Fix reading analysis.active database field (#903)

This field is reported by the database as b'\x00' or b'\x01', both of
which bool(...) returns as True. Use parse_sql_bool() instead; and I've
verified that all other BOOLEAN or BIT fields use parse_sql_bool() too.

Add test case exercising the update_analysis() API fixed in PR #899
and checking that active is returned from the database correctly.

* Also fix typo so grepping finds this comment (trivial)
(Verified that changing this XML comment doesn't affect liquibase's
hash for this changeSet.)

* Bump version: 7.4.0 → 7.4.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 7.4.0
+current_version = 7.4.1
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[A-z0-9-]+)

api/server.py

@@ -25,7 +25,7 @@
 from db.python.utils import get_logger
 
 # This tag is automatically updated by bump2version
-_VERSION = '7.4.0'
+_VERSION = '7.4.1'
 
 
 logger = get_logger()

db/project.xml

@@ -643,7 +643,7 @@
 		<!--		In MariaDB, you can do _conditional_ unique values in a sort of hacky way.
 			You make a combined key, with one of the fields only NOT NULL when the row should participant in
 		the check.
-			IE: if you archive a sequencing group, marking the "nullIfInactitve field to NULL will allow
+			IE: if you archive a sequencing group, marking the "nullIfInactive" field to NULL will allow
 		multiple
 			copies - allowing for us to reuse the same external_ids for multiple sequencing groups. 	-->
 		<createTable tableName="sequencing_group_external_id">

deploy/python/version.txt

@@ -1 +1 @@
-7.4.0
+7.4.1

models/models/analysis.py

@@ -4,7 +4,7 @@
 
 from pydantic import BaseModel
 
-from models.base import SMBase, parse_sql_dict
+from models.base import SMBase, parse_sql_bool, parse_sql_dict
 from models.enums import AnalysisStatus
 from models.utils.cohort_id_format import (
     cohort_id_format_list,
@@ -64,7 +64,7 @@ def from_db(**kwargs):
             timestamp_completed=timestamp_completed,
             project=kwargs.get('project'),
             meta=meta,
-            active=bool(kwargs.get('active')),
+            active=parse_sql_bool(kwargs.get('active')),
             author=kwargs.get('author'),
         )
 

setup.py

@@ -19,7 +19,7 @@
 setup(
     name=PKG,
     # This tag is automatically updated by bump2version
-    version='7.4.0',
+    version='7.4.1',
     description='Python API for interacting with the Sample API system',
     long_description=readme,
     long_description_content_type='text/markdown',

test/test_analysis.py

@@ -2,6 +2,7 @@
 import time
 from test.testbase import DbIsolatedTest, run_as_sync
 
+from api.routes.analysis import AnalysisUpdateModel, update_analysis
 from db.python.filters import GenericFilter
 from db.python.layers.analysis import AnalysisLayer
 from db.python.layers.assay import AssayLayer
@@ -17,6 +18,7 @@
     ParticipantUpsertInternal,
     SampleUpsertInternal,
     SequencingGroupUpsertInternal,
+    parse_sql_bool,
 )
 
 
@@ -323,3 +325,36 @@ async def test_update_analysis(self):
         ]
 
         self.assertEqual(analyses, expected)
+
+    @run_as_sync
+    async def test_route_update_active(self):
+        """
+        Test that update_analysis(active=False) is effective
+        """
+        analysis_id = await self.al.create_analysis(
+            AnalysisInternal(
+                type='cram',
+                status=AnalysisStatus.COMPLETED,
+                sequencing_group_ids=[self.genome_sequencing_group_id],
+            )
+        )
+
+        analyses = await self.connection.connection.fetch_all('SELECT * FROM analysis')
+        self.assertEqual(1, len(analyses))
+        self.assertEqual(analysis_id, analyses[0]['id'])
+        self.assertTrue(parse_sql_bool(analyses[0]['active']))
+
+        inactivate = AnalysisUpdateModel(active=False, status=AnalysisStatus.COMPLETED)
+        await update_analysis(analysis_id, inactivate, self.connection)
+
+        analyses = await self.connection.connection.fetch_all('SELECT * FROM analysis')
+        self.assertEqual(1, len(analyses))
+        self.assertEqual(analysis_id, analyses[0]['id'])
+        self.assertFalse(parse_sql_bool(analyses[0]['active']))
+
+        analyses = await self.al.query(
+            AnalysisFilter(project=GenericFilter(eq=self.project_id))
+        )
+        self.assertEqual(1, len(analyses))
+        self.assertEqual(analysis_id, analyses[0].id)
+        self.assertFalse(analyses[0].active)

web/package.json

@@ -1,6 +1,6 @@
 {
     "name": "metamist",
-    "version": "7.4.0",
+    "version": "7.4.1",
     "private": true,
     "dependencies": {
         "@apollo/client": "^3.7.3",