.display = this.checked ? '' : 'none';
+ }
+ });
+ });
+ });
+
\ No newline at end of file
diff --git a/static/js/searchByLactationStage.js b/static/js/searchByLactationStage.js
new file mode 100644
index 0000000000000000000000000000000000000000..7b34d5911bf1aa7e1a571b721c71501c366a6583
--- /dev/null
+++ b/static/js/searchByLactationStage.js
@@ -0,0 +1,199 @@
+taxon_lt/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTableRev, createTableWithArgRev } from './utils.js';
+
+$("#searchByLactation.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_lactation_taxon').show();
+$('#spinner_lactation_taxon2').show();
+
+var thtable = $('#results_lactation_taxon').DataTable();
+
+var $select = $('#search_lactation').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Colostrum',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_lactation_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_lactation_taxon').hide();
+ $('#spinner_lactation_taxon2').hide();
+ $('#search_lactation option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_lactation_taxon').removeAttr('disabled');
+ $('#spinner_lactation_taxon').show();
+ $('#spinner_lactation_taxon2').show();
+
+ createTableRev(value, 'have_produced_2', 'results_lactation_taxon');
+
+ if ( $('#taxon_lt').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_lactation_taxon').hide();
+ $('#spinner_lactation_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_lactation_taxon').hide();
+ $('#spinner_lactation_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByLactation").val("");
+ $('#filter_lactation_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( lactation !== null ) {
+ $('#spinner_lactation_taxon').show();
+ $('#spinner_lactation_taxon2').show();
+ selectize.setTextboxValue(lactation);
+ $("#search_lactation option:selected").text(lactation);
+ $("#search_lactation option:selected").val(lactation);
+ $('#filter_lactation_taxon').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_lactation_taxon'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let lactationid = l_path[l_path.length-1];
+
+ createTableWithArgRev(lactationid, 'have_produced_2', 'results_lactation_taxon');
+
+ if ( $('#taxon_lt').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_lactation_taxon').hide();
+ $('#spinner_lactation_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_lactation_taxon').hide();
+ $('#spinner_lactation_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByLactation").val("");
+ $('#filter_lactation_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: sources
+// if ( sources !== null ) {
+// $('input.column_source').val(sources.join(";"));
+// }
+// URL: lactation
+if ( taxon !== null ) {
+ $('input.column_filter').val(taxon);
+}
+
+// Filter - taxon
+function filterColumntaxon(i) {
+ $('#results_lactation_taxon').DataTable().column(i).search(
+ $('#taxon_lt').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumntaxon($(this).parents('tr').attr('data-column'));
+} );
+
+// Filter - QPS
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_th]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_stage').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
+
+ // Filter - Sources
+// function filterSourceColumn(i) {
+// $('#results_taxon_stage').DataTable().column(i).search(
+// $('#sources_th').val().replace(/;/g, "|"), true, false
+// ).draw();
+// checkURL();
+// }
+// $('input.column_source').on( 'keyup click', function () {
+// filterSourceColumn(5);
+// });
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_lactation option:selected").text() !== '' ) {
+ url += "?lactation=" + $("#search_lactation option:selected").text();
+ }
+ if ( $("#taxon_lt").val() !== '' ) {
+ url += "&taxon=" + $("#taxon_lt").val();
+ }
+ // if ( $('#qps_th').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ // if ( $("#sources_th").val() !== '' ) {
+ // if ( $("#sources_th").val().includes(";") ) {
+ // let list = $("#sources_th").val().split(";");
+ // for (let s = 0 ; s < list.length ; s++ ) {
+ // if ( list[s] != '' ) {
+ // url += "&source=" + list[s];
+ // }
+ // }
+ // }
+ // else {
+ // url += "&source=" + $("#sources_th").val();
+ // }
+ // }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByOligosaccharideName.js b/static/js/searchByOligosaccharideName.js
new file mode 100644
index 0000000000000000000000000000000000000000..fee6d1c15cf22ec92171bf15539bf0427778c922
--- /dev/null
+++ b/static/js/searchByOligosaccharideName.js
@@ -0,0 +1,146 @@
+taxon_lt/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTableRev, createTableWithArgRev } from './utils.js';
+
+$("#searchByOligosaccharideName.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_oligoname_taxon').show();
+$('#spinner_oligoname_taxon2').show();
+
+var thtable = $('#results_oligoname_taxon').DataTable();
+
+var $select = $('#search_oligoname').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Isoglobotriose',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_oligo_name_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_oligoname_taxon').hide();
+ $('#spinner_oligoname_taxon2').hide();
+ $('#search_oligoname option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_oligoname_taxon').removeAttr('disabled');
+ $('#spinner_oligoname_taxon').show();
+ $('#spinner_oligoname_taxon2').show();
+
+ createTableRev(value, 'have_produced_tmp_1', 'results_oligoname_taxon');
+
+ if ( $('#taxon_lt').val() != '' ) { filterColumntaxon(3); }
+
+ $('#spinner_oligoname_taxon').hide();
+ $('#spinner_oligoname_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_oligoname_taxon').hide();
+ $('#spinner_oligoname_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByOligosaccharideName").val("");
+ $('#filter_oligoname_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( oligoname !== null ) {
+ $('#spinner_oligoname_taxon').show();
+ $('#spinner_oligoname_taxon2').show();
+ selectize.setTextboxValue(oligoname);
+ $("#search_oligoname option:selected").text(oligoname);
+ $("#search_oligoname option:selected").val(oligoname);
+ $('#filter_oligoname_taxon').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_oligo_name_taxon'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let oligonameid = l_path[l_path.length-1];
+
+ createTableWithArgRev(oligonameid, 'have_produced_2', 'results_oligoname_taxon');
+
+ if ( $('#taxon_lt').val() != '' ) { filterColumntaxon(3); }
+
+ $('#spinner_oligoname_taxon').hide();
+ $('#spinner_oligoname_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_oligoname_taxon').hide();
+ $('#spinner_oligoname_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByOligosaccharideName").val("");
+ $('#filter_oligoname_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: oligoname
+if ( taxon !== null ) {
+ $('input.column_filter').val(taxon);
+}
+
+// Filter - taxon
+function filterColumntaxon(i) {
+ $('#results_oligoname_taxon').DataTable().column(i).search(
+ $('#taxon_lt').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumntaxon($(this).parents('tr').attr('data-column'));
+} );
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_oligoname option:selected").text() !== '' ) {
+ url += "?oligoname=" + $("#search_oligoname option:selected").text();
+ }
+ if ( $("#taxon_lt").val() !== '' ) {
+ url += "&taxon=" + $("#taxon_lt").val();
+ }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByOligosaccharideType.js b/static/js/searchByOligosaccharideType.js
new file mode 100644
index 0000000000000000000000000000000000000000..fb80fdc320ebeaa99ddb2630283717fdbf637d5c
--- /dev/null
+++ b/static/js/searchByOligosaccharideType.js
@@ -0,0 +1,146 @@
+taxon_lt/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTableRev, createTableWithArgRev } from './utils.js';
+
+$("#searchByOligosaccharideType.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_oligotype_taxon').show();
+$('#spinner_oligotype_taxon2').show();
+
+var thtable = $('#results_oligotype_taxon').DataTable();
+
+var $select = $('#search_oligotype').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Fucosylated',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_oligo_type_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_oligotype_taxon').hide();
+ $('#spinner_oligotype_taxon2').hide();
+ $('#search_oligotype option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_oligotype_taxon').removeAttr('disabled');
+ $('#spinner_oligotype_taxon').show();
+ $('#spinner_oligotypee_taxon2').show();
+
+ createTableRev(value, 'have_produced_tmp_2', 'results_oligotype_taxon');
+
+ if ( $('#taxon_lt').val() != '' ) { filterColumntaxon(3); }
+
+ $('#spinner_oligotype_taxon').hide();
+ $('#spinner_oligotype_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_oligotype_taxon').hide();
+ $('#spinner_oligotype_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByOligosaccharideType").val("");
+ $('#filter_oligotype_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( oligotype !== null ) {
+ $('#spinner_oligotype_taxon').show();
+ $('#spinner_oligotype_taxon2').show();
+ selectize.setTextboxValue(oligotype);
+ $("#search_oligotype option:selected").text(oligotype);
+ $("#search_oligotype option:selected").val(oligotype);
+ $('#filter_oligotype_taxon').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_oligo_type_taxon'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let oligotypeid = l_path[l_path.length-1];
+
+ createTableWithArgRev(oligotypeid, 'have_produced_2', 'results_oligotype_taxon');
+
+ if ( $('#taxon_lt').val() != '' ) { filterColumntaxon(3); }
+
+ $('#spinner_oligotype_taxon').hide();
+ $('#spinner_oligotype_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_oligotype_taxon').hide();
+ $('#spinner_oligotype_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByOligosaccharideType").val("");
+ $('#filter_oligotype_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: oligotype
+if ( taxon !== null ) {
+ $('input.column_filter').val(taxon);
+}
+
+// Filter - taxon
+function filterColumntaxon(i) {
+ $('#results_oligotype_taxon').DataTable().column(i).search(
+ $('#taxon_lt').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumntaxon($(this).parents('tr').attr('data-column'));
+} );
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_oligotype option:selected").text() !== '' ) {
+ url += "?oligotype=" + $("#search_oligotype option:selected").text();
+ }
+ if ( $("#taxon_lt").val() !== '' ) {
+ url += "&taxon=" + $("#taxon_lt").val();
+ }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByPhysiologicalStage.js b/static/js/searchByPhysiologicalStage.js
new file mode 100644
index 0000000000000000000000000000000000000000..6bbe367b0577208180bc37510f7fba8ef656388d
--- /dev/null
+++ b/static/js/searchByPhysiologicalStage.js
@@ -0,0 +1,199 @@
+/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTableRev, createTableWithArgRev } from './utils.js';
+
+$("#searchByPhysiologicalStage.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_stage_taxon').show();
+$('#spinner_stage_taxon2').show();
+
+var thtable = $('#results_stage_taxon').DataTable();
+
+var $select = $('#search_stage').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Multiparious',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_physio_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_stage_taxon').hide();
+ $('#spinner_stage_taxon2').hide();
+ $('#search_stage option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_stage_taxon').removeAttr('disabled');
+ $('#spinner_stage_taxon').show();
+ $('#spinner_stage_taxon2').show();
+
+ createTableRev(value, 'has_a_physiological_stage', 'results_stage_taxon');
+
+ if ( $('#taxon_ht').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_stage_taxon').hide();
+ $('#spinner_stage_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_stage_taxon').hide();
+ $('#spinner_stage_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByStage").val("");
+ $('#filter_stage_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( stage !== null ) {
+ $('#spinner_stage_taxon').show();
+ $('#spinner_stage_taxon2').show();
+ selectize.setTextboxValue(stage);
+ $("#search_stage option:selected").text(stage);
+ $("#search_stage option:selected").val(stage);
+ $('#filter_stage_taxon').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_physio_taxon'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let stageid = l_path[l_path.length-1];
+
+ createTableWithArgRev(stageid, 'has_a_physiological_stage', 'results_stage_taxon');
+
+ if ( $('#taxon_ht').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_stage_taxon').hide();
+ $('#spinner_stage_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_stage_taxon').hide();
+ $('#spinner_stage_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByStage").val("");
+ $('#filter_stage_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: sources
+// if ( sources !== null ) {
+// $('input.column_source').val(sources.join(";"));
+// }
+// URL: stage
+if ( taxon !== null ) {
+ $('input.column_filter').val(taxon);
+}
+
+// Filter - taxon
+function filterColumntaxon(i) {
+ $('#results_stage_taxon').DataTable().column(i).search(
+ $('#taxon_ht').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumntaxon($(this).parents('tr').attr('data-column'));
+} );
+
+// Filter - QPS
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_th]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_stage').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
+
+ // Filter - Sources
+// function filterSourceColumn(i) {
+// $('#results_taxon_stage').DataTable().column(i).search(
+// $('#sources_th').val().replace(/;/g, "|"), true, false
+// ).draw();
+// checkURL();
+// }
+// $('input.column_source').on( 'keyup click', function () {
+// filterSourceColumn(5);
+// });
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_stage option:selected").text() !== '' ) {
+ url += "?stage=" + $("#search_stage option:selected").text();
+ }
+ if ( $("#taxon_ht").val() !== '' ) {
+ url += "&taxon=" + $("#taxon_ht").val();
+ }
+ // if ( $('#qps_th').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ // if ( $("#sources_th").val() !== '' ) {
+ // if ( $("#sources_th").val().includes(";") ) {
+ // let list = $("#sources_th").val().split(";");
+ // for (let s = 0 ; s < list.length ; s++ ) {
+ // if ( list[s] != '' ) {
+ // url += "&source=" + list[s];
+ // }
+ // }
+ // }
+ // else {
+ // url += "&source=" + $("#sources_th").val();
+ // }
+ // }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByPostpartum.js b/static/js/searchByPostpartum.js
new file mode 100644
index 0000000000000000000000000000000000000000..ac3c7034d2ba58d96dd8e08a30383c7ee3865641
--- /dev/null
+++ b/static/js/searchByPostpartum.js
@@ -0,0 +1,199 @@
+taxon_pt/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTableRev, createTableWithArgRev } from './utils.js';
+
+$("#searchByPostpartum.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_postpartum_taxon').show();
+$('#spinner_postpartum_taxon2').show();
+
+var thtable = $('#results_postpartum_taxon').DataTable();
+
+var $select = $('#search_postpartum').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. first week postpartum',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_postpartum_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_postpartum_taxon').hide();
+ $('#spinner_postpartum_taxon2').hide();
+ $('#search_postpartum option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_postpartum_taxon').removeAttr('disabled');
+ $('#spinner_postpartum_taxon').show();
+ $('#spinner_postpartum_taxon2').show();
+
+ createTableRev(value, 'has_given_birth_since', 'results_postpartum_taxon');
+
+ if ( $('#taxon_pt').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_postpartum_taxon').hide();
+ $('#spinner_postpartum_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_postpartum_taxon').hide();
+ $('#spinner_postpartum_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByPostpartum").val("");
+ $('#filter_postpartum_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( postpartum !== null ) {
+ $('#spinner_postpartum_taxon').show();
+ $('#spinner_postpartum_taxon2').show();
+ selectize.setTextboxValue(postpartum);
+ $("#search_postpartum option:selected").text(postpartum);
+ $("#search_postpartum option:selected").val(postpartum);
+ $('#filter_postpartum_taxon').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_postpartum_taxon'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let postpartumid = l_path[l_path.length-1];
+
+ createTableWithArgRev(postpartumid, 'has_given_birth_since', 'results_postpartum_taxon');
+
+ if ( $('#taxon_pt').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_postpartum_taxon').hide();
+ $('#spinner_postpartum_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_postpartum_taxon').hide();
+ $('#spinner_postpartum_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonByPostpartum").val("");
+ $('#filter_postpartum_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: sources
+// if ( sources !== null ) {
+// $('input.column_source').val(sources.join(";"));
+// }
+// URL: postpartum
+if ( taxon !== null ) {
+ $('input.column_filter').val(taxon);
+}
+
+// Filter - taxon
+function filterColumntaxon(i) {
+ $('#results_postpartum_taxon').DataTable().column(i).search(
+ $('#taxon_pt').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumntaxon($(this).parents('tr').attr('data-column'));
+} );
+
+// Filter - QPS
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_th]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_stage').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
+
+ // Filter - Sources
+// function filterSourceColumn(i) {
+// $('#results_taxon_stage').DataTable().column(i).search(
+// $('#sources_th').val().replace(/;/g, "|"), true, false
+// ).draw();
+// checkURL();
+// }
+// $('input.column_source').on( 'keyup click', function () {
+// filterSourceColumn(5);
+// });
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_postpartum option:selected").text() !== '' ) {
+ url += "?postpartum=" + $("#search_postpartum option:selected").text();
+ }
+ if ( $("#taxon_pt").val() !== '' ) {
+ url += "&taxon=" + $("#taxon_pt").val();
+ }
+ // if ( $('#qps_th').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ // if ( $("#sources_th").val() !== '' ) {
+ // if ( $("#sources_th").val().includes(";") ) {
+ // let list = $("#sources_th").val().split(";");
+ // for (let s = 0 ; s < list.length ; s++ ) {
+ // if ( list[s] != '' ) {
+ // url += "&source=" + list[s];
+ // }
+ // }
+ // }
+ // else {
+ // url += "&source=" + $("#sources_th").val();
+ // }
+ // }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchBySampleType.js b/static/js/searchBySampleType.js
new file mode 100644
index 0000000000000000000000000000000000000000..68e9e93fd49b26c4a79db7faaeb13b37c76fdbec
--- /dev/null
+++ b/static/js/searchBySampleType.js
@@ -0,0 +1,199 @@
+/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTableRev, createTableWithArgRev } from './utils.js';
+
+$("#searchBySampleType.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_sample_taxon').show();
+$('#spinner_sample_taxon2').show();
+
+var thtable = $('#results_sample_taxon').DataTable();
+
+var $select = $('#search_sample').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Pooled milk',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_sample_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_sample_taxon').hide();
+ $('#spinner_sample_taxon2').hide();
+ $('#search_sample option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_sample_taxon').removeAttr('disabled');
+ $('#spinner_sample_taxon').show();
+ $('#spinner_sample_taxon2').show();
+
+ createTableRev(value, 'have_produced_1', 'results_sample_taxon');
+
+ if ( $('#taxon_ut').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_sample_taxon').hide();
+ $('#spinner_sample_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_sample_taxon').hide();
+ $('#spinner_sample_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonBySample").val("");
+ $('#filter_sample_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( sample !== null ) {
+ $('#spinner_sample_taxon').show();
+ $('#spinner_sample_taxon2').show();
+ selectize.setTextboxValue(sample);
+ $("#search_sample option:selected").text(sample);
+ $("#search_sample option:selected").val(sample);
+ $('#filter_sample_taxon').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_sample_taxon'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let sampleid = l_path[l_path.length-1];
+
+ createTableWithArgRev(sampleid, 'have_produced_1', 'results_sample_taxon');
+
+ if ( $('#taxon_ut').val() != '' ) { filterColumntaxon(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_sample_taxon').hide();
+ $('#spinner_sample_taxon2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_sample_taxon').hide();
+ $('#spinner_sample_taxon2').hide();
+ // Clear oracle
+ $("#relationTaxonBySample").val("");
+ $('#filter_sample_taxon').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: sources
+// if ( sources !== null ) {
+// $('input.column_source').val(sources.join(";"));
+// }
+// URL: sample
+if ( taxon !== null ) {
+ $('input.column_filter').val(taxon);
+}
+
+// Filter - taxon
+function filterColumntaxon(i) {
+ $('#results_sample_taxon').DataTable().column(i).search(
+ $('#taxon_ut').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumntaxon($(this).parents('tr').attr('data-column'));
+} );
+
+// Filter - QPS
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_th]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_stage').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
+
+ // Filter - Sources
+// function filterSourceColumn(i) {
+// $('#results_taxon_stage').DataTable().column(i).search(
+// $('#sources_th').val().replace(/;/g, "|"), true, false
+// ).draw();
+// checkURL();
+// }
+// $('input.column_source').on( 'keyup click', function () {
+// filterSourceColumn(5);
+// });
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_sample option:selected").text() !== '' ) {
+ url += "?sample=" + $("#search_sample option:selected").text();
+ }
+ if ( $("#taxon_ut").val() !== '' ) {
+ url += "&taxon=" + $("#taxon_ut").val();
+ }
+ // if ( $('#qps_th').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ // if ( $("#sources_th").val() !== '' ) {
+ // if ( $("#sources_th").val().includes(";") ) {
+ // let list = $("#sources_th").val().split(";");
+ // for (let s = 0 ; s < list.length ; s++ ) {
+ // if ( list[s] != '' ) {
+ // url += "&source=" + list[s];
+ // }
+ // }
+ // }
+ // else {
+ // url += "&source=" + $("#sources_th").val();
+ // }
+ // }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByTaxon.js b/static/js/searchByTaxon.js
index d1ac9ba61e6e3635499223692b7e85d0f49e65d5..6647a78b9f8bff3581520a0c79996978d79099fa 100644
