Merge branch 'develop' into release/v1.4.0

clarity_epp.py

@@ -94,10 +94,17 @@ def export_merge_file(args):
 
 
 def export_removed_samples(args):
-    """Export removed sampels table."""
+    """Export removed samples table."""
     clarity_epp.export.sample.removed_samples(lims, args.output_file)
 
 
+def export_sample_indications(args):
+    """Export sample indication table."""
+    clarity_epp.export.sample.sample_indications(
+        lims, args.output_file, args.artifact_name, args.sequencing_run, args.sequencing_run_project
+    )
+
+
 def export_tapestation(args):
     """Export samplesheets for Tapestation machine."""
     clarity_epp.export.tapestation.samplesheet(lims, args.process_id, args.output_file)
@@ -263,10 +270,21 @@ def placement_complete_step(args):
     parser_export_ped.set_defaults(func=export_ped_file)
 
     parser_export_removed_samples = subparser_export.add_parser(
-        'removed_samples', help='Export removed sampels table', parents=[output_parser]
+        'removed_samples', help='Export removed samples table', parents=[output_parser]
     )
     parser_export_removed_samples.set_defaults(func=export_removed_samples)
 
+    parser_export_sample_indications = subparser_export.add_parser(
+        'sample_indications', help='Export sample indication table.', parents=[output_parser]
+    )
+    parser_export_sample_indications_group = parser_export_sample_indications.add_mutually_exclusive_group(required=True)
+    parser_export_sample_indications_group.add_argument('-a', '--artifact_name', help='Artifact name')
+    parser_export_sample_indications_group.add_argument('-r', '--sequencing_run', help='Sequencing run name')
+    parser_export_sample_indications.add_argument(
+        '-p', '--sequencing_run_project',  nargs='?', help='Sequencing run project name'
+    )
+    parser_export_sample_indications.set_defaults(func=export_sample_indications)
+
     parser_export_tapestation = subparser_export.add_parser(
         'tapestation', help='Create tapestation samplesheets', parents=[output_parser]
     )

clarity_epp/export/sample.py

@@ -120,3 +120,32 @@ def removed_samples(lims, output_file):
                     stage=removed_stage.name,
                     removed_status=sample_removed_status
                 ))
+
+
+def sample_indications(lims, output_file, artifact_name=None, sequencing_run=None, sequencing_run_project=None):
+    """Export table with sample indications. Lookup samples by sample name or sequencing run (project)."""
+    samples = []
+
+    # Get samples by artifact_name
+    if artifact_name:
+        artifacts = lims.get_artifacts(name=artifact_name)
+        samples = {artifact_name: artifact.samples[0] for artifact in artifacts}
+
+    # Get samples by sequencing run
+    elif sequencing_run:
+        udf_query = {'Dx Sequencing Run ID': sequencing_run}
+        if sequencing_run_project:
+            udf_query['Dx Sequencing Run Project'] = sequencing_run_project
+
+        artifacts = lims.get_artifacts(type='Analyte', udf=udf_query)
+        samples = {artifact.name: artifact.samples[0] for artifact in artifacts}
+
+    # Write result
+    if samples:
+        output_file.write('Sample\tIndication\n')
+        for sample_name, sample in samples.items():
+            output_file.write(
+                '{sample}\t{indication}\n'.format(sample=sample_name, indication=sample.udf['Dx Onderzoeksindicatie'])
+            )
+    else:
+        print("Can't find sample(s).")