(PXP-5525): Add blank version of record (#271)

* Update swagger API docs

* First pass implement POST /index/blank/{GUID}

- Create a blank record that is a new version of a previous record
(i.e. shared a baseid with previous record)
- acl/authz carry over from previous record
- requires update permission on previous record
- user must specify uploader field, can optionally specify file_name field
(following convention of POST /index/blank)

* Add unit tests for POST /index/blank/{GUID}

* Fix errors

- Return 201 on success
- Fix syntax error in driver

* Run black

* Remove buggy test

* Test no record found condition

* Run black

* Remove unnecessary guard for duplicate GUID

* Revert deletion of test_create_blank_record_with_baseid

* Run black

* Update indexd/index/blueprint.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* Support specifying guid

- allow specifying guid
- update swagger docs
- check for GUID already exists
- write tests for specifying guid

* Update swagger docs

- Remove unneeded OutputRefWithUrl
- Update index/blank and index/blank/{{GUID}} endpoints to return 201, not 200

* Add test for creating blank version of blank record

* Fix typo, remove unused import, run black

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

indexd/index/blueprint.py

@@ -295,6 +295,31 @@ def post_index_blank_record():
     return flask.jsonify(ret), 201
 
 
+@blueprint.route("/index/blank/<path:record>", methods=["POST"])
+def add_index_blank_record_version(record):
+    """
+    Create a new blank version of the record with this GUID.
+    Authn/authz fields carry over from the previous version of the record.
+    Only uploader and optionally file_name fields are filled.
+    Returns the GUID of the new blank version and the baseid common to all versions
+    of the record.
+    """
+    uploader = flask.request.get_json().get("uploader")
+    file_name = flask.request.get_json().get("file_name")
+    new_did = flask.request.json.get("did")
+    if not uploader:
+        raise UserError("no uploader specified")
+
+    # authorize done in add_blank_version for the existing record's authz
+    did, baseid, rev = blueprint.index_driver.add_blank_version(
+        record, new_did=new_did, uploader=uploader, file_name=file_name
+    )
+
+    ret = {"did": did, "baseid": baseid, "rev": rev}
+
+    return flask.jsonify(ret), 201
+
+
 @blueprint.route("/index/blank/<path:record>", methods=["PUT"])
 def put_index_blank_record(record):
     """

indexd/index/drivers/alchemy.py

@@ -1153,6 +1153,54 @@ def add_version(
 
             return record.did, record.baseid, record.rev
 
+    def add_blank_version(
+        self, current_did, new_did=None, file_name=None, uploader=None
+    ):
+        """
+        Add a blank record version given did.
+        Authn/authz fields carry over from previous version.
+        """
+        with self.session as session:
+            query = session.query(IndexRecord).filter_by(did=current_did)
+
+            try:
+                old_record = query.one()
+            except NoResultFound:
+                raise NoRecordFound("no record found")
+            except MultipleResultsFound:
+                raise MultipleRecordsFound("multiple records found")
+
+            auth.authorize("update", [u.resource for u in old_record.authz])
+
+            # handle the edgecase where new_did matches the original doc's did to
+            # prevent sqlalchemy FlushError
+            if new_did == old_record.did:
+                raise UserError("{did} already exists".format(did=new_did), 400)
+
+            new_record = IndexRecord()
+            did = new_did
+            if not did:
+                did = str(uuid.uuid4())
+                if self.config.get("PREPEND_PREFIX"):
+                    did = self.config["DEFAULT_PREFIX"] + did
+
+            new_record.did = did
+            new_record.baseid = old_record.baseid
+            new_record.rev = str(uuid.uuid4())[:8]
+            new_record.file_name = file_name
+            new_record.uploader = uploader
+
+            new_record.acl = old_record.acl
+            new_record.authz = old_record.authz
+
+            try:
+                session.add(new_record)
+                session.commit()
+            except IntegrityError:
+                raise UserError("{did} already exists".format(did=did), 400)
+
+            return new_record.did, new_record.baseid, new_record.rev
+
     def get_all_versions(self, did):
         """
         Get all record versions (in order of creation) given DID

