Merge pull request #987 from populationgenomics/dev

Release: project_insights multiple family extids fix and register_missing_combiner_analysis.py script

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 7.5.0
+current_version = 7.5.1
 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 = '7.5.0'
+_VERSION = '7.5.1'
 
 
 logger = get_logger()

db/python/layers/project_insights.py

@@ -750,7 +750,7 @@ async def _sequencing_group_details_by_project_and_seq_fields(
     sg.technology as sequencing_technology,
     s.type as sample_type,
     f.id as family_id,
-    f.external_id as family_external_id,
+    fext.external_id as family_external_id,
     fp.participant_id as participant_id,
     pext.external_id as participant_external_id,
     s.id as sample_id,
@@ -759,6 +759,7 @@ async def _sequencing_group_details_by_project_and_seq_fields(
 FROM
     family f
     LEFT JOIN family_participant fp ON f.id = fp.family_id
+    LEFT JOIN family_external_id fext ON f.id = fext.family_id
     LEFT JOIN participant_external_id pext ON fp.participant_id = pext.participant_id
     LEFT JOIN sample s ON fp.participant_id = s.participant_id
     LEFT JOIN sample_external_id sext ON s.id = sext.sample_id

deploy/python/version.txt

@@ -1 +1 @@
-7.5.0
+7.5.1

scripts/register_missing_combiner_analysis.py

@@ -0,0 +1,55 @@
+"""Register a missing combiner analysis in Metamist
+
+Ad-hoc script to register a missing combiner analysis in Metamist.
+Is supremely inflexible since there is a short timeframe for combining previous
+VDS' for the OurDNA browser release.
+"""
+
+from argparse import ArgumentParser
+
+from hail.vds import read_vds
+
+from cpg_utils.hail_batch import config_retrieve, init_batch
+from metamist.apis import AnalysisApi
+from metamist.models import Analysis, AnalysisStatus
+
+
+def get_sg_ids(vds: str) -> list[str]:
+    """Gets all sequencing group IDs from a VDS
+
+    Args:
+        vds (str): The VDS to extract the sequencing group IDs from
+
+    Returns:
+        list[str]: A list of sequencing group IDs.
+    """
+    return read_vds(vds).variant_data.s.collect()
+
+
+def main(vds: str):
+    """Create and register a missing combiner analysis
+
+    Args:
+        vds (str): The existing VDS that needs to be registered
+        dataset (str): The project / dataset to register the analysis in
+    """
+    init_batch()
+    aapi = AnalysisApi()
+    am = Analysis(
+        type='combiner',
+        output=vds,
+        status=AnalysisStatus('completed'),
+        sequencing_group_ids=get_sg_ids(vds),
+        meta={},
+    )
+    dataset: str = config_retrieve(['workflow', 'dataset'])
+    if config_retrieve(['workflow', 'access_level']) == 'test':
+        dataset += '-test'
+    aapi.create_analysis(project=dataset, analysis=am)
+
+
+if __name__ == '__main__':
+    parser = ArgumentParser()
+    parser.add_argument('--vds', help='VDS to register analysis for.')
+    args = parser.parse_args()
+    main(args.vds)

setup.py

@@ -19,7 +19,7 @@
 setup(
     name=PKG,
     # This tag is automatically updated by bump2version
-    version='7.5.0',
+    version='7.5.1',
     description='Python API for interacting with the Sample API system',
     long_description=readme,
     long_description_content_type='text/markdown',

test/test_project_insights.py

@@ -111,3 +111,14 @@ async def test_project_insights_summary(self):
         ]
 
         self.assertEqual(result, expected)
+
+    @run_as_sync
+    async def test_project_insights_details(self):
+        """Test getting the details for all available projects"""
+
+        await self.partl.upsert_participant(get_test_participant())
+
+        # There's not enough data set up to usefully verify the result
+        _ = await self.pil.get_project_insights_details(
+            project_names=[self.project_name], sequencing_types=['genome', 'exome']
+        )

test/test_sequencing_groups.py

@@ -127,10 +127,9 @@ async def test_auto_deprecation_of_old_sequencing_group(self):
                             type='sequencing',
                             external_ids={'second-key': 'second-sequencing-object'},
                             meta={
-                                'second-sequencing-object' 'sequencing_type': 'genome',
+                                'sequencing_type': 'genome',
                                 'sequencing_platform': 'short-read',
                                 'sequencing_technology': 'illumina',
-                                'sequencing_type': 'genome',
                             },
                         ),
                     ],

web/package.json

@@ -1,6 +1,6 @@
 {
     "name": "metamist",
-    "version": "7.5.0",
+    "version": "7.5.1",
     "private": true,
     "dependencies": {
         "@apollo/client": "^3.11.5",