Merge pull request #66 from UMCUGenetics/release/v1.8.0

Release/v1.8.0

clarity_epp.py

@@ -48,7 +48,9 @@ def export_hamilton(args):
 
 def export_illumina(args):
     """Export (updated) illumina samplesheet."""
-    clarity_epp.export.illumina.update_samplesheet(lims, args.process_id, args.artifact_id, args.output_file)
+    clarity_epp.export.illumina.update_samplesheet(
+        lims, args.process_id, args.artifact_id, args.output_file, args.conversion_tool
+    )
 
 
 def export_labels(args):
@@ -59,6 +61,8 @@ def export_labels(args):
         clarity_epp.export.labels.container_sample(lims, args.process_id, args.output_file, args.description)
     elif args.type == 'storage_location':
         clarity_epp.export.labels.storage_location(lims, args.process_id, args.output_file)
+    elif args.type == 'nunc_mix_sample':
+        clarity_epp.export.labels.nunc_mix_sample(lims, args.process_id, args.output_file)
 
 
 def export_magnis(args):
@@ -92,6 +96,8 @@ def export_manual_pipetting(args):
         clarity_epp.export.manual_pipetting.samplesheet_pool_samples(lims, args.process_id, args.output_file)
     elif args.type == 'pool_magnis_pools':
         clarity_epp.export.manual_pipetting.samplesheet_pool_magnis_pools(lims, args.process_id, args.output_file)
+    elif args.type == 'normalization_mix':
+        clarity_epp.export.manual_pipetting.samplesheet_normalization_mix(lims, args.process_id, args.output_file)
 
 
 def export_ped_file(args):
@@ -151,6 +157,8 @@ def upload_tecan_results(args):
         clarity_epp.upload.tecan.results_qc(lims, args.process_id)
     elif args.type == 'purify_normalise':
         clarity_epp.upload.tecan.results_purify_normalise(lims, args.process_id)
+    elif args.type == 'purify_mix':
+        clarity_epp.upload.tecan.results_purify_mix(lims, args.process_id)
 
 
 def upload_tapestation_results(args):
@@ -195,12 +203,14 @@ def placement_automatic(args):
     clarity_epp.placement.plate.copy_layout(lims, args.process_id)
 
 
-def placement_artifact_set_name(args):
-    """Change artifact name to sequence name."""
+def placement_artifact_set(args):
+    """Change artifact name or udf."""
     if args.type == 'sequence_name':
         clarity_epp.placement.artifact.set_sequence_name(lims, args.process_id)
     elif args.type == 'run_id':
         clarity_epp.placement.artifact.set_runid_name(lims, args.process_id)
+    elif args.type == 'norm_udf':
+        clarity_epp.placement.artifact.set_norm_manual_udf(lims, args.process_id)
 
 
 def placement_route_artifact(args):
@@ -219,6 +229,11 @@ def placement_unpooling(args):
     clarity_epp.placement.pool.unpooling(lims, args.process_id)
 
 
+def placement_patient_pools(args):
+    """Create  patient pools for Dx samples."""
+    clarity_epp.placement.pool.create_patient_pools(lims, args.process_id)
+
+
 def placement_complete_step(args):
     """Complete protocol step (Dx Mark protocol complete)."""
     clarity_epp.placement.step.finish_protocol_complete(lims, args.process_id)
@@ -229,6 +244,11 @@ def placement_tecan(args):
     clarity_epp.placement.tecan.place_artifacts(lims, args.process_id)
 
 
+def placement_pipetting(args):
+    """Check pipetted input and output nuncs."""
+    clarity_epp.placement.pipetting.check_nunc_input_nunc_output(lims, args.process_id)
+
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     subparser = parser.add_subparsers()
@@ -271,10 +291,16 @@ def placement_tecan(args):
     )
     parser_export_illumina.add_argument('process_id', help='Clarity lims process id')
     parser_export_illumina.add_argument('artifact_id', help='Clarity lims samplesheet artifact id')
+    parser_export_illumina.add_argument(
+        '-c', '--conversion_tool', choices=['bcl2fastq', 'bclconvert'], default='bcl2fastq', help='Illumina conversion tool'
+    )
     parser_export_illumina.set_defaults(func=export_illumina)
 
