drop box script for creating new Flow cell with n lanes

SVN: 22858

deep_sequencing_unit/dist/etc/data-set-handler-create-flow-cell.py

+'''
+expected incoming Name for HiSeq2000 runs: 110715_SN792_0054_BC035RACXX
+expected incoming Name for GAII runs: 110812_6353WAAXX
+
+Note: 
+print statements go to: ~openbis/sprint/datastore_server/log/startup_log.txt
+'''
+
+import os
+from time import *
+from datetime import *
+import xml.etree.ElementTree as etree
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+IS_HISEQ_RUN=False
+RUNPARAMETERS = 'runParameters.xml'
+RUNINFO = 'RunInfo.xml'
+FLOWCELL_SPACE='/BSSE_FLOWCELLS/'
+FLOWCELL_PROJECT='FLOWCELLS/'
+EXPERIMENT_TYPE_CODE='HT_SEQUENCING'
+
+# Mapping between XML file naming and used in here
+RUNPARAMETERS_XML = {'FLOWCELL':'Flowcell', 'RTAVERSION':'RTAVersion',
+  'CONTROLLANE':'ControlLane', 'SBS':'Sbs', 'INDEX':'Index',
+  'CYCLES_REQUESTED_BY_CUSTOMER':'Read1', 'PE':'Pe'}
+RUNINFO_XML = {'LANECOUNT':'LaneCount', 'SURFACECOUNT':'SurfaceCount',
+   'SWATHCOUNT':'SwathCount', 'TILECOUNT':'TileCount'}
+INSTRUMENT = {'SN792':'RUA', 'BS-DSU-ELLAC':'ELLAC'}
+
+class parseXmlFile: 
+    
+  def __init__(self, xmlFile):
+    self.xmlFile = xmlFile
+    self.tree = etree.parse(self.xmlFile)
+    self.root = self.tree.getroot()
+
+  def getXmlElement (self, elementName):
+    '''
+    Returns the text value of a given XML element
+    '''
+    for e in self.root.getchildren():
+      element = e.find(elementName)
+      if element is None:
+	return 'None'
+      else:
+	return element.text
+
+  def getAllchildren (self, elementName):
+    '''
+    finds all children of a given XML Element and returns them as list
+    '''
+    for e in self.root.getchildren():
+      # the '//' means look recursively for all children not only direct ones
+      childList  = self.tree.findall('//' + elementName)
+    return childList 
+
+# -----------------------------------------------------------------------------
+
+def create_openbis_timestamp (): 
+  ''' 
+  Create an openBIS conform timestamp
+  '''
+  tz=localtime()[3]-gmtime()[3]
+  d=datetime.now()
+  return d.strftime("%Y-%m-%d %H:%M:%S GMT"+"%+.2d" % tz+":00")
+
+# -----------------------------------------------------------------------------
+
+# Create a "transaction" -- a way of grouping operations together so they all
+# happen or none of them do.
+transaction = service.transaction()
+
+incomingPath = incoming.getAbsolutePath()
+
+# Get the incoming name 
+name = incoming.getName()
+
+split=name.split("_")
+if (len(split) == 4):
+  IS_HISEQ_RUN=True
+if (len(split) == 2):
+  pass
+
+# Search for the sample and check if there is already sample with this name
+search_service = transaction.getSearchService()
+sc = SearchCriteria()
+sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, name));
+foundSamples = search_service.searchForSamples(sc)
+if foundSamples.size() > 0:
+  raise NameError('Already found a Flow Cell with the following name: '+ name)  
+
+# Parse the RunInfo.xml file
+runInfo = parseXmlFile(incomingPath + '/' + RUNINFO) 
+
+# Create a new Flow Cell and set the experiment
+newFlowCell = transaction.createNewSample(FLOWCELL_SPACE + name, "ILLUMINA_FLOW_CELL")
+exp = transaction.getExperiment(FLOWCELL_SPACE + FLOWCELL_PROJECT + datetime.now().strftime("%Y.%m"))
+if exp == None:
+  exp = transaction.createNewExperiment(FLOWCELL_SPACE + FLOWCELL_PROJECT + datetime.now().strftime("%Y.%m"),
+             EXPERIMENT_TYPE_CODE)
+newFlowCell.setExperiment(exp)
+ 
+if IS_HISEQ_RUN:
+  run = runInfo.getAllchildren('Run')[0].attrib
+  if (run['Id'] != name):
+    raise NameError('Flowcell names do not match between directory name '+ name +
+          ' and ' + RUNINFO + 'property file: ' + run['Id'])
+
+  # The HiSeq is providing more infos, which we will parse here:
+  runParameters = parseXmlFile(incomingPath + '/' + RUNPARAMETERS)
+  
+  newFlowCell.setPropertyValue("ILLUMINA_PIPELINE_VERSION", runParameters.getXmlElement(RUNPARAMETERS_XML['RTAVERSION']))
+  newFlowCell.setPropertyValue("FLOWCELLTYPE", runParameters.getXmlElement(RUNPARAMETERS_XML['FLOWCELL']))
+  newFlowCell.setPropertyValue("CONTROL_LANE", runParameters.getXmlElement(RUNPARAMETERS_XML['CONTROLLANE']))
+  newFlowCell.setPropertyValue("SBS_KIT", runParameters.getXmlElement(RUNPARAMETERS_XML['SBS']))
+  
+  read1 = runParameters.getAllchildren('Read1')
+  newFlowCell.setPropertyValue("CYCLES_REQUESTED_BY_CUSTOMER", read1[0].text)
+  
+  read2 = runParameters.getAllchildren('Read2')
+  if (str(read2[0].text) == '0'):
+    newFlowCell.setPropertyValue("END_TYPE", "SINGLE_READ") 
+  else:
+    newFlowCell.setPropertyValue("END_TYPE", "PAIRED_END") 
+    newFlowCell.setPropertyValue("PAIRED_END_KIT", runParameters.getXmlElement(RUNPARAMETERS_XML['PE']))
+  
+  indexRead = runParameters.getAllchildren('IndexRead')
+  newFlowCell.setPropertyValue("INDEXREAD", indexRead[0].text) 
+
+  def setFcProperty(searchId, dict):
+    children = runInfo.getAllchildren(searchId) 
+    for element in (dict):
+      if (element <> '') and (dict[element] <> ''):
+        newFlowCell.setPropertyValue(element, children[0].attrib[dict[element]])
+
+  setFcProperty('FlowcellLayout', RUNINFO_XML)
+
+
+sequencer = runInfo.getAllchildren('Instrument')
+newFlowCell.setPropertyValue("SEQUENCER", INSTRUMENT[sequencer[0].text])
+
+newFlowCell.setPropertyValue("FLOW_CELL_SEQUENCED_ON", create_openbis_timestamp())
+if IS_HISEQ_RUN:
+  maxLanes = runInfo.getAllchildren('FlowcellLayout')[0].attrib[RUNINFO_XML['LANECOUNT']]
+else:
+  maxLanes = len(runInfo.getAllchildren('Tiles')[0])
+
+# -----------------------------------------------------------------------------
+
+def registerFlowLane(a_lane):
+  '''
+  Registers a new Flow lane 
+  '''
+  newFlowLane = transaction.createNewSample(FLOWCELL_SPACE + name + ':' + str(a_lane), "ILLUMINA_FLOW_LANE")
+  newFlowLane.setContainer(newFlowCell)
+  
+[registerFlowLane(lane) for lane in range(1,int(maxLanes)+1)]