DEV-2301 externalize enums so that they can be accessed by other modu…

…les (#69)

DEV-2301 externalize enums so that they can be accessed by other modules
* introduce pre-commit isort
* reformat all with isort

.pre-commit-config.yaml

@@ -3,6 +3,11 @@ repos:
     rev: 22.3.0
     hooks:
       - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.11.5
+    hooks:
+      - id: isort
+        args: [--profile, black]
   - repo: git@github.com:Yelp/detect-secrets
     rev: v1.4.0
     hooks:

.secrets.baseline

@@ -20,15 +20,12 @@
     {
       "name": "CloudantDetector"
     },
-    {
-      "name": "DiscordBotTokenDetector"
-    },
     {
       "name": "GitHubTokenDetector"
     },
     {
       "name": "HexHighEntropyString",
-      "limit": 3
+      "limit": 3.0
     },
     {
       "name": "IbmCloudIamDetector"
@@ -109,12 +106,6 @@
     },
     {
       "path": "detect_secrets.filters.heuristic.is_templated_secret"
-    },
-    {
-      "path": "detect_secrets.filters.regex.should_exclude_file",
-      "pattern": [
-        "^.secrets.baseline$"
-      ]
     }
   ],
   "results": {
@@ -144,7 +135,7 @@
         "filename": "gdc_ng_models/alembic/versions/12dbbcac7a1d_change_columns_to_biginteger.py",
         "hashed_secret": "e9a4b5d5cbc26e98f00981d15146f2a23871666b",
         "is_verified": false,
-        "line_number": 14,
+        "line_number": 13,
         "is_secret": false
       }
     ],
@@ -154,10 +145,10 @@
         "filename": "gdc_ng_models/alembic/versions/e9d53a640d5d_add_start_end_datetimes_notifications.py",
         "hashed_secret": "e9a4b5d5cbc26e98f00981d15146f2a23871666b",
         "is_verified": false,
-        "line_number": 13,
+        "line_number": 12,
         "is_secret": false
       }
     ]
   },
-  "generated_at": "2023-08-25T14:30:18Z"
+  "generated_at": "2023-12-01T15:34:13Z"
 }

gdc_ng_models/alembic/env.py

@@ -1,8 +1,7 @@
 from logging.config import fileConfig
 
 from alembic import context
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
+from sqlalchemy import engine_from_config, pool
 
 import gdc_ng_models.models.batch as batch_models
 import gdc_ng_models.models.download_reports as download_reports_models
@@ -15,7 +14,6 @@
 import gdc_ng_models.models.studyrule as studyrule_models
 import gdc_ng_models.models.submission as submission_models
 
-
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
 config = context.config

gdc_ng_models/alembic/versions/12dbbcac7a1d_change_columns_to_biginteger.py

@@ -5,9 +5,8 @@
 Create Date: 2021-03-30 13:16:01.055456
 
 """
-from alembic import op
 import sqlalchemy as sa
-
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "12dbbcac7a1d"

gdc_ng_models/alembic/versions/e9d53a640d5d_add_start_end_datetimes_notifications.py

@@ -5,9 +5,8 @@
 Create Date: 2020-12-11 16:06:21.960486
 
 """
-from alembic import op
 import sqlalchemy as sa
-
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "e9d53a640d5d"

gdc_ng_models/models/audit.py

@@ -1,7 +1,7 @@
 """Common audit metadata for our data models."""
 import datetime
 
-from sqlalchemy import schema, sql, func
+from sqlalchemy import func, schema, sql
 from sqlalchemy.sql import sqltypes
 
 

gdc_ng_models/models/cohort.py

@@ -10,9 +10,11 @@
 """
 
 import uuid
+
 import sqlalchemy
 from sqlalchemy.dialects import postgresql
 from sqlalchemy.ext import declarative
+
 from gdc_ng_models.models import accessed, audit
 
 Base = declarative.declarative_base()

gdc_ng_models/models/download_reports.py

@@ -1,8 +1,8 @@
 import json
+
 import sqlalchemy as db
-from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.dialects.postgresql import JSONB
-
+from sqlalchemy.ext.declarative import declarative_base
 
 Base = declarative_base()
 

gdc_ng_models/models/entity_set.py

@@ -19,11 +19,30 @@
   by the cohort service in the backend system.
 """
 
+import enum
+
 import sqlalchemy
 from sqlalchemy.dialects import postgresql
 from sqlalchemy.ext import declarative
+
 from gdc_ng_models.models import accessed, audit
 
+
+@enum.unique
+class SetType(enum.Enum):
+    ephemeral = 1
+    frozen = 2
+    mutable = 3
+
+
+@enum.unique
+class EntityType(enum.Enum):
+    case = 1
+    file = 2
+    gene = 3
+    ssm = 4
+
+
 Base = declarative.declarative_base()
 
 
@@ -51,19 +70,17 @@ class EntitySet(Base, audit.AuditColumnsMixin, accessed.AccessedColumnMixin):
         primary_key=True,
     )
     type = sqlalchemy.Column(
-        postgresql.ENUM("ephmeral", "frozen", "mutable", name="entity_set_type"),
+        postgresql.ENUM(SetType, name="entity_set_type"),
         nullable=False,
     )
     entity_type = sqlalchemy.Column(
-        postgresql.ENUM("case", "file", "gene", "ssm", name="entity_type"),
+        postgresql.ENUM(EntityType, name="entity_type"),
         nullable=False,
     )
 
