feat: upgrade to sodar core v1 (#1973)

backend/cases_import/models/executors.py

@@ -136,7 +136,7 @@ def __init__(self, project: Project):
     def _build_fs_options(self, project: Project) -> FileSystemOptions:
         """Build `FileSystemOptions` from project settings."""
         app_settings = AppSettingAPI()
-        kwargs = {"app_name": "cases_import", "project": project}
+        kwargs = {"plugin_name": "cases_import", "project": project}
 
         path = app_settings.get(setting_name="import_data_path", **kwargs) or None
         if not path:

backend/cases_import/tests/test_models_executor.py

@@ -51,7 +51,7 @@ def _setUpExecutor(self, action, fac_kwargs=None):
 
         app_settings = AppSettingAPI()
         app_settings.set(
-            app_name="cases_import",
+            plugin_name="cases_import",
             setting_name="import_data_protocol",
             value="file",
             project=self.project,

backend/cases_qc/tests/test_views_api.py

@@ -91,7 +91,7 @@ def _setUpExecutor(self, fac_kwargs: typing.Dict[str, str]):
 
         app_settings = AppSettingAPI()
         app_settings.set(
-            app_name="cases_import",
+            plugin_name="cases_import",
             setting_name="import_data_protocol",
             value="file",
             project=self.project,

backend/genepanels/forms.py

@@ -24,8 +24,11 @@ def __init__(self, *args, **kwargs):
         self.fields["genes"] = self._build_genes_field()
 
     def _build_genes_field(self):
-        rows = [entry.symbol for entry in self.instance.genepanelentry_set.all()]
-        initial_value = "\n".join(rows)
+        if self.instance.pk:
+            rows = [entry.symbol for entry in self.instance.genepanelentry_set.all()]
+            initial_value = "\n".join(rows)
+        else:
+            initial_value = ""
         return forms.CharField(
             label="Genes",
             widget=forms.Textarea,

backend/genepanels/tests/test_models.py

@@ -24,7 +24,9 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         category = GenePanelCategoryFactory()
-        self.assertEqual(category.get_absolute_url(), f"/genepanels/category/{category.sodar_uuid}")
+        self.assertEqual(
+            category.get_absolute_url(), f"/genepanels/category/{category.sodar_uuid}/"
+        )
 
     def test_str(self):
         category = GenePanelCategoryFactory()
@@ -46,7 +48,7 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         panel = GenePanelFactory()
-        self.assertEqual(panel.get_absolute_url(), f"/genepanels/panel/{panel.sodar_uuid}")
+        self.assertEqual(panel.get_absolute_url(), f"/genepanels/panel/{panel.sodar_uuid}/")
 
     def test_get_hgnc_list(self):
         panel = GenePanelFactory()

backend/seqmeta/tests/test_models.py

@@ -12,7 +12,7 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         kit = EnrichmentKitFactory()
-        self.assertEqual(kit.get_absolute_url(), f"/seqmeta/enrichmentkit/{kit.sodar_uuid}")
+        self.assertEqual(kit.get_absolute_url(), f"/seqmeta/enrichmentkit/{kit.sodar_uuid}/")
 
     def test_str(self):
         kit = EnrichmentKitFactory()

backend/varannos/tests/test_models.py

@@ -17,7 +17,7 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         obj = VarAnnoSetFactory()
-        self.assertEqual(obj.get_absolute_url(), f"/varannos/varannoset/details/{obj.sodar_uuid}")
+        self.assertEqual(obj.get_absolute_url(), f"/varannos/varannoset/details/{obj.sodar_uuid}/")
 
     def test_days_since_modification(self):
         with freeze_time((datetime.now() - timedelta(days=10)).strftime("%Y-%m-%d")):

backend/varfish/users/management/commands/initdev.py

@@ -282,7 +282,7 @@ def _create_project(
             for setting_name, value in setting_value.items():
                 if project_settings.get(setting_name) != value:
                     app_settings.set(
-                        app_name="cases_import",
+                        plugin_name="cases_import",
                         setting_name=setting_name,
                         value=value,
                         project=project,

