Merge pull request #18 from UMCUGenetics/develop

v1.2.0

clarity_epp.py

@@ -30,6 +30,12 @@ def export_caliper(args):
         clarity_epp.export.caliper.samplesheet_normalise(lims, args.process_id, args.output_file)
 
 
+def export_email(args):
+    """Export emails"""
+    if args.type == 'sequencing_run':
+        clarity_epp.export.email.sequencing_run(lims, config.email, args.process_id)
+
+
 def export_hamilton(args):
     """Export samplesheets for hamilton machine."""
     if args.type == 'filling_out':
@@ -48,7 +54,7 @@ def export_labels(args):
     if args.type == 'container':
         clarity_epp.export.labels.container(lims, args.process_id, args.output_file, args.description)
     elif args.type == 'container_sample':
-        clarity_epp.export.labels.container_sample(lims, args.process_id, args.output_file)
+        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)
 
@@ -149,6 +155,11 @@ def placement_artifact_set_name(args):
         clarity_epp.placement.artifact.set_runid_name(lims, args.process_id)
 
 
+def placement_route_artifact(args):
+    """Route artifacts to a workflow"""
+    clarity_epp.placement.artifact.route_to_workflow(lims, args.process_id)
+
+
 def placement_barcode(args):
     """Check barcodes."""
     if args.type == 'check_family':
@@ -176,80 +187,84 @@ def placement_complete_step(args):
     parser_export = subparser.add_parser('export', help='Export from lims.')
     subparser_export = parser_export.add_subparsers()
 
-    parser_export_hamilton = subparser_export.add_parser('hamilton', help='Create hamilton samplesheets', parents=[output_parser])
-    parser_export_hamilton.add_argument('type', choices=['filling_out', 'purify'], help='Samplesheet type')
-    parser_export_hamilton.add_argument('process_id', help='Clarity lims process id')
-    parser_export_hamilton.set_defaults(func=export_hamilton)
-
-    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.set_defaults(func=export_tecan)
-
-    parser_export_manual_pipetting = subparser_export.add_parser('manual', help='Create manual pipetting _exports', parents=[output_parser])
-    parser_export_manual_pipetting.add_argument('type', choices=['purify', 'dilute_library_pool', 'multiplex_library_pool', 'multiplex_sequence_pool'], help='Samplesheet type')
-    parser_export_manual_pipetting.add_argument('process_id', help='Clarity lims process id')
-    parser_export_manual_pipetting.set_defaults(func=export_manual_pipetting)
+    parser_export_bioanalyzer = subparser_export.add_parser('bioanalyzer', help='Create bioanalyzer samplesheets', parents=[output_parser])
+    parser_export_bioanalyzer.add_argument('process_id', help='Clarity lims process id')
+    parser_export_bioanalyzer.set_defaults(func=export_bioanalyzer)
 
     parser_export_caliper = subparser_export.add_parser('caliper', help='Create caliper samplesheets', parents=[output_parser])
     parser_export_caliper.add_argument('type', choices=['normalise'], help='Samplesheet type')
     parser_export_caliper.add_argument('process_id', help='Clarity lims process id')
     parser_export_caliper.set_defaults(func=export_caliper)
 
-    parser_export_tapestation = subparser_export.add_parser('tapestation', help='Create tapestation samplesheets', parents=[output_parser])
-    parser_export_tapestation.add_argument('process_id', help='Clarity lims process id')
-    parser_export_tapestation.set_defaults(func=export_tapestation)
+    parser_export_email = subparser_export.add_parser('email', help='Send emails', parents=[output_parser])
+    parser_export_email.add_argument('type', choices=['sequencing_run'], help='Email type')
+    parser_export_email.add_argument('process_id', help='Clarity lims process id')
+    parser_export_email.set_defaults(func=export_email)
 
-    parser_export_bioanalyzer = subparser_export.add_parser('bioanalyzer', help='Create bioanalyzer samplesheets', parents=[output_parser])
-    parser_export_bioanalyzer.add_argument('process_id', help='Clarity lims process id')
-    parser_export_bioanalyzer.set_defaults(func=export_bioanalyzer)
+    parser_export_hamilton = subparser_export.add_parser('hamilton', help='Create hamilton samplesheets', parents=[output_parser])
+    parser_export_hamilton.add_argument('type', choices=['filling_out', 'purify'], help='Samplesheet type')
+    parser_export_hamilton.add_argument('process_id', help='Clarity lims process id')
+    parser_export_hamilton.set_defaults(func=export_hamilton)
+
+    parser_export_illumina = subparser_export.add_parser('illumina', help='Export updated illumina samplesheet.', parents=[output_parser])
+    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.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('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)
 
+    parser_export_manual_pipetting = subparser_export.add_parser('manual', help='Create manual pipetting _exports', parents=[output_parser])
+    parser_export_manual_pipetting.add_argument('type', choices=['purify', 'dilute_library_pool', 'multiplex_library_pool', 'multiplex_sequence_pool'], help='Samplesheet type')
+    parser_export_manual_pipetting.add_argument('process_id', help='Clarity lims process id')
+    parser_export_manual_pipetting.set_defaults(func=export_manual_pipetting)
+
+    parser_export_merge = subparser_export.add_parser('merge', help='Export merge file.', parents=[output_parser])
+    parser_export_merge.add_argument('process_id', help='Clarity lims process id')
+    parser_export_merge.set_defaults(func=export_merge_file)
+
     parser_export_ped = subparser_export.add_parser('ped', help='Export ped file.', parents=[output_parser])
     parser_export_ped.add_argument('process_id', help='Clarity lims process id')
     parser_export_ped.set_defaults(func=export_ped_file)
 
-    parser_export_ped = subparser_export.add_parser('merge', help='Export merge file.', parents=[output_parser])
-    parser_export_ped.add_argument('process_id', help='Clarity lims process id')
-    parser_export_ped.set_defaults(func=export_merge_file)
+    parser_export_removed_samples = subparser_export.add_parser('removed_samples', help='Export removed sampels table.', parents=[output_parser])
+    parser_export_removed_samples.set_defaults(func=export_removed_samples)
+
+    parser_export_tapestation = subparser_export.add_parser('tapestation', help='Create tapestation samplesheets', parents=[output_parser])
+    parser_export_tapestation.add_argument('process_id', help='Clarity lims process id')
+    parser_export_tapestation.set_defaults(func=export_tapestation)
+
+    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.set_defaults(func=export_tecan)
 
     parser_export_workflow = subparser_export.add_parser('workflow', help='Export workflow result file.', parents=[output_parser])
     parser_export_workflow.add_argument('type', choices=['lab', 'data_analysis'], help='Workflow type')
     parser_export_workflow.add_argument('process_id', help='Clarity lims process id')
     parser_export_workflow.set_defaults(func=export_workflow)
 
-    parser_export_illumina = subparser_export.add_parser('illumina', help='Export updated illumina samplesheet.', parents=[output_parser])
-    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.set_defaults(func=export_illumina)
-
-    parser_export_removed_samples = subparser_export.add_parser('removed_samples', help='Export removed sampels table.', parents=[output_parser])
-    parser_export_removed_samples.set_defaults(func=export_removed_samples)
-
     # Sample upload
     parser_upload = subparser.add_parser('upload', help='Upload samples or results to clarity lims')
     subparser_upload = parser_upload.add_subparsers()
 
+    parser_upload_bioanalyzer = subparser_upload.add_parser('bioanalyzer', help='Upload bioanalyzer results')
+    parser_upload_bioanalyzer.add_argument('process_id', help='Clarity lims process id')
+    parser_upload_bioanalyzer.set_defaults(func=upload_bioanalyzer_results)
+
     parser_upload_sample = subparser_upload.add_parser('sample', help='Upload samples from helix export')
     parser_upload_sample.add_argument('input_file', type=argparse.FileType('r'), help='Input file path')
     parser_upload_sample.set_defaults(func=upload_samples)
 
-    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.set_defaults(func=upload_tecan_results)
-
     parser_upload_tapestation = subparser_upload.add_parser('tapestation', help='Upload tapestation results')
     parser_upload_tapestation.add_argument('process_id', help='Clarity lims process id')
     parser_upload_tapestation.set_defaults(func=upload_tapestation_results)
 
-    parser_upload_bioanalyzer = subparser_upload.add_parser('bioanalyzer', help='Upload bioanalyzer results')
-    parser_upload_bioanalyzer.add_argument('process_id', help='Clarity lims process id')
-    parser_upload_bioanalyzer.set_defaults(func=upload_bioanalyzer_results)
+    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.set_defaults(func=upload_tecan_results)
 