--- a/static/js/searchByTaxon.js
+++ b/static/js/searchByTaxon.js
@@ -14,21 +14,23 @@
# limitations under the License.
**/
-import { format_docs } from './utils.js';
+import { format_docs, createTable, createTableWithArg } from './utils.js';
$("#searchByTaxon.nav-item").addClass( "active" );
// Spinner
-$('#spinner_taxon_habitat').show();
-$('#spinner_taxon_habitat2').show();
-// $('#relationHabitatByTaxon').prop('disabled', true);
+$('#spinner_taxon_stage').show();
+$('#spinner_taxon_stage2').show();
+// $('#relationstageByTaxon').prop('disabled', true);
+
+var thtable = $('#results_taxon_stage').DataTable();
var $select = $('#search').selectize({
valueField: 'path',
labelField: 'name',
searchField: 'name',
sortField: 'name',
- placeholder: 'e.g. Bacillus subtilis',
+ placeholder: 'e.g. Sus scrofa',
openOnFocus: false,
create: false,
maxItems: 1,
@@ -37,20 +39,45 @@ var $select = $('#search').selectize({
// $.getJSON($SCRIPT_ROOT + '/_get_list_term',
$.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
- { table: "list_taxon"},
+ { table: "list_taxon_physio"},
function(data) {
data.forEach(function(item) {
that.addOption(item);
});
- $('#spinner_taxon_habitat').hide();
- $('#spinner_taxon_habitat2').hide();
+ $('#spinner_taxon_stage').hide();
+ $('#spinner_taxon_stage2').hide();
$('#search option:selected').prop('disabled', false);
});
},
onChange:function(value){
- if (value != "") {
- createTable(value);
+ if (value != '') {
+
+ $('#filter_taxon_stage').removeAttr('disabled');
+ $('#spinner_taxon_stage').show();
+ $('#spinner_taxon_stage2').show();
+
+ createTable(value, 'has_a_physiological_stage', 'results_taxon_stage');
+
+ if ( $('#stage_th').val() != '' ) { filterColumnstage(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_taxon_stage').hide();
+ $('#spinner_taxon_stage2').hide();
+
+ checkURL();
}
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_stage').hide();
+ $('#spinner_taxon_stage2').hide();
+ // Clear oracle
+ $("#relationstageByTaxon").val("");
+ $('#filter_taxon_stage').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
}
});
@@ -58,404 +85,435 @@ var selectize = $select[0].selectize;
// URL: taxon
if ( taxon !== null ) {
- $('#spinner_taxon_habitat').show();
- $('#spinner_taxon_habitat2').show();
+ $('#spinner_taxon_stage').show();
+ $('#spinner_taxon_stage2').show();
selectize.setTextboxValue(taxon);
$("#search option:selected").text(taxon);
$("#search option:selected").val(taxon);
- $('#filter_taxon_habitat').removeAttr('disabled');
-
- createTable_old(taxon);
-}
-// URL: qps
-if ( qps !== null ) {
- $('input:checkbox').prop('checked', true);
-}
-// URL: sources
-if ( sources !== null ) {
- $('input.column_source').val(sources.join(";"));
-}
-// URL: habitat
-if ( habitat !== null ) {
- $('input.column_filter').val(habitat);
-}
-
-var thtable = $('#results_taxon_habitat').DataTable();
-
-// Datatable
-function createTable(path) {
- if ( path != '' ) {
- let l_path = path.split('/');
- let taxonid = l_path[l_path.length-1];
+ $('#filter_taxon_stage').removeAttr('disabled');
- $('#filter_taxon_habitat').removeAttr('disabled');
- $('#spinner_taxon_habitat').show();
- $('#spinner_taxon_habitat2').show();
-
- $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
- { taxonid: taxonid,
- type: 'habitat'
- },
- function success(relations) {
- $('#hide').css( 'display', 'block' );
- $('#results_taxon_habitat').DataTable().destroy();
- thtable = $('#results_taxon_habitat').DataTable(
- {
- dom: 'lifrtBp', // 'Bfrtip'
- data: relations,
- buttons: [
- {
- extend: 'copyHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'csvHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'excelHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'pdfHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- 'colvis'
- ],
- columns: [
- {"render": function(data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- let docs = "";
- if ( data.includes(', ') ) { docs = data.split(', '); }
- else { docs = data.split(','); }
- let docs_f = "";
- if ( docs.length > 2 ) { // 3
- docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
- }
- else {
- docs_f = docids;
- }
- return docs_f;
- }},
- {"render": function ( data, type, row, meta ) {
- let taxa = row[1].split(', ');
- let taxon = taxa[0];
- if ( row[9].includes("ncbi") ) {
- taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- else if ( row[9].includes("bd") ) {
- taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- return taxon;
- }},
- {"render": function (data, type, row, meta) {
- return row[2];
- }},
- {"render": function (data, type, row, meta) {
- return row[3].split(',')[0];
- }},
- {"orderable": false, "render": function (data, type, row, meta) {
- return row[4];
- }},
- {"render": function (data, type, row, meta) {
- return row[5];
- }},
- {"render": function (data, type, row, meta) {
- let taxs = row[1].split(', ');
- let forms = "";
- for ( let i = 1; i < taxs.length ; i++ ) {
- forms += taxs[i]
- if ( i != taxs.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let elts = row[3].split(', ');
- let forms = "";
- for ( let i = 1; i < elts.length ; i++ ) {
- forms += elts[i]
- if ( i != elts.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- return docids;
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[9];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[7];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[8];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[6];
- }}
- ]
- });
-
- if ( $('#habitat_th').val() != '' ) { filterColumnHabitat(3); }
- if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
- if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
-
- $('#spinner_taxon_habitat').hide();
- $('#spinner_taxon_habitat2').hide();
-
- checkURL();
- });
- }
- else {
- alert("No result for " + taxon);
- // Spinner off
- $('#spinner_taxon_habitat').hide();
- $('#spinner_taxon_habitat2').hide();
- // Clear oracle
- $("#relationHabitatByTaxon").val("");
- $('#filter_taxon_habitat').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
-}
-
-function createTable_old(taxon) {
$.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: taxon, table: 'list_taxon'},
+ {name: taxon, table: 'list_taxon_physio'},
function success(path) {
if ( path != '' ) {
let l_path = path[0].split('/');
let taxonid = l_path[l_path.length-1];
- $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
- { taxonid: taxonid,
- type: 'habitat'
- },
- function success(relations) {
- $('#hide').css( 'display', 'block' );
- $('#results_taxon_habitat').DataTable().destroy();
- thtable = $('#results_taxon_habitat').DataTable(
- {
- dom: 'lifrtBp', // 'Bfrtip'
- data: relations,
- buttons: [
- {
- extend: 'copyHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'csvHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'excelHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'pdfHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- 'colvis'
- ],
- columns: [
- {"render": function(data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- let docs = "";
- if ( data.includes(', ') ) { docs = data.split(', '); }
- else { docs = data.split(','); }
- let docs_f = "";
- if ( docs.length > 2 ) { // 3
- docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
- }
- else {
- docs_f = docids;
- }
- return docs_f;
- }},
- {"render": function ( data, type, row, meta ) {
- let taxa = row[1].split(', ');
- let taxon = taxa[0];
- if ( row[9].includes("ncbi") ) {
- taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- else if ( row[9].includes("bd") ) {
- taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- return taxon;
- }},
- {"render": function (data, type, row, meta) {
- return row[2];
- }},
- {"render": function (data, type, row, meta) {
- return row[3].split(',')[0];
- }},
- {"orderable": false, "render": function (data, type, row, meta) {
- return row[4];
- }},
- {"render": function (data, type, row, meta) {
- return row[5];
- }},
- {"render": function (data, type, row, meta) {
- let taxs = row[1].split(', ');
- let forms = "";
- for ( let i = 1; i < taxs.length ; i++ ) {
- forms += taxs[i]
- if ( i != taxs.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let elts = row[3].split(', ');
- let forms = "";
- for ( let i = 1; i < elts.length ; i++ ) {
- forms += elts[i]
- if ( i != elts.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- return docids;
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[9];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[7];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[8];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[6];
- }}
- ]
- });
+ createTableWithArg(taxonid, 'has_a_physiological_stage', 'results_taxon_stage');
- if ( $('#habitat_th').val() != '' ) { filterColumnHabitat(3); }
- if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
- if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+ if ( $('#stage_th').val() != '' ) { filterColumnstage(3); }
+ // if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ // if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
- $('#spinner_taxon_habitat').hide();
- $('#spinner_taxon_habitat2').hide();
+ $('#spinner_taxon_stage').hide();
+ $('#spinner_taxon_stage2').hide();
- checkURL();
- });
+ checkURL();
}
else {
alert("No result for " + taxon);
// Spinner off
- $('#spinner_taxon_habitat').hide();
- $('#spinner_taxon_habitat2').hide();
+ $('#spinner_taxon_stage').hide();
+ $('#spinner_taxon_stage2').hide();
// Clear oracle
- $("#relationHabitatByTaxon").val("");
- $('#filter_taxon_habitat').attr('disabled', 'disabled');
+ $("#relationstageByTaxon").val("");
+ $('#filter_taxon_stage').attr('disabled', 'disabled');
// Change URL
window.location.replace(window.location.pathname);
}
});
}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: sources
+// if ( sources !== null ) {
+// $('input.column_source').val(sources.join(";"));
+// }
+// URL: stage
+if ( stage !== null ) {
+ $('input.column_filter').val(stage);
+}
-// Filter - Habitat
-function filterColumnHabitat(i) {
- $('#results_taxon_habitat').DataTable().column(i).search(
- $('#habitat_th').val().replace(/;/g, "|"), true, false
+// var thtable = $('#results_taxon_stage').DataTable();
+
+// Datatable
+// function createTable(path) {
+// if ( path != '' ) {
+// let l_path = path.split('/');
+// let taxonid = l_path[l_path.length-1];
+//
+// $('#filter_taxon_stage').removeAttr('disabled');
+// $('#spinner_taxon_stage').show();
+// $('#spinner_taxon_stage2').show();
+//
+// $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+// { taxonid: taxonid,
+// type: 'has_a_physiological_stage'
+// },
+// function success(relations) {
+// $('#hide').css( 'display', 'block' );
+// $('#results_taxon_stage').DataTable().destroy();
+// thtable = $('#results_taxon_stage').DataTable(
+// {
+// dom: 'lifrtBp', // 'Bfrtip'
+// data: relations,
+// buttons: [
+// {
+// extend: 'copyHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'csvHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'excelHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'pdfHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// 'colvis'
+// ],
+// columns: [
+// {"render": function(data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+// else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'stage'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// let docs = "";
+// if ( data.includes(', ') ) { docs = data.split(', '); }
+// else { docs = data.split(','); }
+// let docs_f = "";
+// if ( docs.length > 2 ) { // 3
+// docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+// }
+// else {
+// docs_f = docids;
+// }
+// return docs_f;
+// }},
+// {"render": function ( data, type, row, meta ) {
+// let taxa = row[1].split(', ');
+// let taxon = taxa[0];
+// if ( row[9].includes("ncbi") ) {
+// taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// else if ( row[9].includes("bd") ) {
+// taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// return taxon;
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[2];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[3].split(',')[0];
+// }},
+// {"orderable": false, "render": function (data, type, row, meta) {
+// return row[4];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[5];
+// }},
+// {"render": function (data, type, row, meta) {
+// let taxs = row[1].split(', ');
+// let forms = "";
+// for ( let i = 1; i < taxs.length ; i++ ) {
+// forms += taxs[i]
+// if ( i != taxs.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let elts = row[3].split(', ');
+// let forms = "";
+// for ( let i = 1; i < elts.length ; i++ ) {
+// forms += elts[i]
+// if ( i != elts.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+// else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'stage'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// return docids;
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[9];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[7];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[8];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[6];
+// }}
+// ]
+// });
+//
+// if ( $('#stage_th').val() != '' ) { filterColumnstage(3); }
+// if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+// if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+//
+// $('#spinner_taxon_stage').hide();
+// $('#spinner_taxon_stage2').hide();
+//
+// checkURL();
+// });
+// }
+// else {
+// alert("No result for " + taxon);
+// // Spinner off
+// $('#spinner_taxon_stage').hide();
+// $('#spinner_taxon_stage2').hide();
+// // Clear oracle
+// $("#relationstageByTaxon").val("");
+// $('#filter_taxon_stage').attr('disabled', 'disabled');
+// // Change URL
+// window.location.replace(window.location.pathname);
+// }
+// }
+
+// function createTable_old(taxon) {
+// $.getJSON($SCRIPT_ROOT + '/_get_path',
+// {name: taxon, table: 'list_taxon'},
+// function success(path) {
+// if ( path != '' ) {
+// let l_path = path[0].split('/');
+// let taxonid = l_path[l_path.length-1];
+//
+// $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+// { taxonid: taxonid,
+// type: 'stage'
+// },
+// function success(relations) {
+// $('#hide').css( 'display', 'block' );
+// $('#results_taxon_stage').DataTable().destroy();
+// thtable = $('#results_taxon_stage').DataTable(
+// {
+// dom: 'lifrtBp', // 'Bfrtip'
+// data: relations,
+// buttons: [
+// {
+// extend: 'copyHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'csvHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'excelHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'pdfHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// 'colvis'
+// ],
+// columns: [
+// {"render": function(data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'stage'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// let docs = "";
+// if ( data.includes(', ') ) { docs = data.split(', '); }
+// else { docs = data.split(','); }
+// let docs_f = "";
+// if ( docs.length > 2 ) { // 3
+// docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+// }
+// else {
+// docs_f = docids;
+// }
+// return docs_f;
+// }},
+// {"render": function ( data, type, row, meta ) {
+// let taxa = row[1].split(', ');
+// let taxon = taxa[0];
+// if ( row[9].includes("ncbi") ) {
+// taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// else if ( row[9].includes("bd") ) {
+// taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// return taxon;
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[2];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[3].split(',')[0];
+// }},
+// {"orderable": false, "render": function (data, type, row, meta) {
+// return row[4];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[5];
+// }},
+// {"render": function (data, type, row, meta) {
+// let taxs = row[1].split(', ');
+// let forms = "";
+// for ( let i = 1; i < taxs.length ; i++ ) {
+// forms += taxs[i]
+// if ( i != taxs.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let elts = row[3].split(', ');
+// let forms = "";
+// for ( let i = 1; i < elts.length ; i++ ) {
+// forms += elts[i]
+// if ( i != elts.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'stage'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// return docids;
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[9];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[7];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[8];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[6];
+// }}
+// ]
+// });
+//
+// if ( $('#stage_th').val() != '' ) { filterColumnstage(3); }
+// if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+// if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+//
+// $('#spinner_taxon_stage').hide();
+// $('#spinner_taxon_stage2').hide();
+//
+// checkURL();
+// });
+// }
+// else {
+// alert("No result for " + taxon);
+// // Spinner off
+// $('#spinner_taxon_stage').hide();
+// $('#spinner_taxon_stage2').hide();
+// // Clear oracle
+// $("#relationstageByTaxon").val("");
+// $('#filter_taxon_stage').attr('disabled', 'disabled');
+// // Change URL
+// window.location.replace(window.location.pathname);
+// }
+// });
+// }
+
+// Filter - stage
+function filterColumnstage(i) {
+ $('#results_taxon_stage').DataTable().column(i).search(
+ $('#stage_th').val().replace(/;/g, "|"), true, false
).draw();
checkURL();
}
$('input.column_filter').on( 'keyup click', function () {
- filterColumnHabitat($(this).parents('tr').attr('data-column'));
+ filterColumnstage($(this).parents('tr').attr('data-column'));
} );
// Filter - QPS
-function filterColumnCheck(i) {
- let state = $('input[name=qps_th]').is(':checked');
- let qps = "";
- if ( state == true ) { qps = "yes"; }
- $('#results_taxon_habitat').DataTable().column(i).search(
- qps, true, false
- ).draw();
- checkURL();
-}
-$('input:checkbox').on('change', function () {
- filterColumnCheck(4);
- });
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_th]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_stage').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
// Filter - Sources
-function filterSourceColumn(i) {
- $('#results_taxon_habitat').DataTable().column(i).search(
- $('#sources_th').val().replace(/;/g, "|"), true, false
- ).draw();
- checkURL();
-}
-$('input.column_source').on( 'keyup click', function () {
- filterSourceColumn(5);
-});
+// function filterSourceColumn(i) {
+// $('#results_taxon_stage').DataTable().column(i).search(
+// $('#sources_th').val().replace(/;/g, "|"), true, false
+// ).draw();
+// checkURL();
+// }
+// $('input.column_source').on( 'keyup click', function () {
+// filterSourceColumn(5);
+// });
// Check url
function checkURL() {
@@ -463,24 +521,24 @@ function checkURL() {
if ( $("#search option:selected").text() !== '' ) {
url += "?taxon=" + $("#search option:selected").text();
}
- if ( $("#habitat_th").val() !== '' ) {
- url += "&habitat=" + $("#habitat_th").val();
- }
- if ( $('#qps_th').is(":checked") ) {
- url += "&qps=yes";
- }
- if ( $("#sources_th").val() !== '' ) {
- if ( $("#sources_th").val().includes(";") ) {
- let list = $("#sources_th").val().split(";");
- for (let s = 0 ; s < list.length ; s++ ) {
- if ( list[s] != '' ) {
- url += "&source=" + list[s];
- }
- }
- }
- else {
- url += "&source=" + $("#sources_th").val();
- }
+ if ( $("#stage_th").val() !== '' ) {
+ url += "&stage=" + $("#stage_th").val();
}
+ // if ( $('#qps_th').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ // if ( $("#sources_th").val() !== '' ) {
+ // if ( $("#sources_th").val().includes(";") ) {
+ // let list = $("#sources_th").val().split(";");
+ // for (let s = 0 ; s < list.length ; s++ ) {
+ // if ( list[s] != '' ) {
+ // url += "&source=" + list[s];
+ // }
+ // }
+ // }
+ // else {
+ // url += "&source=" + $("#sources_th").val();
+ // }
+ // }
history.pushState({}, null, url);
}
diff --git a/static/js/searchByTaxonForLactation.js b/static/js/searchByTaxonForLactation.js
new file mode 100644
index 0000000000000000000000000000000000000000..df907e7d7935d51de184780b93d06da4c66e442e
--- /dev/null
+++ b/static/js/searchByTaxonForLactation.js
@@ -0,0 +1,497 @@
+/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not lactation this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTable, createTableWithArg } from './utils.js';
+
+$("#searchByTaxonForLactation.nav-item").addClass( "active" );
+
+$('#spinner_taxon_lactation').show();
+$('#spinner_taxon_lactation2').show();
+
+var thtable = $('#results_taxon_lactation').DataTable();
+
+var $select = $('#search_taxon_lactation').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Equus caballus',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ // $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_taxon_lactation"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_lactation').hide();
+ $('#spinner_taxon_lactation2').hide();
+ $('#search_taxon_lactation').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != "") {
+
+ $('#filter_taxon_lactation').removeAttr('disabled');
+ $('#spinner_taxon_lactation').show();
+ $('#spinner_taxon_lactation2').show();
+
+ createTable(value, 'have_produced_2', 'results_taxon_lactation');
+
+ if ( $('#lactation_tu').val() != '' ) { filterColumnlactation(3); }
+ // if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_taxon_lactation').hide();
+ $('#spinner_taxon_lactation2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_lactation').hide();
+ $('#spinner_taxon_lactation2').hide();
+ // Clear oracle
+ $("#relationlactationByTaxon").val("");
+ $('#filter_taxon_lactation').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( taxon !== null ) {
+ $('#spinner_taxon_lactation').show();
+ $('#spinner_taxon_lactation2').show();
+ selectize.setTextboxValue(taxon);
+ $("#search_taxon_lactation option:selected").text(taxon);
+ $("#search_taxon_lactation option:selected").val(taxon);
+ $('#filter_taxon_lactation').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_taxon_lactation'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ createTableWithArg(taxonid, 'have_produced_2', 'results_taxon_lactation');
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_lactation').hide();
+ $('#spinner_taxon_lactation2').hide();
+ // Clear oracle
+ $("#relationlactationByTaxon").val("");
+ $('#filter_taxon_lactation').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: lactation
+if ( lactation !== null ) {
+ $('input.column_filter').val(lactation);
+}
+
+// var thtable = $('#results_taxon_lactation').DataTable();
+
+// Data table
+// function createTable(path) {
+// if ( path != '' ) {
+// let l_path = path.split('/');
+// let taxonid = l_path[l_path.length-1];
+//
+// $('#filter_taxon_lactation').removeAttr('disabled');
+// $('#spinner_taxon_lactation').show();
+// $('#spinner_taxon_lactation2').show();
+//
+// $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+// { taxonid: taxonid,
+// type: 'lactation'
+// },
+// function success(relations) {
+// $('#hide').css( 'display', 'block' );
+// $('#results_taxon_lactation').DataTable().destroy();
+// thtable = $('#results_taxon_lactation').DataTable(
+// {dom: 'lifrtBp', // 'Bfrtip'
+// data: relations,
+// buttons: [
+// {
+// extend: 'copyHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'csvHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'excelHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'pdfHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// 'colvis'
+// ],
+// columns: [
+// {"render": function(data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'lactation'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// let docs = "";
+// if ( data.includes(', ') ) { docs = data.split(', '); }
+// else { docs = data.split(','); }
+// let docs_f = "";
+// if ( docs.length > 2 ) { // 3
+// docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+// }
+// else {
+// docs_f = docids;
+// }
+// return docs_f;
+// }},
+// {"render": function ( data, type, row, meta ) {
+// let taxa = row[1].split(', ');
+// let taxon = taxa[0];
+// if ( row[9].includes("ncbi") ) {
+// taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// else if ( row[9].includes("bd") ) {
+// taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// return taxon;
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[2];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[3].split(',')[0];
+// }},
+// {"orderable": false, "render": function (data, type, row, meta) {
+// return row[4];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[5];
+// }},
+// {"render": function (data, type, row, meta) {
+// let taxs = row[1].split(', ');
+// let forms = "";
+// for ( let i = 1; i < taxs.length ; i++ ) {
+// forms += taxs[i]
+// if ( i != taxs.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let elts = row[3].split(', ');
+// let forms = "";
+// for ( let i = 1; i < elts.length ; i++ ) {
+// forms += elts[i]
+// if ( i != elts.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'lactation'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// return docids;
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[9];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[7];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[8];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[6];
+// }}
+// ]
+// });
+//
+// if ( $('#lactation_tu').val() != '' ) { filterColumnlactation(3); }
+// if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
+//
+// $('#spinner_taxon_lactation').hide();
+// $('#spinner_taxon_lactation2').hide();
+//
+// checkURL();
+// });
+// }
+// else {
+// alert("No result for " + taxon);
+// // Spinner off
+// $('#spinner_taxon_lactation').hide();
+// $('#spinner_taxon_lactation2').hide();
+// // Clear oracle
+// $("#relationlactationByTaxon").val("");
+// $('#filter_taxon_lactation').attr('disabled', 'disabled');
+// // Change URL
+// window.location.replace(window.location.pathname);
+// }
+// }
+function createTable_old(taxon) {
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_taxon_lactation'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ { taxonid: taxonid,
+ type: 'lactation'
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#results_taxon_lactation').DataTable().destroy();
+ thtable = $('#results_taxon_lactation').DataTable(
+ {dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'lactation'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ {"render": function ( data, type, row, meta ) {
+ let taxa = row[1].split(', ');
+ let taxon = taxa[0];
+ if ( row[9].includes("ncbi") ) {
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ return taxon;
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[3].split(',')[0];
+ }},
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ for ( let i = 1; i < taxs.length ; i++ ) {
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ for ( let i = 1; i < elts.length ; i++ ) {
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'lactation'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }}
+ ]
+ });
+
+ if ( $('#lactation_tu').val() != '' ) { filterColumnlactation(3); }
+ // if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_taxon_lactation').hide();
+ $('#spinner_taxon_lactation2').hide();
+
+ checkURL();
+ });
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_lactation').hide();
+ $('#spinner_taxon_lactation2').hide();
+ // Clear oracle
+ $("#relationlactationByTaxon").val("");
+ $('#filter_taxon_lactation').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+
+// Filter - lactation
+function filterColumnlactation(i) {
+ $('#results_taxon_lactation').DataTable().column(i).search(
+ $('#lactation_tu').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumnlactation($(this).parents('tr').attr('data-column'));
+} );
+
+// Filter - QPS
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_tu]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_lactation').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_taxon_lactation option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search_taxon_lactation option:selected").text();
+ }
+ if ( $("#lactation_tu").val() !== '' ) {
+ url += "&lactation=" + $("#lactation_tu").val();
+ }
+ // if ( $('#qps_tu').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByTaxonForOligosaccharideName.js b/static/js/searchByTaxonForOligosaccharideName.js
new file mode 100644
index 0000000000000000000000000000000000000000..352627e9fbb01fbd0a0ec367a6893294d2837d3d
--- /dev/null
+++ b/static/js/searchByTaxonForOligosaccharideName.js
@@ -0,0 +1,147 @@
+/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTable, createTableWithArg } from './utils.js';
+
+$("#searchByTaxonForOligosaccharideName.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_taxon_oligoname').show();
+$('#spinner_taxon_oligoname2').show();
+
+var thtable = $('#results_taxon_oligoname').DataTable();
+
+var $select = $('#search').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Canis lupus familiaris',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_taxon_oligo_name"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_oligoname').hide();
+ $('#spinner_taxon_oligoname2').hide();
+ $('#search option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_taxon_oligoname').removeAttr('disabled');
+ $('#spinner_taxon_oligoname').show();
+ $('#spinner_taxon_oligoname2').show();
+
+ createTable(value, 'have_produced_tmp_1', 'results_taxon_oligoname');
+
+ if ( $('#oligoname_th').val() != '' ) { filterColumnoligoname(3); }
+
+ $('#spinner_taxon_oligoname').hide();
+ $('#spinner_taxon_oligoname2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_oligoname').hide();
+ $('#spinner_taxon_oligoname2').hide();
+ // Clear oracle
+ $("#relationoligonameByTaxon").val("");
+ $('#filter_taxon_oligoname').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( taxon !== null ) {
+ $('#spinner_taxon_oligoname').show();
+ $('#spinner_taxon_oligoname2').show();
+ selectize.setTextboxValue(taxon);
+ $("#search option:selected").text(taxon);
+ $("#search option:selected").val(taxon);
+ $('#filter_taxon_oligoname').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_taxon_oligo_name'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ createTableWithArg(taxonid, 'have_produced_tmp_1', 'results_taxon_oligoname');
+
+ if ( $('#oligoname_th').val() != '' ) { filterColumnoligoname(3); }
+
+ $('#spinner_taxon_oligoname').hide();
+ $('#spinner_taxon_oligoname2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_oligoname').hide();
+ $('#spinner_taxon_oligoname2').hide();