backend/variants/migrations/0110_drop_variant_summary.py

@@ -0,0 +1,102 @@
+# Generated by Django 4.2.16 on 2024-10-09 13:00
+
+from django.db import connection
+from django.db import migrations, utils
+from django.db.migrations.recorder import MigrationRecorder
+
+def is_migration_applied(app_name, migration_name):
+    recorder = MigrationRecorder(connection)
+    try:
+        return recorder.migration_qs.filter(app=app_name, name=migration_name).exists()
+    except utils.ProgrammingError:
+        return False  # migration table does not exist yet
+
+if not is_migration_applied('projectroles', '0001_initial'):
+    run_before = []  # fresh installation, will run projectroles squashed migrations
+elif is_migration_applied('projectroles', '0032_alter_appsetting_value'):
+    run_before = []  # critical projectroles migration already applied
+else:
+    # We will not execute the squashed projectroles migration 0001..0032 and the
+    # projectroles migration 0032 has not been applied yet.
+    run_before = [
+        ("projectroles", "0032_alter_appsetting_value"),
+    ]
+
+
+SQL_OUTER = r"""
+DROP MATERIALIZED VIEW IF EXISTS variants_smallvariantsummary;
+
+CREATE MATERIALIZED VIEW variants_smallvariantsummary
+AS
+    %s
+WITH NO DATA;
+
+CREATE UNIQUE INDEX variants_smallvariantsummary_id ON variants_smallvariantsummary(id);
+CREATE INDEX variants_smallvariantsummary_coord ON variants_smallvariantsummary(
+    release, chromosome, start, "end", bin, reference, alternative
+);
+"""
+
+
+SQL_INNER = r"""
+WITH excluded_case_ids AS (
+    SELECT DISTINCT variants_case.id AS case_id
+    FROM variants_case
+    JOIN projectroles_project ON variants_case.project_id = projectroles_project.id
+    JOIN projectroles_appsetting ON
+        projectroles_project.id = projectroles_appsetting.project_id AND
+        projectroles_appsetting.name = 'exclude_from_inhouse_db' AND
+        projectroles_appsetting.value = '1'
+)
+SELECT
+    row_number() OVER (PARTITION BY true) AS id,
+    release,
+    chromosome,
+    start,
+    "end",
+    bin,
+    reference,
+    alternative,
+    sum(num_hom_ref) AS count_hom_ref,
+    sum(num_het) AS count_het,
+    sum(num_hom_alt) AS count_hom_alt,
+    sum(num_hemi_ref) AS count_hemi_ref,
+    sum(num_hemi_alt) AS count_hemi_alt
+FROM (
+    SELECT DISTINCT
+        variants.release,
+        variants.chromosome,
+        variants.start,
+        variants."end",
+        variants.bin,
+        variants.reference,
+        variants.alternative,
+        variants.num_hom_ref,
+        variants.num_het,
+        variants.num_hom_alt,
+        variants.num_hemi_ref,
+        variants.num_hemi_alt,
+        variants.case_id
+    FROM variants_smallvariant AS variants
+    WHERE NOT EXISTS (SELECT 1 from excluded_case_ids AS e WHERE e.case_id = variants.case_id)
+) AS variants_per_case
+GROUP BY (release, chromosome, start, "end", bin, reference, alternative)
+"""
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("variants", "0109_alter_clearexpiredexportedfilesbgjob_bg_job_and_more"),
+    ]
+
+    run_before = run_before
+
+    operations = [
+        migrations.RunSQL(
+            """
+            DROP MATERIALIZED VIEW IF EXISTS variants_smallvariantsummary;
+            """,
+            SQL_OUTER % SQL_INNER
+        )
+    ]

backend/variants/migrations/0111_create_variant_summary.py

@@ -0,0 +1,81 @@
+# Generated by Django 4.2.16 on 2024-10-09 13:00
+
+from django.db import migrations
+
+
+SQL_OUTER = r"""
+DROP MATERIALIZED VIEW IF EXISTS variants_smallvariantsummary;
+
+CREATE MATERIALIZED VIEW variants_smallvariantsummary
+AS
+    %s
+WITH NO DATA;
+
+CREATE UNIQUE INDEX variants_smallvariantsummary_id ON variants_smallvariantsummary(id);
+CREATE INDEX variants_smallvariantsummary_coord ON variants_smallvariantsummary(
+    release, chromosome, start, "end", bin, reference, alternative
+);
+"""
+
+
+SQL_INNER = r"""
+WITH excluded_case_ids AS (
+    SELECT DISTINCT variants_case.id AS case_id
+    FROM variants_case
+    JOIN projectroles_project ON variants_case.project_id = projectroles_project.id
+    JOIN projectroles_appsetting ON
+        projectroles_project.id = projectroles_appsetting.project_id AND
+        projectroles_appsetting.name = 'exclude_from_inhouse_db' AND
+        projectroles_appsetting.value = '1'
+)
+SELECT
+    row_number() OVER (PARTITION BY true) AS id,
+    release,
+    chromosome,
+    start,
+    "end",
+    bin,
+    reference,
+    alternative,
+    sum(num_hom_ref) AS count_hom_ref,
+    sum(num_het) AS count_het,
+    sum(num_hom_alt) AS count_hom_alt,
+    sum(num_hemi_ref) AS count_hemi_ref,
+    sum(num_hemi_alt) AS count_hemi_alt
+FROM (
+    SELECT DISTINCT
+        variants.release,
+        variants.chromosome,
+        variants.start,
+        variants."end",
+        variants.bin,
+        variants.reference,
+        variants.alternative,
+        variants.num_hom_ref,
+        variants.num_het,
+        variants.num_hom_alt,
+        variants.num_hemi_ref,
+        variants.num_hemi_alt,
+        variants.case_id
+    FROM variants_smallvariant AS variants
+    WHERE NOT EXISTS (SELECT 1 from excluded_case_ids AS e WHERE e.case_id = variants.case_id)
+) AS variants_per_case
+GROUP BY (release, chromosome, start, "end", bin, reference, alternative)
+"""
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("variants", "0110_drop_variant_summary"),
+        ("projectroles", "0032_alter_appsetting_value"),
+    ]
+
+    operations = [
+        migrations.RunSQL(
+            SQL_OUTER % SQL_INNER,
+            """
+            DROP MATERIALIZED VIEW IF EXISTS variants_smallvariantsummary;
+            """,
+        )
+    ]