genelastic 0.8.0__py3-none-any.whl → 0.10.0__py3-none-any.whl

genelastic/api/specification.yml

@@ -1,39 +1,20 @@
 ---
 openapi: "3.0.3"
 info:
-  description: This is the swagger file for our API
+  description: C'est le fichier Swagger de l'API de la Base Expérimentale (genelastic).
   version: "1.0.1"
-  title: Swagger for ReST API
+  title: API de la Base Expérimentale (genelastic)
 servers:
   - url: "/api"
 
 paths:
-  /ping:
-    get:
-      operationId: genelastic.api.routes.ping
-      tags:
-        - Tests
-      summary: Server status check
-      description: Test route to verify that the server is online
-      responses:
-        200:
-          description: The server is online
-          content:
-            application/json:
-              schema:
-                type: object
-                properties:
-                  message:
-                    type: string
-                    example: pong
 
-  /indices:
+  /indexes:
     get:
-      operationId: genelastic.api.routes.list_indices
+      operationId: genelastic.api.routes.indexes
       tags:
         - Indexes
-      summary: Listing the indexes present in Elasticsearch
-      description: Listing the indexes present in Elasticsearch
+      summary: Renvoie tous les index présents dans Elasticsearch
       responses:
         200:
           description: Success of the request
@@ -46,26 +27,25 @@ paths:
         500:
           description: Internal server error
 
-  /indices/{index_id}/documents/{document_id}:
+  /documents/{index_id}/{document_id}:
     get:
-      operationId: genelastic.api.routes.retrieve_document
+      operationId: genelastic.api.routes.retrieve_document_by_index_and_id
       parameters:
         - in: path
           name: index_id
           schema:
             type: string
           required: true
-          description: The index in which to search for the document
+          description: L'index dans lequel rechercher le document
         - in: path
           name: document_id
           schema:
             type: string
           required: true
-          description: The ID of the document to retrieve
+          description: L'ID du document à récupérer
       tags:
-        - Document
-      summary: Retrieve a document
-      description: Retrieve a specific document from Elasticsearch
+        - Documents
+      summary: Retourne un document selon l'index et l'ID du document
       responses:
         200:
           description: Success in reading the data
@@ -80,8 +60,8 @@ paths:
 
   /wet_processes:
     get:
-      operationId: genelastic.api.routes.list_wet_processes
-      summary: Retrieve a list of wet processes
+      operationId: genelastic.api.routes.wet_processes
+      summary: Renvoie la liste des wet processes
       tags:
         - Wet processes
       responses:
@@ -92,10 +72,55 @@ paths:
               schema:
                 type: array
 
+  /wet_processes/{proc_id}:
+    get:
+      operationId: genelastic.api.routes.get_wet_process
+      summary: Renvoie la liste des détails d'un wet process spécifique
+      tags:
+        - Wet processes
+      parameters:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Wet process ID
+      responses:
+        200:
+          description: List of wet processes
+          content:
+            application/json:
+              schema:
+                type: array
+
+
+  /wet_process/{proc_id}/analyses:
+    get:
+      operationId: genelastic.api.routes.list_analyses_by_wet_process
+      summary: Renvoie les analyses qui contiennent le wet process spécifié
+      tags:
+        - Analyses
+      parameters:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Wet process ID
+      responses:
+        200:
+          description: List of wet processes
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  type: string
+
   /bi_processes:
     get:
-      operationId: genelastic.api.routes.list_bi_processes
-      summary: Retrieve a list of bi processes
+      operationId: genelastic.api.routes.bi_processes
+      summary: Renvoie la liste des bi processes
       tags:
         - Bi processes
       responses:
@@ -106,24 +131,33 @@ paths:
               schema:
                 type: array
 
-  /analyses:
+  /bi_processes/{proc_id}:
     get:
-      operationId: genelastic.api.routes.list_analyses
-      summary: Retrieve a list of analyses
+      operationId: genelastic.api.routes.get_bi_process
+      summary: Renvoie la liste des détails d'un bi process spécifique
       tags:
-        - Analyses
+        - Bi processes
+      parameters:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Bi process ID
       responses:
         200:
-          description: List of analyses
+          description: List of bi processes
           content:
             application/json:
               schema:
-                type: string
+                type: array
+        404:
+          description: Bi process not found
 