+ // Clear oracle
+ $("#relationoligonameByTaxon").val("");
+ $('#filter_taxon_oligoname').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+
+// URL: oligoname
+if ( oligoname !== null ) {
+ $('input.column_filter').val(oligotype);
+}
+
+// Filter - oligoname
+function filterColumnoligoname(i) {
+ $('#results_taxon_oligoname').DataTable().column(i).search(
+ $('#oligoname_th').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumnoligoname($(this).parents('tr').attr('data-column'));
+} );
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search option:selected").text();
+ }
+ if ( $("#oligoname_th").val() !== '' ) {
+ url += "&oligoname=" + $("#oligoname_th").val();
+ }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByTaxonForOligosaccharideType.js b/static/js/searchByTaxonForOligosaccharideType.js
new file mode 100644
index 0000000000000000000000000000000000000000..290ba02a8142a2e5651161e2c7b8b934208d26e1
--- /dev/null
+++ b/static/js/searchByTaxonForOligosaccharideType.js
@@ -0,0 +1,147 @@
+/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTable, createTableWithArg } from './utils.js';
+
+$("#searchByTaxonForOligosaccharideType.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_taxon_oligotype').show();
+$('#spinner_taxon_oligotype2').show();
+
+var thtable = $('#results_taxon_oligotype').DataTable();
+
+var $select = $('#search').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Bos taurus',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_taxon_oligo_type"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_oligotype').hide();
+ $('#spinner_taxon_oligotype2').hide();
+ $('#search option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != '') {
+
+ $('#filter_taxon_oligotype').removeAttr('disabled');
+ $('#spinner_taxon_oligotype').show();
+ $('#spinner_taxon_oligotype2').show();
+
+ createTable(value, 'have_produced_tmp_2', 'results_taxon_oligotype');
+
+ if ( $('#oligotype_th').val() != '' ) { filterColumnoligotype(3); }
+
+ $('#spinner_taxon_oligotype').hide();
+ $('#spinner_taxon_oligotype2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_oligotype').hide();
+ $('#spinner_taxon_oligotype2').hide();
+ // Clear oracle
+ $("#relationoligotypeByTaxon").val("");
+ $('#filter_taxon_oligotype').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( taxon !== null ) {
+ $('#spinner_taxon_oligotype').show();
+ $('#spinner_taxon_oligotype2').show();
+ selectize.setTextboxValue(taxon);
+ $("#search option:selected").text(taxon);
+ $("#search option:selected").val(taxon);
+ $('#filter_taxon_oligotype').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_taxon_oligo_type'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ createTableWithArg(taxonid, 'have_produced_tmp_2', 'results_taxon_oligotype');
+
+ if ( $('#oligotype_th').val() != '' ) { filterColumnoligotype(3); }
+
+ $('#spinner_taxon_oligotype').hide();
+ $('#spinner_taxon_oligotype2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_oligotype').hide();
+ $('#spinner_taxon_oligotype2').hide();
+ // Clear oracle
+ $("#relationvByTaxon").val("");
+ $('#filter_taxon_oligotype').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+
+// URL: oligotype
+if ( oligotype !== null ) {
+ $('input.column_filter').val(oligotype);
+}
+
+// Filter - oligotype
+function filterColumnoligotype(i) {
+ $('#results_taxon_oligotype').DataTable().column(i).search(
+ $('#oligotype_th').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumnoligotype($(this).parents('tr').attr('data-column'));
+} );
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search option:selected").text();
+ }
+ if ( $("#oligotype_th").val() !== '' ) {
+ url += "&oligotype=" + $("#oligotype_th").val();
+ }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByTaxonForPhenotype.js b/static/js/searchByTaxonForPhenotype.js
deleted file mode 100644
index 71f6740b5387c9efce7bb256ae546137dc52f8b8..0000000000000000000000000000000000000000
--- a/static/js/searchByTaxonForPhenotype.js
+++ /dev/null
@@ -1,522 +0,0 @@
-/**
-# Copyright 2022 Sandra Dérozier (INRAE)
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-**/
-
-import { format_docs } from './utils.js';
-
-$("#searchByTaxonForPhenotype.nav-item").addClass( "active" );
-
-$('#spinner_taxon_phenotype').show();
-$('#spinner_taxon_phenotype2').show();
-
-var $select = $('#search_taxon_phenotype').selectize({
- valueField: 'path',
- labelField: 'name',
- searchField: 'name',
- sortField: 'name',
- placeholder: 'e.g. Bacillus subtilis',
- openOnFocus: false,
- create: false,
- maxItems: 1,
- onInitialize: function() {
- var that = this;
-
- // $.getJSON($SCRIPT_ROOT + '/_get_list_term',
- $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
- { table: "list_taxon_phenotype"},
- function(data) {
- data.forEach(function(item) {
- that.addOption(item);
- });
- $('#spinner_taxon_phenotype').hide();
- $('#spinner_taxon_phenotype2').hide();
- $('#search_taxon_phenotype option:selected').prop('disabled', false);
- });
- },
- onChange:function(value){
- if (value != "") {
- createTable(value);
- }
- }
- });
-
-var selectize = $select[0].selectize;
-
-// URL: taxon
-if ( taxon !== null ) {
- $('#spinner_taxon_phenotype').show();
- $('#spinner_taxon_phenotype2').show();
- selectize.setTextboxValue(taxon);
- $("#search_taxon_phenotype option:selected").text(taxon);
- $("#search_taxon_phenotype option:selected").val(taxon);
- $('#filter_taxon_phenotype').removeAttr('disabled');
-
- createTable_old(taxon);
-}
-// URL: qps
-if ( qps !== null ) {
- $('input:checkbox').prop('checked', true);
-}
-// URL: phenotype
-if ( phenotype !== null ) {
- $('input.column_filter').val(phenotype);
-}
-
-var thtable = $('#results_taxon_phenotype').DataTable();
-
-// Datatable
-function createTable(path) {
- if ( path != '' ) {
- let l_path = path.split('/');
- let taxonid = l_path[l_path.length-1];
-
- $('#filter_taxon_phenotype').removeAttr('disabled');
- $('#spinner_taxon_phenotype').show();
- $('#spinner_taxon_phenotype2').show();
-
- $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
- { taxonid: taxonid,
- type: 'phenotype'
- },
- function success(relations) {
- $('#hide').css( 'display', 'block' );
- $('#results_taxon_phenotype').DataTable().destroy();
- thtable = $('#results_taxon_phenotype').DataTable(
- {dom: 'lifrtBp', // 'Bfrtip'
- data: relations,
- buttons: [
- {
- extend: 'copyHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'csvHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'excelHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'pdfHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- 'colvis'
- ],
- columns: [
- {"render": function(data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- let docs = "";
- if ( data.includes(', ') ) { docs = data.split(', '); }
- else { docs = data.split(','); }
- let docs_f = "";
- if ( docs.length > 2 ) { // 3
- docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
- }
- else {
- docs_f = docids;
- }
- return docs_f;
- }},
- {"render": function ( data, type, row, meta ) {
- let taxa = row[1].split(', ');
- let taxon = taxa[0];
- if ( row[9].includes("ncbi") ) {
- taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- else if ( row[9].includes("bd") ) {
- taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- return taxon;
- }},
- {"render": function (data, type, row, meta) {
- return row[2];
- }},
- {"render": function (data, type, row, meta) {
- return row[3].split(',')[0];
- }},
- {"orderable": false, "render": function (data, type, row, meta) {
- return row[4];
- }},
- {"render": function (data, type, row, meta) {
- return row[5];
- }},
- {"render": function (data, type, row, meta) {
- let taxs = row[1].split(', ');
- let forms = "";
- for ( let i = 1; i < taxs.length ; i++ ) {
- forms += taxs[i]
- if ( i != taxs.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let elts = row[3].split(', ');
- let forms = "";
- for ( let i = 1; i < elts.length ; i++ ) {
- forms += elts[i]
- if ( i != elts.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- return docids;
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[9];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[7];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[8];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[6];
- }}
- ]
- });
-
- if ( $('#phenotype_tp').val() != '' ) { filterColumnphenotype(3); }
- if ( $('input[name=qps_tp]').is(':checked') == true ) { filterColumnCheck(4); }
-
- $('#spinner_taxon_phenotype').hide();
- $('#spinner_taxon_phenotype2').hide();
-
- checkURL();
- });
- }
- else {
- alert("No result for " + taxon);
- // Spinner off
- $('#spinner_taxon_phenotype').hide();
- $('#spinner_taxon_phenotype2').hide();
- // Clear oracle
- $("#relationPhenotypeByTaxon").val("");
- $('#filter_taxon_phenotype').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
-}
-function createTable_old(taxon) {
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: taxon, table: 'list_taxon_phenotype'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let taxonid = l_path[l_path.length-1];
-
- $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
- { taxonid: taxonid,
- type: 'phenotype'
- },
- function success(relations) {
- $('#hide').css( 'display', 'block' );
- $('#results_taxon_phenotype').DataTable().destroy();
- thtable = $('#results_taxon_phenotype').DataTable(
- {dom: 'lifrtBp', // 'Bfrtip'
- data: relations,
- buttons: [
- {
- extend: 'copyHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'csvHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'excelHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'pdfHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- 'colvis'
- ],
- columns: [
- {"render": function(data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- let docs = "";
- if ( data.includes(', ') ) { docs = data.split(', '); }
- else { docs = data.split(','); }
- let docs_f = "";
- if ( docs.length > 2 ) { // 3
- docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
- }
- else {
- docs_f = docids;
- }
- return docs_f;
- }},
- {"render": function ( data, type, row, meta ) {
- let taxa = row[1].split(', ');
- let taxon = taxa[0];
- if ( row[9].includes("ncbi") ) {
- taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- else if ( row[9].includes("bd") ) {
- taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- return taxon;
- }},
- {"render": function (data, type, row, meta) {
- return row[2];
- }},
- {"render": function (data, type, row, meta) {
- return row[3].split(',')[0];
- }},
- {"orderable": false, "render": function (data, type, row, meta) {
- return row[4];
- }},
- {"render": function (data, type, row, meta) {
- return row[5];
- }},
- {"render": function (data, type, row, meta) {
- let taxs = row[1].split(', ');
- let forms = "";
- for ( let i = 1; i < taxs.length ; i++ ) {
- forms += taxs[i]
- if ( i != taxs.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let elts = row[3].split(', ');
- let forms = "";
- for ( let i = 1; i < elts.length ; i++ ) {
- forms += elts[i]
- if ( i != elts.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- return docids;
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[9];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[7];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[8];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[6];
- }}
- // {"width": "15%", "targets": 0,
- // render: function(data, type, row, meta) {
- // var docids = format_docs(row, alvisir, 'phenotype');
- // let docs = "";
- // if ( data.includes(', ') ) { docs = data.split(', '); }
- // else { docs = data.split(','); }
- // let docs_f = "";
- // if ( docs.length > 3 ) {
- // docs_f = docids.split(", ").slice(0,3).join(', ') + ", ...";
- // }
- // else {
- // docs_f = docids;
- // }
- //
- // return docs_f;
- // }
- // },
- // {"width": "30%", "targets": 1,
- // "render": function ( data, type, row, meta ) {
- // let taxa = data.split(', ');
- // let taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>: ";
- // let forms = "";
- // for ( let i = 1; i < taxa.length ; i++ ) {
- // forms += taxa[i] + ", "
- // }
- // forms = forms.slice(0, -2);
- //
- // let taxa_f = "";
- // if ( taxa.length > 3 ) {
- // taxa_f = taxon + forms.split(", ").slice(0,2).join(', ') + ", ...";
- // }
- // else {
- // taxa_f = taxon + forms;
- // }
- //
- // return taxa_f;
- // },
- // },
- // {"width": "12%", "targets": 2},
- // {"width": "28%", "targets": 3,
- // "render": function ( data, type, row, meta ) {
- // let elts = data.split(', ');
- // let elt = "<b>"+elts[0]+"</b>: ";
- // let forms = "";
- // for ( let i = 1; i < elts.length ; i++ ) {
- // forms += elts[i] + ", "
- // }
- // forms = forms.slice(0, -2);
- //
- // let elts_f = "";
- // if ( elts.length > 3 ) {
- // elts_f = elt + forms.split(", ").slice(0,2).join(', ') + ", ...";
- // }
- // else {
- // elts_f = elt + forms;
- // }
- // return elts_f;
- // },
- // },
- // {"width": "5%", "targets": 4, "orderable": false,
- // "render": function ( data, type, row, meta ) {
- // let qps = data;
- // return "<center>"+qps+"</center>";
- // },
- // },
- // {"width": "10%", "targets": 5 },
- // {"data": null, "orderable": false,
- // "className": "details-control", "defaultContent": ""}
- ]
- // ,
- // buttons: [
- // 'copy', 'excel', 'pdf', 'print']
- });
-
- if ( $('#phenotype_tp').val() != '' ) { filterColumnphenotype(3); }
- if ( $('input[name=qps_tp]').is(':checked') == true ) { filterColumnCheck(4); }
-
- $('#spinner_taxon_phenotype').hide();
- $('#spinner_taxon_phenotype2').hide();
-
- checkURL();
- });
- }
- else {
- alert("No result for " + taxon);
- // Spinner off
- $('#spinner_taxon_phenotype').hide();
- $('#spinner_taxon_phenotype2').hide();
- // Clear oracle
- $("#relationPhenotypeByTaxon").val("");
- $('#filter_taxon_phenotype').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
- });
-}
-
-// Filter - phenotype
-function filterColumnphenotype(i) {
- $('#results_taxon_phenotype').DataTable().column(i).search(
- $('#phenotype_tp').val().replace(/;/g, "|"), true, false
- ).draw();
- checkURL();
-}
-$('input.column_filter').on( 'keyup click', function () {
- filterColumnphenotype($(this).parents('tr').attr('data-column'));
-} );
-
-// Filter - QPS
-function filterColumnCheck(i) {
- let state = $('input[name=qps_tp]').is(':checked');
- let qps = "";
- if ( state == true ) { qps = "yes"; }
- $('#results_taxon_phenotype').DataTable().column(i).search(
- qps, true, false
- ).draw();
- checkURL();
-}
-$('input:checkbox').on('change', function () {
- filterColumnCheck(4);
- });
-
-// Check url
-function checkURL() {
- var url = window.location.pathname;
- if ( $("#search_taxon_phenotype option:selected").text() !== '' ) {
- url += "?taxon=" + $("#search_taxon_phenotype option:selected").text();
- }
- if ( $("#phenotype_tp").val() !== '' ) {
- url += "&phenotype=" + $("#phenotype_tp").val();
- }
- if ( $('#qps_tp').is(":checked") ) {
- url += "&qps=yes";
- }
- history.pushState({}, null, url);
-}
diff --git a/static/js/searchByTaxonForPostpartum.js b/static/js/searchByTaxonForPostpartum.js
new file mode 100644
index 0000000000000000000000000000000000000000..2fa580ba7c3c59dfdf8a7f9292140186f38bd4c8
--- /dev/null
+++ b/static/js/searchByTaxonForPostpartum.js
@@ -0,0 +1,569 @@
+/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTable, createTableWithArg } from './utils.js';
+
+$("#searchByTaxonForPostpartum.nav-item").addClass( "active" );
+
+// Spinner
+$('#spinner_taxon_postpartum').show();
+$('#spinner_taxon_postpartum2').show();
+
+var thtable = $('#results_taxon_postpartum').DataTable();
+
+var $select = $('#search_taxon_postpartum').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Rattus',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ // $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_taxon_postpartum"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_postpartum').hide();
+ $('#spinner_taxon_postpartum2').hide();
+ $('#search_taxon_postpartum option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != "") {
+
+ $('#filter_taxon_postpartum').removeAttr('disabled');
+ $('#spinner_taxon_postpartum').show();
+ $('#spinner_taxon_postpartum2').show();
+
+ createTable(value, 'has_given_birth_since', 'results_taxon_postpartum');
+
+ if ( $('#postpartum_tp').val() != '' ) { filterColumnpostpartum(3); }
+ // if ( $('input[name=qps_tp]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_taxon_postpartum').hide();
+ $('#spinner_taxon_postpartum2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_postpartum').hide();
+ $('#spinner_taxon_postpartum2').hide();
+ // Clear oracle
+ $("#relationpostpartumByTaxon").val("");
+ $('#filter_taxon_postpartum').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( taxon !== null ) {
+ $('#spinner_taxon_postpartum').show();
+ $('#spinner_taxon_postpartum2').show();
+ selectize.setTextboxValue(taxon);
+ $("#search_taxon_postpartum option:selected").text(taxon);
+ $("#search_taxon_postpartum option:selected").val(taxon);
+ $('#filter_taxon_postpartum').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_taxon_postpartum'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ createTableWithArg(taxonid, 'has_given_birth_since', 'results_taxon_postpartum');
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_postpartum').hide();
+ $('#spinner_taxon_postpartum2').hide();
+ // Clear oracle
+ $("#relationpostpartumByTaxon").val("");
+ $('#filter_taxon_postpartum').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: postpartum
+if ( postpartum !== null ) {
+ $('input.column_filter').val(postpartum);
+}
+
+// var thtable = $('#results_taxon_postpartum').DataTable();
+
+// Datatable
+// function createTable(path) {
+// if ( path != '' ) {
+// let l_path = path.split('/');
+// let taxonid = l_path[l_path.length-1];
+//
+// $('#filter_taxon_postpartum').removeAttr('disabled');
+// $('#spinner_taxon_postpartum').show();
+// $('#spinner_taxon_postpartum2').show();
+//
+// $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+// { taxonid: taxonid,
+// type: 'postpartum'
+// },
+// function success(relations) {
+// $('#hide').css( 'display', 'block' );
+// $('#results_taxon_postpartum').DataTable().destroy();
+// thtable = $('#results_taxon_postpartum').DataTable(
+// {dom: 'lifrtBp', // 'Bfrtip'
+// data: relations,
+// buttons: [
+// {
+// extend: 'copyHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'csvHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'excelHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'pdfHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// 'colvis'
+// ],
+// columns: [
+// {"render": function(data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'postpartum'; }
+// var docids = format_docs(row, alvisir, rtype);
+// let docs = "";
+// if ( data.includes(', ') ) { docs = data.split(', '); }
+// else { docs = data.split(','); }
+// let docs_f = "";
+// if ( docs.length > 2 ) { // 3
+// docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+// }
+// else {
+// docs_f = docids;
+// }
+// return docs_f;
+// }},
+// {"render": function ( data, type, row, meta ) {
+// let taxa = row[1].split(', ');
+// let taxon = taxa[0];
+// if ( row[9].includes("ncbi") ) {
+// taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// else if ( row[9].includes("bd") ) {
+// taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// return taxon;
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[2];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[3].split(',')[0];
+// }},
+// {"orderable": false, "render": function (data, type, row, meta) {
+// return row[4];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[5];
+// }},
+// {"render": function (data, type, row, meta) {
+// let taxs = row[1].split(', ');
+// let forms = "";
+// for ( let i = 1; i < taxs.length ; i++ ) {
+// forms += taxs[i]
+// if ( i != taxs.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let elts = row[3].split(', ');
+// let forms = "";
+// for ( let i = 1; i < elts.length ; i++ ) {
+// forms += elts[i]
+// if ( i != elts.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'postpartum'; }
+// var docids = format_docs(row, alvisir, rtype);
+// return docids;
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[9];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[7];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[8];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[6];
+// }}
+// ]
+// });
+//
+// if ( $('#postpartum_tp').val() != '' ) { filterColumnpostpartum(3); }
+// if ( $('input[name=qps_tp]').is(':checked') == true ) { filterColumnCheck(4); }
+//
+// $('#spinner_taxon_postpartum').hide();
+// $('#spinner_taxon_postpartum2').hide();
+//
+// checkURL();
+// });
+// }
+// else {
+// alert("No result for " + taxon);
+// // Spinner off
+// $('#spinner_taxon_postpartum').hide();
+// $('#spinner_taxon_postpartum2').hide();
+// // Clear oracle
+// $("#relationpostpartumByTaxon").val("");
+// $('#filter_taxon_postpartum').attr('disabled', 'disabled');
+// // Change URL
+// window.location.replace(window.location.pathname);
+// }
+// }
+// function createTable_old(taxon) {
+// $.getJSON($SCRIPT_ROOT + '/_get_path',
+// {name: taxon, table: 'list_taxon_postpartum'},
+// function success(path) {
+// if ( path != '' ) {
+// let l_path = path[0].split('/');
+// let taxonid = l_path[l_path.length-1];
+//
+// $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+// { taxonid: taxonid,
+// type: 'postpartum'
+// },
+// function success(relations) {
+// $('#hide').css( 'display', 'block' );
+// $('#results_taxon_postpartum').DataTable().destroy();
+// thtable = $('#results_taxon_postpartum').DataTable(
+// {dom: 'lifrtBp', // 'Bfrtip'
+// data: relations,
+// buttons: [
+// {
+// extend: 'copyHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'csvHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'excelHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'pdfHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// 'colvis'
+// ],
+// columns: [
+// {"render": function(data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'postpartum'; }
+// var docids = format_docs(row, alvisir, rtype);
+// let docs = "";
+// if ( data.includes(', ') ) { docs = data.split(', '); }
+// else { docs = data.split(','); }
+// let docs_f = "";
+// if ( docs.length > 2 ) { // 3
+// docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+// }
+// else {
+// docs_f = docids;
+// }
+// return docs_f;
+// }},
+// {"render": function ( data, type, row, meta ) {
+// let taxa = row[1].split(', ');
+// let taxon = taxa[0];
+// if ( row[9].includes("ncbi") ) {
+// taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// else if ( row[9].includes("bd") ) {
+// taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// return taxon;
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[2];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[3].split(',')[0];
+// }},
+// {"orderable": false, "render": function (data, type, row, meta) {
+// return row[4];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[5];
+// }},
+// {"render": function (data, type, row, meta) {
+// let taxs = row[1].split(', ');
+// let forms = "";
+// for ( let i = 1; i < taxs.length ; i++ ) {
+// forms += taxs[i]
+// if ( i != taxs.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let elts = row[3].split(', ');
+// let forms = "";
+// for ( let i = 1; i < elts.length ; i++ ) {
+// forms += elts[i]
+// if ( i != elts.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'postpartum'; }
+// var docids = format_docs(row, alvisir, rtype);
+// return docids;
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[9];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[7];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[8];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[6];
+// }}
+// // {"width": "15%", "targets": 0,
+// // render: function(data, type, row, meta) {
+// // var docids = format_docs(row, alvisir, 'postpartum');
+// // let docs = "";
+// // if ( data.includes(', ') ) { docs = data.split(', '); }
+// // else { docs = data.split(','); }
+// // let docs_f = "";
+// // if ( docs.length > 3 ) {
+// // docs_f = docids.split(", ").slice(0,3).join(', ') + ", ...";
+// // }
+// // else {
+// // docs_f = docids;
+// // }
+// //
+// // return docs_f;
+// // }
+// // },
+// // {"width": "30%", "targets": 1,
+// // "render": function ( data, type, row, meta ) {
+// // let taxa = data.split(', ');
+// // let taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>: ";
+// // let forms = "";
+// // for ( let i = 1; i < taxa.length ; i++ ) {
+// // forms += taxa[i] + ", "
+// // }
+// // forms = forms.slice(0, -2);
+// //
+// // let taxa_f = "";
+// // if ( taxa.length > 3 ) {
+// // taxa_f = taxon + forms.split(", ").slice(0,2).join(', ') + ", ...";
+// // }
+// // else {
+// // taxa_f = taxon + forms;
+// // }
+// //
+// // return taxa_f;
+// // },
+// // },
+// // {"width": "12%", "targets": 2},
+// // {"width": "28%", "targets": 3,
+// // "render": function ( data, type, row, meta ) {
+// // let elts = data.split(', ');
+// // let elt = "<b>"+elts[0]+"</b>: ";
+// // let forms = "";
+// // for ( let i = 1; i < elts.length ; i++ ) {
+// // forms += elts[i] + ", "
+// // }
+// // forms = forms.slice(0, -2);
+// //
+// // let elts_f = "";
+// // if ( elts.length > 3 ) {
+// // elts_f = elt + forms.split(", ").slice(0,2).join(', ') + ", ...";
+// // }
+// // else {
+// // elts_f = elt + forms;
+// // }
+// // return elts_f;
+// // },
+// // },
+// // {"width": "5%", "targets": 4, "orderable": false,
+// // "render": function ( data, type, row, meta ) {
+// // let qps = data;
+// // return "<center>"+qps+"</center>";
+// // },
+// // },
+// // {"width": "10%", "targets": 5 },
+// // {"data": null, "orderable": false,
+// // "className": "details-control", "defaultContent": ""}
+// ]
+// // ,
+// // buttons: [
+// // 'copy', 'excel', 'pdf', 'print']
+// });
+//
+// if ( $('#postpartum_tp').val() != '' ) { filterColumnpostpartum(3); }
+// if ( $('input[name=qps_tp]').is(':checked') == true ) { filterColumnCheck(4); }
+//
+// $('#spinner_taxon_postpartum').hide();
+// $('#spinner_taxon_postpartum2').hide();
+//
+// checkURL();
+// });
+// }
+// else {
+// alert("No result for " + taxon);
+// // Spinner off
+// $('#spinner_taxon_postpartum').hide();
+// $('#spinner_taxon_postpartum2').hide();
+// // Clear oracle
+// $("#relationpostpartumByTaxon").val("");
+// $('#filter_taxon_postpartum').attr('disabled', 'disabled');
+// // Change URL
+// window.location.replace(window.location.pathname);
+// }
+// });
+// }
+
+// Filter - postpartum
+function filterColumnpostpartum(i) {
+ $('#results_taxon_postpartum').DataTable().column(i).search(
+ $('#postpartum_tp').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumnpostpartum($(this).parents('tr').attr('data-column'));
+} );
+
+// Filter - QPS
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_tp]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_postpartum').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_taxon_postpartum option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search_taxon_postpartum option:selected").text();
+ }
+ if ( $("#postpartum_tp").val() !== '' ) {
+ url += "&postpartum=" + $("#postpartum_tp").val();
+ }
+ // if ( $('#qps_tp').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByTaxonForSampleType.js b/static/js/searchByTaxonForSampleType.js
new file mode 100644
index 0000000000000000000000000000000000000000..1375a9ea8abdeecb96a8a8e893035aad4ea25a50
--- /dev/null
+++ b/static/js/searchByTaxonForSampleType.js
@@ -0,0 +1,497 @@
+/**
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+import { format_docs, createTable, createTableWithArg } from './utils.js';
+
+$("#searchByTaxonForSampleType.nav-item").addClass( "active" );
+
+$('#spinner_taxon_sample').show();
+$('#spinner_taxon_sample2').show();
+
+var thtable = $('#results_taxon_sample').DataTable();
+
+var $select = $('#search_taxon_sample').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Bos taurus',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ // $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
+ { table: "list_taxon_sample"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_sample').hide();
+ $('#spinner_taxon_sample2').hide();
+ $('#search_taxon_sample').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != "") {
+
+ $('#filter_taxon_sample').removeAttr('disabled');
+ $('#spinner_taxon_sample').show();
+ $('#spinner_taxon_sample2').show();
+
+ createTable(value, 'have_produced_1', 'results_taxon_sample');
+
+ if ( $('#sample_tu').val() != '' ) { filterColumnsample(3); }
+ // if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_taxon_sample').hide();
+ $('#spinner_taxon_sample2').hide();
+
+ checkURL();
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_sample').hide();
+ $('#spinner_taxon_sample2').hide();
+ // Clear oracle
+ $("#relationSampleByTaxon").val("");
+ $('#filter_taxon_sample').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
+
+// URL: taxon
+if ( taxon !== null ) {
+ $('#spinner_taxon_sample').show();
+ $('#spinner_taxon_sample2').show();
+ selectize.setTextboxValue(taxon);
+ $("#search_taxon_sample option:selected").text(taxon);
+ $("#search_taxon_sample option:selected").val(taxon);
+ $('#filter_taxon_sample').removeAttr('disabled');
+
+ $.getJSON($SCRIPT_ROOT + '/_get_path',
+ {name: taxon, table: 'list_taxon_sample'},
+ function success(path) {
+ if ( path != '' ) {
+ let l_path = path[0].split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ createTableWithArg(taxonid, 'have_produced_1', 'results_taxon_sample');
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_sample').hide();
+ $('#spinner_taxon_sample2').hide();
+ // Clear oracle
+ $("#relationSampleByTaxon").val("");
+ $('#filter_taxon_sample').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+ });
+}
+// URL: qps
+// if ( qps !== null ) {
+// $('input:checkbox').prop('checked', true);
+// }
+// URL: sample
+if ( sample !== null ) {
+ $('input.column_filter').val(sample);
+}
+
+// var thtable = $('#results_taxon_sample').DataTable();
+
+// Data table
+// function createTable(path) {
+// if ( path != '' ) {
+// let l_path = path.split('/');
+// let taxonid = l_path[l_path.length-1];
+//
+// $('#filter_taxon_sample').removeAttr('disabled');
+// $('#spinner_taxon_sample').show();
+// $('#spinner_taxon_sample2').show();
+//