     # QC
     parser_qc = subparser.add_parser('qc', help='Set QC values/flags.')
@@ -280,18 +295,22 @@ def placement_complete_step(args):
     parser_placement_artifact.add_argument('process_id', help='Clarity lims process id')
     parser_placement_artifact.set_defaults(func=placement_artifact_set_name)
 
+    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')
+    parser_placement_route_artifact.set_defaults(func=placement_route_artifact)
+
     parser_placement_barcode = subparser_placement.add_parser('barcode_check', help='Check barcode clarity_epp.placement.')
     parser_placement_barcode.add_argument('type', choices=['check_family'], help='Check type')
     parser_placement_barcode.add_argument('process_id', help='Clarity lims process id')
     parser_placement_barcode.set_defaults(func=placement_barcode)
 
-    parser_placement_unpooling = subparser_placement.add_parser('unpooling', help='Unpooling of sequencing pool.')
-    parser_placement_unpooling.add_argument('process_id', help='Clarity lims process id')
-    parser_placement_unpooling.set_defaults(func=placement_unpooling)
-
     parser_placement_complete_step = subparser_placement.add_parser('complete_step', help='Complete step Dx Mark protocol complete.')
     parser_placement_complete_step.add_argument('process_id', help='Clarity lims process id')
     parser_placement_complete_step.set_defaults(func=placement_complete_step)
 
+    parser_placement_unpooling = subparser_placement.add_parser('unpooling', help='Unpooling of sequencing pool.')
+    parser_placement_unpooling.add_argument('process_id', help='Clarity lims process id')
+    parser_placement_unpooling.set_defaults(func=placement_unpooling)
+
     args = parser.parse_args()
     args.func(args)

clarity_epp/export/__init__.py

@@ -2,6 +2,7 @@
 
 import bioanalyzer
 import caliper
+import email
 import hamilton
 import illumina
 import labels

clarity_epp/export/email.py

@@ -0,0 +1,29 @@
+"""Export email functions."""
+from genologics.entities import Process
+
+from .. import send_email
+
+
+def sequencing_run(lims, email_settings, process_id):
+    process = Process(lims, id=process_id)
+    artifact = process.all_inputs()[0]
+
+    subject = "LIMS QC Controle - {0}".format(artifact.name)
+
+    message = "Sequencing Run: {0}\n".format(artifact.name)
+    message += "Date: {0}\n".format(process.date_run)
+    message += "Technician: {0}\n".format(process.technician.name)
+    message += "LIMS Next Action: {0}\n\n".format(process.step.actions.next_actions[0]['action'])
+
+    message += "UDF - Conversie rapport OK?: {0}\n".format(process.udf['Conversie rapport OK?'])
+    if 'Fouten registratie (uitleg)' in process.udf:
+        message += "UDF - Fouten registratie (uitleg): {0}\n".format(process.udf['Fouten registratie (uitleg)'])
+    if 'Fouten registratie (oorzaak)' in process.udf:
+        message += "UDF - Fouten registratie (oorzaak): {0}\n".format(process.udf['Fouten registratie (uitleg)'])
+
+    if process.step.actions.escalation:
+        message += "\nManager Review LIMS:\n"
+        message += "{0}: {1}\n".format(process.step.actions.escalation['author'].name, process.step.actions.escalation['request'])
+        message += "{0}: {1}\n".format(process.step.actions.escalation['reviewer'].name, process.step.actions.escalation['answer'])
+
+    send_email(email_settings['from'], email_settings['to_sequencing_run_complete'], subject, message)

clarity_epp/export/illumina.py

@@ -33,7 +33,7 @@ def get_project(projects, urgent=False):
 
                 # Create family if not exist
                 if family not in families:
-                    families[family] = {'samples': [], 'NICU': False, 'project_type': 'unknown_project', 'split_project_type': False, 'urgent': False}
+                    families[family] = {'samples': [], 'NICU': False, 'project_type': 'unknown_project', 'split_project_type': False, 'urgent': False, 'merge': False}
 
