Merge pull request #30 from UMCUGenetics/release/v1.4.0

v1.4.0

.gitignore

@@ -102,3 +102,6 @@ ENV/
 
 # Mac OS
 .DS_Store
+
+# temp scripts
+tmp

clarity_epp.py

@@ -69,6 +69,18 @@ def export_manual_pipetting(args):
         clarity_epp.export.manual_pipetting.samplesheet_multiplex_library_pool(lims, args.process_id, args.output_file)
     elif args.type == 'multiplex_sequence_pool':
         clarity_epp.export.manual_pipetting.samplesheet_multiplex_sequence_pool(lims, args.process_id, args.output_file)
+    elif args.type == 'normalization':
+        clarity_epp.export.manual_pipetting.samplesheet_normalization(lims, args.process_id, args.output_file)
+    elif args.type == 'capture':
+        clarity_epp.export.manual_pipetting.samplesheet_capture(lims, args.process_id, args.output_file)
+    elif args.type == 'exonuclease':
+        clarity_epp.export.manual_pipetting.sammplesheet_exonuclease(lims, args.process_id, args.output_file)
+    elif args.type == 'pcr_exonuclease':
+        clarity_epp.export.manual_pipetting.sammplesheet_pcr_exonuclease(lims, args.process_id, args.output_file)
+    elif args.type == 'mip_multiplex_pool':
+        clarity_epp.export.manual_pipetting.samplesheet_mip_multiplex_pool(lims, args.process_id, args.output_file)
+    elif args.type == 'mip_dilute_pool':
+        clarity_epp.export.manual_pipetting.samplesheet_mip_pool_dilution(lims, args.process_id, args.output_file)
 
 
 def export_ped_file(args):
@@ -82,10 +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)
@@ -183,13 +202,18 @@ def placement_complete_step(args):
     subparser = parser.add_subparsers()
 
     output_parser = argparse.ArgumentParser(add_help=False)
-    output_parser.add_argument('-o', '--output_file',  nargs='?', type=argparse.FileType('w'), default=sys.stdout, help='Output file path (default=stdout)')
+    output_parser.add_argument(
+        '-o', '--output_file',  nargs='?', type=argparse.FileType('w'), default=sys.stdout,
+        help='Output file path (default=stdout)'
+    )
 
     # export
-    parser_export = subparser.add_parser('export', help='Export from lims.')
+    parser_export = subparser.add_parser('export', help='Export from lims')
     subparser_export = parser_export.add_subparsers()
 
-    parser_export_bioanalyzer = subparser_export.add_parser('bioanalyzer', help='Create bioanalyzer samplesheets', parents=[output_parser])
+    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)
 
@@ -203,47 +227,77 @@ def placement_complete_step(args):
     parser_export_email.add_argument('process_id', help='Clarity lims process id')
     parser_export_email.set_defaults(func=export_email)
 
-    parser_export_hamilton = subparser_export.add_parser('hamilton', help='Create hamilton samplesheets', parents=[output_parser])
+    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 = 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 = 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 = 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', 'normalization',
+            'capture', 'exonuclease', 'pcr_exonuclease', 'mip_multiplex_pool', 'mip_dilute_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 = 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 = 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_removed_samples = subparser_export.add_parser('removed_samples', help='Export removed sampels table.', parents=[output_parser])
+    parser_export_removed_samples = subparser_export.add_parser(
+        'removed_samples', help='Export removed samples 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_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]
+    )
     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 = subparser_export.add_parser(
+        'workflow', help='Export workflow result file', parents=[output_parser]
+    )
     parser_export_workflow.add_argument('type', choices=['all', '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)
@@ -269,48 +323,50 @@ def placement_complete_step(args):
     parser_upload_tecan.set_defaults(func=upload_tecan_results)
 
     # QC
-    parser_qc = subparser.add_parser('qc', help='Set QC values/flags.')
+    parser_qc = subparser.add_parser('qc', help='Set QC values/flags')
     subparser_qc = parser_qc.add_subparsers()
 
-    parser_qc_fragment_length = subparser_qc.add_parser('fragment_length', help='Set fragment length qc flag.')
+    parser_qc_fragment_length = subparser_qc.add_parser('fragment_length', help='Set fragment length qc flag')
     parser_qc_fragment_length.add_argument('process_id', help='Clarity lims process id')
     parser_qc_fragment_length.set_defaults(func=qc_fragment_length)
 
-    parser_qc_illumina = subparser_qc.add_parser('illumina', help='Set average % Bases >=Q30.')
+    parser_qc_illumina = subparser_qc.add_parser('illumina', help='Set average % Bases >=Q30')
     parser_qc_illumina.add_argument('process_id', help='Clarity lims process id')
     parser_qc_illumina.set_defaults(func=qc_illumina)
 
-    parser_qc_qubit = subparser_qc.add_parser('qubit', help='Set qubit qc flag.')
+    parser_qc_qubit = subparser_qc.add_parser('qubit', help='Set qubit qc flag')
     parser_qc_qubit.add_argument('process_id', help='Clarity lims process id')
     parser_qc_qubit.set_defaults(func=qc_qubit)
 
     # placement
-    parser_placement = subparser.add_parser('placement', help='Container placement functions.')
+    parser_placement = subparser.add_parser('placement', help='Container placement functions')
     subparser_placement = parser_placement.add_subparsers()
 
-    parser_placement_automatic = subparser_placement.add_parser('copy', help='Copy container layout from previous step.')
+    parser_placement_automatic = subparser_placement.add_parser('copy', help='Copy container layout from previous step')
     parser_placement_automatic.add_argument('process_id', help='Clarity lims process id')
     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 = 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('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 = 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 = 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_complete_step = subparser_placement.add_parser('complete_step', help='Complete step Dx Mark protocol complete.')
+    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 = 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)
 

clarity_epp/export/__init__.py

@@ -1,15 +1,15 @@
 """Export functions."""
 
-import bioanalyzer
-import caliper
-import email
-import hamilton
-import illumina
-import labels
-import manual_pipetting
-import merge
-import ped
-import sample
-import tapestation
-import tecan
-import workflow
+import clarity_epp.export.bioanalyzer
+import clarity_epp.export.caliper
+import clarity_epp.export.email
+import clarity_epp.export.hamilton
+import clarity_epp.export.illumina
+import clarity_epp.export.labels
+import clarity_epp.export.manual_pipetting
+import clarity_epp.export.merge
+import clarity_epp.export.ped
+import clarity_epp.export.sample
+import clarity_epp.export.tapestation
+import clarity_epp.export.tecan
+import clarity_epp.export.workflow