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 b2394a965ee733cca746c9bc6ec8c8ecbfc75bac..33e3b6d6545382e3c25ac506af35140ab995d914 100644
--- a/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py
+++ b/deep_sequencing_unit/source/Jython/create_QGF_Invoices_simplified.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
'''
Copyright 2012 ETH Zuerich, CISD
@@ -16,7 +17,8 @@ limitations under the License.
@author Manuel Kohler
@description:
-Creates Excel-based invoices for the Quantitative Genomics Facility, D-BSSE, ETH Zurich
+Creates Excel-based invoices for the Quantitative Genomics Facility,
+D-BSSE, ETH Zurich
@attention:
Runs under Jython
@@ -46,8 +48,9 @@ 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"]
+columnHeadersList = ["EXTERNAL_SAMPLE_NAME", "BARCODE", "INDEX2", "CONTACT_PERSON_NAME",
+ "BIOLOGICAL_SAMPLE_ARRIVED", "PREPARED_BY", "KIT", "QC_AT_DBSSE",
+ "CELL_PLASTICITY_SYSTEMSX", "PRICE", "NOTES"]
columnHeadersMap = {"EXTERNAL_SAMPLE_NAME": "Sample Name",
"BARCODE": "Index",
@@ -58,6 +61,7 @@ columnHeadersMap = {"EXTERNAL_SAMPLE_NAME": "Sample Name",
"CONTACT_PERSON_NAME" : "Contact Person",
"NOTES" : "Notes",
"BIOLOGICAL_SAMPLE_ARRIVED": "Received",
+ "CELL_PLASTICITY_SYSTEMSX": "Cell Plasticity",
"PRICE" : "Price"}
class uniqueRow():
@@ -121,8 +125,8 @@ def getVocabulary(service, vocabularyCode):
vocabularyMap[term.getCode()] = term.getLabel()
return vocabularyMap
-def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDict, piSpace,
- flowCellProperties, flowcellName, logger, format="xls"):
+def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDict,
+ piSpace, flowCellProperties, flowcellName, logger,format="xls"):
'''
Writes out all data to an Excel file
'''
@@ -165,7 +169,7 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
sheet.setZoom(3, 2)
writeHeader()
- createRow("Principal Investigator", piName)
+ createRow("Principal Investigator", piName.replace("_", " "))
createRow("Data Space", piSpace)
createRow("Run Folder Name", flowcellName)
createRow()
@@ -182,6 +186,8 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
sampleHeader.getCell(myColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
listofLanes = piDict[piName]
+ listofLanes.sort()
+ logger.debug(listofLanes)
for lane in listofLanes:
singleSampleColumns = uniqueColumn()
@@ -191,8 +197,8 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
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):
+ # if there is a shared lane do not mix them
+ if (sanitizeString(sampleValues['PRINCIPAL_INVESTIGATOR_NAME']) != sanitizeString(piName)):
continue
rowN = sheet.createRow(myRows.getNextRow())
@@ -201,15 +207,14 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(configMap['sampleCodePrefix'] + sample)
rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
-
for column in columnHeadersList:
if (column == 'BIOLOGICAL_SAMPLE_ARRIVED'):
try:
value = sampleValues[column].split(" ")[0]
except:
- value = sampleValues[column]
+ value = sampleValues[column]
else:
- value = sampleValues[column]
+ value = sampleValues[column]
rowN.createCell(singleSampleColumns.getNextColumn()).setCellValue(value)
rowN.getCell(singleSampleColumns.getCurrentColumn()).setCellStyle(setFont(wb, configMap, 10))
@@ -250,6 +255,9 @@ def writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDi
fileOut.close();
def sanitizeString(myString):
+ myString = myString.replace(u'ä', 'ae')
+ myString = myString.replace(u'ü', 'ue')
+ myString = myString.replace(u'ö', 'oe')
return re.sub('[^A-Za-z0-9]+', '_', myString)
def setUpLogger(logPath, logLevel=logging.INFO):
@@ -355,6 +363,7 @@ def getFLowcellData(service, configMap, flowcell, logger):
sampleDict = {}
piDict = {}
spaceDict = {}
+ invoiceDict = {}
for lane in range(1, numberOfLanes + 1):
myLane = flowcell + ":" + str(lane)
@@ -373,8 +382,10 @@ def getFLowcellData(service, configMap, flowcell, logger):
sampleProperties = samples.getProperties()
s[sampleCode.split("-")[-1]] = sampleProperties
sampleDict[lane] = s
- pi = sampleProperties[configMap["pIPropertyName"]]
+ pi = sanitizeString(sampleProperties[configMap["pIPropertyName"]])
+ sentInvoice = {'true': True, 'false': False}.get((sampleProperties['INVOICE']).lower())
logger.debug("PI for " + sampleCode + ": " + pi)
+ logger.debug("Invoice sent for " + sampleCode + ": " + str(sentInvoice))
if piDict.has_key(pi):
piDict[pi].append(lane)
@@ -383,18 +394,26 @@ def getFLowcellData(service, configMap, flowcell, logger):
else:
piDict[pi] = [lane]
- spaceDict[pi] = l.getSpaceCode()
+ if not sentInvoice:
+ if invoiceDict.has_key(pi):
+ invoiceDict[pi].append(lane)
+ # Making the lanes unique
+ invoiceDict[pi] = list(set(invoiceDict[pi]))
+ else:
+ invoiceDict[pi] = [lane]
+ 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)
+ logger.info("Found the following PIs with non-invoiced samples : ")
+ logger.info(invoiceDict)
# simply sort the hashmap
treeMap = TreeMap (flowCellProperties)
- return laneDict, sampleDict, piDict, treeMap, spaceDict
+ return laneDict, sampleDict, piDict, treeMap, spaceDict, invoiceDict
'''
@@ -405,6 +424,7 @@ def main():
# for now setting the format by hand
format = "xlsx"
+ magicString = "@Invoice@"
logger = setUpLogger('log/')
logger.info('Started Creation Invoices...')
@@ -416,12 +436,16 @@ def main():
service = login(logger, configMap)
flowcellName = myoptions.flowcell
- laneDict, sampleDict, piDict, flowCellProperties, spaceDict = getFLowcellData(service, configMap, flowcellName, logger)
+ laneDict, sampleDict, piDict, flowCellProperties, spaceDict, invoiceDict = getFLowcellData(service, configMap, flowcellName, logger)
for piName in piDict:
# create an Excel file for each PI
- writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict, piDict, spaceDict[piName],
- flowCellProperties, flowcellName, logger, format)
+ writeExcel(myoptions, configMap, service, piName, laneDict, sampleDict,
+ piDict, spaceDict[piName], flowCellProperties,
+ flowcellName, logger, format)
+
+ for invoicePi in invoiceDict:
+ print (magicString + invoicePi)
service.logout()