wip

varfish-org · Sep 26, 2023 · 2a6f85a · 2a6f85a
1 parent df26f6b
commit 2a6f85a
Show file tree

Hide file tree

Showing 9 changed files with 26,407 additions and 16,719 deletions.
diff --git a/cases_qc/tests/helpers.py b/cases_qc/tests/helpers.py
@@ -72,7 +72,9 @@ def tearDown(self):
         super().tearDown()
         # recover all factory.Faker random states
         default_faker = factory.Faker._get_faker()
-        for the_factory, generator in zip(default_faker.factories, self._FixRandomSeedMixin__faker_generators):
+        for the_factory, generator in zip(
+            default_faker.factories, self._FixRandomSeedMixin__faker_generators
+        ):
             the_factory._Generator__random = generator
         # recover the random module's state
         random.setstate(self._FixRandomSeedMixin__random_state)

diff --git a/cases_qc/tests/snapshots/snap_test_io_cramino.py b/cases_qc/tests/snapshots/snap_test_io_cramino.py
@@ -4,52 +4,95 @@
 
 from snapshottest import GenericRepr, Snapshot
 
-
 snapshots = Snapshot()
 
-snapshots['CraminoLoadTest::test_load 1'] = [
-    '_state',
-    'id',
-    'sodar_uuid',
-    'date_created',
-    'date_modified',
-    'caseqc_id',
-    'sample',
-    'summary',
-    'chrom_counts'
+snapshots["CraminoLoadTest::test_load 1"] = [
+    "_state",
+    "id",
+    "sodar_uuid",
+    "date_created",
+    "date_modified",
+    "caseqc_id",
+    "sample",
+    "summary",
+    "chrom_counts",
 ]
 
-snapshots['CraminoLoadTest::test_load 2'] = {
-    'chrom_counts': [
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr1', normalized_counts=1.02)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr10', normalized_counts=1.02)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr11', normalized_counts=1.02)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr12', normalized_counts=1.01)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr13', normalized_counts=0.85)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr14', normalized_counts=0.83)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr15', normalized_counts=0.84)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr16', normalized_counts=1.03)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr17', normalized_counts=1.06)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr18', normalized_counts=0.98)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr19', normalized_counts=1.04)"),
+snapshots["CraminoLoadTest::test_load 2"] = {
+    "chrom_counts": [
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr1', normalized_counts=1.02)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr10', normalized_counts=1.02)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr11', normalized_counts=1.02)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr12', normalized_counts=1.01)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr13', normalized_counts=0.85)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr14', normalized_counts=0.83)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr15', normalized_counts=0.84)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr16', normalized_counts=1.03)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr17', normalized_counts=1.06)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr18', normalized_counts=0.98)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr19', normalized_counts=1.04)"
+        ),
         GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr2', normalized_counts=1.0)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr20', normalized_counts=1.09)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr21', normalized_counts=0.92)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr22', normalized_counts=0.8)"),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr20', normalized_counts=1.09)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr21', normalized_counts=0.92)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr22', normalized_counts=0.8)"
+        ),
         GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr3', normalized_counts=1.0)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr4', normalized_counts=0.99)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr5', normalized_counts=0.99)"),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr4', normalized_counts=0.99)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr5', normalized_counts=0.99)"
+        ),
         GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr6', normalized_counts=1.0)"),
         GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr7', normalized_counts=1.0)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr8', normalized_counts=0.99)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chr9', normalized_counts=0.94)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chrEBV', normalized_counts=23.65)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chrMT', normalized_counts=333.16)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chrX', normalized_counts=0.95)"),
-        GenericRepr("CraminoChromNormalizedCountsRecord(chrom_name='chrY', normalized_counts=0.04)")
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr8', normalized_counts=0.99)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chr9', normalized_counts=0.94)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chrEBV', normalized_counts=23.65)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chrMT', normalized_counts=333.16)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chrX', normalized_counts=0.95)"
+        ),
+        GenericRepr(
+            "CraminoChromNormalizedCountsRecord(chrom_name='chrY', normalized_counts=0.04)"
+        ),
     ],
-    'sample': 'sample',
-    'summary': [
+    "sample": "sample",
+    "summary": [
         GenericRepr("CraminoSummaryRecord(key='File name', value='NA12878.bam')"),
         GenericRepr("CraminoSummaryRecord(key='Number of reads', value=41169470)"),
         GenericRepr("CraminoSummaryRecord(key='Yield [Gb]', value=199.86)"),
@@ -63,6 +106,8 @@
         GenericRepr("CraminoSummaryRecord(key='Mean identity', value=97.69)"),
         GenericRepr("CraminoSummaryRecord(key='Path', value='/path/to/NA12878.bam')"),
         GenericRepr("CraminoSummaryRecord(key='Creation time', value='24/04/2023 20:51:37')"),
-        GenericRepr("CraminoSummaryRecord(key='Checksum', value='45EBB3BBD5DABA01A7997558DDF81429')")
-    ]
+        GenericRepr(
+            "CraminoSummaryRecord(key='Checksum', value='45EBB3BBD5DABA01A7997558DDF81429')"
+        ),
+    ],
 }