genelastic 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

genelastic/api/cli_start_api.py

@@ -0,0 +1,18 @@
+from genelastic.common import parse_server_launch_args
+from genelastic.common.server import start_dev_server, start_prod_server
+
+
+def main() -> None:
+    app_module = "genelastic.api.server:app"
+    args = parse_server_launch_args("Start API server.", 8000)
+    if args.env == "dev":
+        start_dev_server(app_module, args)
+    elif args.env == "prod":
+        start_prod_server(app_module, args)
+    else:
+        msg = f"Environment '{args.env}' is not implemented."
+        raise NotImplementedError(msg)
+
+
+if __name__ == "__main__":
+    main()

genelastic/api/extends/example.yml

@@ -0,0 +1,20 @@
+---
+paths:
+  /ping_2:
+    get:
+      operationId: genelastic.api.extends.example.ping_2
+      tags:
+        - Tests
+      summary: Vérification du statut du serveur
+      description: Route de test pour vérifier que le serveur est en ligne
+      responses:
+        200:
+          description: Le serveur est en ligne
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  message:
+                    type: string
+                    example: pong_2

genelastic/api/server.py

@@ -3,6 +3,7 @@ from typing import Any
 
 import connexion
 import yaml
+from connexion import FlaskApp
 
 from genelastic.common import ElasticQueryConn
 
@@ -10,7 +11,7 @@ from genelastic.common 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:
@@ -48,33 +49,35 @@ def aggregate_openapi_specs(
     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"]
 
-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, 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)
+    return connexion_app
 
-if __name__ == "__main__":
-    connexion_app.run(debug=True)
+
+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 +1,350 @@
+---
+openapi: "3.0.3"
+info:
+  description: This is the swagger file for our API
+  version: "1.0.1"
+  title: Swagger for ReST API
+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:
+    get:
+      operationId: genelastic.api.routes.list_indices
+      tags:
+        - Indexes
+      summary: Listing the indexes present in Elasticsearch
+      description: Listing the indexes present in 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
+
+  /indices/{index_id}/documents/{document_id}:
+    get:
+      operationId: genelastic.api.routes.retrieve_document
+      parameters:
+        - in: path
+          name: index_id
+          schema:
+            type: string
+          required: true
+          description: The index in which to search for the document
+        - in: path
+          name: document_id
+          schema:
+            type: string
+          required: true
+          description: The ID of the document to retrieve
+      tags:
+        - Document
+      summary: Retrieve a document
+      description: Retrieve a specific document from Elasticsearch
+      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.list_wet_processes
+      summary: Retrieve a list of wet processes
+      tags:
+        - Wet processes
+      responses:
+        200:
+          description: List of wet processes
+          content:
+            application/json:
+              schema:
+                type: array
+
+  /bi_processes:
+    get:
+      operationId: genelastic.api.routes.list_bi_processes
+      summary: Retrieve a list of bi processes
+      tags:
+        - Bi processes
+      responses:
+        200:
+          description: List of bi processes
+          content:
+            application/json:
+              schema:
+                type: array
+
+  /analyses:
+    get:
+      operationId: genelastic.api.routes.list_analyses
+      summary: Retrieve a list of analyses
+      tags:
+        - Analyses
+      responses:
+        200:
+          description: List of analyses
+          content:
+            application/json:
+              schema:
+                type: string
+
+  /wet_process/{proc_id}:
+    get:
+      operationId: genelastic.api.routes.list_analyses_wet_processes
+      summary: Retrieve a list of analyses of one specific wet process
+      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_process/{proc_id}:
+    get:
+      operationId: genelastic.api.routes.list_analyses_bi_processes
+      summary: Retrieve a list of analyses of one specific bi process
+      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
+
+  /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.get_genelastic_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"

genelastic/common/__init__.py

@@ -1,6 +1,10 @@
 """Genelastic package for common code between API and import scripts."""
 
-from .cli import add_es_connection_args, add_verbose_control_args
+from .cli import (
+    add_es_connection_args,
+    add_verbose_control_args,
+    parse_server_launch_args,
+)
 from .elastic import ElasticImportConn, ElasticQueryConn
 from .exceptions import DBIntegrityError
 from .types import (
@@ -36,4 +40,5 @@ __all__ = [
     "WetProcessesData",
     "add_es_connection_args",
     "add_verbose_control_args",
+    "parse_server_launch_args",
 ]

genelastic/common/cli.py

@@ -2,6 +2,8 @@
 
 import argparse
 
+BASE_LOG_LEVEL = ["critical", "error", "warning", "info", "debug"]
+
 
 def add_verbose_control_args(parser: argparse.ArgumentParser) -> None:
     """Add verbose control arguments to the parser.
@@ -61,3 +63,53 @@ def add_es_connection_args(parser: argparse.ArgumentParser) -> None:
         dest="es_index_prefix",
         help="Add the given prefix to each index created during import.",
     )
+
+
+def parse_server_launch_args(
+    parser_desc: str, default_port: int
+) -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        description=parser_desc,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
+    )
+    parser.add_argument(
+        "--host",
+        type=str,
+        default="127.0.0.1",
+    )
+    parser.add_argument(
+        "--port",
+        type=int,
+        default=default_port,
+    )
+
+    env_subparsers = parser.add_subparsers(dest="env", required=True)
+    dev_parser = env_subparsers.add_parser(
+        "dev",
+        help="Use development environment.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    dev_parser.add_argument(
+        "--log-level",
+        type=str,
+        default="info",
+        choices=[*BASE_LOG_LEVEL, "trace"],
+    )
+
+    prod_parser = env_subparsers.add_parser(
+        "prod",
+        help="Use production environment.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    prod_parser.add_argument(
+        "--log-level", type=str, default="info", choices=BASE_LOG_LEVEL
+    )
+    prod_parser.add_argument(
+        "-w", "--workers", type=int, default=1, help="Number of workers."
+    )
+
+    prod_parser.add_argument("--access-logfile", type=str, default=None)
+    prod_parser.add_argument("--log-file", type=str, default=None)
+
+    return parser.parse_args()

genelastic/common/server.py

@@ -0,0 +1,51 @@
+import argparse
+import subprocess
+import sys
+
+import uvicorn
+
+
+def start_dev_server(app_module: str, args: argparse.Namespace) -> None:
+    """Start the development server using Uvicorn.
+    :args app_module: The module containing the Flask server to start.
+    :args argparse.Namespace: The parsed arguments.
+    """
+    uvicorn.run(
+        app_module,
+        host=args.host,
+        port=args.port,
+        log_level=args.log_level,
+        reload=True,
+    )
+
+
+def start_prod_server(app_module: str, args: argparse.Namespace) -> None:
+    """Start the production server using Gunicorn.
+    It will spawn one primary process and workers
+    :args app_module: The module containing the Flask server to start.
+    :args argparse.Namespace: The parsed arguments.
+    :raises subprocess.CalledProcessError: If gunicorn exits with a non-zero status code.
+    """
+    cmd = [
+        sys.executable,
+        "-m",
+        "gunicorn",
+        "-k",
+        "uvicorn.workers.UvicornWorker",
+        "--workers",
+        str(args.workers),
+        "--log-level",
+        args.log_level,
+        "-b",
+        f"{args.host}:{args.port}",
+        "--capture-output",
+        app_module,
+    ]
+
+    if args.log_file:
+        cmd.extend(["--log-file", args.log_file])
+
+    if args.access_logfile:
+        cmd.extend(["--access-logfile", args.access_logfile])
+
+    subprocess.run(cmd, check=True)  # noqa: S603