                 # Update family information
                 if sample.udf['Dx Onderzoeksreden'] == 'Research':  # Dx research sample
@@ -54,14 +54,20 @@ def get_project(projects, urgent=False):
                         project_type = 'CREv2'
                         families[family]['project_type'] = project_type
                         families[family]['split_project_type'] = True
-
+                    # Set urgent / merge status
                     if 'Dx Spoed' in list(sample.udf) and sample.udf['Dx Spoed']:
                         families[family]['urgent'] = True
+                    if 'Dx Mergen' in list(sample.udf) and sample.udf['Dx Mergen']:
+                        families[family]['merge'] = True
+                        families[family]['urgent'] = False
 
             else:  # Other samples
-                family = sample.project.name
+                if 'GIAB' in sample.name.upper() and not sample.project:  # GIAB control samples
+                    family = 'GIAB'
+                else:
+                    family = sample.project.name
                 if family not in families:
-                    families[family] = {'samples': [], 'NICU': False, 'project_type': family, 'split_project_type': False, 'urgent': False}
+                    families[family] = {'samples': [], 'NICU': False, 'project_type': family, 'split_project_type': False, 'urgent': False, 'merge': False}
 
             # Add sample to family
             families[family]['samples'].append(sample)
@@ -86,16 +92,22 @@ def get_project(projects, urgent=False):
     # Set sample projects
     sample_projects = {}
 
-    # Urgent families / samples
-    for family in [family for family in families.values() if family['urgent']]:
+    # Urgent families / samples, skip merge
+    for family in [family for family in families.values() if family['urgent'] and not family['merge']]:
         family_project = get_project(project_types[family['project_type']]['projects'], urgent=True)
-
+        for sample in family['samples']:
+            sample_projects[get_sequence_name(sample)] = family_project
+            project_types[family['project_type']]['projects'][family_project] += 1
+
+    # Merge families / samples
+    for family in [family for family in families.values() if family['merge']]:
+        family_project = get_project(project_types[family['project_type']]['projects'])
         for sample in family['samples']:
             sample_projects[get_sequence_name(sample)] = family_project
             project_types[family['project_type']]['projects'][family_project] += 1
 
-    # Non urgent families / samples
-    non_urgent_families = [family for family in families.values() if not family['urgent']]
+    # Non urgent and non merge families / samples
+    non_urgent_families = [family for family in families.values() if not family['urgent'] and not family['merge']]
     for family in sorted(non_urgent_families, key=lambda fam: (len(fam['samples'])), reverse=True):
         family_project = get_project(project_types[family['project_type']]['projects'])
         for sample in family['samples']:

clarity_epp/export/labels.py

@@ -1,37 +1,39 @@
 """Export label functions."""
 
-import re
-
 from genologics.entities import Process
 
 
-def container(lims, process_id, output_file, description):
+def container(lims, process_id, output_file, description=''):
     """Generate container label file."""
     process = Process(lims, id=process_id)
-    for container in process.output_containers():
+    for index, container in enumerate(sorted(process.output_containers(), key=lambda container: container.id, reverse=True)):
         if description:
-            output_file.write('{description} {container}\t{container}\r\n'.format(description=description, container=container.name))
+            if ',' in description:
+                output_file.write('{description}\t{container}\r\n'.format(description=description.split(',')[index], container=container.name))
+            else:
+                output_file.write('{description}\t{container}\r\n'.format(description=description, container=container.name))
         else:
             output_file.write('{container}\r\n'.format(container=container.name))
 
 
-def container_sample(lims, process_id, output_file):
+def container_sample(lims, process_id, output_file, description=''):
     """Generate container & artifact name label file."""
     process = Process(lims, id=process_id)
     for container in process.output_containers():
         for artifact in container.placements.values():
-            output_file.write('{container}\t{sample}\r\n'.format(container=container.name, sample=artifact.name))
+            if description:
+                output_file.write('{description}\t{sample}\t{container}\r\n'.format(description=description, container=container.name, sample=artifact.name))
+            else:
+                output_file.write('{sample}\t{container}\r\n'.format(container=container.name, sample=artifact.name))
 
 
 def storage_location(lims, process_id, output_file):
     """Generate storage location label file."""
     process = Process(lims, id=process_id)
-    for artifact in process.all_outputs():
+    for artifact in process.analytes()[0]:
         storage_location = artifact.samples[0].udf['Dx Opslaglocatie']
-        m = re.search('\D+(\d+)\w+: (\d+)', storage_location)
-        output_file.write('{sample}\t{storage_location}\t{tray}\t{tray_position}\n'.format(
+        output_file.write('{sample}\t{storage_location}\t{birth_date}\n'.format(
             sample=artifact.samples[0].name,
             storage_location=storage_location,
-            tray=m.group(1),
-            tray_position=m.group(2)
+            birth_date=artifact.samples[0].udf['Dx Geboortejaar']
         ))