From 94e92edca15249a39eaba1347b36e18ffc8a319f Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Tue, 27 Jun 2023 14:55:58 +0200
Subject: [PATCH 01/17] create analyses schema
---
schemas/analyses/AnalysesResponse.yml | 9 +++++++++
schemas/analyses/Analysis.yml | 27 +++++++++++++++++++++++++++
2 files changed, 36 insertions(+)
create mode 100644 schemas/analyses/AnalysesResponse.yml
create mode 100644 schemas/analyses/Analysis.yml
diff --git a/schemas/analyses/AnalysesResponse.yml b/schemas/analyses/AnalysesResponse.yml
new file mode 100644
index 0000000..9a2727d
--- /dev/null
+++ b/schemas/analyses/AnalysesResponse.yml
@@ -0,0 +1,9 @@
+allOf:
+ - $ref: '../utils/BaseResponse.yml'
+ - type: object
+ - properties:
+ analyses:
+ description: "Array of analyses"
+ type: array
+ items:
+ $ref: '../../schemas/analyses/Analysis.yml'
\ No newline at end of file
diff --git a/schemas/analyses/Analysis.yml b/schemas/analyses/Analysis.yml
new file mode 100644
index 0000000..7a0435d
--- /dev/null
+++ b/schemas/analyses/Analysis.yml
@@ -0,0 +1,27 @@
+type: object
+description: "Analysis object"
+properties:
+ id:
+ description: "id of the analysis"
+ type: integer
+ example: 1
+ name:
+ description: "name of the analysis"
+ type: string
+ example: "My mapping"
+ creation_date:
+ allOf:
+ - $ref: "../utils/DatePattern.yml"
+ description: "date of the creation of the analysis (ISO 8601 full-time format)"
+ edition_date:
+ allOf:
+ - $ref: "../utils/DatePattern.yml"
+ description: "date of the last modification (ISO 8601 full-time format)"
+ desc:
+ description: "description of the analysis"
+ type: string
+ example: "mapping of metabolites on mouse biosource"
+ input:
+ description: "id of the first step of the analysis"
+ type: integer
+ example: 1
\ No newline at end of file
--
GitLab
From d46dcccf42390b1eb044be2006ad966fa39ea91e Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Tue, 27 Jun 2023 15:07:37 +0200
Subject: [PATCH 02/17] create analyses path
---
paths/analyses/get.yml | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
create mode 100644 paths/analyses/get.yml
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
new file mode 100644
index 0000000..3a7071a
--- /dev/null
+++ b/paths/analyses/get.yml
@@ -0,0 +1,25 @@
+get:
+ tags:
+ - Analyses
+ summary: get Analysis
+ description: get from Analysis
+ operationId: getAnalyses
+ x-eov-operation-handler: analyses
+ parameters:
+ - name: id
+ in: query
+ description: id of the analysis
+ required: false
+ schema:
+ type: string
+ # autoriser les caractères spéciaux
+ # pour demander des listes d'identifiants
+ # example: /analyses/123,456,789
+ allowReserved: true
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
--
GitLab
From 89a1f3a145d117cf7cdd588912b354a931fa2c8e Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Tue, 27 Jun 2023 15:12:55 +0200
Subject: [PATCH 03/17] add analyses in metexplore api yaml
---
metexplore3-api.yml | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index e0f9e09..d4308ae 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -33,6 +33,10 @@ paths:
$ref: "paths/users/token_login.yml"
/:
$ref: "paths/root.yml"
+
+ /analyses:
+ $ref: "paths/analyses/get.yml"
+
/biosources:
$ref: "paths/biosources.yml"
--
GitLab
From 39072f8f7f7dba24f9ab916d3c98439e00a3f5c1 Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Wed, 28 Jun 2023 09:59:51 +0200
Subject: [PATCH 04/17] modify to pass parameter in path instead of query
---
metexplore3-api.yml | 2 +-
paths/analyses/get.yml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index d4308ae..0da9c9a 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -34,7 +34,7 @@ paths:
/:
$ref: "paths/root.yml"
- /analyses:
+ /analyses/{id}:
$ref: "paths/analyses/get.yml"
/biosources:
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
index 3a7071a..8651145 100644
--- a/paths/analyses/get.yml
+++ b/paths/analyses/get.yml
@@ -7,7 +7,7 @@ get:
x-eov-operation-handler: analyses
parameters:
- name: id
- in: query
+ in: path
description: id of the analysis
required: false
schema:
--
GitLab
From 1ede536b54bcbd1b545a4253e6bd8b1bdb0cd119 Mon Sep 17 00:00:00 2001
From: JeanClement <jeanclement.gallardo@inrae.fr>
Date: Wed, 28 Jun 2023 10:19:16 +0200
Subject: [PATCH 05/17] add steps methods
---
metexplore3-api.yml | 3 +++
paths/steps/get.yml | 21 +++++++++++++++++++++
schemas/steps/Step.yml | 29 +++++++++++++++++++++++++++++
schemas/steps/StepResponse.yml | 9 +++++++++
schemas/steps/Steps.yml | 17 +++++++++++++++++
schemas/steps/StepsResponse.yml | 9 +++++++++
6 files changed, 88 insertions(+)
create mode 100644 paths/steps/get.yml
create mode 100644 schemas/steps/Step.yml
create mode 100644 schemas/steps/StepResponse.yml
