genelastic 0.7.0__py3-none-any.whl → 0.9.0__py3-none-any.whl

genelastic/api/server.py

@@ -3,14 +3,16 @@ from typing import Any
 
 import connexion
 import yaml
+from connexion import FlaskApp
 
-from genelastic.common import ElasticQueryConn
+from genelastic.api.errors import register_error_handlers
+from genelastic.common.elastic import ElasticQueryConn
 
 
 def load_yaml(file_path: Path) -> Any:  # noqa: ANN401
     """Load a YAML file and return its content."""
     content = None
-    with Path.open(file_path, encoding="utf-8") as f:
+    with file_path.open(encoding="utf-8") as f:
         try:
             content = yaml.safe_load(f)
         except yaml.YAMLError as exc:
@@ -42,39 +44,45 @@ def aggregate_openapi_specs(
 
         content = load_yaml(entry)
 
-        if "paths" in content:
+        if content and "paths" in content:
             main_spec["paths"].update(content["paths"])
 
     return main_spec
 
 
-# Initialiser l'application Connexion
-connexion_app = connexion.FlaskApp(__name__)
-connexion_app.app.config.from_object("src.genelastic.api.settings.Config")
+def create_app() -> FlaskApp:
+    # Initialiser l'application Connexion
+    connexion_app = connexion.FlaskApp(__name__)
+    connexion_app.app.config.from_object("genelastic.api.settings")
 
-# Initialiser le client Elasticsearch
-es_url = connexion_app.app.config["GENAPI_ES_URL"]
-es_cert_fp = connexion_app.app.config["GENAPI_ES_CERT_FP"]
-es_api_key = connexion_app.app.config["GENAPI_ES_ENCODED_API_KEY"]
+    # Initialiser le client Elasticsearch
+    es_url = connexion_app.app.config["GENAPI_ES_URL"]
+    es_cert_fp = connexion_app.app.config["GENAPI_ES_CERT_FP"]
+    es_api_key = connexion_app.app.config["GENAPI_ES_ENCODED_API_KEY"]
+    index_prefix = connexion_app.app.config["GENAPI_ES_INDEX_PREFIX"]
 
-connexion_app.app.elastic_query_conn = ElasticQueryConn(
-    es_url, es_cert_fp, api_key=es_api_key
-)
+    connexion_app.app.elastic_query_conn = ElasticQueryConn(
+        es_url, es_cert_fp, index_prefix, api_key=es_api_key
+    )
 
-connexion_app.app.logger.debug(
-    "Successfully connected to Elasticsearch server: %s",
-    connexion_app.app.elastic_query_conn.client.info(),
-)
+    connexion_app.app.logger.debug(
+        "Successfully connected to Elasticsearch server: %s",
+        connexion_app.app.elastic_query_conn.client.info(),
+    )
 
-# Chemins des fichiers YAML
-main_yaml_file = Path(__file__).parents[0] / "specification.yml"
-additional_yaml_dir = Path(__file__).parents[0] / "extends"
+    # Chemins des fichiers YAML
+    main_yaml_file = Path(__file__).parents[0] / "specification.yml"
+    additional_yaml_dir = Path(__file__).parents[0] / "extends"
 
-# Charger et combiner les fichiers YAML
-yaml_spec = aggregate_openapi_specs(main_yaml_file, additional_yaml_dir)
+    # Charger et combiner les fichiers YAML
+    yaml_spec = aggregate_openapi_specs(main_yaml_file, additional_yaml_dir)
 
-# Ajouter la spécification vers OpenAPI
-connexion_app.add_api(yaml_spec)
+    # Ajouter la spécification vers OpenAPI
+    connexion_app.add_api(yaml_spec)
 
-if __name__ == "__main__":
-    connexion_app.run(debug=True)
+    register_error_handlers(connexion_app.app)
+
+    return connexion_app
+
+
+app = create_app()

genelastic/api/settings.py

@@ -3,12 +3,8 @@ from environs import Env
 env = Env()
 env.read_env()
 
-
-class Config:
-    """Flask config class."""
-
-    # Charger toutes les variables d'environnement nécessaires
-    GENAPI_ES_URL = env.url("GENAPI_ES_URL").geturl()
-    GENAPI_ES_ENCODED_API_KEY = env.str("GENAPI_ES_ENCODED_API_KEY")
-    GENAPI_ES_INDEX_PREFIX = env.str("GENAPI_ES_INDEX_PREFIX")
-    GENAPI_ES_CERT_FP = env.str("GENAPI_ES_CERT_FP")
+# Load required environment variables.
+GENAPI_ES_URL = env.url("GENAPI_ES_URL").geturl()
+GENAPI_ES_ENCODED_API_KEY = env.str("GENAPI_ES_ENCODED_API_KEY")
+GENAPI_ES_INDEX_PREFIX = env.str("GENAPI_ES_INDEX_PREFIX")
+GENAPI_ES_CERT_FP = env.str("GENAPI_ES_CERT_FP")

