From 80b6654d29b9dcc493d184cdba287a655e64da61 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 1 Dec 2016 10:25:47 +0000
Subject: [PATCH] - regular samples need to be unique - Pools not as these
should have the lane information (same pool on different lanes)
SVN: 37423
---
.../Jython/create_QGF_Invoices_simplified.py | 49 +++++++++----------
1 file changed, 23 insertions(+), 26 deletions(-)
diff --git a/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py b/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py
index e3083417947..1cca5dd3f75 100644
--- a/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py
+++ b/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py
@@ -219,9 +219,11 @@ def write_samples(configMap, myRows, wb, sheet, setFont, sample, sampleValues, w
if write_lane:
rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(str(sampleValues['LANE']))
- rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
+ rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
+ rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(configMap['sampleCodePrefix'] + sample.split("_")[1])
+ else:
+ rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(configMap['sampleCodePrefix'] + sample)
- rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(configMap['sampleCodePrefix'] + sample)
rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
for code, label in working_column_headers_dict.iteritems():
if (code == 'BIOLOGICAL_SAMPLE_ARRIVED'):
@@ -313,29 +315,24 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
logger.debug(listofLanes)
for lane in listofLanes:
- accumulated_pi_dict = merge_two_dicts(accumulated_pi_dict, sampleDict[lane])
-
- # sort the dictionary by keys and taking the key as an integer
- for sample in sorted(accumulated_pi_dict.iterkeys(), key=int):
- sampleValues = accumulated_pi_dict[sample]
- logger.debug(sampleValues['PRINCIPAL_INVESTIGATOR_NAME'])
- logger.debug(piName)
- logger.debug(sample)
- # if there is a shared lane do not mix them
- if (sanitizeString(sampleValues['PRINCIPAL_INVESTIGATOR_NAME']) != sanitizeString(piName)):
- continue
-
- # Find the Pools:
- try:
- if sampleValues['BARCODE'] != 'NOINDEX':
- regular_samples[sample] = sampleValues
- else:
- pool_samples[sample] = sampleValues
- except:
- if int(sampleValues['NCBI_ORGANISM_TAXONOMY']) != 10847:
- pool_samples[sample] = sampleValues
- else:
- regular_samples[sample] = sampleValues
+ for sample_code in sampleDict[lane]:
+ sampleValues = sampleDict[lane][sample_code]
+
+ # if there is a shared lane do not mix them
+ if (sanitizeString(sampleValues['PRINCIPAL_INVESTIGATOR_NAME']) != sanitizeString(piName)):
+ continue
+
+ # Find the Pools:
+ try:
+ if sampleValues['BARCODE'] != 'NOINDEX':
+ regular_samples[sample_code] = sampleValues
+ else:
+ pool_samples[lane + "_" + sample_code] = sampleValues
+ except:
+ if int(sampleValues['NCBI_ORGANISM_TAXONOMY']) != 10847:
+ pool_samples[lane + "_" + sample_code] = sampleValues
+ else:
+ regular_samples[sample_code] = sampleValues
logger.debug("Found {0} samples.".format(len(regular_samples)))
logger.debug("Found {0} pools.".format(len(pool_samples)))
@@ -351,7 +348,7 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
logger.debug("check_empty_columns_dict: {0}".format(check_empty_columns_dict))
write_sample_column_header(configMap, working_column_headers_dict, myRows, wb, sheet)
- for reg_sample in regular_samples:
+ for reg_sample in sorted(regular_samples):
value = write_samples(configMap, myRows, wb, sheet, setFont, reg_sample, regular_samples[reg_sample], working_column_headers_dict, lane)
write_intermediate_section(configMap, flowCellProperties, myRows, wb, sheet)
--
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