+// $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+// { taxonid: taxonid,
+// type: 'sample'
+// },
+// function success(relations) {
+// $('#hide').css( 'display', 'block' );
+// $('#results_taxon_sample').DataTable().destroy();
+// thtable = $('#results_taxon_sample').DataTable(
+// {dom: 'lifrtBp', // 'Bfrtip'
+// data: relations,
+// buttons: [
+// {
+// extend: 'copyHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'csvHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'excelHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'pdfHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// 'colvis'
+// ],
+// columns: [
+// {"render": function(data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'sample'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// let docs = "";
+// if ( data.includes(', ') ) { docs = data.split(', '); }
+// else { docs = data.split(','); }
+// let docs_f = "";
+// if ( docs.length > 2 ) { // 3
+// docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+// }
+// else {
+// docs_f = docids;
+// }
+// return docs_f;
+// }},
+// {"render": function ( data, type, row, meta ) {
+// let taxa = row[1].split(', ');
+// let taxon = taxa[0];
+// if ( row[9].includes("ncbi") ) {
+// taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// else if ( row[9].includes("bd") ) {
+// taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// return taxon;
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[2];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[3].split(',')[0];
+// }},
+// {"orderable": false, "render": function (data, type, row, meta) {
+// return row[4];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[5];
+// }},
+// {"render": function (data, type, row, meta) {
+// let taxs = row[1].split(', ');
+// let forms = "";
+// for ( let i = 1; i < taxs.length ; i++ ) {
+// forms += taxs[i]
+// if ( i != taxs.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let elts = row[3].split(', ');
+// let forms = "";
+// for ( let i = 1; i < elts.length ; i++ ) {
+// forms += elts[i]
+// if ( i != elts.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'sample'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// return docids;
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[9];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[7];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[8];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[6];
+// }}
+// ]
+// });
+//
+// if ( $('#sample_tu').val() != '' ) { filterColumnsample(3); }
+// if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
+//
+// $('#spinner_taxon_sample').hide();
+// $('#spinner_taxon_sample2').hide();
+//
+// checkURL();
+// });
+// }
+// else {
+// alert("No result for " + taxon);
+// // Spinner off
+// $('#spinner_taxon_sample').hide();
+// $('#spinner_taxon_sample2').hide();
+// // Clear oracle
+// $("#relationsampleByTaxon").val("");
+// $('#filter_taxon_sample').attr('disabled', 'disabled');
+// // Change URL
+// window.location.replace(window.location.pathname);
+// }
+// }
+// function createTable_old(taxon) {
+// $.getJSON($SCRIPT_ROOT + '/_get_path',
+// {name: taxon, table: 'list_taxon_sample'},
+// function success(path) {
+// if ( path != '' ) {
+// let l_path = path[0].split('/');
+// let taxonid = l_path[l_path.length-1];
+//
+// $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+// { taxonid: taxonid,
+// type: 'sample'
+// },
+// function success(relations) {
+// $('#hide').css( 'display', 'block' );
+// $('#results_taxon_sample').DataTable().destroy();
+// thtable = $('#results_taxon_sample').DataTable(
+// {dom: 'lifrtBp', // 'Bfrtip'
+// data: relations,
+// buttons: [
+// {
+// extend: 'copyHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'csvHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'excelHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// {
+// extend: 'pdfHtml5',
+// exportOptions: { columns: function ( idx, data, node ) {
+// var table_id = node.getAttribute('aria-controls');
+// if ( idx == 0 ) { return false; } // Never Source Text
+// else if ( idx == 6 ) { return true; } // Always Full Source Text
+// return $('#' + table_id).DataTable().column( idx ).visible(); }
+// },
+// title: 'Omnicrobe_V_'+version
+// },
+// 'colvis'
+// ],
+// columns: [
+// {"render": function(data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'sample'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// let docs = "";
+// if ( data.includes(', ') ) { docs = data.split(', '); }
+// else { docs = data.split(','); }
+// let docs_f = "";
+// if ( docs.length > 2 ) { // 3
+// docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+// }
+// else {
+// docs_f = docids;
+// }
+// return docs_f;
+// }},
+// {"render": function ( data, type, row, meta ) {
+// let taxa = row[1].split(', ');
+// let taxon = taxa[0];
+// if ( row[9].includes("ncbi") ) {
+// taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// else if ( row[9].includes("bd") ) {
+// taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+// }
+// return taxon;
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[2];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[3].split(',')[0];
+// }},
+// {"orderable": false, "render": function (data, type, row, meta) {
+// return row[4];
+// }},
+// {"render": function (data, type, row, meta) {
+// return row[5];
+// }},
+// {"render": function (data, type, row, meta) {
+// let taxs = row[1].split(', ');
+// let forms = "";
+// for ( let i = 1; i < taxs.length ; i++ ) {
+// forms += taxs[i]
+// if ( i != taxs.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let elts = row[3].split(', ');
+// let forms = "";
+// for ( let i = 1; i < elts.length ; i++ ) {
+// forms += elts[i]
+// if ( i != elts.length - 1 ) { forms += ", " }
+// }
+// return forms;
+// }},
+// {"render": function (data, type, row, meta) {
+// let rtype = '';
+// if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+// else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'sample'; }
+// else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+// var docids = format_docs(row, alvisir, rtype);
+// return docids;
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[9];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[7];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[8];
+// }},
+// {"visible": false, "render": function (data, type, row, meta) {
+// return row[6];
+// }}
+// ]
+// });
+//
+// if ( $('#sample_tu').val() != '' ) { filterColumnsample(3); }
+// if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
+//
+// $('#spinner_taxon_sample').hide();
+// $('#spinner_taxon_sample2').hide();
+//
+// checkURL();
+// });
+// }
+// else {
+// alert("No result for " + taxon);
+// // Spinner off
+// $('#spinner_taxon_sample').hide();
+// $('#spinner_taxon_sample2').hide();
+// // Clear oracle
+// $("#relationsampleByTaxon").val("");
+// $('#filter_taxon_sample').attr('disabled', 'disabled');
+// // Change URL
+// window.location.replace(window.location.pathname);
+// }
+// });
+// }
+
+// Filter - sample
+function filterColumnsample(i) {
+ $('#results_taxon_sample').DataTable().column(i).search(
+ $('#sample_tu').val().replace(/;/g, "|"), true, false
+ ).draw();
+ checkURL();
+}
+$('input.column_filter').on( 'keyup click', function () {
+ filterColumnsample($(this).parents('tr').attr('data-column'));
+} );
+
+// Filter - QPS
+// function filterColumnCheck(i) {
+// let state = $('input[name=qps_tu]').is(':checked');
+// let qps = "";
+// if ( state == true ) { qps = "yes"; }
+// $('#results_taxon_sample').DataTable().column(i).search(
+// qps, true, false
+// ).draw();
+// checkURL();
+// }
+// $('input:checkbox').on('change', function () {
+// filterColumnCheck(4);
+// });
+
+// Check url
+function checkURL() {
+ var url = window.location.pathname;
+ if ( $("#search_taxon_sample option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search_taxon_sample option:selected").text();
+ }
+ if ( $("#sample_tu").val() !== '' ) {
+ url += "&sample=" + $("#sample_tu").val();
+ }
+ // if ( $('#qps_tu').is(":checked") ) {
+ // url += "&qps=yes";
+ // }
+ history.pushState({}, null, url);
+}
diff --git a/static/js/searchByTaxonForUse.js b/static/js/searchByTaxonForUse.js
deleted file mode 100644
index 265128d29e206cc246b69854f3e89d440ac8f773..0000000000000000000000000000000000000000
--- a/static/js/searchByTaxonForUse.js
+++ /dev/null
@@ -1,450 +0,0 @@
-/**
-# Copyright 2022 Sandra Dérozier (INRAE)
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-**/
-
-import { format_docs } from './utils.js';
-
-$("#searchByTaxonForUse.nav-item").addClass( "active" );
-
-$('#spinner_taxon_use').show();
-$('#spinner_taxon_use2').show();
-
-var $select = $('#search_taxon_use').selectize({
- valueField: 'path',
- labelField: 'name',
- searchField: 'name',
- sortField: 'name',
- placeholder: 'e.g. Bacillus subtilis',
- openOnFocus: false,
- create: false,
- maxItems: 1,
- onInitialize: function() {
- var that = this;
-
- // $.getJSON($SCRIPT_ROOT + '/_get_list_term',
- $.getJSON($SCRIPT_ROOT + '/_get_list_obt_class',
- { table: "list_taxon_use"},
- function(data) {
- data.forEach(function(item) {
- that.addOption(item);
- });
- $('#spinner_taxon_use').hide();
- $('#spinner_taxon_use2').hide();
- $('#search_taxon_use').prop('disabled', false);
- });
- },
- onChange:function(value){
- if (value != "") {
- createTable(value);
- }
- }
- });
-
-var selectize = $select[0].selectize;
-
-// URL: taxon
-if ( taxon !== null ) {
- $('#spinner_taxon_use').show();
- $('#spinner_taxon_use2').show();
- selectize.setTextboxValue(taxon);
- $("#search_taxon_use option:selected").text(taxon);
- $("#search_taxon_use option:selected").val(taxon);
- $('#filter_taxon_use').removeAttr('disabled');
- createTable_old(taxon);
-}
-// URL: qps
-if ( qps !== null ) {
- $('input:checkbox').prop('checked', true);
-}
-// URL: use
-if ( use !== null ) {
- $('input.column_filter').val(use);
-}
-
-var thtable = $('#results_taxon_use').DataTable();
-
-// Data table
-function createTable(path) {
- if ( path != '' ) {
- let l_path = path.split('/');
- let taxonid = l_path[l_path.length-1];
-
- $('#filter_taxon_use').removeAttr('disabled');
- $('#spinner_taxon_use').show();
- $('#spinner_taxon_use2').show();
-
- $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
- { taxonid: taxonid,
- type: 'use'
- },
- function success(relations) {
- $('#hide').css( 'display', 'block' );
- $('#results_taxon_use').DataTable().destroy();
- thtable = $('#results_taxon_use').DataTable(
- {dom: 'lifrtBp', // 'Bfrtip'
- data: relations,
- buttons: [
- {
- extend: 'copyHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'csvHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'excelHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'pdfHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- 'colvis'
- ],
- columns: [
- {"render": function(data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- let docs = "";
- if ( data.includes(', ') ) { docs = data.split(', '); }
- else { docs = data.split(','); }
- let docs_f = "";
- if ( docs.length > 2 ) { // 3
- docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
- }
- else {
- docs_f = docids;
- }
- return docs_f;
- }},
- {"render": function ( data, type, row, meta ) {
- let taxa = row[1].split(', ');
- let taxon = taxa[0];
- if ( row[9].includes("ncbi") ) {
- taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- else if ( row[9].includes("bd") ) {
- taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- return taxon;
- }},
- {"render": function (data, type, row, meta) {
- return row[2];
- }},
- {"render": function (data, type, row, meta) {
- return row[3].split(',')[0];
- }},
- {"orderable": false, "render": function (data, type, row, meta) {
- return row[4];
- }},
- {"render": function (data, type, row, meta) {
- return row[5];
- }},
- {"render": function (data, type, row, meta) {
- let taxs = row[1].split(', ');
- let forms = "";
- for ( let i = 1; i < taxs.length ; i++ ) {
- forms += taxs[i]
- if ( i != taxs.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let elts = row[3].split(', ');
- let forms = "";
- for ( let i = 1; i < elts.length ; i++ ) {
- forms += elts[i]
- if ( i != elts.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- return docids;
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[9];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[7];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[8];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[6];
- }}
- ]
- });
-
- if ( $('#use_tu').val() != '' ) { filterColumnuse(3); }
- if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
-
- $('#spinner_taxon_use').hide();
- $('#spinner_taxon_use2').hide();
-
- checkURL();
- });
- }
- else {
- alert("No result for " + taxon);
- // Spinner off
- $('#spinner_taxon_use').hide();
- $('#spinner_taxon_use2').hide();
- // Clear oracle
- $("#relationUseByTaxon").val("");
- $('#filter_taxon_use').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
-}
-function createTable_old(taxon) {
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: taxon, table: 'list_taxon_use'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let taxonid = l_path[l_path.length-1];
-
- $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
- { taxonid: taxonid,
- type: 'use'
- },
- function success(relations) {
- $('#hide').css( 'display', 'block' );
- $('#results_taxon_use').DataTable().destroy();
- thtable = $('#results_taxon_use').DataTable(
- {dom: 'lifrtBp', // 'Bfrtip'
- data: relations,
- buttons: [
- {
- extend: 'copyHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'csvHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'excelHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
- },
- title: 'Omnicrobe_V_'+version
- },
- {
- extend: 'pdfHtml5',
- exportOptions: { columns: function ( idx, data, node ) {
- var table_id = node.getAttribute('aria-controls');
- if ( idx == 0 ) { return false; } // Never Source Text
- else if ( idx == 6 ) { return true; } // Always Full Source Text
- return $('#' + table_id).DataTable().column( idx ).visible(); }
- },
- title: 'Omnicrobe_V_'+version
- },
- 'colvis'
- ],
- columns: [
- {"render": function(data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- let docs = "";
- if ( data.includes(', ') ) { docs = data.split(', '); }
- else { docs = data.split(','); }
- let docs_f = "";
- if ( docs.length > 2 ) { // 3
- docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
- }
- else {
- docs_f = docids;
- }
- return docs_f;
- }},
- {"render": function ( data, type, row, meta ) {
- let taxa = row[1].split(', ');
- let taxon = taxa[0];
- if ( row[9].includes("ncbi") ) {
- taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- else if ( row[9].includes("bd") ) {
- taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
- }
- return taxon;
- }},
- {"render": function (data, type, row, meta) {
- return row[2];
- }},
- {"render": function (data, type, row, meta) {
- return row[3].split(',')[0];
- }},
- {"orderable": false, "render": function (data, type, row, meta) {
- return row[4];
- }},
- {"render": function (data, type, row, meta) {
- return row[5];
- }},
- {"render": function (data, type, row, meta) {
- let taxs = row[1].split(', ');
- let forms = "";
- for ( let i = 1; i < taxs.length ; i++ ) {
- forms += taxs[i]
- if ( i != taxs.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let elts = row[3].split(', ');
- let forms = "";
- for ( let i = 1; i < elts.length ; i++ ) {
- forms += elts[i]
- if ( i != elts.length - 1 ) { forms += ", " }
- }
- return forms;
- }},
- {"render": function (data, type, row, meta) {
- let rtype = '';
- if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
- else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
- else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
- var docids = format_docs(row, alvisir, rtype);
- return docids;
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[9];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[7];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[8];
- }},
- {"visible": false, "render": function (data, type, row, meta) {
- return row[6];
- }}
- ]
- });
-
- if ( $('#use_tu').val() != '' ) { filterColumnuse(3); }
- if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
-
- $('#spinner_taxon_use').hide();
- $('#spinner_taxon_use2').hide();
-
- checkURL();
- });
- }
- else {
- alert("No result for " + taxon);
- // Spinner off
- $('#spinner_taxon_use').hide();
- $('#spinner_taxon_use2').hide();
- // Clear oracle
- $("#relationUseByTaxon").val("");
- $('#filter_taxon_use').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
- });
-}
-
-// Filter - use
-function filterColumnuse(i) {
- $('#results_taxon_use').DataTable().column(i).search(
- $('#use_tu').val().replace(/;/g, "|"), true, false
- ).draw();
- checkURL();
-}
-$('input.column_filter').on( 'keyup click', function () {
- filterColumnuse($(this).parents('tr').attr('data-column'));
-} );
-
-// Filter - QPS
-function filterColumnCheck(i) {
- let state = $('input[name=qps_tu]').is(':checked');
- let qps = "";
- if ( state == true ) { qps = "yes"; }
- $('#results_taxon_use').DataTable().column(i).search(
- qps, true, false
- ).draw();
- checkURL();
-}
-$('input:checkbox').on('change', function () {
- filterColumnCheck(4);
- });
-
-// Check url
-function checkURL() {
- var url = window.location.pathname;
- if ( $("#search_taxon_use option:selected").text() !== '' ) {
- url += "?taxon=" + $("#search_taxon_use option:selected").text();
- }
- if ( $("#use_tu").val() !== '' ) {
- url += "&use=" + $("#use_tu").val();
- }
- if ( $('#qps_tu').is(":checked") ) {
- url += "&qps=yes";
- }
- history.pushState({}, null, url);
-}
diff --git a/static/js/sheet.js b/static/js/sheet.js
new file mode 100644
index 0000000000000000000000000000000000000000..99b65f78d98a77362f0086680cc51c34e51e2002
--- /dev/null
+++ b/static/js/sheet.js
@@ -0,0 +1,107 @@
+document.addEventListener('DOMContentLoaded', function() {
+ // Initial setup
+ initializeApp();
+
+ // Event listeners for global elements
+ setupEventListeners();
+});
+
+function initializeApp() {
+ // Show initial section
+ toggleSection('oligo');
+
+ // Load initial structure
+ loadStructure('2\'-Fucosyllactose');
+}
+
+function setupEventListeners() {
+ // Navigation buttons are handled by inline onclick in HTML
+
+ // Setup download buttons
+ const downloadButtons = document.querySelectorAll('.download-btn');
+ downloadButtons.forEach(button => {
+ button.addEventListener('click', () => downloadCSV());
+ });
+}
+
+// Section visibility toggle
+window.toggleSection = function(sectionType) {
+ const sections = document.querySelectorAll('.section');
+ sections.forEach(section => section.classList.add('hidden'));
+
+ const activeSection = document.getElementById(`${sectionType}-section`);
+ if (activeSection) {
+ activeSection.classList.remove('hidden');
+ }
+}
+
+// CSV Download functionality
+window.downloadCSV = function() {
+ const section = document.querySelector('.section:not(.hidden)');
+ if (!section) return;
+
+ try {
+ const data = collectSectionData(section);
+ const csvContent = convertToCSV(data);
+ triggerDownload(csvContent, `${section.id}_data.csv`);
+ } catch (error) {
+ console.error('Error generating CSV:', error);
+ alert('Error generating CSV file. Please try again.');
+ }
+}
+
+function collectSectionData(section) {
+ const data = [];
+ const infoItems = section.querySelectorAll('.info-item');
+
+ infoItems.forEach(item => {
+ const label = item.querySelector('.info-label').textContent.trim();
+ const value = item.querySelector('.info-value').textContent.trim();
+ data.push([label, value]);
+ });
+
+ return data;
+}
+
+function convertToCSV(data) {
+ // Add header
+ const rows = [['Label', 'Value'], ...data];
+
+ // Convert to CSV format
+ return rows
+ .map(row =>
+ row.map(cell =>
+ `"${(cell || '').replace(/"/g, '""')}"`)
+ .join(','))
+ .join('\n');
+}
+
+function triggerDownload(content, filename) {
+ const blob = new Blob([content], { type: 'text/csv;charset=utf-8;' });
+ const link = document.createElement('a');
+ link.href = URL.createObjectURL(blob);
+ link.download = filename;
+ document.body.appendChild(link);
+ link.click();
+ document.body.removeChild(link);
+}
+
+// Structure loading functionality
+async function loadStructure(compoundName) {
+ try {
+ // Example using PubChem API
+ const searchUrl = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${encodeURIComponent(compoundName)}/PNG`;
+
+ const structureImage = document.getElementById('structure-image');
+ if (structureImage) {
+ structureImage.src = searchUrl;
+ structureImage.alt = `${compoundName} structure`;
+ }
+ } catch (error) {
+ console.error('Error loading structure:', error);
+ const structureImage = document.getElementById('structure-image');
+ if (structureImage) {
+ structureImage.alt = 'Error loading structure';
+ }
+ }
+}
\ No newline at end of file
diff --git a/static/js/utils.js b/static/js/utils.js
index cc575f7b5098c5c8f093090a8aad93414be7fd2b..4d83bacf7073fbd72263b622307ec92194f35499 100644
--- a/static/js/utils.js
+++ b/static/js/utils.js
@@ -43,6 +43,9 @@ export function format_docs(relation, alvisir, rtype) {
docids += "<a target='_blank' class='doc' href='https://collection-cirmbia.fr/page/Display_souches/"+cirmid+"'>"+cirmid+"</a>, ";
}
}
+ else {
+ docids = relation[0] + ", "
+ }
// CIRM-Levures
// CIRM-CBPF
}
@@ -50,3 +53,651 @@ export function format_docs(relation, alvisir, rtype) {
return docids;
}
+
+export function createTable(path, rel_type, tablename) {
+ let l_path = path.split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ { taxonid: taxonid,
+ type: rel_type
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#'+tablename).DataTable().destroy();
+ $('#'+tablename).DataTable(
+ {
+ dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ // Source text
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced tmp 2' ) { rtype = 'Oligosaccharide_type'; }
+ else if ( row[2] == 'Have produced tmp 1' ) { rtype = 'Oligosaccharide_name'; }
+ else if ( row[2] == 'Have produced 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Have produced 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ // Scientific name of taxon
+ {"render": function ( data, type, row, meta ) {
+ // let taxa = row[1].split(', ');
+ // let taxon = taxa[0];
+ let taxa = row[12];
+ if ( row[9].includes("ncbi") ) {
+ // taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ // taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa+"</a>";
+ }
+ return taxon;
+ }},
+ // Relation type
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ // Reference class
+ {"render": function (data, type, row, meta) {
+ //return row[3].split(',')[0];
+ return row[11];
+ }},
+ // QPS
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ // Source
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ // Form taxon
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( rel_type == 'have_produced_tmp_2' || rel_type == 'have_produced_tmp_1' || rel_type == 'have_produced_2' || rel_type == 'have_produced_1' || rel_type == 'has_a_physiological_stage' || rel_type == 'has_given_birth_since' ) { i = 0; }
+ for ( i ; i < taxs.length ; i++ ) { //let i = 1;
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ // Form reference
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( rel_type == 'have_produced_tmp_2' || rel_type == 'have_produced_tmp_1' || rel_type == 'have_produced_2' || rel_type == 'have_produced_1' || rel_type == 'has_a_physiological_stage' || rel_type == 'has_given_birth_since' ) { i = 0; }
+ for ( i ; i < elts.length ; i++ ) { //let i = 1;
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ // Full source text
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced tmp 2' ) { rtype = 'Oligosaccharide_type'; }
+ else if ( row[2] == 'Have produced tmp 1' ) { rtype = 'Oligosaccharide_name'; }
+ else if ( row[2] == 'Have produced 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Have produced 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }}
+ ]
+ });
+ });
+}
+
+export function createTableRev(path, rel_type, tablename) {
+
+ let l_path = path.split('/');
+ let ontobiotopeid = l_path[l_path.length-1];
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ {
+ ontobiotopeid: ontobiotopeid,
+ type: rel_type
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#'+tablename).DataTable().destroy();
+ $('#'+tablename).DataTable(
+ {dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced tmp 2' ) { rtype = 'Oligosaccharide_type'; }
+ else if ( row[2] == 'Have produced tmp 1' ) { rtype = 'Oligosaccharide_name'; }
+ else if ( row[2] == 'Have produced 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Have produced 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ {"render": function (data, type, row, meta) {
+ // return row[3].split(',')[0];
+ return row[11];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ {"render": function ( data, type, row, meta ) {
+ // let taxa = row[1].split(', ');
+ // let taxon = taxa[0];
+ let taxa = row[12];
+ if ( row[9].includes("ncbi") ) {
+ // taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ // taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa+"</a>";
+ }
+ return taxon;
+ }},
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( rel_type == 'have_produced_tmp_2' || rel_type == 'have_produced_tmp_1' || rel_type == 'have_produced_2' || rel_type == 'have_produced_1' || rel_type == 'has_a_physiological_stage' || rel_type == 'has_given_birth_since' ) { i = 0; }
+ for ( i ; i < elts.length ; i++ ) { //let i = 1;
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( rel_type == 'have_produced_tmp_2' || rel_type == 'have_produced_tmp_1' || rel_type == 'have_produced_2' || rel_type == 'have_produced_1' || rel_type == 'has_a_physiological_stage' || rel_type == 'has_given_birth_since' ) { i = 0; }
+ for ( i ; i < taxs.length ; i++ ) { //let i = 1;
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced tmp 2' ) { rtype = 'Oligosaccharide_type'; }
+ else if ( row[2] == 'Have produced tmp 1' ) { rtype = 'Oligosaccharide_name'; }
+ else if ( row[2] == 'Have produced 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Have produced 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }}
+ ]
+ });
+ });
+}
+
+export function createTableWithArg(taxonid, etype, tablename) {
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ { taxonid: taxonid,
+ type: etype//'habitat'
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#'+tablename).DataTable().destroy();
+ $('#'+tablename).DataTable(
+ {
+ dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced tmp 2' ) { rtype = 'Oligosaccharide_type'; }
+ else if ( row[2] == 'Have produced tmp 1' ) { rtype = 'Oligosaccharide_name'; }
+ else if ( row[2] == 'Have produced 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Have produced 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ {"render": function ( data, type, row, meta ) {
+ // let taxa = row[1].split(', ');
+ // let taxon = taxa[0];
+ if ( row[9].includes("ncbi") ) {
+ // taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+row[12]+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ // taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+row[12]+"</a>";
+ }
+ return taxon;
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ {"render": function (data, type, row, meta) {
+ // return row[3].split(',')[0];
+ return row[11];
+ }},
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( etype == 'have_produced_tmp_2' || etype == 'have_produced_tmp_1' || etype == 'have_produced_2' || etype == 'have_produced_1' || etype == 'has_a_physiological_stage' || etype == 'has_given_birth_since' ) { i = 0; }
+ for ( i ; i < taxs.length ; i++ ) {
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( etype == 'have_produced_tmp_2' || etype == 'have_produced_tmp_1' || etype == 'have_produced_2' || etype == 'have_produced_1' || etype == 'has_a_physiological_stage' || etype == 'has_given_birth_since' ) { i = 0; }
+ for ( i ; i < elts.length ; i++ ) {
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced tmp 2' ) { rtype = 'Oligosaccharide_type'; }
+ else if ( row[2] == 'Have produced tmp 1' ) { rtype = 'Oligosaccharide_name'; }
+ else if ( row[2] == 'Has product 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Has product 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }}
+ ]
+ });
+ });
+}
+
+export function createTableWithArgRev(ontobiotopeid, etype, tablename) {
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ { ontobiotopeid: ontobiotopeid,
+ type: etype
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#'+tablename).DataTable().destroy();
+ $('#'+tablename).DataTable(
+ {dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Have produced 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[3].split(',')[0];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ {"render": function ( data, type, row, meta ) {
+ let taxa = row[1].split(', ');
+ let taxon = taxa[0];
+ if ( row[9].includes("ncbi") ) {
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ return taxon;
+ }},
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( etype == 'have_produced_2' || etype == 'have_produced_1' || etype == 'has_a_physiological_stage' || etype == 'has_given_birth_since' ) { i = 0; }
+ for ( let i = 1; i < elts.length ; i++ ) {
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ let i = 1;
+ if ( etype == 'have_produced_2' || etype == 'have_produced_1' || etype == 'has_a_physiological_stage' || etype == 'has_given_birth_since' ) { i = 0; }
+ for ( let i = 1; i < taxs.length ; i++ ) {
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Have produced 2' ) { rtype = 'lactationstage'; }
+ else if ( row[2] == 'Have produced 1' ) { rtype = 'sampletype'; }
+ else if ( row[2] == 'Has given birth since' ) { rtype = 'postpartumage'; }
+ else if ( row[2] == 'Has a physiological stage' ) { rtype = 'physiologicalstage'; }
+ else if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }}
+ ]
+ });
+ });
+}
diff --git a/templates/about.html b/templates/about.html
index 773ab71f26363a732c54c1af6dabbcc990247aaf..3a8882ebe98f716310794c2055b3a45f6e6e3398 100644
--- a/templates/about.html
+++ b/templates/about.html
@@ -26,6 +26,10 @@
<div style="margin-left: 5%;margin-right: 5%;">
+ <div class="alert alert-info" role="alert">
+ The content of this page will be adapted at a later date!