genelastic/api/specification.yml

@@ -0,0 +1,512 @@
+---
+openapi: "3.0.3"
+info:
+  description: C'est le fichier Swagger de l'API de la Base Expérimentale (genelastic).
+  version: "1.0.1"
+  title: API de la Base Expérimentale (genelastic)
+servers:
+  - url: "/api"
+
+paths:
+
+  /indexes:
+    get:
+      operationId: genelastic.api.routes.indexes
+      tags:
+        - Indexes
+      summary: Renvoie tous les index présents dans Elasticsearch
+      responses:
+        200:
+          description: Success of the request
+          content:
+            application/json:
+              schema:
+                type: object
+        400:
+          description: The server could not understand the request due to invalid syntax.
+        500:
+          description: Internal server error
+
+  /documents/{index_id}/{document_id}:
+    get:
+      operationId: genelastic.api.routes.retrieve_document_by_index_and_id
+      parameters:
+        - in: path
+          name: index_id
+          schema:
+            type: string
+          required: true
+          description: L'index dans lequel rechercher le document
+        - in: path
+          name: document_id
+          schema:
+            type: string
+          required: true
+          description: L'ID du document à récupérer
+      tags:
+        - Documents
+      summary: Retourne un document selon l'index et l'ID du document
+      responses:
+        200:
+          description: Success in reading the data
+          content:
+            application/json:
+              schema:
+                type: object
+        404:
+          description: Document not found
+        500:
+          description: Internal server error
+
+  /wet_processes:
+    get:
+      operationId: genelastic.api.routes.wet_processes
+      summary: Renvoie la liste des wet processes
+      tags:
+        - Wet processes
+      responses:
+        200:
+          description: List of wet processes
+          content:
+            application/json:
+              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.bi_processes
+      summary: Renvoie la liste des bi processes
+      tags:
+        - Bi processes
+      responses:
+        200:
+          description: List of bi processes
+          content:
+            application/json:
+              schema:
+                type: array
+
+  /bi_processes/{proc_id}:
+    get:
+      operationId: genelastic.api.routes.get_bi_process
+      summary: Renvoie la liste des détails d'un bi process spécifique
+      tags:
+        - Bi processes
+      parameters:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Bi process ID
+      responses:
+        200:
+          description: List of bi processes
+          content:
+            application/json:
+              schema:
+                type: array
+        404:
+          description: Bi process not found
+
+  /bi_process/{proc_id}/analyses:
+    get:
+      operationId: genelastic.api.routes.list_analyses_by_bi_process
+      summary: Renvoie les analyses qui contiennent le bi process spécifié
+      tags:
+        - Analyses
+      parameters:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Bi process ID
+      responses:
+        200:
+          description: List of bi processes
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  type: string
+
+  /bi_process/{proc_id}/analyses/esql_query:
+    get:
+      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:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Bi process ID
+      responses:
+        200:
+          description: List of bi processes
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  type: string
+
+  /bi_process/{proc_id}/analyses/sql_query:
+    get:
+      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:
+        - Analyses
+      parameters:
+        - in: path
+          name: proc_id
+          schema:
+            type: string
+          required: true
+          description: Bi process ID
+      responses:
+        200:
+          description: List of bi processes
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  type: string
+
+
+  /analyses:
+    get:
+      operationId: genelastic.api.routes.analyses
+      summary: Renvoie une liste de toutes les analyses présentes dans Elasticsearch
+      tags:
+        - Analyses
+      responses:
+        200:
+          description: List of analyses
+          content:
+            application/json:
+              schema:
+                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"
+
+  /analyses/key_value_analyses_index:
+    get:
+      operationId: genelastic.api.routes.key_value_analyses_index
+      tags:
+        - 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: Success
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  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:
+                        error:
+                          type: string
+
+  /wet_processes/count_key_value_wet_processes_index:
+    get:
+      operationId: genelastic.api.routes.count_wet_process_fields
+      tags:
+        - 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: Success
+          content:
+            application/json:
+              schema:
+                type: object
+                additionalProperties:
+                  oneOf:
+                    - type: object
+                      additionalProperties:
+                        type: integer
+                    - type: object
+                      properties:
+                        error:
+                          type: string
+
+  /bi_processes/count_key_value_bi_processes_index:
+    get:
+      operationId: genelastic.api.routes.count_bi_process_fields
+      tags:
+        - 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
+          content:
+            application/json:
+              schema:
+                type: object
+                additionalProperties:
+                  oneOf:
+                    - type: object
+                      additionalProperties:
+                        type: integer
+                    - type: object
+                      properties:
+                        error:
+                          type: string

genelastic/common/__init__.py

@@ -1,39 +0,0 @@
-"""Genelastic package for common code between API and import scripts."""
-
-from .cli import add_es_connection_args, add_verbose_control_args
-from .elastic import ElasticImportConn, ElasticQueryConn
-from .exceptions import DBIntegrityError
-from .types import (
-    AnalysisDocument,
-    AnalysisMetaData,
-    BioInfoProcessData,
-    Bucket,
-    BulkItems,
-    BundleDict,
-    MetadataDocument,
-    ProcessDocument,
-    RandomAnalysisData,
-    RandomBiProcessData,
-    RandomWetProcessData,
-    WetProcessesData,
-)
-
-__all__ = [
-    "AnalysisDocument",
-    "AnalysisMetaData",
-    "BioInfoProcessData",
-    "Bucket",
-    "BulkItems",
-    "BundleDict",
-    "DBIntegrityError",
-    "ElasticImportConn",
-    "ElasticQueryConn",
-    "MetadataDocument",
-    "ProcessDocument",
-    "RandomAnalysisData",
-    "RandomBiProcessData",
-    "RandomWetProcessData",
-    "WetProcessesData",
-    "add_es_connection_args",
-    "add_verbose_control_args",
-]