create mode 100644 schemas/steps/Steps.yml
create mode 100644 schemas/steps/StepsResponse.yml
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index e0f9e09..afc9c62 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -57,6 +57,9 @@ paths:
/filter:
$ref: "paths/filters/get.yml"
+ /steps:
+ $ref: "paths/steps/get.yml"
+
components:
securitySchemes:
jwtAuth:
diff --git a/paths/steps/get.yml b/paths/steps/get.yml
new file mode 100644
index 0000000..35bdb0b
--- /dev/null
+++ b/paths/steps/get.yml
@@ -0,0 +1,21 @@
+get:
+ tags:
+ - Steps
+ summary: Get specific step of an analysis
+ operationId: getSteps
+ x-eov-operation-handler: steps
+ description: Get a specific step of an analysis
+ parameters:
+ - name: id
+ in: query
+ description: the id for the step
+ required: true
+ schema:
+ type: integer
+ responses:
+ 200:
+ description: success
+ content:
+ application/json:
+ schema:
+ $ref: "../../schemas/steps/StepResponse.yml"
\ No newline at end of file
diff --git a/schemas/steps/Step.yml b/schemas/steps/Step.yml
new file mode 100644
index 0000000..aaf0d6a
--- /dev/null
+++ b/schemas/steps/Step.yml
@@ -0,0 +1,29 @@
+type: object
+description: "A step from an analysis"
+properties:
+ id:
+ description: "step id"
+ type: integer
+ format: int64
+ example: 22
+ id_analysis:
+ description: "analysis id"
+ type: integer
+ format: int64
+ example: 14
+ name:
+ description: "name of the step"
+ type: string
+ example: "Input"
+ root:
+ description: "Boolean that determined if its the first step of analysis or not"
+ type: boolean
+ example: false
+ type:
+ description: "Determine what types (data, job, ...) is this step"
+ type: string
+ example: "data"
+ description:
+ description: "Description of the step"
+ type: string
+ example: "Input value for next job"
\ No newline at end of file
diff --git a/schemas/steps/StepResponse.yml b/schemas/steps/StepResponse.yml
new file mode 100644
index 0000000..25c0d81
--- /dev/null
+++ b/schemas/steps/StepResponse.yml
@@ -0,0 +1,9 @@
+allOf:
+ - $ref: "../utils/BaseResponse.yml"
+ - type: object
+ - properties:
+ steps:
+ description: "Specific step of an analysis"
+ type: object
+ items:
+ $ref: "Step.yml"
diff --git a/schemas/steps/Steps.yml b/schemas/steps/Steps.yml
new file mode 100644
index 0000000..822f307
--- /dev/null
+++ b/schemas/steps/Steps.yml
@@ -0,0 +1,17 @@
+type: object
+description: "Array of steps"
+properties:
+ id_analysis:
+ description: "analysis id"
+ type: integer
+ format: int64
+ example: 14
+ name:
+ description: "name of the analysis"
+ type: string
+ example: "Input"
+ steps:
+ description: "Array of step"
+ type: array
+ example: [{id: 134, id_analysis: 123, name: "Input", root: true, type: "data", description: "Input value for mapping"},
+ {id: 135, id_analysis: 123, name: "Mapping", root: false, type: "job", description: "Mapping on metabolites"}]
\ No newline at end of file
diff --git a/schemas/steps/StepsResponse.yml b/schemas/steps/StepsResponse.yml
new file mode 100644
index 0000000..97911c8
--- /dev/null
+++ b/schemas/steps/StepsResponse.yml
@@ -0,0 +1,9 @@
+allOf:
+ - $ref: "../utils/BaseResponse.yml"
+ - type: object
+ - properties:
+ steps:
+ description: "All steps of an analysis"
+ type: array
+ items:
+ $ref: "Steps.yml"
--
GitLab
From 30323c725dcbec950dd6d1e7b79fc227e7999a4d Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Wed, 28 Jun 2023 10:21:45 +0200
Subject: [PATCH 06/17] change get to post
---
metexplore3-api.yml | 4 ++--
paths/analyses/get.yml | 25 -------------------------
paths/analyses/post.yml | 21 +++++++++++++++++++++
3 files changed, 23 insertions(+), 27 deletions(-)
delete mode 100644 paths/analyses/get.yml
create mode 100644 paths/analyses/post.yml
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index 0da9c9a..b116a19 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -34,8 +34,8 @@ paths:
/:
$ref: "paths/root.yml"
- /analyses/{id}:
- $ref: "paths/analyses/get.yml"
+ /analyses:
+ $ref: "paths/analyses/post.yml"
/biosources:
$ref: "paths/biosources.yml"
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
deleted file mode 100644
index 8651145..0000000
--- a/paths/analyses/get.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-get:
- tags:
- - Analyses
- summary: get Analysis
- description: get from Analysis
- operationId: getAnalyses
- x-eov-operation-handler: analyses
- parameters:
- - name: id
- in: path
- description: id of the analysis
- required: false
- schema:
- type: string
- # autoriser les caractères spéciaux
- # pour demander des listes d'identifiants
- # example: /analyses/123,456,789
- allowReserved: true
- responses:
- 200:
- description: successful operation
- content:
- application/json:
- schema:
- $ref: ../../schemas/analyses/AnalysesResponse.yml