     parser_export_labels = subparser_export.add_parser('labels', help='Export container labels', parents=[output_parser])
-    parser_export_labels.add_argument('type', choices=['container', 'container_sample', 'storage_location'], help='Label type')
+    parser_export_labels.add_argument(
+        'type', 
+        choices=['container', 'container_sample', 'storage_location', 'nunc_mix_sample'], 
+        help='Label type')
     parser_export_labels.add_argument('process_id', help='Clarity lims process id')
     parser_export_labels.add_argument('-d', '--description',  nargs='?', help='Container name description')
     parser_export_labels.set_defaults(func=export_labels)
@@ -293,7 +319,7 @@ def placement_tecan(args):
         choices=[
             'purify', 'dilute_library_pool', 'multiplex_library_pool', 'multiplex_sequence_pool', 'normalization',
             'capture', 'exonuclease', 'pcr_exonuclease', 'mip_multiplex_pool', 'mip_dilute_pool', 'pool_samples',
-            'pool_magnis_pools'
+            'pool_magnis_pools', 'normalization_mix'
         ],
         help='Samplesheet type'
     )
@@ -338,7 +364,9 @@ def placement_tecan(args):
 
     parser_export_tecan = subparser_export.add_parser('tecan', help='Create tecan samplesheets', parents=[output_parser])
     parser_export_tecan.add_argument('process_id', help='Clarity lims process id')
-    parser_export_tecan.add_argument('type', choices=['qc', 'purify_normalise'], help='Samplesheet type')
+    parser_export_tecan.add_argument(
+        'type', choices=['qc', 'purify_normalise', 'filling_out_purify', 'normalise'], help='Samplesheet type'
+    )
     parser_export_tecan.set_defaults(func=export_tecan)
 
     parser_export_workflow = subparser_export.add_parser(
@@ -366,7 +394,7 @@ def placement_tecan(args):
 
     parser_upload_tecan = subparser_upload.add_parser('tecan', help='Upload tecan results')
     parser_upload_tecan.add_argument('process_id', help='Clarity lims process id')
-    parser_upload_tecan.add_argument('type', choices=['qc', 'purify_normalise'], help='Tecan process type')
+    parser_upload_tecan.add_argument('type', choices=['qc', 'purify_normalise', 'purify_mix'], help='Tecan process type')
     parser_upload_tecan.set_defaults(func=upload_tecan_results)
 
     parser_upload_magnis = subparser_upload.add_parser('magnis', help='Upload magnis results')
@@ -404,9 +432,9 @@ def placement_tecan(args):
     parser_placement_automatic.set_defaults(func=placement_automatic)
 
     parser_placement_artifact = subparser_placement.add_parser('artifact', help='Change artifact name to sequence name')
-    parser_placement_artifact.add_argument('type', choices=['sequence_name', 'run_id'], help='Check type')
+    parser_placement_artifact.add_argument('type', choices=['sequence_name', 'run_id', 'norm_udf'], help='Check type')
     parser_placement_artifact.add_argument('process_id', help='Clarity lims process id')
-    parser_placement_artifact.set_defaults(func=placement_artifact_set_name)
+    parser_placement_artifact.set_defaults(func=placement_artifact_set)
 
     parser_placement_route_artifact = subparser_placement.add_parser('route_artifact', help='Route artifact to a workflow')
     parser_placement_route_artifact.add_argument('process_id', help='Clarity lims process id')
@@ -428,9 +456,17 @@ def placement_tecan(args):
     parser_placement_unpooling.add_argument('process_id', help='Clarity lims process id')
     parser_placement_unpooling.set_defaults(func=placement_unpooling)
 
+    parser_placement_patient_pools = subparser_placement.add_parser('patient_pools', help='Create patient pools for Dx samples')
+    parser_placement_patient_pools.add_argument('process_id', help='Clarity lims process id')
+    parser_placement_patient_pools.set_defaults(func=placement_patient_pools)
+
     parser_placement_tecan = subparser_placement.add_parser('tecan', help='Placement of samples in tecan step')
     parser_placement_tecan.add_argument('process_id', help='Clarity lims process id')
     parser_placement_tecan.set_defaults(func=placement_tecan)
 
