Merge pull request #353 from uc-cdis/bug/PXP-6421-Revert-description

bug(PXP-6421): Reverting description changes for DRS
uc-cdis · Mar 17, 2023 · 899654a · 899654a
2 parents f09ede1 + 78164d7
commit 899654a
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Showing 21 changed files with 635 additions and 825 deletions.
diff --git a/.gitignore b/.gitignore
@@ -67,9 +67,3 @@ docs/_build/
 local_settings.py
 settings.yaml
 *.sq3
-
-# IDE
-.idea
-
-# pyenv
-.python-version
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -128,15 +128,6 @@
         "line_number": 104
       }
     ],
-    "indexd/utils.py": [
-      {
-        "type": "Basic Auth Credentials",
-        "filename": "indexd/utils.py",
-        "hashed_secret": "5d0fa74acf95d1d6bebd0d37f76a94e77d604fd9",
-        "is_verified": false,
-        "line_number": 87
-      }
-    ],
     "tests/test_aliases_endpoints.py": [
       {
         "type": "Hex High Entropy String",
@@ -168,77 +159,77 @@
         "filename": "tests/test_client.py",
         "hashed_secret": "5666c088b494f26cd8f63ace013992f5fc391ce0",
         "is_verified": false,
-        "line_number": 23
+        "line_number": 19
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "15a6d8daad1278efcaadc0d6e3d1dd2d9ebbc262",
         "is_verified": false,
-        "line_number": 1090
+        "line_number": 1084
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "1b0d1a618b5c213dd792bbc3aa96ffa6bc370ef3",
         "is_verified": false,
-        "line_number": 1306
+        "line_number": 1300
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "1170ace44158ff189902ff44597efef121623353",
         "is_verified": false,
-        "line_number": 1737
+        "line_number": 1731
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "ff9c79b737b3ea7386618cc9437d3fb0a772182b",
         "is_verified": false,
-        "line_number": 2414
+        "line_number": 2406
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "c8176f1e75e62e15dabaa4087fb7194451c8f6d2",
         "is_verified": false,
-        "line_number": 2417
+        "line_number": 2409
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "d5198f8eddb1cbeb437899cd99e5ee97ab8531b4",
         "is_verified": false,
-        "line_number": 2417
+        "line_number": 2409
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "02dc196562514eaa3e2feac1f441ccf6ad81e09d",
         "is_verified": false,
-        "line_number": 2421
+        "line_number": 2413
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "f1cb2d91a95165a2ab909eadd9f7b65f312c7e2d",
         "is_verified": false,
-        "line_number": 2422
+        "line_number": 2414
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "58db546de03270b55a4c889a5c5e6296b29fef25",
         "is_verified": false,
-        "line_number": 2423
+        "line_number": 2415
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_client.py",
         "hashed_secret": "b6c0bd08fde409c18760f32bef8705191840c402",
         "is_verified": false,
-        "line_number": 2424
+        "line_number": 2416
       }
     ],
     "tests/test_deprecated_aliases_endpoints.py": [
@@ -269,5 +260,5 @@
       }
     ]
   },
-  "generated_at": "2023-03-09T21:25:06Z"
+  "generated_at": "2023-03-17T18:42:05Z"
 }
diff --git a/bin/index_admin.py b/bin/index_admin.py
@@ -39,7 +39,6 @@ def main(path, action=None, username=None, password=None):
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser()
 
     parser.add_argument(

diff --git a/indexd/blueprint.py b/indexd/blueprint.py
@@ -65,7 +65,6 @@ def get_record(record):
 
 
 def dist_get_record(record):
-
     # Sort the list of distributed ID services
     # Ones with which the request matches a hint will be first
     # Followed by those that don't match the hint

diff --git a/indexd/drs/blueprint.py b/indexd/drs/blueprint.py
@@ -129,7 +129,7 @@ def indexd_to_drs(record, expand=False):
 
     form = record["form"] if "form" in record else "bundle"
 
-    description = record["description"] if "description" in record else ""
+    description = record["description"] if "description" in record else None
 
     alias = (
         record["alias"]
@@ -141,6 +141,7 @@ def indexd_to_drs(record, expand=False):
 
     drs_object = {
         "id": did,
+        "description": "",
         "mime_type": "application/json",
         "name": name,
         "created_time": created_time,
@@ -154,6 +155,9 @@ def indexd_to_drs(record, expand=False):
         "description": description,
     }
 
+    if "description" in record:
+        drs_object["description"] = record["description"]
+
     if "bundle_data" in record:
         drs_object["contents"] = []
         for bundle in record["bundle_data"]:

diff --git a/indexd/index/blueprint.py b/indexd/index/blueprint.py
@@ -7,7 +7,7 @@
 
 from indexd import auth
 
-from indexd.errors import AuthError, AuthzError, IndexdUnexpectedError
+from indexd.errors import AuthError, AuthzError
 from indexd.errors import UserError
 
 from .schema import PUT_RECORD_SCHEMA
@@ -243,7 +243,7 @@ def get_urls():
 
