genelastic 0.7.0__tar.gz → 0.8.0__tar.gz

genelastic-0.8.0/MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include src *.yml
+recursive-include src *.html

{genelastic-0.7.0 → genelastic-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: genelastic
-Version: 0.7.0
+Version: 0.8.0
 Summary: Generate and store genetic data into an Elasticsearch database.
 Author: CNRGH
 Author-email: Pierrick ROGER <pierrick.roger@cnrgh.fr>, Maxime BLANCHON <maxime.blanchon@cnrgh.fr>
@@ -16,7 +16,7 @@ Requires-Dist: elasticsearch
 Requires-Dist: PyVCF3
 Requires-Dist: schema
 Requires-Dist: PyYAML
-Requires-Dist: biophony>=1.2.1
+Requires-Dist: biophony<1.4,>=1.3.0
 Requires-Dist: colorlog
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
@@ -27,7 +27,7 @@ Requires-Dist: types-PyYAML; extra == "tests"
 Requires-Dist: ruff<0.9,>=0.8.1; extra == "tests"
 Requires-Dist: pre-commit<4.1,>=4.0.1; extra == "tests"
 Requires-Dist: types-requests; extra == "tests"
-Requires-Dist: ansible<10.5,>=10.4.0; extra == "tests"
+Requires-Dist: ansible-core>=2.17.0; extra == "tests"
 Requires-Dist: ansible-lint<25,>=24.12.2; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
@@ -38,10 +38,14 @@ Requires-Dist: flask; extra == "api"
 Requires-Dist: elasticsearch; extra == "api"
 Requires-Dist: environs; extra == "api"
 Requires-Dist: connexion[flask,swagger-ui,uvicorn]; extra == "api"
+Requires-Dist: gunicorn; extra == "api"
 Provides-Extra: ui
 Requires-Dist: flask; extra == "ui"
 Requires-Dist: requests; extra == "ui"
 Requires-Dist: environs; extra == "ui"
+Requires-Dist: uvicorn; extra == "ui"
+Requires-Dist: asgiref; extra == "ui"
+Requires-Dist: gunicorn; extra == "ui"
 
 # genelastic
 

{genelastic-0.7.0 → genelastic-0.8.0}/pyproject.toml

@@ -4,13 +4,13 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "genelastic"
-version = "0.7.0"
+version = "0.8.0"
 dependencies = [
     "elasticsearch",
     "PyVCF3",
     "schema",
     "PyYAML",
-    "biophony>=1.2.1",
+    "biophony >= 1.3.0, < 1.4",
     "colorlog",
 ]
 requires-python = ">= 3.11"
@@ -39,7 +39,7 @@ tests = [
     "ruff >= 0.8.1, < 0.9",
     "pre-commit >= 4.0.1, < 4.1",
     "types-requests",
-    "ansible >= 10.4.0, < 10.5",
+    "ansible-core >= 2.17.0",
     "ansible-lint >= 24.12.2, < 25"
 ]
 docs = [
@@ -52,13 +52,17 @@ api = [
     "flask",
     "elasticsearch",
     "environs",
-    "connexion[flask,swagger-ui,uvicorn]"
+    "connexion[flask,swagger-ui,uvicorn]",
+    "gunicorn"
 ]
 
 ui = [
     "flask",
     "requests",
-    "environs"
+    "environs",
+    "uvicorn",
+    "asgiref",
+    "gunicorn"
 ]
 
 [project.scripts]
@@ -66,8 +70,16 @@ gnl-data = "genelastic.import_data.cli_gen_data:main"
 gnl-import = "genelastic.import_data.cli_import:main"
 gnl-info = "genelastic.import_data.cli_info:main"
 gnl-integrity = "genelastic.import_data.cli_integrity:main"
+gnl-start-api = "genelastic.api.cli_start_api:main"
+gnl-start-ui = "genelastic.ui.cli_start_ui:main"
 gnl-validate = "genelastic.import_data.cli_validate:main"
 
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
 [tool.ruff]
 line-length = 80
 target-version = "py311"

genelastic-0.8.0/src/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-0.8.0/src/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-0.8.0/src/genelastic/api/server.py

@@ -0,0 +1,83 @@
+from pathlib import Path
+from typing import Any
+
+import connexion
+import yaml
+from connexion import FlaskApp
+
+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 file_path.open(encoding="utf-8") as f:
+        try:
+            content = yaml.safe_load(f)
+        except yaml.YAMLError as exc:
+            raise SystemExit(exc) from exc
+    return content
+
+
+def aggregate_openapi_specs(
+    main_spec_file: Path, additional_spec_path: Path
+) -> Any:  # noqa: ANN401
+    """Aggregate OpenAPI specifications from a main file and a directory
+    of additional specifications.
+    """
+    main_spec = load_yaml(main_spec_file)
+    try:
+        entries = additional_spec_path.iterdir()
+    except OSError as exc:
+        raise SystemExit(exc) from exc
+
+    if "paths" not in main_spec:
+        main_spec["paths"] = []
+
+    for entry in entries:
+        if not entry.is_file():
+            continue
+
+        if entry.suffix not in [".yml", ".yaml"]:
+            continue
+
+        content = load_yaml(entry)
+
+        if "paths" in content:
+            main_spec["paths"].update(content["paths"])
+
+    return main_spec
+
+
+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"]
+
+    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(),
+    )
+
+    # 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)
+
+    # Ajouter la spécification vers OpenAPI
+    connexion_app.add_api(yaml_spec)
+    return connexion_app
+
+
+app = create_app()

genelastic-0.8.0/src/genelastic/api/settings.py

@@ -0,0 +1,10 @@
+from environs import Env
+
+env = Env()
+env.read_env()
+
+# 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-0.8.0/src/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-0.7.0 → genelastic-0.8.0}/src/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-0.7.0 → genelastic-0.8.0}/src/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()