Reformat with the latest black

Clinical-Genomics · Feb 9, 2024 · 196652a · 196652a
1 parent 9bf98ee
commit 196652a
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Showing 4 changed files with 43 additions and 43 deletions.
diff --git a/src/chanjo2/endpoints/overview.py b/src/chanjo2/endpoints/overview.py
@@ -78,9 +78,9 @@ async def gene_overview(
     form_dict: dict = jsonable_encoder(form_data)
     validated_form = GeneReportForm(**form_dict)
 
-    gene_overview_content: Dict[
-        str, List[GeneCoverage]
-    ] = get_gene_overview_coverage_stats(form_data=validated_form, session=db)
+    gene_overview_content: Dict[str, List[GeneCoverage]] = (
+        get_gene_overview_coverage_stats(form_data=validated_form, session=db)
+    )
 
     return templates.TemplateResponse(
         "gene-overview.html",

diff --git a/src/chanjo2/meta/handle_load_intervals.py b/src/chanjo2/meta/handle_load_intervals.py
@@ -149,9 +149,9 @@ async def update_transcripts(
                 refseq_mrna_pred=items[6],
                 refseq_ncrna=items[7],
                 refseq_mane_select=items[8] if build == Builds.build_38 else None,
-                refseq_mane_plus_clinical=items[9]
-                if build == Builds.build_38
-                else None,
+                refseq_mane_plus_clinical=(
+                    items[9] if build == Builds.build_38 else None
+                ),
                 build=build,
             )
             transcripts_bulk.append(transcript)

diff --git a/src/chanjo2/meta/handle_report_contents.py b/src/chanjo2/meta/handle_report_contents.py
@@ -288,14 +288,14 @@ def get_genes_overview_incomplete_coverage_rows(
                 completeness_at_level: float = gene_cov_stats.completeness.get(
                     cov_level
                 )
-                overview_line: Optional[
-                    List[str]
-                ] = _get_incomplete_gene_coverage_overview_line(
-                    hgnc_symbol=gene_cov_stats.hgnc_symbol,
-                    hgnc_id=gene_cov_stats.hgnc_id,
-                    interval_id=gene_cov_stats.hgnc_id,
-                    sample=sample_name,
-                    completeness=completeness_at_level,
+                overview_line: Optional[List[str]] = (
+                    _get_incomplete_gene_coverage_overview_line(
+                        hgnc_symbol=gene_cov_stats.hgnc_symbol,
+                        hgnc_id=gene_cov_stats.hgnc_id,
+                        interval_id=gene_cov_stats.hgnc_id,
+                        sample=sample_name,
+                        completeness=completeness_at_level,
+                    )
                 )
 
                 genes_overview_rows.append(overview_line)
@@ -305,14 +305,14 @@ def get_genes_overview_incomplete_coverage_rows(
                     completeness_at_level: float = (
                         inner_interval_stats.completeness.get(cov_level)
                     )
-                    overview_line: Optional[
-                        List[str]
-                    ] = _get_incomplete_gene_coverage_overview_line(
-                        hgnc_symbol=gene_cov_stats.hgnc_symbol,
-                        hgnc_id=gene_cov_stats.hgnc_id,
-                        interval_id=inner_interval_stats.interval_id,
-                        sample=sample_name,
-                        completeness=completeness_at_level,
+                    overview_line: Optional[List[str]] = (
+                        _get_incomplete_gene_coverage_overview_line(
+                            hgnc_symbol=gene_cov_stats.hgnc_symbol,
+                            hgnc_id=gene_cov_stats.hgnc_id,
+                            interval_id=inner_interval_stats.interval_id,
+                            sample=sample_name,
+                            completeness=completeness_at_level,
+                        )
                     )
 
                     genes_overview_rows.append(overview_line)
@@ -357,9 +357,9 @@ def get_gene_overview_coverage_stats(form_data: GeneReportForm, session: Session
         )
         for sample, d4_file in samples_d4_files
     }
-    gene_stats[
-        "samples_coverage_stats_by_interval"
-    ] = get_gene_coverage_stats_by_interval(coverage_by_sample=samples_coverage_stats)
+    gene_stats["samples_coverage_stats_by_interval"] = (
+        get_gene_coverage_stats_by_interval(coverage_by_sample=samples_coverage_stats)
+    )
     return gene_stats
 
 

diff --git a/tests/src/chanjo2/meta/test_handle_report_contents.py b/tests/src/chanjo2/meta/test_handle_report_contents.py
@@ -38,10 +38,10 @@ def test_get_report_level_completeness_rows(
     assert samples_coverage_stats
 
     # THEN it should be possible to retrieve stats for the default coverage level:
-    default_level_samples_coverage_stats: List[
-        Tuple[str, float, str]
-    ] = get_report_level_completeness_rows(
-        samples_coverage_stats=samples_coverage_stats, level=DEFAULT_COVERAGE_LEVEL
+    default_level_samples_coverage_stats: List[Tuple[str, float, str]] = (
+        get_report_level_completeness_rows(
+            samples_coverage_stats=samples_coverage_stats, level=DEFAULT_COVERAGE_LEVEL
+        )
     )
     for (
         sample,
@@ -76,11 +76,11 @@ def test_get_report_completeness_rows(
     assert samples_coverage_stats
 
     # THEN completeness rows should contain the expected stats for each sample
-    samples_completeness_rows: List[
-        Tuple[str, Dict[str, float]]
-    ] = get_report_completeness_rows(
-        samples_coverage_stats=samples_coverage_stats,
-        levels=DEFAULT_COMPLETENESS_LEVELS,
+    samples_completeness_rows: List[Tuple[str, Dict[str, float]]] = (
+        get_report_completeness_rows(
+            samples_coverage_stats=samples_coverage_stats,
+            levels=DEFAULT_COMPLETENESS_LEVELS,
+        )
     )
     for sample, stats in samples_completeness_rows:
         assert sample == samples_d4_list[0][0]
@@ -125,12 +125,12 @@ def test_get_genes_overview_incomplete_coverage_rows(
     assert samples_coverage_stats
 
     # THEN it should be possible to retrieve stats for the transcripts that are not fully covered at the given threshold
-    genes_overview_lines: List[
-        Tuple[Union[str, int, float]]
-    ] = get_genes_overview_incomplete_coverage_rows(
-        samples_coverage_stats=samples_coverage_stats,
-        interval_type=SQLTranscript,
-        cov_level=DEFAULT_COMPLETENESS_LEVELS[0],
+    genes_overview_lines: List[Tuple[Union[str, int, float]]] = (
+        get_genes_overview_incomplete_coverage_rows(
+            samples_coverage_stats=samples_coverage_stats,
+            interval_type=SQLTranscript,
+            cov_level=DEFAULT_COMPLETENESS_LEVELS[0],
+        )
     )
 
     # THEN each transcript line should contain the expected values
@@ -168,9 +168,9 @@ def test_get_gene_coverage_stats_by_interval(
     }
 
     # WHEN passed to the get_gene_coverage_stats_by_interval function:
-    intervals_coverage_stats: Dict[
-        str, List[Tuple]
-    ] = get_gene_coverage_stats_by_interval(coverage_by_sample=samples_coverage_stats)
+    intervals_coverage_stats: Dict[str, List[Tuple]] = (
+        get_gene_coverage_stats_by_interval(coverage_by_sample=samples_coverage_stats)
+    )
 
     # THEN the returned data should have the expected format
     for interval_id, stats_tuples in intervals_coverage_stats.items():