diff --git a/paths/analyses/post.yml b/paths/analyses/post.yml
new file mode 100644
index 0000000..99d9774
--- /dev/null
+++ b/paths/analyses/post.yml
@@ -0,0 +1,21 @@
+post:
+ tags:
+ - Analyses
+ summary: post Analysis
+ description: post from Analysis
+ operationId: postAnalyses
+ x-eov-operation-handler: analyses
+ requestBody:
+ content:
+ application/json:
+ schema:
+ type: object
+ items:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
--
GitLab
From a9107eb0fca0a4d20b8dc3b2ede6592296204a42 Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Wed, 28 Jun 2023 11:17:43 +0200
Subject: [PATCH 07/17] back to get with path
---
metexplore3-api.yml | 4 ++--
paths/analyses/get.yml | 25 +++++++++++++++++++++++++
paths/analyses/post.yml | 21 ---------------------
3 files changed, 27 insertions(+), 23 deletions(-)
create mode 100644 paths/analyses/get.yml
delete mode 100644 paths/analyses/post.yml
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index 3d7c0a4..2e3bf2c 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -34,8 +34,8 @@ paths:
/:
$ref: "paths/root.yml"
- /analyses:
- $ref: "paths/analyses/post.yml"
+ /analyses/{id}:
+ $ref: "paths/analyses/get.yml"
/biosources:
$ref: "paths/biosources.yml"
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
new file mode 100644
index 0000000..8651145
--- /dev/null
+++ b/paths/analyses/get.yml
@@ -0,0 +1,25 @@
+get:
+ tags:
+ - Analyses
+ summary: get Analysis
+ description: get from Analysis
+ operationId: getAnalyses
+ x-eov-operation-handler: analyses
+ parameters:
+ - name: id
+ in: path
+ description: id of the analysis
+ required: false
+ schema:
+ type: string
+ # autoriser les caractères spéciaux
+ # pour demander des listes d'identifiants
+ # example: /analyses/123,456,789
+ allowReserved: true
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
diff --git a/paths/analyses/post.yml b/paths/analyses/post.yml
deleted file mode 100644
index 99d9774..0000000
--- a/paths/analyses/post.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-post:
- tags:
- - Analyses
- summary: post Analysis
- description: post from Analysis
- operationId: postAnalyses
- x-eov-operation-handler: analyses
- requestBody:
- content:
- application/json:
- schema:
- type: object
- items:
- $ref: ../../schemas/analyses/AnalysesResponse.yml
- responses:
- 200:
- description: successful operation
- content:
- application/json:
- schema:
- $ref: ../../schemas/analyses/AnalysesResponse.yml
--
GitLab
From 3c5f349331b380ac4a8326d8ec4103bcbcac0e1f Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Wed, 28 Jun 2023 11:23:58 +0200
Subject: [PATCH 08/17] back to query
---
metexplore3-api.yml | 2 +-
paths/analyses/get.yml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index 2e3bf2c..01238a2 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -34,7 +34,7 @@ paths:
/:
$ref: "paths/root.yml"
- /analyses/{id}:
+ /analyses:
$ref: "paths/analyses/get.yml"
/biosources:
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
index 8651145..3a7071a 100644
--- a/paths/analyses/get.yml
+++ b/paths/analyses/get.yml
@@ -7,7 +7,7 @@ get:
x-eov-operation-handler: analyses
parameters:
- name: id
- in: path
+ in: query
description: id of the analysis
required: false
schema:
--
GitLab
From 78e511665b7932dd5613bdd4aa08b38b6505c57e Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Wed, 28 Jun 2023 14:25:59 +0200
Subject: [PATCH 09/17] analyses add, update and delete
---
metexplore3-api.yml | 2 +-
paths/analyses/add.yml | 20 +++++++++++++++
paths/analyses/analyses.yml | 15 ++++++++++++
paths/analyses/del.yml | 20 +++++++++++++++
paths/analyses/get.yml | 49 ++++++++++++++++++-------------------
paths/analyses/update.yml | 20 +++++++++++++++
6 files changed, 100 insertions(+), 26 deletions(-)
create mode 100644 paths/analyses/add.yml
create mode 100644 paths/analyses/analyses.yml
create mode 100644 paths/analyses/del.yml
create mode 100644 paths/analyses/update.yml
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index 01238a2..c5da294 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -35,7 +35,7 @@ paths:
$ref: "paths/root.yml"
/analyses:
- $ref: "paths/analyses/get.yml"
+ $ref: "paths/analyses/analyses.yml"
/biosources:
$ref: "paths/biosources.yml"
diff --git a/paths/analyses/add.yml b/paths/analyses/add.yml
new file mode 100644
index 0000000..e52e7cf
--- /dev/null
+++ b/paths/analyses/add.yml
@@ -0,0 +1,20 @@
+tags:
+ - Analyses
+summary: add Analysis
+description: add for Analysis
+operationId: addAnalyses
+x-eov-operation-handler: analyses
+requestBody:
+ content:
+ application/json:
+ schema:
+ type: object
+ items:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
+responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