-  /wet_process/{proc_id}:
+  /bi_process/{proc_id}/analyses:
     get:
-      operationId: genelastic.api.routes.list_analyses_wet_processes
-      summary: Retrieve a list of analyses of one specific wet process
+      operationId: genelastic.api.routes.list_analyses_by_bi_process
+      summary: Renvoie les analyses qui contiennent le bi process spécifié
       tags:
         - Analyses
       parameters:
@@ -132,10 +166,10 @@ paths:
           schema:
             type: string
           required: true
-          description: Wet process ID
+          description: Bi process ID
       responses:
         200:
-          description: List of wet processes
+          description: List of bi processes
           content:
             application/json:
               schema:
@@ -143,10 +177,10 @@ paths:
                 items:
                   type: string
 
-  /bi_process/{proc_id}:
+  /bi_process/{proc_id}/analyses/esql_query:
     get:
-      operationId: genelastic.api.routes.list_analyses_bi_processes
-      summary: Retrieve a list of analyses of one specific bi process
+      operationId: genelastic.api.routes.list_analyses_by_bi_process_esql
+      summary: Renvoie les analyses qui contiennent le bi process spécifié (via une requête ESQL)
       tags:
         - Analyses
       parameters:
@@ -166,177 +200,300 @@ paths:
                 items:
                   type: string
 
-  /snvs_documents:
+  /bi_process/{proc_id}/analyses/sql_query:
     get:
-      operationId: genelastic.api.routes.list_snv_documents
-      summary: Retrieve all documents containing an insertion (INS), a deletion (DEL) or a mutation
-        at a single position (SNV)
+      operationId: genelastic.api.routes.list_analyses_by_bi_process_sql
+      summary: Renvoie les analyses qui contiennent le bi process spécifié (via une requête SQL)
       tags:
-        - Documents
+        - Analyses
+      parameters:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Bi process ID
       responses:
         200:
-          description: Complete list of documents containing an insertion (INS), a deletion (DEL) or a mutation
-            at a single position (SNV)
+          description: List of bi processes
           content:
             application/json:
               schema:
                 type: array
                 items:
-                  type: object
-                  properties:
-                    type:
-                      type: string
-                    chr:
-                      type: string
-                    pos:
-                      type: integer
-                    alt:
-                      type: array
-                      items:
-                        type: string
-                    info:
-                      type: object
-                      additionalProperties:
-                        type: string
-        400:
-          description: Invalid request
-        500:
-          description: Internal server error
+                  type: string
+
 