openapis/swagger.yaml

@@ -236,7 +236,7 @@ paths:
           schema:
             $ref: '#/definitions/InputBlankInfo'
       responses:
-        '200':
+        '201':
           description: successful operation
           schema:
             $ref: '#/definitions/OutputRef'
@@ -245,6 +245,39 @@ paths:
       security:
         - basic_auth: []
   '/index/blank/{GUID}':
+    post:
+      tags:
+        - index
+      summary: Create a new, blank version for the document associated to the provided uuid.
+      description: Creates a new blank version of a record with the provided GUID. Returns the GUID of the new version of the record and the baseid common to all versions of the record. Authorization (acl/authz fields) carry over from the original record to the new blank version. No other metadata (md5sum, etc) carries over from the original record to the new blank version.
+      operationId: addNewBlankVersion
+      consumes:
+        - application/json
+      produces:
+        - application/json
+      parameters:
+        - name: GUID
+          in: path
+          description: the uuid associated to the record needed to have new version
+          required: true
+          type: string
+        - in: body
+          name: body
+          description: Metadata object that needs to be added to the store
+          required: true
+          schema:
+            $ref: '#/definitions/InputBlankVersionInfo'
+      responses:
+        '201':
+          description: successful operation
+          schema:
+            $ref: '#/definitions/OutputRef'
+        '400':
+          description: Invalid status value
+        '404':
+          description: GUID does not exist
+      security:
+        - basic_auth: []
     put:
       tags:
         - index
@@ -898,7 +931,7 @@ paths:
         - DOS
   '/ga4gh/drs/v1/objects':
     get:
-      summary: List all DrsObject. 
+      summary: List all DrsObject.
       description: 'Url field here contains their location and not the presigned url.'
       operationId: ListDrsObject
       responses:
@@ -966,13 +999,13 @@ paths:
           type: boolean
           default: false
           description: >-
-            NOT IMPLEMENTED YET. 
-            
+            NOT IMPLEMENTED YET.
+
             If false and the object_id refers to a bundle, then the ContentsObject array
             contains only those objects directly contained in the bundle. That is, if the
             bundle contains other bundles, those other bundles are not recursively
             included in the result.
-            
+
             If true and the object_id refers to a bundle, then the entire set of objects
             in the bundle is expanded. That is, if the bundle contains aother bundles,
             then those other bundles are recursively expanded and included in the result.
@@ -1047,7 +1080,7 @@ paths:
       tags:
         - DRS
       x-swagger-router-controller: ga4gh.drs.server
-    
+
   '/bulk/documents':
     post:
       tags:
@@ -1071,7 +1104,7 @@ paths:
         '400':
           description: Invalid status value
       security: []
-  
+
   '/_query/urls/q':
     get:
       tags:
@@ -1311,6 +1344,18 @@ definitions:
       file_name:
         type: string
         description: name of the uploaded file
+  InputBlankVersionInfo:
+    type: object
+    properties:
+      uploader:
+        type: string
+        description: user who uploaded this file
+      file_name:
+        type: string
+        description: optional; name of the uploaded file
+      did:
+        type: string
+        description: optional; specify the GUID of the new blank version that is created.
   UpdateInputInfo:
     type: object
     properties:
@@ -1790,7 +1835,7 @@ definitions:
         format: date-time
         description: |-
           Timestamp of content creation in RFC3339.
-          (This is the creation time of the underlying content, not of the JSON object.) 
+          (This is the creation time of the underlying content, not of the JSON object.)
       updated_time:
         type: string
         format: date-time
@@ -1909,7 +1954,7 @@ definitions:
           A name declared by the bundle author that must be
           used when materialising this object,
           overriding any name directly associated with the object itself.
-          The name must be unique with the containing bundle. 
+          The name must be unique with the containing bundle.
           This string is made up of uppercase and lowercase letters, decimal digits, hypen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable filenames].
       id:
         type: string
@@ -1936,7 +1981,7 @@ definitions:
         items:
           example:
             {}
-        
+
     required:
       - name
   Error:
@@ -1949,15 +1994,15 @@ definitions:
         description: A detailed error message.
       status_code:
         type: integer
-        description: The integer representing the HTTP status code (e.g. 200, 404).  
+        description: The integer representing the HTTP status code (e.g. 200, 404).
   ListDrsObject:
     type: object
     properties:
-      drs_objects: 
+      drs_objects:
         type: array
         items:
           $ref: '#/definitions/DrsObject'
-          
+
   ListRecords:
     type: object
     properties: