genelastic 0.6.1__py3-none-any.whl → 0.8.0__py3-none-any.whl

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

@@ -1,12 +1,44 @@
 """Genelastic package for common code between API and import scripts."""
-from .elastic import ElasticQueryConn, ElasticImportConn
-from .types import (BundleDict, AnalysisMetaData, BioInfoProcessData, WetProcessesData,
-                    MetadataDocument, AnalysisDocument, BulkItems, ProcessDocument, Bucket)
-from .cli import add_verbose_control_args, add_es_connection_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 (
+    AnalysisDocument,
+    AnalysisMetaData,
+    BioInfoProcessData,
+    Bucket,
+    BulkItems,
+    BundleDict,
+    MetadataDocument,
+    ProcessDocument,
+    RandomAnalysisData,
+    RandomBiProcessData,
+    RandomWetProcessData,
+    WetProcessesData,
+)
 
-__all__ = ['ElasticQueryConn', 'ElasticImportConn', 'BundleDict', 'AnalysisMetaData',
-           'BioInfoProcessData', 'WetProcessesData', 'MetadataDocument', 'AnalysisDocument',
-           'BulkItems', 'ProcessDocument', 'Bucket', 'add_verbose_control_args',
-           'add_es_connection_args', 'DBIntegrityError'
-           ]
+__all__ = [
+    "AnalysisDocument",
+    "AnalysisMetaData",
+    "BioInfoProcessData",
+    "Bucket",
+    "BulkItems",
+    "BundleDict",
+    "DBIntegrityError",
+    "ElasticImportConn",
+    "ElasticQueryConn",
+    "MetadataDocument",
+    "ProcessDocument",
+    "RandomAnalysisData",
+    "RandomBiProcessData",
+    "RandomWetProcessData",
+    "WetProcessesData",
+    "add_es_connection_args",
+    "add_verbose_control_args",
+    "parse_server_launch_args",
+]

genelastic/common/cli.py

@@ -1,35 +1,115 @@
 """Utility functions for CLI scripts."""
+
 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.
+    """Add verbose control arguments to the parser.
     Arguments are added to the parser by using its reference.
     """
-    parser.add_argument('-q', '--quiet', dest='verbose', action='store_const',
-                        const=0, default=1,
-                        help='Set verbosity to 0 (quiet mode).')
-    parser.add_argument('-v', '--verbose', dest='verbose', action='count',
-                        default=1,
-                        help=('Verbose level. -v for information, -vv for debug,' +
-                              ' -vvv for trace.'))
+    parser.add_argument(
+        "-q",
+        "--quiet",
+        dest="verbose",
+        action="store_const",
+        const=0,
+        default=1,
+        help="Set verbosity to 0 (quiet mode).",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        dest="verbose",
+        action="count",
+        default=1,
+        help=(
+            "Verbose level. -v for information, -vv for debug, -vvv for trace."
+        ),
+    )
 
 
 def add_es_connection_args(parser: argparse.ArgumentParser) -> None:
-    """
-    Add arguments to the parser needed to gather ElasticSearch server connection parameters.
+    """Add arguments to the parser needed to gather ElasticSearch server connection parameters.
     Arguments are added to the parser by using its reference.
     """
-    parser.add_argument('--es-host', dest='es_host', default='localhost',
-                        help='Address of Elasticsearch host.')
-    parser.add_argument('--es-port', type=int, default=9200, dest='es_port',
-                        help='Elasticsearch port.')
-    parser.add_argument('--es-usr', dest='es_usr', default='elastic',
-                        help='Elasticsearch user.')
-    parser.add_argument('--es-pwd', dest='es_pwd', required=True,
-                        help='Elasticsearch password.')
-    parser.add_argument('--es-cert-fp', dest='es_cert_fp',
-                        help='Elasticsearch sha256 certificate fingerprint.')
-    parser.add_argument('--es-index-prefix', dest='es_index_prefix',
-                        help='Add the given prefix to each index created during import.')
+    parser.add_argument(
+        "--es-host",
+        dest="es_host",
+        default="localhost",
+        help="Address of Elasticsearch host.",
+    )
+    parser.add_argument(
+        "--es-port",
+        type=int,
+        default=9200,
+        dest="es_port",
+        help="Elasticsearch port.",
+    )
+    parser.add_argument(
+        "--es-usr", dest="es_usr", default="elastic", help="Elasticsearch user."
+    )
+    parser.add_argument(
+        "--es-pwd", dest="es_pwd", required=True, help="Elasticsearch password."
+    )
+    parser.add_argument(
+        "--es-cert-fp",
+        dest="es_cert_fp",
+        help="Elasticsearch sha256 certificate fingerprint.",
+    )
+    parser.add_argument(
+        "--es-index-prefix",
+        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()