 # NOTE: /index/<record>/deeper-route methods are above /index/<record> so that routing
 # prefers these first. Without this ordering, newer versions of the web framework
-# were interpreting index/e383a3aa-316e-4a51-975d-d699eff41bd2/aliases/ as routing
+# were interpretting index/e383a3aa-316e-4a51-975d-d699eff41bd2/aliases/ as routing
 # to /index/<record> where <record> was "e383a3aa-316e-4a51-975d-d699eff41bd2/aliases/"
 
 
@@ -407,7 +407,6 @@ def post_index_record():
     version = flask.request.json.get("version")
     baseid = flask.request.json.get("baseid")
     uploader = flask.request.json.get("uploader")
-    description = flask.request.json.get("description")
 
     did, rev, baseid = blueprint.index_driver.add(
         form,
@@ -423,7 +422,6 @@ def post_index_record():
         hashes=hashes,
         baseid=baseid,
         uploader=uploader,
-        description=description,
     )
 
     ret = {"did": did, "rev": rev, "baseid": baseid}
@@ -555,7 +553,6 @@ def add_index_record_version(record):
     metadata = flask.request.json.get("metadata")
     urls_metadata = flask.request.json.get("urls_metadata")
     version = flask.request.json.get("version")
-    description = flask.request.json.get("description")
 
     # authorize done in add_version for both the old and new authz
     did, baseid, rev = blueprint.index_driver.add_version(
@@ -571,7 +568,6 @@ def add_index_record_version(record):
         urls_metadata=urls_metadata,
         version=version,
         hashes=hashes,
-        description=description,
     )
 
     ret = {"did": did, "baseid": baseid, "rev": rev}

diff --git a/indexd/index/drivers/alchemy.py b/indexd/index/drivers/alchemy.py
@@ -77,7 +77,6 @@ class IndexRecord(Base):
     file_name = Column(String, index=True)
     version = Column(String, index=True)
     uploader = Column(String, index=True)
-    description = Column(String)
 
     urls = relationship(
         "IndexRecordUrl", backref="index_record", cascade="all, delete-orphan"
@@ -136,7 +135,6 @@ def to_document_dict(self):
             "form": self.form,
             "created_date": created_date,
             "updated_date": updated_date,
-            "description": self.description,
         }
 
 
@@ -684,7 +682,6 @@ def add(
         hashes=None,
         baseid=None,
         uploader=None,
-        description=None,
     ):
         """
         Creates a new record given size, urls, acl, authz, hashes, metadata,
@@ -744,9 +741,6 @@ def add(
                 IndexRecordMetadata(did=record.did, key=m_key, value=m_value)
                 for m_key, m_value in metadata.items()
             ]
-
-            record.description = description
-
             session.merge(base_version)
 
             try:
@@ -1273,7 +1267,6 @@ def add_version(
         acl=None,
         authz=None,
         hashes=None,
-        description=None,
     ):
         """
         Add a record version given did
@@ -1312,7 +1305,6 @@ def add_version(
             record.size = size
             record.file_name = file_name
             record.version = version
-            record.description = description
 
             record.urls = [IndexRecordUrl(did=record.did, url=url) for url in urls]
 

diff --git a/indexd/index/drivers/query/urls.py b/indexd/index/drivers/query/urls.py
@@ -35,7 +35,6 @@ def query_urls(
         fields="did,urls",
         **kwargs
     ):
-
         if kwargs:
             raise UserError(
                 "Unexpected query parameter(s) {}".format(list(kwargs.keys()))
@@ -102,7 +101,6 @@ def query_metadata_by_key(
         fields="did,urls,rev",
         **kwargs
     ):
-
         if kwargs:
             raise UserError(
                 "Unexpected query parameter(s) {}".format(list(kwargs.keys()))

diff --git a/indexd/index/schema.py b/indexd/index/schema.py
@@ -31,10 +31,6 @@
             "description": "optional version string of the object",
             "type": "string",
         },
-        "description": {
-            "description": "optional description string of the object",
-            "type": "string",
-        },
         "uploader": {
             "description": "optional uploader of the object",
             "type": "string",
@@ -86,7 +82,6 @@
         "uploader": {"type": ["string", "null"]},
         "metadata": {"type": "object"},
         "urls_metadata": {"type": "object"},
-        "description": {"type": ["string", "null"]},
     },
 }
 

diff --git a/indexd/utils.py b/indexd/utils.py
@@ -16,7 +16,6 @@ def hint_match(record, hints):
 def try_drop_test_data(
     user, database, root_user="postgres", host=""
 ):  # pragma: no cover
-
     engine = create_engine(
         "postgres://{user}@{host}/postgres".format(user=root_user, host=host)
     )

diff --git a/openapis/swagger.yaml b/openapis/swagger.yaml
@@ -1449,8 +1449,6 @@ definitions:
         type: object
       version:
         type: string
-      description:
-        type: string
       urls:
         type: array
         items:
@@ -2352,11 +2350,7 @@ definitions:
         type: array
         items:
           $ref: '#/definitions/Checksum'
-      description:
-        type: string
-      version:
-        type: string
-        description: optional version string of the object
+
       bundles:
         type: array
         items: