finalize PR

drs_filer/api/additional.data_repository_service.swagger.yaml

@@ -4,7 +4,7 @@ paths:
       summary: Create object.
       description: |-
         Register metadata of a data object.
-      operationId: RegisterObjects
+      operationId: PostObject
       responses:
         '200':
           description: The `DrsObject` was successfully created.

drs_filer/ga4gh/drs/endpoints/register_objects.py

@@ -0,0 +1,153 @@
+"""Controller for registering new DRS objects."""
+
+import logging
+from random import choice
+import string
+from typing import (Dict, List, Optional)
+
+from flask import current_app
+from pymongo.errors import DuplicateKeyError
+
+from drs_filer.errors.exceptions import InternalServerError
+
+logger = logging.getLogger(__name__)
+
+
+def register_object(
+    data: Dict,
+    object_id: Optional[str] = None,
+    retries: int = 9,
+) -> str:
+    """Register data object.
+
+    Args:
+        data: Request object of type `DrsObjectRegister`.
+        object_id: DRS object identifier. Auto-generated if not provided.
+        retries: If `object_id` is not supplied, how many times should the
+            generation of a random identifier and insertion into the database
+            be retried in case of `DuplicateKeyError`s.
+
+    Returns:
+        A unique identifier for the object.
+    """
+    # Set parameters
+    db_collection = (
+        current_app.config['FOCA'].db.dbs['drsStore'].
+        collections['objects'].client
+    )
+    url_prefix = current_app.config['FOCA'].endpoints['url_prefix']
+    external_host = current_app.config['FOCA'].endpoints['external_host']
+    external_port = current_app.config['FOCA'].endpoints['external_port']
+    api_path = current_app.config['FOCA'].endpoints['api_path']
+
+    # Set flags and parameters for POST/PUT routes
+    replace = True
+    was_replaced = False
+    if object_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)))
+
+    # Add unique access identifiers for each access method
+    if 'access_methods' in data:
+        data['access_methods'] = __add_access_ids(
+            data=data['access_methods']
+        )
+
+    # Try to generate unique ID and insert object into database
+    for i in range(retries + 1):
+        logger.debug(f"Trying to insert/update object: try {i}")
+
+        # Set or generate object identifier
+        data['id'] = object_id if object_id is not None else generate_id(
+            charset=id_charset,  # type: ignore
+            length=id_length,  # type: ignore
+        )
+
+        # Generate DRS URL
+        data['self_uri'] = (
+            f"{url_prefix}://{external_host}:{external_port}/"
+            f"{api_path}/{data['id']}"
+        )
+
+        # Replace or insert object, then return (PUT)
+        if replace:
+            result_object = db_collection.replace_one(
+                filter={'id': data['id']},
+                replacement=data,
+                upsert=True,
+            )
+            if result_object.modified_count:
+                was_replaced = True
+            break
+
+        # Try to insert new object (POST); continue with next iteration if
+        # key exists
+        try:
+            db_collection.insert_one(data)
+            break
+        except DuplicateKeyError:
+            continue
+
+    else:
+        logger.error(
+            f"Could not generate unique identifier. Tried {retries + 1} times."
+        )
+        raise InternalServerError
+
+    if was_replaced:
+        logger.info(f"Replaced object with id '{data['id']}'.")
+    else:
+        logger.info(f"Added object with id '{data['id']}'.")
+    return data['id']
+
+
+def __add_access_ids(data: List) -> List:
+    """Add access identifiers to posted access methods metadata.
+
+    Args:
+        data: List of access method metadata objects.
+
+    Returns:
+        Access methods metadata complete with unique access identifiers.
+    """
+    id_charset = eval(
+        current_app.config['FOCA'].endpoints['access_methods']['id_charset']
+    )
+    id_length = (
+        current_app.config['FOCA'].endpoints['access_methods']['id_length']
+    )
+    access_ids = []
+    for method in data:
+        access_id = generate_id(id_charset, id_length)
+        if access_id not in access_ids:
+            method['access_id'] = access_id
+            access_ids.append(access_id)
+
+    return data
+
+
+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

@@ -13,19 +13,13 @@
     URLNotFound,
     BadRequest,
 )
-from drs_filer.ga4gh.drs.endpoints.register_new_objects import (
-    register_new_objects,
+from drs_filer.ga4gh.drs.endpoints.register_objects import (
+    register_object,
 )
 
 logger = logging.getLogger(__name__)
 
 
-@log_traffic
-def RegisterObjects() -> str:
-    """Register new DRS object."""
-    return register_new_objects(request)
-
-
 @log_traffic
 def GetObject(object_id: str) -> Dict:
     """Get DRS object.
@@ -150,6 +144,12 @@ def DeleteAccessMethod(object_id: str, access_id: str) -> str:
         raise InternalServerError
 
 
+@log_traffic
+def PostObject() -> str:
+    """Register new DRS object."""
+    return register_object(data=request.json)
+
+
 @log_traffic
 def PutObject(object_id: str):
     """Add/replace DRS object with a user-supplied ID.
@@ -161,4 +161,7 @@ def PutObject(object_id: str):
         Identifier of created/updated DRS object.
 
     """
-    return register_new_objects(request, object_id)
+    return register_object(
+        data=request.json,
+        object_id=object_id,
+    )