+ </div>
+
<h2><span style="color: #21517A;">About Omnicrobe</span></h2><br/>
<IMG ALIGN="LEFT" SRC="{{ url_for('static', filename='img/textmining.png') }}" width="50" height="50"/><div class="text-info" class="text-info" style="padding-top: 10px;"><h4> Context</h4></div>
diff --git a/templates/advancedSearch.html b/templates/advancedSearch.html
index 1c5ba1b49297d49ad0e24c5e66cc4b3d6ab102eb..5a8dd6e3fa95db642499b69387e5dc882b9201ac 100644
--- a/templates/advancedSearch.html
+++ b/templates/advancedSearch.html
@@ -29,13 +29,21 @@
<link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
<link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
- <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />"
- <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/font-awesome@4.7.0/css/font-awesome.css" />
- <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/jQuery-QueryBuilder@2.5.2/dist/css/query-builder.default.css" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/research.css') }}" />
+ <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.5.1/css/all.min.css" />
- <script type="text/javascript" src="https://cdn.jsdelivr.net/npm/sql-parser-mistic@1.2.3/browser/sql-parser.js"></script>
- <script type="text/javascript" src="https://cdn.jsdelivr.net/npm/interactjs@1.6.2/dist/interact.js"></script>
- <script src="https://cdn.jsdelivr.net/npm/jQuery-QueryBuilder@2.5.2/dist/js/query-builder.standalone.js"></script>
+<!-- jQuery QueryBuilder -->
+ <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jQuery-QueryBuilder/2.7.0/css/query-builder.default.min.css" />
+
+<!-- Interact.js -->
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/interact.js/1.10.26/interact.min.js"></script>
+
+<!-- jQuery QueryBuilder -->
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/jQuery-QueryBuilder/2.7.0/js/query-builder.standalone.min.js"></script>
+
+<!-- Selectize.js -->
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.15.2/js/selectize.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script type="module" src="{{ url_for('static', filename='js/advancedSearch.js') }}"></script>
@@ -47,10 +55,24 @@
.rule-value-container{ display: inline }
</style>
+<body>
+
+ <div class="main-content2">
+ <section class="info-section">
+ <div class="info-box">
+ <div class="search-icon">
+ <i class="fas fa-search"></i>
+ </div>
+ <h2>Advanced Search</h2>
+ <p> Build complex queries with multiple criteria and filters. Ideal for research and detailed analysis of oligosaccharide data.</p>
+ </div>
+ </section>
+
+
<div style="margin:80px 0;"></div>
<div style="margin-left: 5%;margin-right: 5%;">
- <h3><span style="color: #21517A;">Advanced search</span></h3>
+ <!-- <h3><span style="color: #21517A;">Advanced search</span></h3> -->
<div style="margin-left: 2%;margin-right: 2%;">
<div class="d-flex justify-content-center text-info">
diff --git a/templates/footer b/templates/footer
index d3a64a525ce6c5f7734f783ea9781993432d6a09..30bad55a01613e3e6727a62ccd8d325cd0f9a78a 100644
--- a/templates/footer
+++ b/templates/footer
@@ -19,7 +19,7 @@
<table width="100%" border=0>
<tr>
<td width="25%"><a target="_blank"href="http://maiage.inrae.fr"><img align="left" src="{{ url_for('static', filename='img/logo_maiage_blanc.png') }}" height="30px"/></a></td>
- <td width="50%"><div align="center" style="font-size: small;color: white;" class='color'>Copyright © 2023 <a class='color' style="color: white;" target="_blank"href="http://inrae.fr">INRAE</a> - <a class='color' style="color: white;" target="_blank"href="http://maiage.inrae.fr">MaIAGE</a><br/><a class='color' style="color: white;" href="mailto:omnicrobe@inrae.fr">omnicrobe@inrae.fr</a></div></td>
+ <td width="50%"><div align="center" style="font-size: small;color: white;" class='color'>Copyright © 2024 <a class='color' style="color: white;" target="_blank"href="http://inrae.fr">INRAE</a> - <a class='color' style="color: white;" target="_blank"href="http://maiage.inrae.fr">MaIAGE</a><br/><a class='color' style="color: white;" href="mailto:omnicrobe@inrae.fr">omnicrobe@inrae.fr</a></div></td>
<td width="25%"><a target="_blank"href="http://inrae.fr"><img align="right" src="{{ url_for('static', filename='img/logo-inrae-blanc.png') }}" height="30px"/></a></td>
</tr>
</table>
diff --git a/templates/header b/templates/header
index 5d0f4acd55ef33c8f7b963a672eca03a6f83ad19..cc1f9af78210f6af9df323a4574d6ecc5d107cee 100644
--- a/templates/header
+++ b/templates/header
@@ -18,8 +18,8 @@
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="robots" content="noindex" />
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
- <meta name="description" property="schema:description" resource="#OMNICROBE" content="Omnicrobe"/>
- <title>Omnicrobe</title>
+ <meta name="description" property="schema:description" resource="#OMNICROBE" content="HoloOligo"/>
+ <title>HoloOligo</title>
<script>
$(document).prop('title', 'Omnicrobe');
</script>
diff --git a/templates/home.html b/templates/home.html
new file mode 100644
index 0000000000000000000000000000000000000000..ea9fa5a02cae665ee18a3fd74267ae8682395250
--- /dev/null
+++ b/templates/home.html
@@ -0,0 +1,74 @@
+{% extends 'main2' %} {% block content %}
+<script type="text/javascript">
+ $SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+</script>
+
+<script src="{{ url_for('static', filename='js/home.js') }}" defer></script>
+<link
+ rel="stylesheet"
+ href="{{ url_for('static', filename='css/home.css') }}"
+/>
+
+<!-- Header Section -->
+<section class="hero-section py-5 text-white text-center">
+ <div class="container">
+ <img
+ src="{{ url_for('static', filename='img/logo_Omnicrobe_3_resize.png') }}"
+ alt="Omnicrobe"
+ class="logo mb-4"
+ />
+ <h1 class="display-4 font-weight-bold mb-3">
+ Welcome to HoloOligo Database
+ </h1>
+ <p class="description mx-auto">
+ Explore comprehensive information on milk oligosaccharides across
+ mammalian species. Discover their roles in nutrition, gut health, and
+ immune modulation through curated data from scientific sources.
+ </p>
+ <a href="about" class="btn btn-info btn-lg mt-3">Learn More</a>
+ </div>
+</section>
+
+<!-- Data Visualization Section -->
+<section class="data-overview my-5">
+ <div class="container">
+ <h2 class="text-center section-title mb-5">HoloOligo Data Overview</h2>
+ <div class="row visualization-row">
+ <div class="col-md-4">
+ <div class="viz-card1">
+ <h3>Entities Overview</h3>
+ <div class="table-wrapper">
+ <table id="entitiesTable" class="table table-striped">
+ <thead>
+ <tr>
+ <th>Entity</th>
+ <th>Count</th>
+ </tr>
+ </thead>
+ <tbody id="entitiesTableBody"></tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="col-md-4">
+ <div class="viz-card">
+ <h3>Oligosaccharide Types</h3>
+ <canvas id="taxonsChart"></canvas>
+ </div>
+ </div>
+
+ <div class="col-md-4">
+ <div class="viz-card">
+ <h3>Species Distribution</h3>
+ <div class="coming-soon">
+ <i class="fas fa-chart-line"></i>
+ <p>Coming Soon</p>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+</section>
+
+{% endblock %}
diff --git a/templates/index.html b/templates/index.html
index a74516bac30cdb4e22a8751ad0ca5c32a7cbb53d..737a32b139fe33bfbb290b3cf165bc990d939b7f 100644
--- a/templates/index.html
+++ b/templates/index.html
@@ -26,8 +26,8 @@
<div class="row no-gutters bg-light position-relative align-items-center">
<div class="col-md-9 mb-md-0 p-md-4 align-middle">
- <h4 style="color: #21517A;">Omnicrobe is a database of habitats, phenotypes and uses</h4><br/>
- <p class="text-justify ">The Omnicrobe database gathers comprehensive information on habitats, phenotypes and usages of microorganisms as automatically extracted from text sources (PubMed, GenBank, DSMZ, CIRM-BIA, CIRM-CFBP, CIRM-Levures). The search offers you access to the information and their sources. <a class="text-info" href='about'>More information.</a>
+ <h4 style="color: #21517A;">HoloOligo is a database of oligosaccharides</h4><br/>
+ <p class="text-justify ">The HoloOligo database gathers comprehensive information on milk oligosaccharides of mammalian species as automatically extracted from text sources. The search offers you access to the information and their sources. <a class="text-info" href='about'>More information.</a>
</p>
</div>
<div class="col-md-3 position-relative p-4 pl-md-0">
@@ -42,8 +42,8 @@
<div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
<div class="card-body">
<center><img align="center" src="{{ url_for('static', filename='img/bacteria.png') }}" width="80" height="80"/></br></br>
- <h6 class="card-title">Where does a microbe live?<br/><br/><br/><br/></h6>
- <a href="searchByTaxon" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon lives in Habitat</a></center>
+ <h6 class="card-title">Search Oligosaccharide name by Taxon<br/><br/><br/><br/></h6>
+ <a href="searchByTaxonForOligosaccharideName" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Oligosaccharide name by Taxon</a></center>
</div>
</div>
</div>
@@ -51,8 +51,8 @@
<div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
<div class="card-body">
<center><img align="center" src="{{ url_for('static', filename='img/apple.png') }}" width="80" height="80"/></br></br>
- <h6 class="card-title">Which microbes can be found in a given habitat?<br/><br/><br/></h6>
- <a href="searchByHabitat" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Habitat contains Taxon</a></center>
+ <h6 class="card-title">Search Taxon by Oligosaccharide name<br/><br/><br/></h6>
+ <a href="searchByOligosaccharideName" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon by Oligosaccharide name</a></center>
</div>
</div>
</div>
@@ -60,8 +60,49 @@
<div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
<div class="card-body">
<center><img align="center" src="{{ url_for('static', filename='img/bacteria.png') }}" width="80" height="80"/></br></br>
- <h6 class="card-title">What are the phenotypes of a given microbe?<br/><br/><br/></h6>
- <a href="searchByTaxonForPhenotype" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon exhibits Phenotype</a></center>
+ <h6 class="card-title">Search Oligosaccharide type by Taxon<br/><br/><br/><br/></h6>
+ <a href="searchByTaxonForOligosaccharideType" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Oligosaccharide type by Taxon</a></center>
+ </div>
+ </div>
+ </div>
+ <div class="col-sm-2 d-flex">
+ <div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ <div class="card-body">
+ <center><img align="center" src="{{ url_for('static', filename='img/apple.png') }}" width="80" height="80"/></br></br>
+ <h6 class="card-title">Search Taxon by Oligosaccharide type<br/><br/><br/></h6>
+ <a href="searchByOligosaccharideType" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon by Oligosaccharide type</a></center>
+ </div>
+ </div>
+ </div>
+ <div class="col-sm-2 d-flex">
+ <div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ <div class="card-body">
+ <center><img align="center" src="{{ url_for('static', filename='img/bacteria.png') }}" width="80" height="80"/></br></br>
+ <h6 class="card-title">Search Physiological stage by Taxon<br/><br/><br/><br/></h6>
+ <a href="searchByTaxon" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Physiological stage by Taxon</a></center>
+ </div>
+ </div>
+ </div>
+ <div class="col-sm-2 d-flex">
+ <div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ <div class="card-body">
+ <center><img align="center" src="{{ url_for('static', filename='img/apple.png') }}" width="80" height="80"/></br></br>
+ <h6 class="card-title">Search Taxon by Physiological stage<br/><br/><br/></h6>
+ <a href="searchByPhysiologicalStage" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon by Physiological stage</a></center>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <br/>
+
+ <div class="row">
+ <div class="col-sm-2 d-flex">
+ <div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ <div class="card-body">
+ <center><img align="center" src="{{ url_for('static', filename='img/bacteria.png') }}" width="80" height="80"/></br></br>
+ <h6 class="card-title">Search Postpartum age by Taxon<br/><br/><br/></h6>
+ <a href="searchByTaxonForPostpartum" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Postpartum age by Taxon</a></center>
</div>
</div>
</div>
@@ -69,8 +110,26 @@
<div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
<div class="card-body">
<center><img align="center" src="{{ url_for('static', filename='img/life-stage.png') }}" width="80" height="80"/></br></br>
- <h6 class="card-title">Which microbes have this phenotype?<br/><br/><br/></h6>
- <a href="searchByPhenotype" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Phenotype is exhibited by Taxon</a></center>
+ <h6 class="card-title">Search Taxon by Postpartum age<br/><br/><br/></h6>
+ <a href="searchByPostpartum" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon by Postpartum age</a></center>
+ </div>
+ </div>
+ </div>
+ <div class="col-sm-2 d-flex">
+ <div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ <div class="card-body">
+ <center><img align="center" src="{{ url_for('static', filename='img/bacteria.png') }}" width="80" height="80"/></br></br>
+ <h6 class="card-title">Search Sample type by Taxon<br/><br/><br/><br/></h6>
+ <a href="searchByTaxonForSampleType" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Sample type by Taxon</a></center>
+ </div>
+ </div>
+ </div>
+ <div class="col-sm-2 d-flex">
+ <div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ <div class="card-body">
+ <center><img align="center" src="{{ url_for('static', filename='img/apple.png') }}" width="80" height="80"/></br></br>
+ <h6 class="card-title">Search Taxon by Sample type<br/><br/><br/></h6>
+ <a href="searchBySampleType" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon by Sample type</a></center>
</div>
</div>
</div>
@@ -78,17 +137,17 @@
<div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
<div class="card-body">
<center><img align="center" src="{{ url_for('static', filename='img/bacteria.png') }}" width="80" height="80"/></br></br>
- <h6 class="card-title">For which use is this microbe studied?<br/><br/><br/></h6>
- <a href="searchByTaxonForUse" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon studied for Use</a></center>
+ <h6 class="card-title">Search Lactation stage by Taxon<br/><br/><br/></h6>
+ <a href="searchByTaxonForLactation" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Lactation stage by Taxon</a></center>
</div>
</div>
</div>
<div class="col-sm-2 d-flex">
<div class="card" style="background-color: #21517A; border-color: #21517A; color: #fff;">
<div class="card-body">
- <center><img align="center" src="{{ url_for('static', filename='img/medicine.png') }}" width="80" height="80"/></br></br>
- <h6 class="card-title">Which microbe is involved in this use?<br/><br/><br/></h6>
- <a href="searchByUse" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Use involves Taxon</a></center>
+ <center><img align="center" src="{{ url_for('static', filename='img/life-stage.png') }}" width="80" height="80"/></br></br>
+ <h6 class="card-title">Search Taxon by Lactation stage<br/><br/><br/></h6>
+ <a href="searchByLactation" style="background-color: #fff; border-color: #fff; color: black;" class="btn btn-sm btn-fix">Search Taxon by Lactation stage</a></center>
</div>
</div>
</div>
diff --git a/templates/main2 b/templates/main2
index 55c99cb7f1ff9368d105f6f59664438c4d5c89c3..0ccd73e0e72e531aa8f220d4f0d7136ceaabdcc9 100644
--- a/templates/main2
+++ b/templates/main2
@@ -17,27 +17,41 @@
<!DOCTYPE html>
<html lang="en">
- <!-- CSS -->
- <link href="https://cdn.datatables.net/1.10.23/css/jquery.dataTables.min.css" rel="stylesheet" type="text/css" />
- <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.5.3/dist/css/bootstrap.min.css" integrity="sha384-TX8t27EcRE3e/ihU7zmQxVncDAy5uIKz4rEkgIXeMed4M0jlfIDPvg6uqKI2xXr2" crossorigin="anonymous">
- <link rel="stylesheet" href="//code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" />
- <link rel="stylesheet" href="{{ url_for('static', filename='css/main.css') }}">
- <link rel="stylesheet" href="https://cdn.datatables.net/buttons/1.6.5/css/buttons.dataTables.min.css" />
- <link rel="stylesheet" href="https://cdn.datatables.net/responsive/2.2.9/css/responsive.dataTables.min.css" />
-
- <!-- JS -->
- <script src="https://code.jquery.com/jquery-3.5.1.slim.min.js" integrity="sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj" crossorigin="anonymous"></script>
- <script src="https://cdn.jsdelivr.net/npm/bootstrap@4.5.3/dist/js/bootstrap.min.js" integrity="sha384-w1Q4orYjBQndcko6MimVbzY0tgp4pWB4lZ7lr30WKz0vr/aWKhXdBNmNb5D92v7s" crossorigin="anonymous"></script>
- <script src="https://code.jquery.com/jquery-3.5.1.js"></script>
- <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
- <script src="https://cdn.datatables.net/1.10.23/js/jquery.dataTables.min.js"></script>
- <script src="https://cdn.datatables.net/buttons/2.0.0/js/dataTables.buttons.min.js"></script>
- <script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
- <script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/pdfmake.min.js"></script>
- <script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/vfs_fonts.js"></script>
- <script src="https://cdn.datatables.net/buttons/2.0.0/js/buttons.html5.min.js"></script>
- <script src="https://cdn.datatables.net/buttons/2.0.0/js/buttons.colVis.min.js"></script>
- <script src="https://cdn.datatables.net/responsive/2.2.9/js/dataTables.responsive.min.js"></script>s
+<!-- CSS -->
+<link href="https://cdn.datatables.net/1.10.23/css/jquery.dataTables.min.css" rel="stylesheet" type="text/css" />
+<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.5.3/dist/css/bootstrap.min.css" integrity="sha384-TX8t27EcRE3e/ihU7zmQxVncDAy5uIKz4rEkgIXeMed4M0jlfIDPvg6uqKI2xXr2" crossorigin="anonymous">
+<link rel="stylesheet" href="//code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" />
+<link rel="stylesheet" href="{{ url_for('static', filename='css/main.css') }}">
+<link rel="stylesheet" href="https://cdn.datatables.net/buttons/1.6.5/css/buttons.dataTables.min.css" />
+<link rel="stylesheet" href="https://cdn.datatables.net/responsive/2.2.9/css/responsive.dataTables.min.css" />
+<link rel="stylesheet" href="{{ url_for('static', filename='css/home.css') }}">
+<link rel="stylesheet" href="{{ url_for('static', filename='css/research.css') }}">
+<link rel="stylesheet" href="{{ url_for('static', filename='css/results.css') }}">
+<link rel="stylesheet" href="{{ url_for('static', filename='css/sheet.css') }}">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0-beta3/css/all.min.css" rel="stylesheet">
+
+<!-- JS -->
+<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js" integrity="sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj" crossorigin="anonymous"></script>
+<script src="https://cdn.jsdelivr.net/npm/bootstrap@4.5.3/dist/js/bootstrap.min.js" integrity="sha384-w1Q4orYjBQndcko6MimVbzY0tgp4pWB4lZ7lr30WKz0vr/aWKhXdBNmNb5D92v7s" crossorigin="anonymous"></script>
