From 03a1a26342b3335d107b92cc4ea6935554ea2d54 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Fri, 22 Feb 2013 16:14:44 +0000
Subject: [PATCH] - added list for sorted header - reduced header font size -
take into account that more than one PI is sharing a lane - trim the
'Received' time stamp simply to date - removed the date from the file name -
fixed debug flag - added debug messages
SVN: 28415
---
.../Jython/create_QGF_Invoices_simplified.py | 56 ++++++++++++++-----
1 file changed, 43 insertions(+), 13 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 da5ce6ce54a..b2394a965ee 100644
--- a/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py
+++ b/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py
@@ -45,13 +45,19 @@ from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SampleFetchOption
excelFormats = {"xls": "HSSFWorkbook()" , "xlsx": "XSSFWorkbook()"}
+# This list is imply used to keep the order of elements of the 'columnHeadersMap'
+columnHeadersList = ["BARCODE", "INDEX2", "PREPARED_BY", "EXTERNAL_SAMPLE_NAME", "BIOLOGICAL_SAMPLE_ARRIVED", "QC_AT_DBSSE",
+ "CONTACT_PERSON_NAME", "KIT", "PRICE", "NOTES"]
+
columnHeadersMap = {"EXTERNAL_SAMPLE_NAME": "Sample Name",
"BARCODE": "Index",
"INDEX2": "Index2",
"PREPARED_BY" : "Prepared by",
"KIT" : "Kit",
+ "QC_AT_DBSSE" : "QC at D-BSSE",
"CONTACT_PERSON_NAME" : "Contact Person",
"NOTES" : "Notes",
+ "BIOLOGICAL_SAMPLE_ARRIVED": "Received",
"PRICE" : "Price"}
class uniqueRow():
@@ -116,7 +122,7 @@ def getVocabulary(service, vocabularyCode):
return vocabularyMap
def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDict, piSpace,
- flowCellProperties, flowcellName, format="xls"):
+ flowCellProperties, flowcellName, logger, format="xls"):
'''
Writes out all data to an Excel file
'''
@@ -130,7 +136,7 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
# Write header
row = sheet.createRow(myRows.getNextRow())
row.createCell(0).setCellValue(configMap["facilityName"] + ", " + configMap["facilityInstitution"])
- row.getCell(0).setCellStyle(setFont(wb, configMap, 14))
+ row.getCell(0).setCellStyle(setFont(wb, configMap, 10))
row1 = sheet.createRow(myRows.getNextRow())
row1.createCell(0).setCellValue(getDate())
row1.getCell(0).setCellStyle(setFont(wb, configMap, 10))
@@ -171,7 +177,7 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
sampleHeader.getCell(myColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
sampleHeader.createCell(myColumns.getNextColumn()).setCellValue("Sample Code")
sampleHeader.getCell(myColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
- for c in columnHeadersMap:
+ for c in columnHeadersList:
sampleHeader.createCell(myColumns.getNextColumn()).setCellValue(columnHeadersMap[c])
sampleHeader.getCell(myColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
@@ -181,16 +187,31 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
# sort the dictionary by keys and taking the key as an integer
for sample in sorted(sampleDict[lane].iterkeys(), key=int):
+ sampleValues = sampleDict[lane][sample]
+ logger.debug(sampleValues['PRINCIPAL_INVESTIGATOR_NAME'])
+ logger.debug(piName)
+ logger.debug(sample)
+ # if there is a shared lane do not mix them
+ if (sampleValues['PRINCIPAL_INVESTIGATOR_NAME'] != piName):
+ continue
+
rowN = sheet.createRow(myRows.getNextRow())
rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(flowcellName + ":" + str(lane))
rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(configMap['sampleCodePrefix'] + sample)
rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
- sampleValues = sampleDict[lane][sample]
- for column in columnHeadersMap.keys():
- rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(sampleValues[column])
+ for column in columnHeadersList:
+ if (column == 'BIOLOGICAL_SAMPLE_ARRIVED'):
+ try:
+ value = sampleValues[column].split(" ")[0]
+ except:
+ value = sampleValues[column]
+ else:
+ value = sampleValues[column]
+
+ rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(value)
rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
singleSampleColumns = uniqueColumn()
@@ -217,9 +238,10 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
writeFooter(service, sheet)
+ # sanitizeString(piName) + datetime.now().strftime("_%d_%m_%Y.") + format
# Write the output to a file
fileName = myoptions.outdir + configMap["facilityNameShort"] + "_" + flowcell + "_" + \
- sanitizeString(piName) + datetime.now().strftime("_%d_%m_%Y.") + format
+ sanitizeString(piName) + "." + format
fileOut = FileOutputStream(fileName)
# need this print for use as an openBIS webapp
print fileName
@@ -352,14 +374,20 @@ def getFLowcellData(service, configMap, flowcell, logger):
s[sampleCode.split("-")[-1]] = sampleProperties
sampleDict[lane] = s
pi = sampleProperties[configMap["pIPropertyName"]]
+ logger.debug("PI for " + sampleCode + ": " + pi)
- if piDict.has_key(pi):
- piDict[pi].append(lane)
- else:
- piDict[pi] = [lane]
+ if piDict.has_key(pi):
+ piDict[pi].append(lane)
+ # Making the lanes unique
+ piDict[pi] = list(set(piDict[pi]))
+ else:
+ piDict[pi] = [lane]
- spaceDict[pi] = l.getSpaceCode()
+ spaceDict[pi] = l.getSpaceCode()
+ logger.debug(spaceDict)
+ logger.debug("piDictionary:")
+ logger.debug(piDict)
logger.info("Found the following PIs on the lanes: ")
logger.info(piDict)
@@ -383,6 +411,8 @@ def main():
myoptions = parseOptions(logger)
configMap = readConfig(logger)
+ if myoptions.debug:
+ logger.setLevel(logging.DEBUG)
service = login(logger, configMap)
flowcellName = myoptions.flowcell
@@ -391,7 +421,7 @@ def main():
for piName in piDict:
# create an Excel file for each PI
writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDict, spaceDict[piName],
- flowCellProperties, flowcellName, format)
+ flowCellProperties, flowcellName, logger, format)
service.logout()
--
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