     # entity_ids are UUIDs that are 36 characters long.
-    # Postgres is more performant when the data sizes are not dynamic
-    entity_ids = sqlalchemy.Column(
-        postgresql.ARRAY(sqlalchemy.String(36)), nullable=False
-    )
+    #  However, postgres does not use lengths in its arrays
+    entity_ids = sqlalchemy.Column(postgresql.ARRAY(sqlalchemy.String), nullable=False)
 
     def __repr__(self):
         return (
@@ -76,8 +93,8 @@ def __repr__(self):
             "updated_datetime={updated_datetime}), "
             "accessed_datetime={accessed_datetime})>".format(
                 id=self.id,
-                type=self.type,
-                entity_type=self.entity_type,
+                type=self.type.name,
+                entity_type=self.entity_type.name,
                 entity_ids=self.entity_ids,
                 created_datetime=self.created_datetime.isoformat()
                 if self.created_datetime
@@ -94,8 +111,8 @@ def __repr__(self):
     def to_json(self):
         return {
             "id": str(self.id),
-            "type": str(self.type),
-            "entity_type": str(self.entity_type),
+            "type": self.type.name,
+            "entity_type": self.entity_type.name,
             "entity_ids": [str(entity_id) for entity_id in self.entity_ids],
             "created_datetime": self.created_datetime.isoformat()
             if self.created_datetime

gdc_ng_models/models/misc.py

@@ -1,7 +1,6 @@
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy import BigInteger, Column, DateTime, Index, String, Text, Sequence
+from sqlalchemy import BigInteger, Column, DateTime, Index, Sequence, String, Text
 from sqlalchemy.dialects.postgresql import JSONB
-
+from sqlalchemy.ext.declarative import declarative_base
 
 Base = declarative_base()
 

gdc_ng_models/models/notifications.py

@@ -2,17 +2,16 @@
 
 from sqlalchemy import (
     BigInteger,
+    Boolean,
     Column,
+    DateTime,
+    Sequence,
     String,
     Text,
-    DateTime,
     text,
-    Boolean,
-    Sequence,
 )
-from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.dialects.postgresql import ARRAY
-
+from sqlalchemy.ext.declarative import declarative_base
 
 Base = declarative_base()
 

gdc_ng_models/models/qcreport.py

@@ -5,15 +5,14 @@
     DateTime,
     Enum,
     ForeignKey,
+    Sequence,
     String,
     Text,
     text,
-    Sequence,
 )
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import relationship, validates
-from sqlalchemy.dialects.postgresql import JSONB
-
 
 Base = declarative_base()
 SEVERITY = Enum("CRITICAL", "WARNING", "PASSED", name="error_severity")

gdc_ng_models/models/redaction.py

@@ -1,21 +1,21 @@
 from datetime import datetime
+
 from sqlalchemy import (
-    Boolean,
     BigInteger,
+    Boolean,
     Column,
     DateTime,
     Enum,
     ForeignKey,
+    Sequence,
     String,
     Text,
     text,
-    Sequence,
 )
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.ext.hybrid import hybrid_property
 from sqlalchemy.orm import relationship
 
-
 Base = declarative_base()
 
 

gdc_ng_models/models/reports.py

@@ -1,8 +1,7 @@
-from sqlalchemy import BigInteger, Column, Text, DateTime, text, Index, func, Sequence
+from sqlalchemy import BigInteger, Column, DateTime, Index, Sequence, Text, func, text
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.ext.hybrid import hybrid_property
-from sqlalchemy.dialects.postgresql import JSONB
-
 
 Base = declarative_base()
 

gdc_ng_models/models/submission.py

@@ -5,26 +5,28 @@
 Models for submission TransactionLogs
 """
 
-from distutils.version import StrictVersion
 from datetime import datetime
-from json import loads, dumps
+from distutils.version import StrictVersion
+from json import dumps, loads
+
 import pytz
 import sqlalchemy as db
-from sqlalchemy import func, Sequence
-from sqlalchemy.ext.declarative import declarative_base, declared_attr
-from sqlalchemy.ext.hybrid import hybrid_property
-from sqlalchemy.orm import relationship, deferred
 from sqlalchemy import (
     BigInteger,
     Boolean,
     Column,
     DateTime,
     ForeignKey,
-    Integer,
     Index,
+    Integer,
+    Sequence,
     Text,
+    func,
     text,
 )
+from sqlalchemy.ext.declarative import declarative_base, declared_attr
+from sqlalchemy.ext.hybrid import hybrid_property
+from sqlalchemy.orm import deferred, relationship
 
 if StrictVersion(db.__version__) >= StrictVersion("1.3.4"):
     from sqlalchemy.dialects.postgresql.json import JSONB

gdc_ng_models/snacks/database.py

@@ -5,7 +5,6 @@
 
 from gdc_ng_models.utils.decorators import try_or_log_error
 
-
 logger = getLogger(__name__)
 
 PERMISSIONS = dict(READ="SELECT", WRITE="SELECT, INSERT, UPDATE, DELETE")

tests/integration/models/test_cohort.py

@@ -1,10 +1,12 @@
 import enum
 import json
 import uuid
+
 import pytest
-from gdc_ng_models.models import cohort
 from sqlalchemy import exc
 
+from gdc_ng_models.models import cohort
+
 
 class CohortType(enum.Enum):
     static = 1

tests/integration/models/test_download_reports_models.py

@@ -1,10 +1,8 @@
 from datetime import date
 
 from cdisutils.dictionary import sort_dict
-from gdc_ng_models.models.download_reports import (
-    DataDownloadReport,
-    DataUsageReport,
-)
+
+from gdc_ng_models.models.download_reports import DataDownloadReport, DataUsageReport
 
 
 def test_create_usage_reports(create_reports_db, db_session):