diff --git a/paths/analyses/analyses.yml b/paths/analyses/analyses.yml
new file mode 100644
index 0000000..63d178c
--- /dev/null
+++ b/paths/analyses/analyses.yml
@@ -0,0 +1,15 @@
+# GET
+get:
+ $ref: ./get.yml
+
+# ADD
+post:
+ $ref: ./add.yml
+
+# DELETE
+delete:
+ $ref: ./del.yml
+
+# PATCH
+patch:
+ $ref: ./update.yml
diff --git a/paths/analyses/del.yml b/paths/analyses/del.yml
new file mode 100644
index 0000000..2b1780a
--- /dev/null
+++ b/paths/analyses/del.yml
@@ -0,0 +1,20 @@
+tags:
+ - Analyses
+summary: del Analysis
+description: delete for Analysis
+operationId: delAnalyses
+x-eov-operation-handler: analyses
+parameters:
+ - name: id
+ in: query
+ description: the id for the Analysis
+ required: true
+ schema:
+ type: integer
+responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
index 3a7071a..2ec94bf 100644
--- a/paths/analyses/get.yml
+++ b/paths/analyses/get.yml
@@ -1,25 +1,24 @@
-get:
- tags:
- - Analyses
- summary: get Analysis
- description: get from Analysis
- operationId: getAnalyses
- x-eov-operation-handler: analyses
- parameters:
- - name: id
- in: query
- description: id of the analysis
- required: false
- schema:
- type: string
- # autoriser les caractères spéciaux
- # pour demander des listes d'identifiants
- # example: /analyses/123,456,789
- allowReserved: true
- responses:
- 200:
- description: successful operation
- content:
- application/json:
- schema:
- $ref: ../../schemas/analyses/AnalysesResponse.yml
+tags:
+ - Analyses
+summary: get Analysis
+description: get from Analysis
+operationId: getAnalyses
+x-eov-operation-handler: analyses
+parameters:
+ - name: id
+ in: query
+ description: id of the analysis
+ required: false
+ schema:
+ type: string
+ # autoriser les caractères spéciaux
+ # pour demander des listes d'identifiants
+ # example: /analyses/123,456,789
+ allowReserved: true
+responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
diff --git a/paths/analyses/update.yml b/paths/analyses/update.yml
new file mode 100644
index 0000000..8b02763
--- /dev/null
+++ b/paths/analyses/update.yml
@@ -0,0 +1,20 @@
+tags:
+ - Analyses
+summary: add Analysis
+description: update for Analysis
+operationId: updateAnalysis
+x-eov-operation-handler: analyses
+requestBody:
+ content:
+ application/json:
+ schema:
+ type: object
+ items:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
+responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/analyses/AnalysesResponse.yml
--
GitLab
From c8b1772387f145cb937e799c1bdb69f1c81cc72a Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Thu, 29 Jun 2023 09:26:50 +0200
Subject: [PATCH 10/17] update analysis attributes to match DB and add 404
responses
---
paths/analyses/add.yml | 6 ++++++
paths/analyses/del.yml | 6 ++++++
paths/analyses/get.yml | 6 ++++++
paths/analyses/update.yml | 6 ++++++
schemas/analyses/Analysis.yml | 20 ++++++++++----------
5 files changed, 34 insertions(+), 10 deletions(-)
diff --git a/paths/analyses/add.yml b/paths/analyses/add.yml
index e52e7cf..5075298 100644
--- a/paths/analyses/add.yml
+++ b/paths/analyses/add.yml
@@ -18,3 +18,9 @@ responses:
application/json:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
+ 404:
+ description: error
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/BaseResponse.yml
diff --git a/paths/analyses/del.yml b/paths/analyses/del.yml
index 2b1780a..4fa421b 100644
--- a/paths/analyses/del.yml
+++ b/paths/analyses/del.yml
@@ -18,3 +18,9 @@ responses:
application/json:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
+ 404:
+ description: error
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/BaseResponse.yml
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
index 2ec94bf..ac2c742 100644
--- a/paths/analyses/get.yml
+++ b/paths/analyses/get.yml
@@ -22,3 +22,9 @@ responses:
application/json:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
+ 404:
+ description: error
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/BaseResponse.yml
diff --git a/paths/analyses/update.yml b/paths/analyses/update.yml
index 8b02763..dbc7717 100644
--- a/paths/analyses/update.yml
+++ b/paths/analyses/update.yml
@@ -18,3 +18,9 @@ responses:
application/json:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
+ 404:
+ description: error
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/BaseResponse.yml
diff --git a/schemas/analyses/Analysis.yml b/schemas/analyses/Analysis.yml
index 7a0435d..3467db0 100644
--- a/schemas/analyses/Analysis.yml
+++ b/schemas/analyses/Analysis.yml
@@ -9,19 +9,19 @@ properties:
description: "name of the analysis"
type: string
example: "My mapping"
- creation_date:
+ description:
+ description: "description of the analysis"
+ type: string
+ example: "mapping of metabolites on mouse biosource"
+ url:
+ description: "url of the analysis"
+ type: string
+ example: "http://localhost:3000/mapping/metabolites/23"
+ creationDate:
allOf:
- $ref: "../utils/DatePattern.yml"
description: "date of the creation of the analysis (ISO 8601 full-time format)"
- edition_date:
+ editionDate:
allOf:
- $ref: "../utils/DatePattern.yml"
description: "date of the last modification (ISO 8601 full-time format)"
- desc:
- description: "description of the analysis"
- type: string
- example: "mapping of metabolites on mouse biosource"
- input:
- description: "id of the first step of the analysis"
- type: integer
- example: 1
\ No newline at end of file
--
GitLab
From 76b3c7ddd984cfa01eec62721608769a5ac00756 Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Thu, 29 Jun 2023 13:17:02 +0200
Subject: [PATCH 11/17] reponse 404
---
paths/analyses/add.yml | 6 +-----
paths/analyses/del.yml | 6 +-----
paths/analyses/get.yml | 6 +-----
paths/analyses/update.yml | 6 +-----
paths/biosources.yml | 4 +++-
paths/enzymes/get.yml | 2 ++
paths/filters/get.yml | 2 ++
paths/genes/get.yml | 2 ++
paths/metabolites/get.yml | 2 ++
paths/pathways/get.yml | 2 ++
paths/proteins/get.yml | 2 ++
paths/reactions/get.yml | 2 ++
paths/root.yml | 4 +++-
paths/steps/get.yml | 4 +++-
paths/users/create.yml | 4 +++-
paths/users/login.yml | 4 +++-
paths/users/token_login.yml | 4 +++-
responses/notFound.yml | 5 +++++
18 files changed, 41 insertions(+), 26 deletions(-)
create mode 100644 responses/notFound.yml
diff --git a/paths/analyses/add.yml b/paths/analyses/add.yml
index 5075298..950a917 100644
--- a/paths/analyses/add.yml
+++ b/paths/analyses/add.yml
@@ -19,8 +19,4 @@ responses:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
404:
- description: error
- content:
- application/json:
- schema:
- $ref: ../../schemas/utils/BaseResponse.yml
+ $ref: ../../responses/notFound.yml
diff --git a/paths/analyses/del.yml b/paths/analyses/del.yml
index 4fa421b..67f5436 100644
--- a/paths/analyses/del.yml
+++ b/paths/analyses/del.yml
@@ -19,8 +19,4 @@ responses:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
404:
- description: error
- content:
- application/json:
- schema:
- $ref: ../../schemas/utils/BaseResponse.yml
+ $ref: ../../responses/notFound.yml
\ No newline at end of file
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
index ac2c742..81d9cff 100644
--- a/paths/analyses/get.yml
+++ b/paths/analyses/get.yml
@@ -23,8 +23,4 @@ responses:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
404:
- description: error
- content:
- application/json:
- schema:
- $ref: ../../schemas/utils/BaseResponse.yml
+ $ref: ../../responses/notFound.yml
diff --git a/paths/analyses/update.yml b/paths/analyses/update.yml
index dbc7717..b59f8e3 100644
--- a/paths/analyses/update.yml
+++ b/paths/analyses/update.yml
@@ -19,8 +19,4 @@ responses:
schema:
$ref: ../../schemas/analyses/AnalysesResponse.yml
404:
- description: error
- content:
- application/json:
- schema:
- $ref: ../../schemas/utils/BaseResponse.yml
+ $ref: ../../responses/notFound.yml
diff --git a/paths/biosources.yml b/paths/biosources.yml
index 55b3bfd..e161857 100644
--- a/paths/biosources.yml
+++ b/paths/biosources.yml
@@ -6,9 +6,11 @@ get:
x-eov-operation-handler: "biosources"
description: "get all biosources"
responses:
- "200":
+ 200:
description: successful operation
content:
application/json:
schema:
$ref: '../schemas/biosources/BioSourcesResponse.yml'
+ 404:
+ $ref: ../responses/notFound.yml
diff --git a/paths/enzymes/get.yml b/paths/enzymes/get.yml
index 242f018..cb1db3a 100644
--- a/paths/enzymes/get.yml
+++ b/paths/enzymes/get.yml
@@ -32,3 +32,5 @@ get:
application/json:
schema:
$ref: ../../schemas/enzymes/EnzymesResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/filters/get.yml b/paths/filters/get.yml
index d4ff4c2..4d8cdf8 100644
--- a/paths/filters/get.yml
+++ b/paths/filters/get.yml
@@ -27,3 +27,5 @@ get:
application/json:
schema:
$ref: ../../schemas/filters/FiltersResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/genes/get.yml b/paths/genes/get.yml
index 4d559f0..f888c83 100644
--- a/paths/genes/get.yml
+++ b/paths/genes/get.yml
@@ -32,3 +32,5 @@ get:
application/json:
schema:
$ref: ../../schemas/genes/GenesResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/metabolites/get.yml b/paths/metabolites/get.yml
index 99ff130..94ef17c 100644
--- a/paths/metabolites/get.yml
+++ b/paths/metabolites/get.yml
@@ -32,3 +32,5 @@ get:
application/json:
schema:
$ref: ../../schemas/metabolites/MetabolitesResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/pathways/get.yml b/paths/pathways/get.yml
index 3df5a5d..a583318 100644
--- a/paths/pathways/get.yml
+++ b/paths/pathways/get.yml
@@ -32,3 +32,5 @@ get:
application/json:
schema:
$ref: ../../schemas/pathways/PathwaysResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/proteins/get.yml b/paths/proteins/get.yml
index a2ea2e2..e570b85 100644
--- a/paths/proteins/get.yml
+++ b/paths/proteins/get.yml
@@ -32,3 +32,5 @@ get:
application/json:
schema:
$ref: ../../schemas/proteins/ProteinsResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/reactions/get.yml b/paths/reactions/get.yml
index 476600c..16a1263 100644
--- a/paths/reactions/get.yml
+++ b/paths/reactions/get.yml
@@ -32,3 +32,5 @@ get:
application/json:
schema:
$ref: ../../schemas/reactions/ReactionsResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/root.yml b/paths/root.yml
index d946a35..4ea2c9e 100644
--- a/paths/root.yml
+++ b/paths/root.yml
@@ -5,9 +5,11 @@ get:
operationId: "root"
x-eov-operation-handler: "root"
responses:
- "200":
+ 200:
description: OK
content:
application/json:
schema:
$ref: "../schemas/utils/BaseResponse.yml"
+ 404:
+ $ref: ../responses/notFound.yml
diff --git a/paths/steps/get.yml b/paths/steps/get.yml
index 35bdb0b..dc06399 100644
--- a/paths/steps/get.yml
+++ b/paths/steps/get.yml
@@ -18,4 +18,6 @@ get:
content:
application/json:
schema:
- $ref: "../../schemas/steps/StepResponse.yml"
\ No newline at end of file
+ $ref: "../../schemas/steps/StepResponse.yml"
+ 404:
+ $ref: ../../responses/notFound.yml
\ No newline at end of file
diff --git a/paths/users/create.yml b/paths/users/create.yml
index 84f610b..a2a1474 100644
--- a/paths/users/create.yml
+++ b/paths/users/create.yml
@@ -12,9 +12,11 @@ post:
items:
$ref: '../../schemas/users/User.yml'
responses:
- "200":
+ 200:
description: successful operation
content:
application/json:
schema:
$ref: '../../schemas/users/UserResponse.yml'
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/users/login.yml b/paths/users/login.yml
index 2346637..d16c4a0 100644
--- a/paths/users/login.yml
+++ b/paths/users/login.yml
@@ -12,9 +12,11 @@ post:
items:
$ref: '../../schemas/users/User.yml'
responses:
- "200":
+ 200:
description: successful operation
content:
application/json:
schema:
$ref: '../../schemas/users/UserResponse.yml'
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/users/token_login.yml b/paths/users/token_login.yml
index e94c103..804a223 100644
--- a/paths/users/token_login.yml
+++ b/paths/users/token_login.yml
@@ -14,9 +14,11 @@ post:
schema:
type: string
responses:
- "200":
+ 200:
description: successful operation
content:
application/json:
schema:
$ref: "../../schemas/users/UserResponse.yml"
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/responses/notFound.yml b/responses/notFound.yml
new file mode 100644
index 0000000..e45accd
--- /dev/null
+++ b/responses/notFound.yml
@@ -0,0 +1,5 @@
+description: not found
+content:
+ application/json:
+ schema:
+ $ref: ../schemas/utils/BaseResponse.yml
\ No newline at end of file
--
GitLab
From b7b0ab90664c86568a441cdd7ca69b1ced8467dc Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Thu, 29 Jun 2023 13:24:41 +0200
Subject: [PATCH 12/17] get analysis authorize one id integer
---
paths/analyses/get.yml | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
index 81d9cff..71566c9 100644
--- a/paths/analyses/get.yml
+++ b/paths/analyses/get.yml
@@ -10,11 +10,7 @@ parameters:
description: id of the analysis
required: false
schema:
- type: string
- # autoriser les caractères spéciaux
- # pour demander des listes d'identifiants
- # example: /analyses/123,456,789
- allowReserved: true
+ type: integer
responses:
200:
description: successful operation
--
GitLab
From eb3621bb2958bee2fbcac24da650b07d963deaf2 Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Thu, 29 Jun 2023 13:27:05 +0200
Subject: [PATCH 13/17] add example for dates
---
schemas/analyses/Analysis.yml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/schemas/analyses/Analysis.yml b/schemas/analyses/Analysis.yml
index 3467db0..9015b6f 100644
--- a/schemas/analyses/Analysis.yml
+++ b/schemas/analyses/Analysis.yml
@@ -21,7 +21,9 @@ properties:
allOf:
- $ref: "../utils/DatePattern.yml"
description: "date of the creation of the analysis (ISO 8601 full-time format)"
+ example: "2023-06-29 13:26:00"
editionDate:
allOf:
- $ref: "../utils/DatePattern.yml"
description: "date of the last modification (ISO 8601 full-time format)"
+ example: "2023-06-29 13:26:00"
--
GitLab
From 7c459bf354271898a44f101b811b18232224a7af Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Thu, 29 Jun 2023 13:38:28 +0200
Subject: [PATCH 14/17] update methods description
---
paths/analyses/add.yml | 2 +-
paths/analyses/del.yml | 4 ++--
paths/analyses/get.yml | 2 +-
paths/analyses/update.yml | 4 ++--
4 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/paths/analyses/add.yml b/paths/analyses/add.yml
index 950a917..d4c06eb 100644
--- a/paths/analyses/add.yml
+++ b/paths/analyses/add.yml
@@ -1,7 +1,7 @@
tags:
- Analyses
summary: add Analysis
-description: add for Analysis
+description: "add an Analysis with data in the body of the request as json (name, description and url)"
operationId: addAnalyses
x-eov-operation-handler: analyses
requestBody:
diff --git a/paths/analyses/del.yml b/paths/analyses/del.yml
index 67f5436..1d6789b 100644
--- a/paths/analyses/del.yml
+++ b/paths/analyses/del.yml
@@ -1,7 +1,7 @@
tags:
- Analyses
-summary: del Analysis
-description: delete for Analysis
+summary: delete Analysis
+description: "delete the Analysis with its id"
operationId: delAnalyses
x-eov-operation-handler: analyses
parameters:
diff --git a/paths/analyses/get.yml b/paths/analyses/get.yml
index 71566c9..faf4274 100644
--- a/paths/analyses/get.yml
+++ b/paths/analyses/get.yml
@@ -1,7 +1,7 @@
tags:
- Analyses
summary: get Analysis
-description: get from Analysis
+description: "get data from Analysis : if no id specified, all the analysis ; else only the one with corresponding id"
operationId: getAnalyses
x-eov-operation-handler: analyses
parameters:
diff --git a/paths/analyses/update.yml b/paths/analyses/update.yml
index b59f8e3..ba82626 100644
--- a/paths/analyses/update.yml
+++ b/paths/analyses/update.yml
@@ -1,7 +1,7 @@
tags:
- Analyses
-summary: add Analysis
-description: update for Analysis
+summary: update Analysis
+description: "update one Analysis with its id, the data to modify is passed in the body of the request in json format (name, description, url)"
operationId: updateAnalysis
x-eov-operation-handler: analyses
requestBody:
--
GitLab
From 9732f2773bb7bbd9fc1cb5a5274966ae461cfe46 Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Thu, 6 Jul 2023 11:34:15 +0200
Subject: [PATCH 15/17] change requestBody schema
---
paths/analyses/add.yml | 4 +---
paths/analyses/update.yml | 4 +---
2 files changed, 2 insertions(+), 6 deletions(-)
diff --git a/paths/analyses/add.yml b/paths/analyses/add.yml
index d4c06eb..d7887c6 100644
--- a/paths/analyses/add.yml
+++ b/paths/analyses/add.yml
@@ -8,9 +8,7 @@ requestBody:
content:
application/json:
schema:
- type: object
- items:
- $ref: ../../schemas/analyses/AnalysesResponse.yml
+ $ref: ../../schemas/analyses/Analysis.yml
responses:
200:
description: successful operation
diff --git a/paths/analyses/update.yml b/paths/analyses/update.yml
index ba82626..b889d39 100644
--- a/paths/analyses/update.yml
+++ b/paths/analyses/update.yml
@@ -8,9 +8,7 @@ requestBody:
content:
application/json:
schema:
- type: object
- items:
- $ref: ../../schemas/analyses/AnalysesResponse.yml
+ $ref: ../../schemas/analyses/Analysis.yml
responses:
200:
description: successful operation
--
GitLab
From 7ce301f6bd539066a86d4bd70c626a2c8e104c88 Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Wed, 19 Jul 2023 11:25:26 +0200
Subject: [PATCH 16/17] add count paths and schema
---
metexplore3-api.yml | 12 ++++++++++++
paths/enzymes/count.yml | 23 +++++++++++++++++++++++
paths/genes/count.yml | 23 +++++++++++++++++++++++
paths/metabolites/count.yml | 23 +++++++++++++++++++++++
paths/pathways/count.yml | 23 +++++++++++++++++++++++
paths/proteins/count.yml | 23 +++++++++++++++++++++++
paths/reactions/count.yml | 23 +++++++++++++++++++++++
schemas/utils/CountResponse.yml | 6 ++++++
8 files changed, 156 insertions(+)
create mode 100644 paths/enzymes/count.yml
create mode 100644 paths/genes/count.yml
create mode 100644 paths/metabolites/count.yml
create mode 100644 paths/pathways/count.yml
create mode 100644 paths/proteins/count.yml
create mode 100644 paths/reactions/count.yml
create mode 100644 schemas/utils/CountResponse.yml
diff --git a/metexplore3-api.yml b/metexplore3-api.yml
index 411c0b1..798f132 100644
--- a/metexplore3-api.yml
+++ b/metexplore3-api.yml
@@ -42,21 +42,33 @@ paths:
/pathways:
$ref: "paths/pathways/get.yml"
+ /pathways/count:
+ $ref: "paths/pathways/count.yml"
/reactions:
$ref: "paths/reactions/get.yml"
+ /reactions/count:
+ $ref: "paths/reactions/count.yml"
/metabolites:
$ref: "paths/metabolites/get.yml"
+ /metabolites/count:
+ $ref: "paths/metabolites/count.yml"
/enzymes:
$ref: "paths/enzymes/get.yml"
+ /enzymes/count:
+ $ref: "paths/enzymes/count.yml"
/proteins:
$ref: "paths/proteins/get.yml"
+ /proteins/count:
+ $ref: "paths/proteins/count.yml"
/genes:
$ref: "paths/genes/get.yml"
+ /genes/count:
+ $ref: "paths/genes/count.yml"
/filter:
$ref: "paths/filters/get.yml"
diff --git a/paths/enzymes/count.yml b/paths/enzymes/count.yml
new file mode 100644
index 0000000..5c86c6a
--- /dev/null
+++ b/paths/enzymes/count.yml
@@ -0,0 +1,23 @@
+get:
+ tags:
+ - Enzymes