+<script src="https://code.jquery.com/jquery-3.5.1.js"></script>
+<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
+<script src="https://cdn.datatables.net/1.10.23/js/jquery.dataTables.min.js"></script>
+<script src="https://cdn.datatables.net/buttons/2.0.0/js/dataTables.buttons.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/pdfmake.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/vfs_fonts.js"></script>
+<script src="https://cdn.datatables.net/buttons/2.0.0/js/buttons.html5.min.js"></script>
+<script src="https://cdn.datatables.net/buttons/2.0.0/js/buttons.colVis.min.js"></script>
+<script src="https://cdn.datatables.net/responsive/2.2.9/js/dataTables.responsive.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/chartjs-chart-matrix@1.1.0"></script>
+<script src="https://cdn.jsdelivr.net/npm/chartjs-chart-boxplot@1.0.0/dist/chartjs-chart-boxplot.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/chartjs-plugin-datalabels/2.0.0/chartjs-plugin-datalabels.js"></script>
+<script src="https://unpkg.com/@sgratzl/chartjs-chart-boxplot@3.6.0/build/index.umd.min.js"></script>
+<script src="js/chartjs-chart-box-and-violin-plot.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jspdf/2.4.0/jspdf.umd.min.js"></script>
+
+
<body>
<div id="left-div">
diff --git a/templates/nav b/templates/nav
index 5b8c85a004d2b9f256dd6e6393f4cd204dd05c02..1e16583fbdde94ae204af098479a53ed77299a1f 100644
--- a/templates/nav
+++ b/templates/nav
@@ -13,52 +13,131 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-->
+ <!--
+ <a class="dropdown-item" href="searchByTaxonForOligosaccharideName" id="searchByTaxonForOligosaccharideName">Taxon : Oligosaccharide Name</a>
+ <a class="dropdown-item" href="searchByOligosaccharideName" id="searchByOligosaccharideName">Oligosaccharide Name:Taxon</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="searchByTaxonForOligosaccharideType" id="searchByTaxonForOligosaccharideType">Taxon :Oligosaccharide Type</a>
+ <a class="dropdown-item" href="searchByOligosaccharideType" id="searchByOligosaccharideType">Oligosaccharide Type : Taxon</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="searchByTaxon" id="searchByTaxon">Taxon : Physiological Stage</a>
+ <a class="dropdown-item" href="searchByPhysiologicalStage" id="searchByPhysiologicalStage">Physiological Stage :Taxon</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="searchByTaxonForPostpartum" id="searchByTaxonForPostpartum">Taxon : Postpartum Age</a>
+ <a class="dropdown-item" href="searchByPostpartum" id="searchByPostpartum">Postpartum Age : Taxon</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="searchByTaxonForSampleType" id="searchByTaxonForSampleType">Taxon : Sample Type</a>
+ <a class="dropdown-item" href="searchBySampleType" id="searchBySampleType">Sample Type : Taxon</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="searchByTaxonForLactation" id="searchByTaxonForLactation">Taxon : Lactation stage</a>
+ <a class="dropdown-item" href="searchByLactation" id="searchByLactation">Lactation Stage : Taxon</a>
+ -->
+
+ <!DOCTYPE html>
+ <html lang="en">
+ <head>
+ <meta charset="UTF-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <title>HoloOligo</title>
+
+ <style>
+ /* Style de la Navbar */
+ .navbar {
+ background-color:rgb(25, 70, 101) !important; /* Couleur de fond de la navbar */
+ }
+
+ .navbar-nav .nav-link {
+ font-size: 1.2rem; /* Taille du texte des liens */
+ color: white !important; /* Couleur des liens */
+ }
+
+ .navbar-nav .nav-link:hover {
+ color: #ffdd57 !important; /* Couleur au survol des liens */
+ }
+
+ /* Personnalisation des éléments du dropdown */
+ .dropdown-menu {
+ background-color:rgb(73, 122, 157); /* Fond du menu déroulant */
+ }
+
+ .dropdown-item {
+ color: white; /* Couleur des éléments du menu déroulant */
+ }
+
+ .dropdown-item:hover {
+ background-color:rgb(255, 255, 255); /* Couleur de fond au survol */
+ }
+
+ /* Style du logo de la navbar */
+ .navbar-brand img {
+ height: 40px; /* Ajuster la taille du logo */
+ }
+
+ /* Modifier la couleur de fond et du texte du bouton burger sur mobile */
+ .navbar-toggler-icon {
+ background-color: white; /* Couleur du menu hamburger */
+ }
+
+ /* Navbar active */
+ .nav-item.active .nav-link {
+ color: #ffdd57 !important; /* Couleur des liens actifs */
+ }
+ </style>
+ </head>
+ <body>
+ <!-- Navbar Section -->
+ <nav class="navbar navbar-expand-lg navbar-dark bg-info fixed-top">
+ <a class="navbar-brand" href="home_page" id="main">
+ <img src="{{ url_for('static', filename='img/logo_Omnicrobe_blanc_small.png') }}" /> HoloOligo
+ </a>
+ <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
+ <span class="navbar-toggler-icon"></span>
+ </button>
+
+ <div class="collapse navbar-collapse" id="navbarSupportedContent">
+ <ul class="navbar-nav mr-auto">
+ <li class="nav-item dropdown">
+ <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+ Search
+ </a>
+ <div class="dropdown-menu" aria-labelledby="navbarDropdown">
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="research" id="research">Simple search</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="advancedSearch" id="advancedSearch">Advanced search</a>
+ </div>
+ </li>
+ <li class="nav-item dropdown">
+ <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+ About
+ </a>
+ <div class="dropdown-menu" aria-labelledby="navbarDropdown">
+ <a class="dropdown-item" href="about">About</a>
+ <a class="dropdown-item" href="release">Release Notes</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="help">Help</a>
+ <div class="dropdown-divider"></div>
+ <a class="dropdown-item" href="contact" id="contact">Contact</a>
+ </div>
+ </li>
+ </ul>
+ </div>
+ </nav>
+
+ <!-- Your page content goes here -->
+
+ <!-- Scripts for Bootstrap -->
+ <!-- Utilisez jQuery complet pour activer les fonctionnalités Bootstrap -->
+ <script src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
+ <script src="https://cdn.jsdelivr.net/npm/bootstrap@4.5.2/dist/js/bootstrap.bundle.min.js"></script>
+ </body>
+ </html>
-<nav class="navbar navbar-expand-lg navbar-dark bg-info fixed-top">
+
+ <!-- Your page content goes here -->
- <a class="navbar-brand" href="index" id="main"><img src="{{ url_for('static', filename='img/logo_Omnicrobe_blanc_small.png') }}" /> Omnicrobe</a>
- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
- <span class="navbar-toggler-icon"></span>
- </button>
-
- <div class="collapse navbar-collapse" id="navbarSupportedContent">
- <ul class="navbar-nav mr-auto">
- <li class="nav-item dropdown">
- <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
- Search
- </a>
- <div class="dropdown-menu" aria-labelledby="navbarDropdown">
- <a class="dropdown-item" href="searchByTaxon" id="searchByTaxon">Taxon lives in Habitat</a>
- <a class="dropdown-item" href="searchByHabitat" id="searchByHabitat">Habitat contains Taxon</a>
- <div class="dropdown-divider"></div>
- <a class="dropdown-item" href="searchByTaxonForPhenotype" id="searchByTaxonForPhenotype">Taxon exhibits Phenotype</a>
- <a class="dropdown-item" href="searchByPhenotype" id="searchByPhenotype">Phenotype is exhibited by Taxon</a>
- <div class="dropdown-divider"></div>
- <a class="dropdown-item" href="searchByTaxonForUse" id="searchByTaxonForUse">Taxon studied for Use</a>
- <a class="dropdown-item" href="searchByUse" id="searchByUse">Use involves Taxon</a>
- <div class="dropdown-divider"></div>
- <a class="dropdown-item" href="advancedSearch" id="advancedSearch">Advanced search</a>
- </div>
- </li>
- <li class="nav-item dropdown">
- <a class="nav-link" href="api" id="navbarDropdown" role="button" aria-haspopup="true">
- Web services
- </a>
- </li>
- <li class="nav-item dropdown">
- <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
- About
- </a>
- <div class="dropdown-menu" aria-labelledby="navbarDropdown">
- <a class="dropdown-item" href="about">About</a>
- <a class="dropdown-item" href="release">Release Notes</a>
- <div class="dropdown-divider"></div>
- <a class="dropdown-item" href="help">Help</a>
- <!--a class="dropdown-item" href="demo">Website usage documentation</a-->
- <div class="dropdown-divider"></div>
- <a class="dropdown-item" href="contact" id="contact">Contact</a>
- </div>
- </li>
- </ul>
- </div>
-</nav>
+ <!-- Scripts for Bootstrap -->
+ <script src="https://code.jquery.com/jquery-3.5.1.slim.min.js"></script>
+ <script src="https://cdn.jsdelivr.net/npm/bootstrap@4.5.2/dist/js/bootstrap.bundle.min.js"></script>
+</body>
+</html>
diff --git a/templates/nav_tabs b/templates/nav_tabs
index 6e7178120a7194373b0846477a5d4f914f155529..0798a05ebae4ce89c02adb595f3bf49b3c1c132c 100644
--- a/templates/nav_tabs
+++ b/templates/nav_tabs
@@ -14,30 +14,55 @@
# limitations under the License.
-->
-<div style="margin-left: 5%; margin-right: 5%;" align="center">
+<div style="margin-left: 2%; margin-right: 2%;" align="center">
<ul class="nav nav-pills flex-column flex-sm-row" id="pills-tab" role="tablist">
+ <li class="nav-item" role="presentation" id="searchByTaxonForOligosaccharideName">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxonForOligosaccharideName">Taxon -> Oligosaccharide name</a>
+ </li>
+ <li> </li>
+ <li class="nav-item" role="presentation" id="searchByOligosaccharideName">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByOligosaccharideName">Oligosaccharide name -> Taxon</a>
+ </li>
+ <li> </li>
+
+ <li class="nav-item" role="presentation" id="searchByTaxonForOligosaccharideType">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxonForOligosaccharideType">Taxon -> Oligosaccharide type</a>
+ </li>
+ <li> </li>
+ <li class="nav-item" role="presentation" id="searchByOligosaccharideType">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByOligosaccharideType">Oligosaccharide type -> Taxon</a>
+ </li>
+ <li> </li>
<li class="nav-item" role="presentation" id="searchByTaxon">
- <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxon">Taxon lives in Habitat</a>
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxon">Taxon -> Physiological stage</a>
+ </li>
+ <li> </li>
+ <li class="nav-item" role="presentation" id="searchByPhysiologicalStage">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByPhysiologicalStage">Physiological stage -> Taxon</a>
+ </li>
+ <li> </li>
+ <li class="nav-item" role="presentation" id="searchByTaxonForPostpartum">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxonForPostpartum">Taxon -> Postpartum age</a>
</li>
<li> </li>
- <li class="nav-item" role="presentation" id="searchByHabitat">
- <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByHabitat">Habitat contains Taxon</a>
+ <li class="nav-item" role="presentation" id="searchByPostpartum">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByPostpartum">Postpartum age -> Taxon</a>
</li>
<li> </li>
- <li class="nav-item" role="presentation" id="searchByTaxonForPhenotype">
- <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxonForPhenotype">Taxon exhibits Phenotype</a>
+ <li class="nav-item" role="presentation" id="searchByTaxonForSampleType">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxonForSampleType">Taxon -> Sample type</a>
</li>
<li> </li>
- <li class="nav-item" role="presentation" id="searchByPhenotype">
- <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByPhenotype">Phenotype is exhibited by Taxon</a>
+ <li class="nav-item" role="presentation" id="searchBySampleType">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchBySampleType">Sample type -> Taxon</a>
</li>
<li> </li>
- <li class="nav-item" role="presentation" id="searchByTaxonForUse">
- <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxonForUse">Taxon studied for Use</a>
+ <li class="nav-item" role="presentation" id="searchByTaxonForLactation">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByTaxonForLactation">Taxon -> Lactation stage</a>
</li>
<li> </li>
- <li class="nav-item" role="presentation" id="searchByUse">
- <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByUse">Use involves Taxon</a>
+ <li class="nav-item" role="presentation" id="searchByLactation">
+ <a class="flex-sm-fill text-sm-center nav-link" aria-current="page" href="searchByLactation">Lactation stage -> Taxon</a>
</li>
</ul>
</div>
diff --git a/templates/release.html b/templates/release.html
index 47b66fdf00ebcefc868081a00abc5b3b782616eb..9ae3221c0260a66ff3b1d6ebebef47092635bc2a 100644
--- a/templates/release.html
+++ b/templates/release.html
@@ -31,92 +31,66 @@
<div class="card" style="border-color: #21517A;">
<div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
- Omnicrobe 1.2 (<i>current release</i>)
+ HoloOligo 0.1 (<i>current release</i>)
</div>
<div class="card-body">
<p align='justify'>
<h5 class="text-info">Information about the data</h5>
- <ul>
+ <!--ul>
<li>Ontologies used: <a href="http://agroportal.lirmm.fr/ontologies/ONTOBIOTOPE" target="_blank">OntoBiotope</a> version 2022-04-28 & <a href="https://forgemia.inra.fr/omnicrobe/extended-microorganisms-taxonomy" target="_blank">Taxonomy</a> version 2023-02-24.</li>
- </ul>
- <div style="margin-left: 15%;margin-right: 15%;">
+ </ul-->
+ <div style="margin-left: 35%;margin-right: 35%;">
<table class="table table-sm table-striped">
- <caption class="text-center">Versions and number of relationships per source</caption>
+ <caption class="text-center">Number of relationships per type</caption>
<thead>
<tr>
<th scope="col"></th>
- <th class="text-right" scope="col">PubMed</th>
- <th class="text-right" scope="col">GenBank</th>
- <th class="text-right" scope="col">DSMZ</th>
- <th class="text-right" scope="col">CIRM-BIA</th>
- <th class="text-right" scope="col">CIRM-CFBP</th>
- <th class="text-right" scope="col">CIRM-Levures</th>
+ <th class="text-right" scope="col">WoS / PubMed</th>
</tr>
</thead>
<tbody>
<tr>
- <th scope="row">Version</th>
- <td class="text-right">2023-03-27</td>
- <td class="text-right">2023-03-27</td>
- <td class="text-right">2023-03-27</td>
- <td class="text-right">2023-02-09</td>
- <td class="text-right">2023-03-16</td>
- <td class="text-right">2022-10-14</td>
+ <th scope="row">Taxa - Oligo name</th>
+ <td class="text-center">157</td>
</tr>
<tr>
- <th scope="row">Taxa - Habitat relations</th>
- <td class="text-right">764,796</td>
- <td class="text-right">268,781</td>
- <td class="text-right">51,176</td>
- <td class="text-right">682</td>
- <td class="text-right">1,223</td>
- <td class="text-right">942</td>
+ <th scope="row">Taxa - Oligo type</th>
+ <td class="text-center">36</td>
</tr>
<tr>
- <th scope="row">Taxa - Phenotype relations</th>
- <td class="text-right">53,377</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
+ <th scope="row">Taxa - Physiological stage</th>
+ <td class="text-center">1</td>
</tr>
<tr>
- <th scope="row">Taxa - Use relations</th>
- <td class="text-right">18,145</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
- <td class="text-right">-</td>
+ <th scope="row">Taxa - Postpartum age</th>
+ <td class="text-center">12</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Sample type</th>
+ <td class="text-center">38</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Lactation stage</th>
+ <td class="text-center">25</td>
</tr>
</tbody>
</table>
</div>
- <h5 class="text-info">New features and improvements in this release</h5>
+ <!--h5 class="text-info">New features and improvements in this release</h5>
<ul>
<li>improved extraction quality</li>
<li>fixed bugs</li>
<li>updated taxonomy</li>
- </ul>
- <!-- <h5 class="text-info">Fixed in this release</h5>
- <ul>
- <li>...</li>
- </ul> -->
- <!--h5 class="text-info">Source code</h5>
- <ul>
- <li>Text-mining workflow: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
- <li>Web interface: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
</ul-->
</p>
</div>
<div class="card-footer text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
- 6 April 2023
+ 5 June 2024
</div>
</div>
<br/>
- <p><h4 class="text-info">Previous releases</h4></p>
+ <!--p><h4 class="text-info">Previous releases</h4></p>
<div class="card" style="border-color: #21517A;">
<div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
@@ -268,15 +242,6 @@
<li>updated taxonomy</li>
<li>updated OntoBiotope</li>
</ul>
- <!-- <h5 class="text-info">Fixed in this release</h5>
- <ul>
- <li>...</li>
- </ul> -->
- <!--h5 class="text-info">Source code</h5>
- <ul>
- <li>Text-mining workflow: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
- <li>Web interface: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
- </ul-->
</p>
</div>
<div class="card-footer text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
@@ -436,7 +401,7 @@
<div class="card-footer text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
22 september 2021
</div>
- </div>
+ </div-->
</div>
<div style="margin:80px 0;"></div>
diff --git a/templates/research.html b/templates/research.html
new file mode 100644
index 0000000000000000000000000000000000000000..42badcfcdbca3f165bbd61c0af2d9aa8ddc2b6fc
--- /dev/null
+++ b/templates/research.html
@@ -0,0 +1,128 @@
+{% extends 'main2' %} {% block content %}
+
+<head>
+ <link
+ rel="stylesheet"
+ href="{{ url_for('static', filename='css/research.css') }}"
+ />
+ <script
+ src="{{ url_for('static', filename='js/research.js') }}"
+ defer
+ ></script>
+</head>
+
+<script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
+
+<script
+ type="application/javascript"
+ src="https://cdn.jsdelivr.net/npm/chartjs-chart-boxplot@4.0.0/dist/chartjs-chart-boxplot.min.js"
+></script>
+
+<script
+ type="application/javascript"
+ src="/static/js/chartjs-chart-box-and-violin-plot.min.js"
+></script>
+
+<body>
+ <div class="main-content2">
+ <section class="info-section">
+ <div class="info-box">
+ <div class="search-icon">
+ <i class="fas fa-search"></i>
+ </div>
+ <h2>Simple Search</h2>
+ <p>
+ Quickly find oligosaccharides by name, type, species, or lactation
+ stage. Perfect for direct queries when you know what you're looking
+ for.
+ </p>
+ </div>
+ </section>
+
+ <!-- Section "Getting Started"
+ <section class="getting-started">
+ <div class="info-box">
+ <h3>Getting Started</h3>
+ <ul>
+ <li>Select your search type from the dropdown menu</li>
+ <li>Enter your search terms in the search bar</li>
+ <li>Use the autocomplete suggestions for accurate results</li>
+ <li>Click search to view your results</li>
+ </ul>
+ </div>
+ </section>-->
+
+ <!-- Simple Search Form -->
+ <section id="simple-search-section" class="search-section">
+ <div class="search-bar2">
+ <span>Search By:</span>
+ <select id="simple-search-type">
+ <option value="oligosaccharide_name">Oligosaccharide Name</option>
+ <option value="oligosaccharide_type">Oligosaccharide Type</option>
+ <option value="species">Species</option>
+ <option value="samples">Samples</option>
+ <option value="lactation-stage">Lactation Stage</option>
+ </select>
+ <input
+ type="text"
+ id="simple-search"
+ placeholder="Enter a keyword to begin..."