-  /snvs_insertion_documents:
+  /analyses:
     get:
-      operationId: genelastic.api.routes.list_snv_insertion_documents
-      summary: Retrieve all documents containing an insertion (INS) at a single position (SNV)
+      operationId: genelastic.api.routes.analyses
+      summary: Renvoie une liste de toutes les analyses présentes dans Elasticsearch
       tags:
-        - Documents
+        - Analyses
       responses:
         200:
-          description: Complete list of documents containing an insertion (INS) at a single position (SNV)
+          description: List of analyses
           content:
             application/json:
               schema:
-                type: array
-                items:
-                  type: object
-                  properties:
-                    type:
-                      type: string
-                    chr:
-                      type: string
-                    pos:
-                      type: integer
-                    alt:
-                      type: array
-                      items:
-                        type: string
-                    info:
-                      type: object
-                      properties:
-                        SVTYPE:
-                          type: string
-                        END:
-                          type: integer
-                        SVLEN:
-                          type: array
-                          items:
-                            type: integer
-        400:
-          description: Invalid request
-        500:
-          description: Internal server error
+                type: string
+
+  #  /snvs_documents:
+  #    get:
+  #      operationId: genelastic.api.routes.list_snv_documents
+  #      summary: Retrieve all documents containing an insertion (INS), a deletion (DEL) or a mutation
+  #        at a single position (SNV)
+  #      tags:
+  #        - Documents
+  #      responses:
+  #        200:
+  #          description: Complete list of documents containing an insertion (INS), a deletion (DEL) or a mutation
+  #            at a single position (SNV)
+  #          content:
+  #            application/json:
+  #              schema:
+  #                type: array
+  #                items:
+  #                  type: object
+  #                  properties:
+  #                    type:
+  #                      type: string
+  #                    chr:
+  #                      type: string
+  #                    pos:
+  #                      type: integer
+  #                    alt:
+  #                      type: array
+  #                      items:
+  #                        type: string
+  #                    info:
+  #                      type: object
+  #                      additionalProperties:
+  #                        type: string
+  #        400:
+  #          description: Invalid request
+  #        500:
+  #          description: Internal server error
+  #
+  #  /snvs_insertion_documents:
+  #    get:
+  #      operationId: genelastic.api.routes.list_snv_insertion_documents
+  #      summary: Retrieve all documents containing an insertion (INS) at a single position (SNV)
+  #      tags:
+  #        - Documents
+  #      responses:
+  #        200:
+  #          description: Complete list of documents containing an insertion (INS) at a single position (SNV)
+  #          content:
+  #            application/json:
+  #              schema:
+  #                type: array
+  #                items:
+  #                  type: object
+  #                  properties:
+  #                    type:
+  #                      type: string
+  #                    chr:
+  #                      type: string
+  #                    pos:
+  #                      type: integer
+  #                    alt:
+  #                      type: array
+  #                      items:
+  #                        type: string
+  #                    info:
+  #                      type: object
+  #                      properties:
+  #                        SVTYPE:
+  #                          type: string
+  #                        END:
+  #                          type: integer
+  #                        SVLEN:
+  #                          type: array
+  #                          items:
+  #                            type: integer
+  #        400:
+  #          description: Invalid request
+  #        500:
+  #          description: Internal server error
+  #
+  #  /snvs_deletion_documents:
+  #    get:
+  #      operationId: genelastic.api.routes.list_snv_deletion_documents
+  #      summary: Retrieve all documents containing a deletion (DEL) at a single position (SNV)
+  #      tags:
+  #        - Documents
+  #      responses:
+  #        200:
+  #          description: Complete list of documents containing a deletion (DEL) at a single position (SNV)
+  #          content:
+  #            application/json:
+  #              schema:
+  #                type: array
+  #                items:
+  #                  type: object
+  #                  properties:
+  #                    type:
+  #                      type: string
+  #                    chr:
+  #                      type: string
+  #                    pos:
+  #                      type: integer
+  #                    alt:
+  #                      type: array
+  #                      items:
+  #                        type: string
+  #                    info:
+  #                      type: object
+  #                      properties:
+  #                        SVTYPE:
+  #                          type: string
+  #                        END:
+  #                          type: integer
+  #                        SVLEN:
+  #                          type: array
+  #                          items:
+  #                            type: integer
+  #        400:
+  #          description: Invalid request
+  #        500:
+  #          description: Internal server error
+  #
+  #  /snvs_mutation_documents:
+  #    get:
+  #      operationId: genelastic.api.routes.list_snv_mutation_documents
+  #      summary: Retrieve all documents containing a mutation at a single position (SNV)
+  #      tags:
+  #        - Documents
+  #      responses:
+  #        200:
+  #          description: Complete list of documents containing a mutation at a single position (SNV)
+  #          content:
+  #            application/json:
+  #              schema:
+  #                type: array
+  #                items:
+  #                  type: object
+  #                  properties:
+  #                    type:
+  #                      type: string
+  #                    chr:
+  #                      type: string
+  #                    pos:
+  #                      type: integer
+  #                    alt:
+  #                      type: array
+  #                      items:
+  #                        type: string
+  #                    info:
+  #                      type: object
+  #                      properties:
+  #                        SVTYPE:
+  #                          type: string
+  #                        END:
+  #                          type: integer
+  #                        SVLEN:
+  #                          type: array
+  #                          items:
+  #                            type: integer
+  #        400:
+  #          description: Invalid request due to incorrect parameters or format
+  #        500:
+  #          description: Internal server error
+
+  /version:
+    get:
+      operationId: genelastic.api.routes.version
+      tags:
+        - Version
+      summary: Get the genelastic package version
+      description: Return the installed version of the genelastic package
+      responses:
+        200:
+          description: Success
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  version:
+                    type: string
+                    example: "1.0.0"
 