+    parser_placement_pipetting = subparser_placement.add_parser('pipetting', help='Check pipetting input and output')
+    parser_placement_pipetting.add_argument('process_id', help='Clarity lims process id')
+    parser_placement_pipetting.set_defaults(func=placement_pipetting)
+
     args = parser.parse_args()
     args.func(args)

clarity_epp/__init__.py

@@ -4,41 +4,69 @@
 from email.mime.multipart import MIMEMultipart
 from email.mime.base import MIMEBase
 from email.mime.text import MIMEText
+import re
 import smtplib
 import mimetypes
 
+from genologics.entities import Artifact
+
+
+def get_sequence_name(artifact):
+    """Generate sequence name, for combined or single samples."""
+    sample_numbers = []
+    for sample in artifact.samples:
+        if 'Dx Monsternummer' in sample.udf:  # Use monsternummer for Dx samples
+            sample_numbers.append(sample.udf['Dx Monsternummer'])
+
+    if sample_numbers:  # Merge monsternummer for Dx samples
+        sequence_name = '-'.join(sorted(sample_numbers))
+    else:  # Use sample name for non Dx samples
+        sequence_name = artifact.samples[0].name
 
-def get_sequence_name(sample):
-    """Generate sequence name."""
-    try:
-        # Set fam_status
-        if sample.udf['Dx Familie status'] == 'Kind':
-            fam_status = 'C'
-        elif sample.udf['Dx Familie status'] == 'Ouder':
-            fam_status = 'P'
-
-        # Set sex
-        if sample.udf['Dx Geslacht'] == 'Man':
-            sex = 'M'
-        elif sample.udf['Dx Geslacht'] == 'Vrouw':
-            sex = 'F'
-        elif sample.udf['Dx Geslacht'] == 'Onbekend':
-            sex = 'O'
-    except KeyError:  # None DX sample, use sample.name as sequence name.
-        sequence_name = sample.name
-    else:
-        if not sample.name.startswith(sample.udf['Dx Familienummer']):
-            sequence_name = '{familienummer}{fam_status}{sex}{monsternummer}'.format(
-                familienummer=sample.udf['Dx Familienummer'],
-                fam_status=fam_status,
-                sex=sex,
-                monsternummer=sample.udf['Dx Monsternummer']
-            )
-        else:
-            sequence_name = sample.name
     return sequence_name
 
 
+def get_sample_artifacts_from_pool(lims, pool_artifact):
+    """Get sample artifacts from (sequence) pool."""
+    sample_artifacts = []
+    pool_artifact_demux = lims.get(pool_artifact.uri + '/demux')
+    for node in pool_artifact_demux.getiterator('artifact'):
+        if node.find('samples'):
+            if len(node.find('samples').findall('sample')) in [1, 2]:
+                sample_artifact = Artifact(lims, uri=node.attrib['uri'])
+
+                # Check if sample_artifact with 2 samples are from the same person
+                if len(sample_artifact.samples) == 2:
+                    if (
+                        'Dx Persoons ID' in sample_artifact.samples[0].udf or
+                        'Dx Persoons ID' in sample_artifact.samples[1].udf or
+                        sample_artifact.samples[0].udf['Dx Persoons ID'] == sample_artifact.samples[1].udf['Dx Persoons ID']
+                    ):
+                        sample_artifacts.append(sample_artifact)
+                else:
+                    sample_artifacts.append(sample_artifact)
+    return sample_artifacts
+
+
+def get_mix_sample_barcode(artifact):
+    """Generate mix sample shortened barcode name."""
+    sample_names = {}
+    for sample in artifact.samples:
+        if 'Dx Monsternummer' in sample.udf:
+            monster = sample.udf['Dx Monsternummer']
+            if re.match(r'\d{4}D\d+', monster):
+                sample_names[sample] = monster[2:4], monster[5:]
+            elif monster.startswith('D'):
+                sample_names[sample] = monster
+
+    barcode_name = ''
+    if sample_names:
+        for sample in artifact.samples:
+            barcode_name += ''.join(sample_names[sample])
+
+    return barcode_name
+
+
 def send_email(server, sender, receivers, subject, text, attachment=None):
     """Send emails."""
     mail = MIMEMultipart()