feat: add "POST ../access" & "PUT ../{access_id}"

drs_filer/api/additional.data_repository_service.swagger.yaml

@@ -115,6 +115,50 @@ paths:
         - DRS-Filer
       x-swagger-router-controller: ga4gh.drs.server
   '/objects/{object_id}/access/{access_id}':
+    put:
+      summary: Create or update an access method.
+      description: |-
+        Create a access method with a predefined ID. Overwrites any
+        existing access method with the same ID.
+      operationId: PutAccessMethod
+      responses:
+        '200':
+          description: The `AccessMethod` was successfully created/updated.
+          schema:
+            type: string
+        '400':
+          description: The request is malformed.
+          schema:
+            $ref: '#/definitions/Error'
+        '401':
+          description: The request is unauthorized.
+          schema:
+            $ref: '#/definitions/Error'
+        '403':
+          description: The requester is not authorized to perform this action.
+          schema:
+            $ref: '#/definitions/Error'
+        '500':
+          description: An unexpected error occurred.
+          schema:
+            $ref: '#/definitions/Error'
+      parameters:
+        - name: object_id
+          in: path
+          required: true
+          type: string
+        - name: access_id
+          in: path
+          required: true
+          type: string
+        - in: body
+          name: AccessMethodRegister
+          description: Access method metadata.
+          schema:
+            $ref: '#/definitions/AccessMethodRegister'
+      tags:
+        - DRS-Filer
+      x-swagger-router-controller: ga4gh.drs.server
     delete:
       summary: Delete object's access method.
       description: >-
@@ -156,7 +200,53 @@ paths:
           type: string
       tags:
         - DRS-Filer
-      x-swagger-router-controller: ga4gh.drs.server    
+      x-swagger-router-controller: ga4gh.drs.server  
+
+  '/objects/{object_id}/access':
+    post:
+      summary: Add an object's access method.
+      description: >-
+        Add `AccessMethod` of an existing `DrsObject`.
+      operationId: PostAccessMethod
+      responses:
+        '200':
+            description: The `AccessMethod` was successfully added.
+            schema:
+              type: string
+        '400':
+            description: The request is malformed.
+            schema:
+              $ref: '#/definitions/Error'
+        '401':
+            description: The request is unauthorized.
+            schema:
+              $ref: '#/definitions/Error'
+        '403':
+            description: The requester is not authorized to perform this action.
+            schema:
+              $ref: '#/definitions/Error'
+        '404':
+            description: The requested resource was not found.
+            schema:
+              $ref: '#/definitions/Error'
+        '500':
+            description: An unexpected error occurred.
+            schema:
+              $ref: '#/definitions/Error'
+      parameters:
+        - name: object_id
+          in: path
+          required: true
+          type: string
+        - in: body
+          name: AccessMethodRegister
+          description: Access method metadata.
+          schema:
+            $ref: '#/definitions/AccessMethodRegister'
+      tags:
+        - DRS-Filer
+      x-swagger-router-controller: ga4gh.drs.server
+
 definitions:
   DrsObjectRegister:
     type: object

drs_filer/ga4gh/drs/endpoints/register_access_methods.py

@@ -0,0 +1,133 @@
+import logging
+from random import choice
+import string
+from typing import Dict, Optional
+
+from flask import current_app
+
+from drs_filer.errors.exceptions import (
+    ObjectNotFound,
+    InternalServerError
+)
+
+logger = logging.getLogger(__name__)
+
+
+def register_access_method(
+    data: Dict,
+    object_id: str,
+    access_id: Optional[str] = None,
+    retries: int = 9
+) -> str:
+    """Register access method.
+
+    Args:
+        data: Request object of type `AccessMethodRegister`.
+        object_id: DRS object identifier.
+        access_id: Access method identifier. Auto-generated if not provided.
+        retries: If `access_id` is not supplied, how many times should the
+            generation of a random identifier and insertion into the database
+            be retried in case of duplicate access_ids.
+
+    Returns:
+        A unique identifier for the access method.
+    """
+    # Set parameters
+    db_collection = (
+        current_app.config['FOCA'].db.dbs['drsStore'].
+        collections['objects'].client
+    )
+    obj = db_collection.find_one({"id": object_id})
+    if not obj:
+        logger.error(f"DRS object with id: {object_id} not found.")
+        raise ObjectNotFound
+
+    # Set flags and parameters for POST/PUT routes
+    replace = True
+    if access_id is None:
+        replace = False
+        id_length = (
+            current_app.config['FOCA'].endpoints['objects']['id_length']
+        )
+        id_charset: str = (
+            current_app.config['FOCA'].endpoints['objects']['id_charset']
+        )
+        # evaluate character set expression or interpret literal string as set
+        try:
+            id_charset = eval(id_charset)
+        except Exception:
+            id_charset = ''.join(sorted(set(id_charset)))
+
+    # Try to generate unique ID and insert object into database
+    for i in range(retries + 1):
+        logger.debug(f"Trying to insert/update access method: try {i}")
+        # Set or generate object identifier
+        if access_id is not None:
+            data['access_id'] = access_id
+        else:
+            data['access_id'] = generate_id(
+                charset=id_charset,  # type: ignore
+                length=id_length,  # type: ignore
+            )
+        # Replace access method, then return (PUT)
+        if replace:
+            result_replace = db_collection.update_one(
+                filter={'id': object_id},
+                update={
+                    '$set': {
+                        'access_methods.$[element]': data
+                    }
+                },
+                array_filters=[{'element.access_id': data['access_id']}],
+            )
+
+            if(result_replace.modified_count):
+                logger.info(
+                    f"Replaced access method with access_id: "
+                    f"{data['access_id']} of DRS object with id: {object_id}"
+                )
+                break
+
+        # Try inserting the access method incase of POST or incase
+        # no element matches with the filter incase of PUT.
+        result_insert = db_collection.update_one(
+            filter={
+                'id': object_id,
+                'access_methods.access_id': {'$ne': data['access_id']}
+            },
+            update={
+                '$push': {
+                    'access_methods': data
+                }
+            }
+        )
+        if(result_insert.modified_count):
+            logger.info(
+                f"Added access method with access_id: {data['access_id']}"
+                f" to DRS object with id: {object_id}"
+            )
+            break
+    # Access method neither added nor updated.
+    else:
+        logger.error(
+            f"Could not generate unique identifier. Tried {retries + 1} times."
+        )
+        raise InternalServerError
+    return data['access_id']
+
+
+def generate_id(
+    charset: str = ''.join([string.ascii_letters, string.digits]),
+    length: int = 6
+) -> str:
+    """Generate random string based on allowed set of characters.
+
+    Args:
+        charset: String of allowed characters.
+        length: Length of returned string.
+
+    Returns:
+        Random string of specified length and composed of defined set of
+        allowed characters.
+    """
+    return ''.join(choice(charset) for __ in range(length))

drs_filer/ga4gh/drs/server.py

@@ -1,5 +1,8 @@
 """Controllers for DRS endpoints."""
 
+from drs_filer.ga4gh.drs.endpoints.register_access_methods import (
+    register_access_method
+)
 import logging
 from typing import Dict
 
@@ -165,3 +168,40 @@ def PutObject(object_id: str):
         data=request.json,
         object_id=object_id,
     )
+
+
+@log_traffic
+def PostAccessMethod(object_id: str):
+    """Add a new `AccessMethod` in an existing DRS object
+
+    Args:
+        object_id: Identifier of the DRS object, in which the
+        `AccessMethod` is to be added.
+
+    Returns:
+        Identifier of the added `AccessMethod`.
+    """
+    return register_access_method(
+        data=request.json,
+        object_id=object_id
+    )
+
+
+@log_traffic
+def PutAccessMethod(object_id: str, access_id: str):
+    """Add/replace an `AccessMethod` in an existing DRS object
+
+    Args:
+        object_id: Identifier of the DRS object, to which the
+            `AccessMethod` is to be added.
+        access_id: Identifier of the `AccessMethod` which is to
+            be added/updated.
+
+    Returns:
+        Identifier of the added/updated `AccessMethod`.
+    """
+    return register_access_method(
+        data=request.json,
+        object_id=object_id,
+        access_id=access_id
+    )