-  /snvs_deletion_documents:
+  /analyses/key_value_analyses_index:
     get:
-      operationId: genelastic.api.routes.list_snv_deletion_documents
-      summary: Retrieve all documents containing a deletion (DEL) at a single position (SNV)
+      operationId: genelastic.api.routes.key_value_analyses_index
       tags:
-        - Documents
+        - Analyses
+      summary: Get all metadata fields of analyses
+      description: Return a list of all flattened metadata key-value documents from the analyses index
       responses:
         200:
-          description: Complete list of documents containing a deletion (DEL) at a single position (SNV)
+          description: Success
           content:
             application/json:
               schema:
                 type: array
                 items:
                   type: object
-                  properties:
-                    type:
-                      type: string
-                    chr:
-                      type: string
-                    pos:
-                      type: integer
-                    alt:
-                      type: array
-                      items:
-                        type: string
-                    info:
-                      type: object
+                  additionalProperties:
+                    type: string
+
+  /analyses/count_key_value_analyses_index:
+    get:
+      operationId: genelastic.api.routes.count_key_value_analyses_index
+      tags:
+        - Analyses
+      summary: Count all key-value pairs of analyses metadata for aggregation
+      description: Return counts of each unique value for selected metadata fields in the analyses index
+      responses:
+        200:
+          description: Success
+          content:
+            application/json:
+              schema:
+                type: object
+                additionalProperties:
+                  oneOf:
+                    - type: object
+                      additionalProperties:
+                        type: integer
+                    - type: object
                       properties:
-                        SVTYPE:
+                        error:
                           type: string
-                        END:
-                          type: integer
-                        SVLEN:
-                          type: array
-                          items:
-                            type: integer
-        400:
-          description: Invalid request
-        500:
-          description: Internal server error
 
-  /snvs_mutation_documents:
+  /wet_processes/count_key_value_wet_processes_index:
     get:
-      operationId: genelastic.api.routes.list_snv_mutation_documents
-      summary: Retrieve all documents containing a mutation at a single position (SNV)
+      operationId: genelastic.api.routes.count_wet_process_fields
       tags:
-        - Documents
+        - Wet processes
+      summary: Count all key-value pairs of wet processes metadata for aggregation
+      description: Return counts of each unique value for selected metadata fields in the wet-processes index
       responses:
         200:
-          description: Complete list of documents containing a mutation at a single position (SNV)
+          description: Success
           content:
             application/json:
               schema:
-                type: array
-                items:
-                  type: object
-                  properties:
-                    type:
-                      type: string
-                    chr:
-                      type: string
-                    pos:
-                      type: integer
-                    alt:
-                      type: array
-                      items:
-                        type: string
-                    info:
-                      type: object
+                type: object
+                additionalProperties:
+                  oneOf:
+                    - type: object
+                      additionalProperties:
+                        type: integer
+                    - type: object
                       properties:
-                        SVTYPE:
+                        error:
                           type: string
-                        END:
-                          type: integer
-                        SVLEN:
-                          type: array
-                          items:
-                            type: integer
-        400:
-          description: Invalid request due to incorrect parameters or format
-        500:
-          description: Internal server error
-
 
-  /version:
+  /bi_processes/count_key_value_bi_processes_index:
     get:
-      operationId: genelastic.api.routes.get_genelastic_version
+      operationId: genelastic.api.routes.count_bi_process_fields
       tags:
-        - Version
-      summary: Get the genelastic package version
-      description: Return the installed version of the genelastic package
+        - Bi processes
+      summary: Count all key-value pairs of bi processes metadata for aggregation
+      description: Return counts of each unique value for selected metadata fields in the bi-processes index
       responses:
         200:
           description: Success
@@ -344,7 +501,12 @@ paths:
             application/json:
               schema:
                 type: object
-                properties:
-                  version:
-                    type: string
-                    example: "1.0.0"
+                additionalProperties:
+                  oneOf:
+                    - type: object
+                      additionalProperties:
+                        type: integer
+                    - type: object
+                      properties:
+                        error:
+                          type: string