+ onkeyup="autocompleteSearch(this.value)"
+ />
+ <div id="autocomplete-suggestions" class="autocomplete-box"></div>
+ <button class="search-btn" onclick="showSimpleSearchResults()">
+ Search
+ </button>
+ <div id="suggestion-box" class="autocomplete-box"></div>
+ </div>
+ </section>
+
+ <!-- Results Section -->
+ <section id="results-section" class="results-section">
+ <h2>Search Results</h2>
+ <div id="column-toggles">
+ <label
+ ><input type="checkbox" data-column="0" checked /> Oligosaccharide
+ Name</label
+ >
+ <label
+ ><input type="checkbox" data-column="1" checked /> Oligosaccharide
+ Type</label
+ >
+ <label><input type="checkbox" data-column="2" checked /> Sample</label>
+ <label><input type="checkbox" data-column="3" checked /> Species</label>
+ <label
+ ><input type="checkbox" data-column="4" checked /> Lactation
+ Stage</label
+ >
+ <label><input type="checkbox" data-column="5" checked /> Details</label>
+ </div>
+
+ <table class="results-table">
+ <thead>
+ <tr>
+ <th onclick="sortTable(0)">
+ Oligosaccharide Name <i class="fas fa-sort"></i>
+ </th>
+ <th onclick="sortTable(1)">
+ Oligosaccharide Type <i class="fas fa-sort"></i>
+ </th>
+ <th onclick="sortTable(2)">Sample <i class="fas fa-sort"></i></th>
+ <th onclick="sortTable(3)">Species <i class="fas fa-sort"></i></th>
+ <th onclick="sortTable(4)">
+ Lactation Stage <i class="fas fa-sort"></i>
+ </th>
+ <th onclick="sortTable(5)">Details <i class="fas fa-sort"></i></th>
+ </tr>
+ </thead>
+ <tbody id="results-body">
+ <!-- Rows will be dynamically populated by JavaScript -->
+ </tbody>
+ </table>
+
+ <div id="pagination" style="margin-top: 20px; text-align: center"></div>
+ </section>
+ </div>
+</body>
+
+{% endblock %}
diff --git a/templates/searchByLactationStage.html b/templates/searchByLactationStage.html
new file mode 100644
index 0000000000000000000000000000000000000000..ed22462aa4bf79753e3cd71d92a3d105c5b1dff8
--- /dev/null
+++ b/templates/searchByLactationStage.html
@@ -0,0 +1,142 @@
+<!--
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+-->
+
+{% extends 'main' %}
+{% block content %}
+<section>
+
+ <script type=text/javascript>
+ $SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+ </script>
+
+ <script>
+ var lactation = JSON.parse('{{ lactation | tojson | safe }}');
+ var taxon = JSON.parse('{{ taxon | tojson | safe }}');
+ var version = JSON.parse('{{ version | tojson | safe }}');
+ var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
+ </script>
+
+ <link href="{{ url_for('static', filename='css/simpleTree.css') }}" rel="stylesheet">
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
+ <script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByLactationStage.js') }}"></script>
+
+ <div style="margin:30px 0;"></div>
+
+ <div style="margin-left: 5%;margin-right: 5%;">
+ <h3><span style="color: #21517A;">Lactation stage --> Taxon</span></h3>
+ <div style="margin-left: 2%;margin-right: 2%;">
+ <div class="d-flex justify-content-center text-info">
+ <div id="spinner_lactation_taxon" class="spinner-border" role="status" style="display: none;">
+ <span class="sr-only">Loading...</span>
+ </div>
+ <div id="spinner_lactation_taxon2" style="display: none;"><strong> Loading...</strong></div>
+ </div>
+ <div style="margin:40px 0;"></div>
+ </div>
+
+ <div class="container">
+ <div class="row justify-content-center">
+ <div class="col-8">
+ <div class="input-group">
+ <label class="button-select input-group-text" for="relationTaxonByLactation">Search relations by lactation stage</label>
+ <select class="form-select" id="search_lactation"></select>
+ <button id="filter_lactation_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ </div>
+ </div>
+ </div>
+ <!-- <div class="row justify-content-center">
+ <div class="col-8">
+ <div class="p-2">
+ <img width="3%" src="{{ url_for('static', filename='img/treeTest.png') }}" data-toggle="modal" data-target="#treeModalHabitat" style="cursor: pointer;"><a class="link-info link-cur" data-toggle="modal" data-target="#treeModalHabitat">OntoBiotope navigation</a>
+ </div>
+ </div>
+ </div> -->
+ </div>
+
+ <div id="demo" class="collapse" style="margin-top: 1%;" align="center">
+ <table align="center">
+ <tr id="filter_col4" data-column="3">
+ <!-- <td>
+ <div style="float:left;">Filter by sources </div>
+ <div style="float:left;" title="Available sources: PubMed, GenBank, DSMZ, CIRM-BIA, CIRM-CFBP, CIRM-Levures">
+ <svg width='1em' height='1em' viewBox='0 0 16 16' class='bi bi-info-circle-fill' fill='currentColor' xmlns='http://www.w3.org/2000/svg'> \
+ <path fill-rule='evenodd' d='M8 16A8 8 0 1 0 8 0a8 8 0 0 0 0 16zm.93-9.412l-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM8 5.5a1 1 0 1 0 0-2 1 1 0 0 0 0 2z'/> \
+ </svg>
+ </div>
+ </td> -->
+ <!-- <td align="center"><input type="text" class="column_source" id="sources_ht"></td> -->
+ <td> Filter by Taxon </td>
+ <td align="center"><input type="text" class="column_filter" id="taxon_lt"></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_ht" id="qps_ht" value="yes" /></td> -->
+ </tr>
+ </table>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can use ";" for "or" (example: "sows;gorilla" for taxon).</small>
+ </div>
+ <div id="hide" style="display:none">
+ <br/>
+ <table id="results_lactation_taxon" class="display responsive nowrap collapsed" style="width:100%"> <!-- visibility="none" -->
+ <thead>
+ <tr>
+ <th>Source text</th>
+ <th>Reference class</th>
+ <th>Relation type</th>
+ <th>Scientific name of taxon</th>
+ <th>QPS</th>
+ <th>Source</th>
+ <th>Occurrence in text (lactation)</th>
+ <th>Occurrence in text (taxon)</th>
+ <th>Full source text</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
+ <th>TaxonID</th>
+ <th>Taxonomy hierarchical path</th>
+ </tr>
+ </thead>
+ </table>
+ </div>
+ </div>
+
+ <div style="margin:80px 0;"></div>
+
+ <!-- Tree navigation (modal) -->
+ <!-- <div class="modal fade" id="treeModalHabitat" tabindex="-1" aria-labelledby="treeModalHabitatLabel" aria-hidden="true">
+ <div class="modal-dialog modal-dialog-centered modal-lg">
+ <div class="modal-content">
+ <div class="modal-header">
+ <h5 class="modal-title text-info" id="treeModalHabitatLabel">OntoBiotope navigation</h5>
+ <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
+ <div class="modal-body">
+ <div class="input-group">
+ <label style="background-color: #21517A; border-color: #21517A; color: #fff;" class="input-group-text" for="searchtreehabitat">Search OntoBiotope class</label>
+ <input type="search" class="form-control" id="searchtreehabitat">
+ </div>
+ <div id="habitattree"></div>
+ </div>
+ </div>
+ </div>
+ </div> -->
+
+</section>
+{% endblock %}
diff --git a/templates/searchByOligosaccharideName.html b/templates/searchByOligosaccharideName.html
new file mode 100644
index 0000000000000000000000000000000000000000..8381b8210fee24ea66e73cbf9e67830a8a920da6
--- /dev/null
+++ b/templates/searchByOligosaccharideName.html
@@ -0,0 +1,103 @@
+<!--
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+-->
+
+{% extends 'main' %}
+{% block content %}
+<section>
+
+ <script type=text/javascript>
+ $SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+ </script>
+
+ <script>
+ var oligoname = JSON.parse('{{ oligoname | tojson | safe }}');
+ var taxon = JSON.parse('{{ taxon | tojson | safe }}');
+ var version = JSON.parse('{{ version | tojson | safe }}');
+ var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
+ </script>
+
+ <link href="{{ url_for('static', filename='css/simpleTree.css') }}" rel="stylesheet">
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
+ <script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByOligosaccharideName.js') }}"></script>
+
+ <div style="margin:30px 0;"></div>
+
+ <div style="margin-left: 5%;margin-right: 5%;">
+ <h3><span style="color: #21517A;">Oligosaccharide Name --> Taxon</span></h3>
+ <div style="margin-left: 2%;margin-right: 2%;">
+ <div class="d-flex justify-content-center text-info">
+ <div id="spinner_oligoname_taxon" class="spinner-border" role="status" style="display: none;">
+ <span class="sr-only">Loading...</span>
+ </div>
+ <div id="spinner_oligoname_taxon2" style="display: none;"><strong> Loading...</strong></div>
+ </div>
+ <div style="margin:40px 0;"></div>
+ </div>
+
+ <div class="container">
+ <div class="row justify-content-center">
+ <div class="col-8">
+ <div class="input-group">
+ <label class="button-select input-group-text" for="relationTaxonByOligoname">Search relations by oligosaccharide Name</label>
+ <select class="form-select" id="search_oligoname"></select>
+ <button id="filter_oligoname_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div id="demo" class="collapse" style="margin-top: 1%;" align="center">
+ <table align="center">
+ <tr id="filter_col4" data-column="3">
+ <td> Filter by Taxon </td>
+ <td align="center"><input type="text" class="column_filter" id="taxon_lt"></td>
+ </tr>
+ </table>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can use ";" for "or" (example: "arctos;maritimus" for taxon).</small>
+ </div>
+ <div id="hide" style="display:none">
+ <br/>
+ <table id="results_oligoname_taxon" class="display responsive nowrap collapsed" style="width:100%">
+ <thead>
+ <tr>
+ <th>Source text</th>
+ <th>Reference class</th>
+ <th>Relation type</th>
+ <th>Scientific name of taxon</th>
+ <th>QPS</th>
+ <th>Source</th>
+ <th>Occurrence in text (oligosaccharide name)</th>
+ <th>Occurrence in text (taxon)</th>
+ <th>Full source text</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
+ <th>TaxonID</th>
+ <th>Taxonomy hierarchical path</th>
+ </tr>
+ </thead>
+ </table>
+ </div>
+ </div>
+
+ <div style="margin:80px 0;"></div>
+
+</section>
+{% endblock %}
diff --git a/templates/searchByOligosaccharideType.html b/templates/searchByOligosaccharideType.html
new file mode 100644
index 0000000000000000000000000000000000000000..6e5796ee69518da0ac9748bc79b254e9d06db0cd
--- /dev/null
+++ b/templates/searchByOligosaccharideType.html
@@ -0,0 +1,103 @@
+<!--
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+-->
+
+{% extends 'main' %}
+{% block content %}
+<section>
+
+ <script type=text/javascript>
+ $SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+ </script>
+
+ <script>
+ var oligotype = JSON.parse('{{ oligotype | tojson | safe }}');
+ var taxon = JSON.parse('{{ taxon | tojson | safe }}');
+ var version = JSON.parse('{{ version | tojson | safe }}');
+ var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
+ </script>
+
+ <link href="{{ url_for('static', filename='css/simpleTree.css') }}" rel="stylesheet">
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
+ <script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByOligosaccharideType.js') }}"></script>
+
+ <div style="margin:30px 0;"></div>
+
+ <div style="margin-left: 5%;margin-right: 5%;">
+ <h3><span style="color: #21517A;">Oligosaccharide Type --> Taxon</span></h3>
+ <div style="margin-left: 2%;margin-right: 2%;">
+ <div class="d-flex justify-content-center text-info">
+ <div id="spinner_oligotype_taxon" class="spinner-border" role="status" style="display: none;">
+ <span class="sr-only">Loading...</span>
+ </div>
+ <div id="spinner_oligotype_taxon2" style="display: none;"><strong> Loading...</strong></div>
+ </div>
+ <div style="margin:40px 0;"></div>
+ </div>
+
+ <div class="container">
+ <div class="row justify-content-center">
+ <div class="col-8">
+ <div class="input-group">
+ <label class="button-select input-group-text" for="relationTaxonByOligotype">Search relations by oligosaccharide Type</label>
+ <select class="form-select" id="search_oligotype"></select>
+ <button id="filter_oligotype_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div id="demo" class="collapse" style="margin-top: 1%;" align="center">
+ <table align="center">
+ <tr id="filter_col4" data-column="3">
+ <td> Filter by Taxon </td>
+ <td align="center"><input type="text" class="column_filter" id="taxon_lt"></td>
+ </tr>
+ </table>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can use ";" for "or" (example: "elephas;ovis" for taxon).</small>
+ </div>
+ <div id="hide" style="display:none">
+ <br/>
+ <table id="results_oligotype_taxon" class="display responsive nowrap collapsed" style="width:100%">
+ <thead>
+ <tr>
+ <th>Source text</th>
+ <th>Reference class</th>
+ <th>Relation type</th>
+ <th>Scientific name of taxon</th>
+ <th>QPS</th>
+ <th>Source</th>
+ <th>Occurrence in text (oligosaccharide type)</th>
+ <th>Occurrence in text (taxon)</th>
+ <th>Full source text</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
+ <th>TaxonID</th>
+ <th>Taxonomy hierarchical path</th>
+ </tr>
+ </thead>
+ </table>
+ </div>
+ </div>
+
+ <div style="margin:80px 0;"></div>
+
+</section>
+{% endblock %}
diff --git a/templates/searchByHabitat.html b/templates/searchByPhysiologicalStage.html
similarity index 75%
rename from templates/searchByHabitat.html
rename to templates/searchByPhysiologicalStage.html
index d6880610c1455c4209a814e27bc344b2c91b187d..d64b8d9727b1022ee81dfe18273822c0f55657d5 100644
--- a/templates/searchByHabitat.html
+++ b/templates/searchByPhysiologicalStage.html
@@ -23,10 +23,8 @@
</script>
<script>
- var habitat = JSON.parse('{{ habitat | tojson | safe }}');
+ var stage = JSON.parse('{{ stage | tojson | safe }}');
var taxon = JSON.parse('{{ taxon | tojson | safe }}');
- var qps = JSON.parse('{{ qps | tojson | safe }}');
- var sources = JSON.parse('{{ sources | tojson | safe }}');
var version = JSON.parse('{{ version | tojson | safe }}');
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
@@ -38,18 +36,18 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
- <script type="module" src="{{ url_for('static', filename='js/searchByHabitat.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByPhysiologicalStage.js') }}"></script>
<div style="margin:30px 0;"></div>
<div style="margin-left: 5%;margin-right: 5%;">
- <h3><span style="color: #21517A;">Habitat contains Taxon</span></h3>
+ <h3><span style="color: #21517A;">Physiological Stage --> Taxon</span></h3>
<div style="margin-left: 2%;margin-right: 2%;">
<div class="d-flex justify-content-center text-info">
- <div id="spinner_habitat_taxon" class="spinner-border" role="status" style="display: none;">
+ <div id="spinner_stage_taxon" class="spinner-border" role="status" style="display: none;">
<span class="sr-only">Loading...</span>
</div>
- <div id="spinner_habitat_taxon2" style="display: none;"><strong> Loading...</strong></div>
+ <div id="spinner_stage_taxon2" style="display: none;"><strong> Loading...</strong></div>
</div>
<div style="margin:40px 0;"></div>
</div>
@@ -58,57 +56,57 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label class="button-select input-group-text" for="relationTaxonByHabitat">Search relations by habitat</label>
- <select class="form-select" id="search_habitat"></select>
- <button id="filter_habitat_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationTaxonByStage">Search relations by physiological stage</label>
+ <select class="form-select" id="search_stage"></select>
+ <button id="filter_stage_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
- <div class="row justify-content-center">
+ <!-- <div class="row justify-content-center">
<div class="col-8">
<div class="p-2">
<img width="3%" src="{{ url_for('static', filename='img/treeTest.png') }}" data-toggle="modal" data-target="#treeModalHabitat" style="cursor: pointer;"><a class="link-info link-cur" data-toggle="modal" data-target="#treeModalHabitat">OntoBiotope navigation</a>
</div>
</div>
- </div>
+ </div> -->
</div>
<div id="demo" class="collapse" style="margin-top: 1%;" align="center">
<table align="center">
<tr id="filter_col4" data-column="3">
- <td>
+ <!-- <td>
<div style="float:left;">Filter by sources </div>
<div style="float:left;" title="Available sources: PubMed, GenBank, DSMZ, CIRM-BIA, CIRM-CFBP, CIRM-Levures">
<svg width='1em' height='1em' viewBox='0 0 16 16' class='bi bi-info-circle-fill' fill='currentColor' xmlns='http://www.w3.org/2000/svg'> \
<path fill-rule='evenodd' d='M8 16A8 8 0 1 0 8 0a8 8 0 0 0 0 16zm.93-9.412l-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM8 5.5a1 1 0 1 0 0-2 1 1 0 0 0 0 2z'/> \
</svg>
</div>
- </td>
- <td align="center"><input type="text" class="column_source" id="sources_ht"></td>
+ </td> -->
+ <!-- <td align="center"><input type="text" class="column_source" id="sources_ht"></td> -->
<td> Filter by Taxon </td>
<td align="center"><input type="text" class="column_filter" id="taxon_ht"></td>
- <td> QPS only </td>
- <td><input type="checkbox" name="qps_ht" id="qps_ht" value="yes" /></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_ht" id="qps_ht" value="yes" /></td> -->
</tr>
</table>
- <small id="help" class="form-text text-muted"><b>Note:</b> to filter by sources and to filter by taxon, you can use ";" for "or" (example: "genbank;dsmz" for sources and "delbrueckii;thermophilus" for taxon).</small>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can use ";" for "or" (example: "delbrueckii;thermophilus" for taxon).</small>
</div>
<div id="hide" style="display:none">
<br/>
- <table id="results_habitat_taxon" class="display responsive nowrap collapsed" style="width:100%"> <!-- visibility="none" -->
+ <table id="results_stage_taxon" class="display responsive nowrap collapsed" style="width:100%"> <!-- visibility="none" -->
<thead>
<tr>
<th>Source text</th>
- <th>OntoBiotope class</th>
+ <th>Reference class</th>
<th>Relation type</th>
<th>Scientific name of taxon</th>
<th>QPS</th>
<th>Source</th>
- <th>Occurrence in text (habitat)</th>
+ <th>Occurrence in text (stage)</th>
<th>Occurrence in text (taxon)</th>
<th>Full source text</th>
- <th>ID OntoBiotope</th>
- <th>OntoBiotope hierarchical path</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
<th>TaxonID</th>
<th>Taxonomy hierarchical path</th>
</tr>
@@ -120,7 +118,7 @@
<div style="margin:80px 0;"></div>
<!-- Tree navigation (modal) -->
- <div class="modal fade" id="treeModalHabitat" tabindex="-1" aria-labelledby="treeModalHabitatLabel" aria-hidden="true">
+ <!-- <div class="modal fade" id="treeModalHabitat" tabindex="-1" aria-labelledby="treeModalHabitatLabel" aria-hidden="true">
<div class="modal-dialog modal-dialog-centered modal-lg">
<div class="modal-content">
<div class="modal-header">
@@ -138,7 +136,7 @@
</div>
</div>
</div>
- </div>
+ </div> -->
</section>
{% endblock %}
diff --git a/templates/searchByPhenotype.html b/templates/searchByPostpartum.html
similarity index 77%
rename from templates/searchByPhenotype.html
rename to templates/searchByPostpartum.html
index 4aa96ca26f89a692abc7e1fab997ab3f2c2bd953..a29e0ee8ca25cbe8c90e9e34afef3b7af6b8ca47 100644
--- a/templates/searchByPhenotype.html
+++ b/templates/searchByPostpartum.html
@@ -23,9 +23,8 @@
</script>
<script>
- var phenotype = JSON.parse('{{ phenotype | tojson | safe }}');
+ var postpartum = JSON.parse('{{ postpartum | tojson | safe }}');
var taxon = JSON.parse('{{ taxon | tojson | safe }}');
- var qps = JSON.parse('{{ qps | tojson | safe }}');
var version = JSON.parse('{{ version | tojson | safe }}');
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
@@ -36,18 +35,18 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
- <script type="module" src="{{ url_for('static', filename='js/searchByPhenotype.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByPostpartum.js') }}"></script>
<div style="margin:30px 0;"></div>
<div style="margin-left: 5%;margin-right: 5%;">
- <h3><span style="color: #21517A;">Phenotype is exhibited by Taxon</span></h3>
+ <h3><span style="color: #21517A;">Postpartum Age --> Taxon</span></h3>
<div style="margin-left: 2%;margin-right: 2%;">
<div class="d-flex justify-content-center text-info">
- <div id="spinner_phenotype_taxon" class="spinner-border" role="status" style="display: none;">
+ <div id="spinner_postpartum_taxon" class="spinner-border" role="status" style="display: none;">
<span class="sr-only">Loading...</span>
</div>
- <div id="spinner_phenotype_taxon2" style="display: none;"><strong> Loading...</strong></div>
+ <div id="spinner_postpartum_taxon2" style="display: none;"><strong> Loading...</strong></div>
</div>
<div style="margin:40px 0;"></div>
</div>
@@ -56,19 +55,19 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label class="button-select input-group-text" for="relationTaxonByPhenotype">Search relations by phenotype</label>
- <select class="form-select" id="search_phenotype"></select>
- <button id="filter_phenotype_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationTaxonByPostpartum">Search relations by postpartum</label>
+ <select class="form-select" id="search_postpartum"></select>
+ <button id="filter_postpartum_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
- <div class="row justify-content-center">
+ <!-- <div class="row justify-content-center">
<div class="col-8">
<div class="p-2">
<img width="3%" src="{{ url_for('static', filename='img/treeTest.png') }}" data-toggle="modal" data-target="#treeModalPhenotype" style="cursor: pointer;"><a class="link-info link-cur" data-toggle="modal" data-target="#treeModalPhenotype">OntoBiotope navigation</a>
</div>
</div>
- </div>
+ </div> -->
</div>
<div id="demo" class="collapse" style="margin-top: 1%;" align="center">
@@ -76,15 +75,15 @@
<tr id="filter_col4" data-column="3">
<td> Filter by Taxon </td>
<td align="center"><input type="text" class="column_filter" id="taxon_pt"></td>
- <td> QPS only </td>
- <td><input type="checkbox" name="qps_pt" id="qps_pt" value="yes" /></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_pt" id="qps_pt" value="yes" /></td> -->
</tr>
</table>
- <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can use ";" for "or" (example: "delbrueckii;thermophilus" for taxon).</small>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can use ";" for "or" (example: "rat;cows" for taxon).</small>
</div>
<div id="hide" style="display:none">
<br/>
- <table id="results_phenotype_taxon" class="display responsive nowrap collapsed" style="width:100%"> <!-- width="100%" visibility="none"-->
+ <table id="results_postpartum_taxon" class="display responsive nowrap collapsed" style="width:100%"> <!-- width="100%" visibility="none"-->
<thead>
<tr>
<th>Source text</th>
@@ -93,7 +92,7 @@
<th>Scientific name of taxon</th>
<th>QPS</th>
<th>Source</th>
- <th>Occurrence in text (phenotype)</th>
+ <th>Occurrence in text (postpartum)</th>
<th>Occurrence in text (taxon)</th>
<th>Full source text</th>
<th>ID OntoBiotope</th>
@@ -109,7 +108,7 @@
<div style="margin:80px 0;"></div>
<!-- Tree navigation (modal) -->
- <div class="modal fade" id="treeModalPhenotype" tabindex="-1" aria-labelledby="treeModalPhenotypeLabel" aria-hidden="true">
+ <!-- <div class="modal fade" id="treeModalPhenotype" tabindex="-1" aria-labelledby="treeModalPhenotypeLabel" aria-hidden="true">
<div class="modal-dialog modal-dialog-centered modal-lg">
<div class="modal-content">
<div class="modal-header">
@@ -127,7 +126,7 @@
</div>
</div>
</div>
- </div>
+ </div> -->
</section>
{% endblock %}
diff --git a/templates/searchByUse.html b/templates/searchBySampleType.html
similarity index 78%
rename from templates/searchByUse.html
rename to templates/searchBySampleType.html
index da7b9711e9f8b18c4bb1ab507979d44d9f11f72b..b955e7dd8cbb0cb31ad78f3c4eb45d65c211a1c5 100644
--- a/templates/searchByUse.html
+++ b/templates/searchBySampleType.html
@@ -23,9 +23,8 @@
</script>
<script>
- var use = JSON.parse('{{ use | tojson | safe }}');
+ var sample = JSON.parse('{{ sample | tojson | safe }}');
var taxon = JSON.parse('{{ taxon | tojson | safe }}');
- var qps = JSON.parse('{{ qps | tojson | safe }}');
var version = JSON.parse('{{ version | tojson | safe }}');
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
@@ -37,19 +36,19 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
- <script type="module" src="{{ url_for('static', filename='js/searchByUse.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchBySampleType.js') }}"></script>
<div style="margin:30px 0;"></div>
<div style="margin-left: 5%;margin-right: 5%;">
- <h3><span style="color: #21517A;">Use involves Taxon</span></h3>
+ <h3><span style="color: #21517A;">Sample Type --> Taxon</span></h3>
<div style="margin-left: 2%;margin-right: 2%;">
<div class="d-flex justify-content-center text-info">
- <div id="spinner_use_taxon" class="spinner-border" role="status" style="display: none;">
+ <div id="spinner_sample_taxon" class="spinner-border" role="status" style="display: none;">
<span class="sr-only">Loading...</span>
</div>
- <div id="spinner_use_taxon2" style="display: none;"><strong> Loading...</strong></div>
+ <div id="spinner_sample_taxon2" style="display: none;"><strong> Loading...</strong></div>
</div>
<div style="margin:40px 0;"></div>
</div>
@@ -58,19 +57,19 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label class="button-select input-group-text" for="relationTaxonByUse">Search relations by use</label>
- <select class="form-select" id="search_use"></select>
- <button id="filter_use_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationTaxonBySample">Search relations by sample</label>
+ <select class="form-select" id="search_sample"></select>
+ <button id="filter_sample_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
- <div class="row justify-content-center">
+ <!-- <div class="row justify-content-center">
<div class="col-8">
<div class="p-2">
<img width="3%" src="{{ url_for('static', filename='img/treeTest.png') }}" data-toggle="modal" data-target="#treeModalUse" style="cursor: pointer;"><a class="link-info link-cur" data-toggle="modal" data-target="#treeModalUse">OntoBiotope navigation</a>
</div>
</div>
- </div>
+ </div> -->
</div>
<div id="demo" class="collapse" style="margin-top: 1%;" align="center">
@@ -78,15 +77,15 @@
<tr id="filter_col4" data-column="3">
<td> Filter by Taxon </td>
<td align="center"><input type="text" class="column_filter" id="taxon_ut"></td>
- <td> QPS only </td>
- <td><input type="checkbox" name="qps_ut" id="qps_ut" value="yes" /></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_ut" id="qps_ut" value="yes" /></td> -->
</tr>
</table>
- <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can use ";" for "or" (example: "delbrueckii;thermophilus" for taxon).</small>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by taxon, you can sample ";" for "or" (example: "cows;dog" for taxon).</small>
</div>
<div id="hide" style="display:none">
<br/>
- <table id="results_use_taxon" class="display responsive nowrap collapsed" style="width:100%"> <!--width="100%" visibility="none"-->
+ <table id="results_sample_taxon" class="display responsive nowrap collapsed" style="width:100%"> <!--width="100%" visibility="none"-->
<thead>
<tr>
<th>Source text</th>
@@ -95,7 +94,7 @@