+ summary: count ligns Enzyme
+ description: get the number of enzymes for one biosource
+ operationId: countEnzymes
+ x-eov-operation-handler: enzymes
+ parameters:
+ - name: idBioSource
+ in: query
+ description: the idBioSource for the Enzyme
+ required: true
+ schema:
+ type: integer
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/CountResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/genes/count.yml b/paths/genes/count.yml
new file mode 100644
index 0000000..49c9d9b
--- /dev/null
+++ b/paths/genes/count.yml
@@ -0,0 +1,23 @@
+get:
+ tags:
+ - Genes
+ summary: count ligns Genes
+ description: get the number of genes for one biosource
+ operationId: countGenes
+ x-eov-operation-handler: genes
+ parameters:
+ - name: idBioSource
+ in: query
+ description: the idBioSource for the genes
+ required: true
+ schema:
+ type: integer
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/CountResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/metabolites/count.yml b/paths/metabolites/count.yml
new file mode 100644
index 0000000..393b777
--- /dev/null
+++ b/paths/metabolites/count.yml
@@ -0,0 +1,23 @@
+get:
+ tags:
+ - Metabolites
+ summary: count ligns Metabolites
+ description: get the number of metabolites for one biosource
+ operationId: countMetabolites
+ x-eov-operation-handler: metabolites
+ parameters:
+ - name: idBioSource
+ in: query
+ description: the idBioSource for the metabolites
+ required: true
+ schema:
+ type: integer
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/CountResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/pathways/count.yml b/paths/pathways/count.yml
new file mode 100644
index 0000000..1fcd3e1
--- /dev/null
+++ b/paths/pathways/count.yml
@@ -0,0 +1,23 @@
+get:
+ tags:
+ - Pathways
+ summary: count ligns Pathways
+ description: get the number of pathways for one biosource
+ operationId: countPathways
+ x-eov-operation-handler: pathways
+ parameters:
+ - name: idBioSource
+ in: query
+ description: the idBioSource for the pathways
+ required: true
+ schema:
+ type: integer
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/CountResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/proteins/count.yml b/paths/proteins/count.yml
new file mode 100644
index 0000000..afff9f6
--- /dev/null
+++ b/paths/proteins/count.yml
@@ -0,0 +1,23 @@
+get:
+ tags:
+ - Proteins
+ summary: count ligns Proteins
+ description: get the number of proteins for one biosource
+ operationId: countProteins
+ x-eov-operation-handler: proteins
+ parameters:
+ - name: idBioSource
+ in: query
+ description: the idBioSource for the proteins
+ required: true
+ schema:
+ type: integer
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/CountResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/paths/reactions/count.yml b/paths/reactions/count.yml
new file mode 100644
index 0000000..d3d1548
--- /dev/null
+++ b/paths/reactions/count.yml
@@ -0,0 +1,23 @@
+get:
+ tags:
+ - Reactions
+ summary: count ligns Reactions
+ description: get the number of reactions for one biosource
+ operationId: countReactions
+ x-eov-operation-handler: reactions
+ parameters:
+ - name: idBioSource
+ in: query
+ description: the idBioSource for the reactions
+ required: true
+ schema:
+ type: integer
+ responses:
+ 200:
+ description: successful operation
+ content:
+ application/json:
+ schema:
+ $ref: ../../schemas/utils/CountResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
diff --git a/schemas/utils/CountResponse.yml b/schemas/utils/CountResponse.yml
new file mode 100644
index 0000000..390800b
--- /dev/null
+++ b/schemas/utils/CountResponse.yml
@@ -0,0 +1,6 @@
+allOf:
+ - $ref: '../utils/BaseResponse.yml'
+ - type: object
+ - properties:
+ count:
+ type: integer
--
GitLab
From 686a334df6530f896612e4fc046bd0227c5f3895 Mon Sep 17 00:00:00 2001
From: "marion.liotier" <marion.liotier@inrae.fr>
Date: Wed, 19 Jul 2023 11:53:05 +0200
Subject: [PATCH 17/17] add 404 response
---
paths/steps/add.yml | 4 +++-
paths/steps/get.yml | 2 ++
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/paths/steps/add.yml b/paths/steps/add.yml
index 0237d42..b830653 100644
--- a/paths/steps/add.yml
+++ b/paths/steps/add.yml
@@ -17,4 +17,6 @@ responses:
content:
application/json:
schema:
- $ref: ../../schemas/steps/StepResponse.yml
\ No newline at end of file
+ $ref: ../../schemas/steps/StepResponse.yml
+ 404:
+ $ref: ../../responses/notFound.yml
\ No newline at end of file
diff --git a/paths/steps/get.yml b/paths/steps/get.yml
index ad66a0f..086ff15 100644
--- a/paths/steps/get.yml
+++ b/paths/steps/get.yml
@@ -24,3 +24,5 @@ responses:
application/json:
schema:
$ref: "../../schemas/steps/StepResponse.yml"
+ 404:
+ $ref: ../../responses/notFound.yml
--
GitLab