New bug fixes feature gendercheckY

clarity_epp.py

@@ -115,9 +115,9 @@ def export_removed_samples(args):
     clarity_epp.export.sample.removed_samples(lims, args.output_file)
 
 
-def export_sample_udf(args):
-    "Export sample udf table."""
-    clarity_epp.export.sample.sample_udf(
+def export_sample_udf_dx(args):
+    "Export table sample udf (Dx-udf only)"""
+    clarity_epp.export.sample.sample_udf_dx(
         lims,
         args.output_file,
         args.artifact_name,
@@ -341,18 +341,18 @@ def placement_pipetting(args):
     )
     parser_export_removed_samples.set_defaults(func=export_removed_samples)
 
-    parser_export_sample_udf = subparser_export.add_parser(
-        'sample_udf', help='Export sample udf table.', parents=[output_parser]
+    parser_export_sample_udf_dx = subparser_export.add_parser(
+        'sample_udf_dx', help='Export sample udf table (Dx-udf only).', parents=[output_parser]
     )
-    parser_export_sample_udf_group = parser_export_sample_udf.add_mutually_exclusive_group(required=True)
-    parser_export_sample_udf_group.add_argument('-a', '--artifact_name', help='Artifact name')
-    parser_export_sample_udf_group.add_argument('-r', '--sequencing_run', help='Sequencing run name')
-    parser_export_sample_udf.add_argument(
+    parser_export_sample_udf_dx_group = parser_export_sample_udf_dx.add_mutually_exclusive_group(required=True)
+    parser_export_sample_udf_dx_group.add_argument('-a', '--artifact_name', help='Artifact name')
+    parser_export_sample_udf_dx_group.add_argument('-r', '--sequencing_run', help='Sequencing run name')
+    parser_export_sample_udf_dx.add_argument(
         '-p', '--sequencing_run_project',  nargs='?', help='Sequencing run project name'
     )
-    parser_export_sample_udf.add_argument('-u', '--udf', help='udf to query')
-    parser_export_sample_udf.add_argument('-c', '--column_name', help='naming of column')
-    parser_export_sample_udf.set_defaults(func=export_sample_udf)
+    parser_export_sample_udf_dx.add_argument('-u', '--udf', help='udf to query (limited to only Dx-udf)')
+    parser_export_sample_udf_dx.add_argument('-c', '--column_name', help='naming of column')
+    parser_export_sample_udf_dx.set_defaults(func=export_sample_udf_dx)
 
     parser_export_sample_related_mip = subparser_export.add_parser(
         'sample_related_mip', help='Export related mip samples.', parents=[output_parser]

clarity_epp/export/sample.py

@@ -145,20 +145,30 @@ def get_samples(lims, artifact_name=None, sequencing_run=None, sequencing_run_pr
     return samples
 
 
-def sample_udf(lims, output_file, artifact_name=None, sequencing_run=None, sequencing_run_project=None, udf=None, column_name=None):
-    """Export table with sample udf."""
+def sample_udf_dx(lims, output_file, artifact_name=None, sequencing_run=None, sequencing_run_project=None, udf=None, column_name=None):
+    """Export table with sample udf (Dx-udf only)."""
     samples = get_samples(lims, artifact_name, sequencing_run, sequencing_run_project)
     # Write result
     if samples:
         output_file.write(f'Sample\t{column_name}\n')
         for sample_name, sample in samples.items():
             if udf in sample.udf:
-                output_file.write(
-                    '{sample}\t{udf_value}\n'.format(
-                        sample=sample_name,
+                if 'Dx' in udf:
+                    if type (sample.udf[udf]) == str:
                         udf_value=sample.udf[udf].split(';')[0]  # select newest udf value
+                    else:
+                        udf_value=sample.udf[udf]
+
+                    output_file.write(
+                        '{sample}\t{udf_value}\n'.format(
+                            sample=sample_name,
+                            udf_value=udf_value
+                         )
+                    )
+                else:
+                    output_file.write(
+                        f'Warning, udf is not type \'Dx\'\n'
                     )
-                )
             else:
                 output_file.write(
                     '{sample}\t{udf_value}\n'.format(

tests/test_export_sample.py

@@ -9,41 +9,51 @@ def __init__(self, udf):
 
 
 def test_sample_udf_withudf(mocker, capsys):
-    # Test output for sample with known udf in database
+    # Test output for sample with known Dx-udf in database
+    samples_mock[sample_name] = MyMock({"Dx geslacht": "Vrouw"})
     patched_clarity_epp = mocker.patch(
         'clarity_epp.export.sample.get_samples',
         return_value=samples_mock
     )
-    sample.sample_udf("lims", sys.stdout, udf=udf_value, column_name=column_name)
+    sample.sample_udf_dx("lims", sys.stdout, udf="Dx geslacht", column_name=column_name)
     captured = capsys.readouterr()
-    assert captured.out == f"Sample\t{column_name}\n{sample_name}\t{geslacht}\n"
+    assert captured.out == f"Sample\t{column_name}\n{sample_name}\tVrouw\n"
 
 
 def test_sample_udf_withoutudf(mocker, capsys):
     # Test output for sample with no known udf in database
+    samples_mock[sample_name] = MyMock({"Dx geslacht": "Vrouw"})
     patched_clarity_epp = mocker.patch(
         'clarity_epp.export.sample.get_samples',
         return_value=samples_mock
     )
-    sample.sample_udf("lims", sys.stdout, udf="udf2", column_name=column_name)
+    sample.sample_udf_dx("lims", sys.stdout, udf="udf2", column_name=column_name)
     captured = capsys.readouterr()
     assert captured.out == f"Sample\t{column_name}\n{sample_name}\tunknown\n"
 
+def test_sample_udf_withoutdxudf(mocker, capsys):
+    # Test output for sample with known udf in database, but not Dx-udf
+    samples_mock[sample_name] = MyMock({"Geslacht": "Vrouw"})
+    patched_clarity_epp = mocker.patch(
+        'clarity_epp.export.sample.get_samples',
+        return_value=samples_mock
+    )
+    sample.sample_udf_dx("lims", sys.stdout, udf="Geslacht", column_name=column_name)
+    captured = capsys.readouterr()
+    assert captured.out == f"Sample\t{column_name}\nWarning, udf is not type \'Dx\'\n"
+
 
 def test_sample_udf_nosamples(mocker, capsys):
     # Test output for sample not known in database
+    samples_mock[sample_name] = MyMock({"Dx geslacht": "Vrouw"})
     patched_clarity_epp = mocker.patch(
         'clarity_epp.export.sample.get_samples',
         return_value=None
     )
-    sample.sample_udf("lims", sys.stdout)
+    sample.sample_udf_dx("lims", sys.stdout)
     captured = capsys.readouterr()
     assert captured.out == "no_sample_found\n"
 
-
 column_name = "test_column"
 sample_name = "test_sample"
-udf_value = "Dx geslacht"
-geslacht = "Vrouw"
 samples_mock = {}
-samples_mock[sample_name] = MyMock({udf_value: geslacht})