<th>Scientific name of taxon</th>
<th>QPS</th>
<th>Source</th>
- <th>Occurrence in text (use)</th>
+ <th>Occurrence in text (sample)</th>
<th>Occurrence in text (taxon)</th>
<th>Full source text</th>
<th>ID OntoBiotope</th>
@@ -111,7 +110,7 @@
<div style="margin:80px 0;"></div>
<!-- Tree navigation (modal) -->
- <div class="modal fade" id="treeModalUse" tabindex="-1" aria-labelledby="treeModalUseLabel" aria-hidden="true">
+ <!-- <div class="modal fade" id="treeModalUse" tabindex="-1" aria-labelledby="treeModalUseLabel" aria-hidden="true">
<div class="modal-dialog modal-dialog-centered modal-lg">
<div class="modal-content">
<div class="modal-header">
@@ -129,7 +128,7 @@
</div>
</div>
</div>
- </div>
+ </div> -->
</section>
{% endblock %}
diff --git a/templates/searchByTaxon.html b/templates/searchByTaxon.html
index 95b66d14a8b2cba0dba87262620bb585d1b004a2..17c9c74bb7d0ed67f331cc51a8dc69bf0f866c88 100644
--- a/templates/searchByTaxon.html
+++ b/templates/searchByTaxon.html
@@ -24,9 +24,7 @@
<script>
var taxon = JSON.parse('{{ taxon | tojson | safe }}');
- var habitat = JSON.parse('{{ habitat | tojson | safe }}');
- var qps = JSON.parse('{{ qps | tojson | safe }}');
- var sources = JSON.parse('{{ sources | tojson | safe }}');
+ var stage = JSON.parse('{{ stage | tojson | safe }}');
var version = JSON.parse('{{ version | tojson | safe }}');
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
@@ -41,12 +39,13 @@
<div style="margin:30px 0;"></div>
<div style="margin-left: 5%;margin-right: 5%;">
- <h3><span style="color: #21517A;">Taxon lives in Habitat</span></h3>
+ <!-- <h3><span style="color: #21517A;">Taxon lives in stage</span></h3> -->
+ <h3><span style="color: #21517A;">Taxon -> Physiological Stage</span></h3>
<div class="d-flex justify-content-center text-info">
- <div id="spinner_taxon_habitat" class="spinner-border" role="status" style="display: none;">
+ <div id="spinner_taxon_stage" class="spinner-border" role="status" style="display: none;">
<span class="sr-only">Loading...</span>
</div>
- <div id="spinner_taxon_habitat2" style="display: none;"><strong> Loading...</strong></div>
+ <div id="spinner_taxon_stage2" style="display: none;"><strong> Loading...</strong></div>
</div>
<div style="margin:40px 0;">
@@ -54,9 +53,9 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group mb-3">
- <label class="button-select input-group-text" for="relationHabitatByTaxon">Search relations by taxon</label>
+ <label class="button-select input-group-text" for="relationstageByTaxon">Search relations by taxon</label>
<select class="form-select" id="search"></select>
- <button id="filter_taxon_habitat" type="button" class="btn btn-info button-select-filter" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <button id="filter_taxon_stage" type="button" class="btn btn-info button-select-filter" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
@@ -65,7 +64,7 @@
<div id="demo" class="collapse" style="margin-top: 1%;" align="center">
<table align="center">
<tr id="filter_col4" data-column="3">
- <td>
+ <!-- <td>
<div style="float:left;">Filter by sources </div>
<div style="float:left;" title="Available sources: PubMed, GenBank, DSMZ, CIRM-BIA, CIRM-CFBP, CIRM-Levures">
<svg width='1em' height='1em' viewBox='0 0 16 16' class='bi bi-info-circle-fill' fill='currentColor' xmlns='http://www.w3.org/2000/svg'> \
@@ -73,33 +72,33 @@
</svg>
</div>
</td>
- <td align="center"><input type="text" class="column_source" id="sources_th"></td>
- <td> Filter by Habitat </td>
- <td align="center"><input type="text" class="column_filter" id="habitat_th"></td>
- <td> QPS only </td>
- <td><input type="checkbox" name="qps_th" id="qps_th" value="yes" /></td>
+ <td align="center"><input type="text" class="column_source" id="sources_th"></td> -->
+ <td> Filter by Physiological stage </td>
+ <td align="center"><input type="text" class="column_filter" id="stage_th"></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_th" id="qps_th" value="yes" /></td> -->
</tr>
</table>
- <small id="help" class="form-text text-muted"><b>Note:</b> to filter by sources and to filter by habitat, you can use ";" for "or" (example: "genbank;dsmz" for sources and "cow;horse" for habitat).</small><br/>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by stage, you can use ";" for "or" (example: "bred;multiparous" for physiological stage).</small><br/>
</div>
<div id="hide" style="display:none">
- <table id="results_taxon_habitat" class="display responsive nowrap collapsed" style="width:100%"> <!--width="100%" visibility="none"-->
+ <table id="results_taxon_stage" class="display responsive nowrap collapsed" style="width:100%"> <!--width="100%" visibility="none"-->
<thead>
<tr>
<th>Source text</th>
<th>Scientific name of taxon</th>
<th>Relation type</th>
- <th>OntoBiotope class</th>
+ <th>Reference class</th>
<th>QPS</th>
<th>Source</th>
<th>Occurrence in text (taxon)</th>
- <th>Occurrence in text (habitat)</th>
+ <th>Occurrence in text (physiological stage)</th>
<th>Full source text</th>
<th>TaxonID</th>
<th>Taxonomy hierarchical path</th>
- <th>ID OntoBiotope</th>
- <th>OntoBiotope hierarchical path</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
</tr>
</thead>
</table>
diff --git a/templates/searchByTaxonForPhenotype.html b/templates/searchByTaxonForLactation.html
similarity index 68%
rename from templates/searchByTaxonForPhenotype.html
rename to templates/searchByTaxonForLactation.html
index a35c6507b377b10271a098ed1c125c8b15fd26f9..7edb31ad2b76797fe8ee2858af89744d153e5884 100644
--- a/templates/searchByTaxonForPhenotype.html
+++ b/templates/searchByTaxonForLactation.html
@@ -2,7 +2,7 @@
# Copyright 2022 Sandra Dérozier (INRAE)
#
# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
+# you may not lactation this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
@@ -23,10 +23,9 @@
</script>
<script>
- var taxon = JSON.parse('{{ taxon | tojson | safe }}');
- var phenotype = JSON.parse('{{ phenotype | tojson | safe }}');
- var qps = JSON.parse('{{ qps | tojson | safe }}');
- var version = JSON.parse('{{ version | tojson | safe }}');
+ var taxon = JSON.parse('{{ taxon | tojson | safe }}');
+ var lactation = JSON.parse('{{ lactation | tojson | safe }}');
+ var version = JSON.parse('{{ version | tojson | safe }}');
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
@@ -35,18 +34,18 @@
<link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
- <script type="module" src="{{ url_for('static', filename='js/searchByTaxonForPhenotype.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByTaxonForLactation.js') }}"></script>
<div style="margin:30px 0;"></div>
<div style="margin-left: 5%;margin-right: 5%;">
- <h3><span style="color: #21517A;">Taxon exhibits Phenotype</span></h3>
+ <h3><span style="color: #21517A;">Taxon -> Lactation Stage</span></h3>
<div class="d-flex justify-content-center text-info">
- <div id="spinner_taxon_phenotype" class="spinner-border" role="status" style="display: none;">
+ <div id="spinner_taxon_lactation" class="spinner-border" role="status" style="display: none;">
<span class="sr-only">Loading...</span>
</div>
- <div id="spinner_taxon_phenotype2" style="display: none;"><strong> Loading...</strong></div>
+ <div id="spinner_taxon_lactation2" style="display: none;"><strong> Loading...</strong></div>
</div>
<div style="margin:40px 0;">
@@ -54,41 +53,43 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label class="button-select input-group-text" for="relationPhenotypeByTaxon">Search relations by taxon</label>
- <select class="form-select" id="search_taxon_phenotype"></select>
- <button id="filter_taxon_phenotype" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationlactationByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search_taxon_lactation"></select>
+ <button id="filter_taxon_lactation" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
</div>
+
<div id="demo" class="collapse" style="margin-top: 1%;" align="center">
<table align="center">
<tr id="filter_col4" data-column="3">
- <td> Filter by Phenotype </td>
- <td align="center"><input type="text" class="column_filter" id="phenotype_tp"></td>
- <td> QPS only </td>
- <td><input type="checkbox" name="qps_tp" id="qps_tp" value="yes" /></td>
+ <td> Filter by Lactation stage </td>
+ <td align="center"><input type="text" class="column_filter" id="lactation_tu"></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_tu" id="qps_tu" value="yes" /></td> -->
</tr>
</table>
- <small id="help" class="form-text text-muted"><b>Note:</b> to filter by phenotype, you can use ";" for "or" (example: "acidophile;adherent" for phenotype).</small><br/>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by lactation stage, you can use ";" for "or" (example: "colostrum;milk" for lactation stage).</small><br/>
</div>
+
<div id="hide" style="display:none">
- <table id="results_taxon_phenotype" class="display responsive nowrap collapsed" style="width:100%"><!-- width="100%" visibility="none"-->
+ <table id="results_taxon_lactation" class="display responsive nowrap collapsed" style="width:100%"><!-- width="100%" visibility="none"-->
<thead>
<tr>
<th>Source text</th>
<th>Scientific name of taxon</th>
<th>Relation type</th>
- <th>OntoBiotope class</th>
+ <th>Reference class</th>
<th>QPS</th>
<th>Source</th>
<th>Occurrence in text (taxon)</th>
- <th>Occurrence in text (phenotype)</th>
+ <th>Occurrence in text (lactation)</th>
<th>Full source text</th>
<th>TaxonID</th>
<th>Taxonomy hierarchical path</th>
- <th>ID OntoBiotope</th>
- <th>OntoBiotope hierarchical path</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
</tr>
</thead>
</table>
diff --git a/templates/searchByTaxonForOligosaccharideName.html b/templates/searchByTaxonForOligosaccharideName.html
new file mode 100644
index 0000000000000000000000000000000000000000..c91563e91286a46531a8a4103afddf219bba6fb3
--- /dev/null
+++ b/templates/searchByTaxonForOligosaccharideName.html
@@ -0,0 +1,100 @@
+<!--
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+-->
+
+{% extends 'main' %}
+{% block content %}
+<section>
+
+ <script type=text/javascript>
+ $SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+ </script>
+
+ <script>
+ var taxon = JSON.parse('{{ taxon | tojson | safe }}');
+ var oligoname = JSON.parse('{{ oligoname | tojson | safe }}');
+ var version = JSON.parse('{{ version | tojson | safe }}');
+ var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
+ </script>
+
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByTaxonForOligosaccharideName.js') }}"></script>
+
+ <div style="margin:30px 0;"></div>
+
+ <div style="margin-left: 5%;margin-right: 5%;">
+ <h3><span style="color: #21517A;">Taxon -> Oligosaccharide name</span></h3>
+ <div class="d-flex justify-content-center text-info">
+ <div id="spinner_taxon_oligoname" class="spinner-border" role="status" style="display: none;">
+ <span class="sr-only">Loading...</span>
+ </div>
+ <div id="spinner_taxon_oligoname2" style="display: none;"><strong> Loading...</strong></div>
+ </div>
+
+ <div style="margin:40px 0;">
+ <div class="container">
+ <div class="row justify-content-center">
+ <div class="col-8">
+ <div class="input-group mb-3">
+ <label class="button-select input-group-text" for="relationoligonameByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search"></select>
+ <button id="filter_taxon_oligoname" type="button" class="btn btn-info button-select-filter" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div id="demo" class="collapse" style="margin-top: 1%;" align="center">
+ <table align="center">
+ <tr id="filter_col4" data-column="3">
+ <td> Filter by Oligosaccharide name </td>
+ <td align="center"><input type="text" class="column_filter" id="oligoname_th"></td>
+ </tr>
+ </table>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by oligosaccharide name, you can use ";" for "or" (example: "fucosyl;asialo" for oligosaccharide name).</small><br/>
+ </div>
+
+ <div id="hide" style="display:none">
+ <table id="results_taxon_oligoname" class="display responsive nowrap collapsed" style="width:100%"> <!--width="100%" visibility="none"-->
+ <thead>
+ <tr>
+ <th>Source text</th>
+ <th>Scientific name of taxon</th>
+ <th>Relation type</th>
+ <th>Reference class</th>
+ <th>QPS</th>
+ <th>Source</th>
+ <th>Occurrence in text (taxon)</th>
+ <th>Occurrence in text (oligosaccharide name)</th>
+ <th>Full source text</th>
+ <th>TaxonID</th>
+ <th>Taxonomy hierarchical path</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
+ </tr>
+ </thead>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div style="margin:80px 0;"></div>
+
+</section>
+{% endblock %}
diff --git a/templates/searchByTaxonForOligosaccharideType.html b/templates/searchByTaxonForOligosaccharideType.html
new file mode 100644
index 0000000000000000000000000000000000000000..b72b164343d035dbf34c7a44bac088cd2f1e6c63
--- /dev/null
+++ b/templates/searchByTaxonForOligosaccharideType.html
@@ -0,0 +1,100 @@
+<!--
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+-->
+
+{% extends 'main' %};
+{% block content %}
+<section>
+
+ <script type=text/javascript>
+ $SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+ </script>
+
+ <script>
+ var taxon = JSON.parse('{{ taxon | tojson | safe }}');
+ var oligotype = JSON.parse('{{ oligotype | tojson | safe }}');
+ var version = JSON.parse('{{ version | tojson | safe }}');
+ var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
+ </script>
+
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByTaxonForOligosaccharideType.js') }}"></script>
+
+ <div style="margin:30px 0;"></div>
+
+ <div style="margin-left: 5%;margin-right: 5%;">
+ <h3><span style="color: #21517A;">Taxon -> Oligosaccharide type</span></h3>
+ <div class="d-flex justify-content-center text-info">
+ <div id="spinner_taxon_oligotype" class="spinner-border" role="status" style="display: none;">
+ <span class="sr-only">Loading...</span>
+ </div>
+ <div id="spinner_taxon_oligotype2" style="display: none;"><strong> Loading...</strong></div>
+ </div>
+
+ <div style="margin:40px 0;">
+ <div class="container">
+ <div class="row justify-content-center">
+ <div class="col-8">
+ <div class="input-group mb-3">
+ <label class="button-select input-group-text" for="relationoligotypeByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search"></select>
+ <button id="filter_taxon_oligotype" type="button" class="btn btn-info button-select-filter" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div id="demo" class="collapse" style="margin-top: 1%;" align="center">
+ <table align="center">
+ <tr id="filter_col4" data-column="3">
+ <td> Filter by Oligosaccharide type </td>
+ <td align="center"><input type="text" class="column_filter" id="oligotype_th"></td>
+ </tr>
+ </table>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by oligosaccharide type, you can use ";" for "or" (example: "fuco;sialy" for oligosaccharide type).</small><br/>
+ </div>
+
+ <div id="hide" style="display:none">
+ <table id="results_taxon_oligotype" class="display responsive nowrap collapsed" style="width:100%"> <!--width="100%" visibility="none"-->
+ <thead>
+ <tr>
+ <th>Source text</th>
+ <th>Scientific name of taxon</th>
+ <th>Relation type</th>
+ <th>Reference class</th>
+ <th>QPS</th>
+ <th>Source</th>
+ <th>Occurrence in text (taxon)</th>
+ <th>Occurrence in text (oligosaccharide type)</th>
+ <th>Full source text</th>
+ <th>TaxonID</th>
+ <th>Taxonomy hierarchical path</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
+ </tr>
+ </thead>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div style="margin:80px 0;"></div>
+
+</section>
+{% endblock %}
diff --git a/templates/searchByTaxonForPostpartum.html b/templates/searchByTaxonForPostpartum.html
new file mode 100644
index 0000000000000000000000000000000000000000..de4dced64ae43d032101cf5ee66e178b2ea1fcd8
--- /dev/null
+++ b/templates/searchByTaxonForPostpartum.html
@@ -0,0 +1,101 @@
+<!--
+# Copyright 2022 Sandra Dérozier (INRAE)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+-->
+
+{% extends 'main' %}
+{% block content %}
+<section>
+
+ <script type=text/javascript>
+ $SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+ </script>
+
+ <script>
+ var taxon = JSON.parse('{{ taxon | tojson | safe }}');
+ var postpartum = JSON.parse('{{ postpartum | tojson | safe }}');
+ var version = JSON.parse('{{ version | tojson | safe }}');
+ var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
+ </script>
+
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByTaxonForPostpartum.js') }}"></script>
+
+ <div style="margin:30px 0;"></div>
+
+ <div style="margin-left: 5%;margin-right: 5%;">
+ <h3><span style="color: #21517A;">Taxon -> Postpartum Age</span></h3>
+
+ <div class="d-flex justify-content-center text-info">
+ <div id="spinner_taxon_postpartum" class="spinner-border" role="status" style="display: none;">
+ <span class="sr-only">Loading...</span>
+ </div>
+ <div id="spinner_taxon_postpartum2" style="display: none;"><strong> Loading...</strong></div>
+ </div>
+
+ <div style="margin:40px 0;">
+ <div class="container">
+ <div class="row justify-content-center">
+ <div class="col-8">
+ <div class="input-group">
+ <label class="button-select input-group-text" for="relationpostpartumByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search_taxon_postpartum"></select>
+ <button id="filter_taxon_postpartum" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div id="demo" class="collapse" style="margin-top: 1%;" align="center">
+ <table align="center">
+ <tr id="filter_col4" data-column="3">
+ <td> Filter by Postpartum age </td>
+ <td align="center"><input type="text" class="column_filter" id="postpartum_tp"></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_tp" id="qps_tp" value="yes" /></td> -->
+ </tr>
+ </table>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by postpartum, you can use ";" for "or" (example: "7;12" for postpartum age).</small><br/>
+ </div>
+ <div id="hide" style="display:none">
+ <table id="results_taxon_postpartum" class="display responsive nowrap collapsed" style="width:100%"><!-- width="100%" visibility="none"-->
+ <thead>
+ <tr>
+ <th>Source text</th>
+ <th>Scientific name of taxon</th>
+ <th>Relation type</th>
+ <th>Reference class</th>
+ <th>QPS</th>
+ <th>Source</th>
+ <th>Occurrence in text (taxon)</th>
+ <th>Occurrence in text (postpartum age)</th>
+ <th>Full source text</th>
+ <th>TaxonID</th>
+ <th>Taxonomy hierarchical path</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
+ </tr>
+ </thead>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div style="margin:80px 0;"></div>
+
+</section>
+{% endblock %}
diff --git a/templates/searchByTaxonForUse.html b/templates/searchByTaxonForSampleType.html
similarity index 67%
rename from templates/searchByTaxonForUse.html
rename to templates/searchByTaxonForSampleType.html
index 930eceb8639bb5cfe572ea9850053c514f152cc8..3e6e7223dfca261b8478b13dccc0a05b75a55c11 100644
--- a/templates/searchByTaxonForUse.html
+++ b/templates/searchByTaxonForSampleType.html
@@ -2,7 +2,7 @@
# Copyright 2022 Sandra Dérozier (INRAE)
#
# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
+# you may not sample this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
@@ -24,8 +24,7 @@
<script>
var taxon = JSON.parse('{{ taxon | tojson | safe }}');
- var use = JSON.parse('{{ use | tojson | safe }}');
- var qps = JSON.parse('{{ qps | tojson | safe }}');
+ var sample = JSON.parse('{{ sample | tojson | safe }}');
var version = JSON.parse('{{ version | tojson | safe }}');
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
@@ -35,18 +34,18 @@
<link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
- <script type="module" src="{{ url_for('static', filename='js/searchByTaxonForUse.js') }}"></script>
+ <script type="module" src="{{ url_for('static', filename='js/searchByTaxonForSampleType.js') }}"></script>
<div style="margin:30px 0;"></div>
<div style="margin-left: 5%;margin-right: 5%;">
- <h3><span style="color: #21517A;">Taxon studied for Use</span></h3>
+ <h3><span style="color: #21517A;">Taxon -> Sample Type</span></h3>
<div class="d-flex justify-content-center text-info">
- <div id="spinner_taxon_use" class="spinner-border" role="status" style="display: none;">
+ <div id="spinner_taxon_sample" class="spinner-border" role="status" style="display: none;">
<span class="sr-only">Loading...</span>
</div>
- <div id="spinner_taxon_use2" style="display: none;"><strong> Loading...</strong></div>
+ <div id="spinner_taxon_sample2" style="display: none;"><strong> Loading...</strong></div>
</div>
<div style="margin:40px 0;">
@@ -54,9 +53,9 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label class="button-select input-group-text" for="relationUseByTaxon">Search relations by taxon</label>
- <select class="form-select" id="search_taxon_use"></select>
- <button id="filter_taxon_use" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationSampleByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search_taxon_sample"></select>
+ <button id="filter_taxon_sample" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
@@ -65,32 +64,32 @@
<div id="demo" class="collapse" style="margin-top: 1%;" align="center">
<table align="center">
<tr id="filter_col4" data-column="3">
- <td> Filter by Use </td>
- <td align="center"><input type="text" class="column_filter" id="use_tu"></td>
- <td> QPS only </td>
- <td><input type="checkbox" name="qps_tu" id="qps_tu" value="yes" /></td>
+ <td> Filter by Sample type </td>
+ <td align="center"><input type="text" class="column_filter" id="sample_tu"></td>
+ <!-- <td> QPS only </td>
+ <td><input type="checkbox" name="qps_tu" id="qps_tu" value="yes" /></td> -->
</tr>
</table>
- <small id="help" class="form-text text-muted"><b>Note:</b> to filter by use, you can use ";" for "or" (example: "antimicrobial activity;antiviral activity" for use).</small><br/>
+ <small id="help" class="form-text text-muted"><b>Note:</b> to filter by sample, you can use ";" for "or" (example: "mixed;pooled" for sample type).</small><br/>
</div>
<div id="hide" style="display:none">
- <table id="results_taxon_use" class="display responsive nowrap collapsed" style="width:100%"><!-- width="100%" visibility="none"-->
+ <table id="results_taxon_sample" class="display responsive nowrap collapsed" style="width:100%"><!-- width="100%" visibility="none"-->
<thead>
<tr>
<th>Source text</th>
<th>Scientific name of taxon</th>
<th>Relation type</th>
- <th>OntoBiotope class</th>
+ <th>Reference class</th>
<th>QPS</th>
<th>Source</th>
<th>Occurrence in text (taxon)</th>
- <th>Occurrence in text (use)</th>
+ <th>Occurrence in text (sample)</th>
<th>Full source text</th>
<th>TaxonID</th>
<th>Taxonomy hierarchical path</th>
- <th>ID OntoBiotope</th>
- <th>OntoBiotope hierarchical path</th>
+ <th>ID Reference</th>
+ <th>Reference hierarchical path</th>
</tr>
</thead>
</table>
diff --git a/templates/sheet.html b/templates/sheet.html
new file mode 100644
index 0000000000000000000000000000000000000000..dbe9808ea284738899ec2df18469d88bae2b7994
--- /dev/null
+++ b/templates/sheet.html
@@ -0,0 +1,123 @@
+{% extends 'main2' %}
+{% block content %}
+<script src="{{ url_for('static', filename='js/sheet.js') }}" defer></script>
+<link href="{{ url_for('static', filename='css/sheet.css') }}" rel="stylesheet"/>
+
+<main class="main-container">
+ <!-- Navigation Sidebar -->
+ <nav class="sidebar">
+ <ul class="nav-menu">
+ <li><button class="nav-btn" onclick="toggleSection('oligo')">Oligosaccharides</button></li>
+ <li><button class="nav-btn" onclick="toggleSection('species')">Species</button></li>
+ <li><button class="nav-btn" onclick="toggleSection('samples')">Samples</button></li>
+ </ul>
+ </nav>
+
+ <!-- Content Area -->
+ <div class="content">
+ <!-- Oligosaccharides Section -->
+ <section id="oligo-section" class="section">
+ <div class="info-card">
+ <h2 class="card-header">Oligosaccharide Information</h2>
+ <div class="info-grid">
+ {% for label, value in [
+ ('Milk Oligosaccharide ID', 'OLIGO0137'),
+ ('Milk Oligosaccharide Normalized Name', '2\'-Fucosyllactose'),
+ ('Abbreviated Normalized MO Name', '2\'-FL'),
+ ('Formula', 'C18H32O15'),
+ ('Synonyms', '2\'FL | 2\'fucosyllactose | 2FL')
+ ] %}
+ <div class="info-item">
+ <span class="info-label">{{ label }}</span>
+ <span class="info-value">{{ value }}</span>
+ </div>
+ {% endfor %}
+ </div>
+ </div>
+
+ <div class="info-card">
+ <h2 class="card-header">Matched Information</h2>
+ <div class="info-grid">
+ {% for label, value in [
+ ('Text Occurrence', 'fucosyllactose'),
+ ('Reference Class', '2\'-Fucosyllactose'),
+ ('Species', 'Rabbit'),
+ ('MO Type', 'XX'),
+ ('MO Samples', 'Unidentified'),
+ ('Methods of Analysis', 'HPAEC-PAD'),
+ ('Text Snippet', 'HPAEC-PAD was used to quantify 2\'-fucosyllactose (2\'-FL)'),
+ ('Number of Occurrences', '2'),
+ ('Number of Matched Documents', '13')
+ ] %}
+ <div class="info-item">
+ <span class="info-label">{{ label }}</span>
+ <span class="info-value">{{ value }}</span>
+ </div>
+ {% endfor %}
+ </div>
+ </div>
+
+ <div class="info-card">
+ <h2 class="card-header">3D Structure</h2>
+ <div class="structure-viewer">
+ <img id="structure-image" class="structure-image" alt="3D Structure">
+ </div>
+ </div>
+
+ <div class="action-bar">
+ <button class="download-btn" onclick="downloadCSV()">Download CSV</button>
+ </div>
+ </section>
+
+ <!-- Species Section -->
+ <section id="species-section" class="section hidden">
+ <div class="info-card">
+ <h2 class="card-header">Species Information</h2>
+ <div class="info-grid">
+ {% for label, value in [
+ ('Species ID', ''),
+ ('Species Scientific Name', ''),
+ ('Number Of Occurrence', ''),
+ ('Physiological Stage', ''),
+ ('Breed', ''),
+ ('Geography', ''),
+ ('Postpartum age', '')
+ ] %}
+ <div class="info-item">
+ <span class="info-label">{{ label }}</span>
+ <span class="info-value">{{ value }}</span>
+ </div>
+ {% endfor %}
+ </div>
+ </div>
+ <div class="action-bar">
+ <button class="download-btn" onclick="downloadCSV()">Download CSV</button>
+ </div>
+ </section>
+
+ <!-- Samples Section -->
+ <section id="samples-section" class="section hidden">
+ <div class="info-card">
+ <h2 class="card-header">Samples Information</h2>
+ <div class="info-grid">
+ {% for label, value in [
+ ('Samples ID', ''),
+ ('Samples Scientific Name', ''),
+ ('Associated Species', ''),
+ ('MO Normalization Method', ''),
+ ('Lactation Stage', '')
+ ] %}
+ <div class="info-item">
+ <span class="info-label">{{ label }}</span>
+ <span class="info-value">{{ value }}</span>
+ </div>
+ {% endfor %}
+ </div>
+ </div>
+ <div class="action-bar">
+ <button class="download-btn" onclick="downloadCSV()">Download CSV</button>
+ </div>
+ </section>
+ </div>
+</main>
+{% endblock %}
\ No newline at end of file