def create(definition, projectDict=None):
classString = "ProjectFactoryCreate"
MU.logMsg(classString, "Submitting project definition for validation and object creation", "info")
validator = ExperimentDefinitionValidator(definition)
definition = validator.getExperimentDefinition()
isValid, validMsg = validator.validateDefinition()
MU.logMsg(classString, "Project definition validation result: %s" % validMsg, "info")
if not isValid:
msg = "Invalid definition, cannot create project! %s" % validMsg
MU.logMsg(classString, msg, "error")
raise ProjectError(msg)
# If valid csv, start to populate database objects
csv = definition
csvType = validator.getDefinitionType()
def createProject(pDict):
if pDict is None:
pDict = {}
projects = Project.objects.count()
if projects:
lastProject = Project.objects.all().order_by("-projectID")[0]
projectID = lastProject.projectID + 1
else:
projectID = 1
project = Project(
projectID=projectID,
name=pDict.get("name", "dummy"),
description=pDict.get("description", "dummy"),
tags=pDict.get("tags", None),
status=pDict.get("status", enums.getChoice(enums.PROJECT_STATUS, "INSTANTIATED")),
)
project.save()
return project
def createSecondaryJobs():
secondaryJobObjects = {}
# Do it by condition
conditions = n.unique(csv["Name"])
newJobDefs = {}
for cond in conditions:
condRows = csv[csv["Name"] == cond]
# If this is a new secondary job, populate the necessary database tables
if csvType == "newJob":
uniqueJobs = n.unique(
zip(
condRows["SecondaryServerName"],
condRows["SecondaryProtocol"],
condRows["SecondaryReference"],
)
)
for job in uniqueJobs:
msg = "Creating SecondaryJob for job info: %s" % str(job)
MU.logMsg(classString, msg, "info")
# First make the job, but don't save it
serverName = job[0]
protocol = job[1]
reference = job[2]
secondaryServer = SecondaryAnalysisServer.objects.get(serverName=serverName)
sjs = SecondaryJobServiceFactory.create(secondaryServer)
# protocolEntry = sjs.getModelProtocolInfo(job[1])
# referenceEntry = sjs.getModelReferenceInfo(job[2])
#
# jobDef = {'protocol' : simplejson.dumps(protocolEntry),
# 'reference' : simplejson.dumps(referenceEntry),
# 'server' : secondaryServer}
jobDef = {"protocol": protocol, "reference": reference, "server": secondaryServer}
# Now add the cells
jobRows = condRows[
(condRows["SecondaryServerName"] == serverName)
& (condRows["SecondaryProtocol"] == protocol)
& (condRows["SecondaryReference"] == reference)
]
jobCells = n.unique(zip(jobRows["SMRTCellPath"], jobRows["PrimaryFolder"]))
smrtCells = []
for c in jobCells:
path, primaryFolder = tuple(c)
msg = "Creating or accessing SMRTCell for data path: %s" % os.path.join(path, primaryFolder)
MU.logMsg(classString, msg, "info")
if os.path.exists(path):
# This is a data path
limsCode = LIMSMapper.limsCodeFromCellPath(path)
cell = SMRTCell.objects.get_or_create(
path=path, primaryFolder=primaryFolder, limsCode=limsCode
)
smrtCells.append(cell[0])
else:
# this is a LIMS Code
dataPath = LIMSMapper.cellPathFromLimsCode(path)
cell = SMRTCell.objects.get_or_create(
path=dataPath, primaryFolder=primaryFolder, limsCode=path
)
smrtCells.append(cell[0])
# Add the SMRT Cells
jobDef["cells"] = smrtCells
hasJob = False
for pk, jd in newJobDefs.iteritems():
if jobDef == jd:
hasJob = True
jobObj = SecondaryJob.objects.get(id=pk)
if not hasJob:
cells = jobDef.pop("cells")
jobObj = SecondaryJob(**jobDef)
jobObj.save()
jobObj.cells.add(*cells)
jobDef["cells"] = cells
newJobDefs[jobObj.id] = jobDef
msg = "Successfully created and saved SecondaryJob: %s" % str(model_to_dict(jobObj))
MU.logMsg(classString, msg, "info")
# Link secondary job to condition
if not secondaryJobObjects.has_key(cond):
secondaryJobObjects[cond] = [jobObj]
else:
secondaryJobObjects[cond].append(jobObj)
else:
# Job already exists
for job, serverName in zip(condRows["SecondaryJobID"], condRows["SecondaryServerName"]):
server = SecondaryAnalysisServer.objects.get(serverName=serverName)
newJob, created = SecondaryJob.objects.get_or_create(jobID=job, server=server)
# Add other job info in here if job was newly created...
if True: # created:
sjs = SecondaryJobServiceFactory.create(server)
jobID = newJob.jobID
jobInfo = sjs.getModelJobInfo(jobID)
# Add protocol and reference info
# protocol = SecondaryJobService.getSingleItem(jobInfo.get('protocol', {'name' : 'unknown'}))
# reference = SecondaryJobService.getSingleItem(jobInfo.get('reference', {'name' : 'unknown'}))
# newJob.protocol = simplejson.dumps(protocol)
# newJob.reference = simplejson.dumps(reference)
newJob.protocol = jobInfo.get("protocol", "unknown")
newJob.reference = jobInfo.get("reference", "unknown")
newJob.save()
# Get the SMRT Cells
smrtCells = jobInfo.get("inputs", [])
smrtCellObjs = []
for c in smrtCells:
cell = SMRTCell.objects.get_or_create(
path=c["SMRTCellPath"], primaryFolder=c["PrimaryFolder"], limsCode=c["LIMSCode"]
)
smrtCellObjs.append(cell[0])
# Now add the SMRT Cells to the new job
[newJob.cells.add(x) for x in smrtCellObjs]
# Link secondary job to condition
if not secondaryJobObjects.has_key(cond):
secondaryJobObjects[cond] = [newJob]
else:
secondaryJobObjects[cond].append(newJob)
return secondaryJobObjects
def createConditions(secondaryJobs, project):
conditionObjects = []
for cond, jobs in secondaryJobs.iteritems():
condRows = csv[csv["Name"] == cond]
extraCols = filter(lambda x: x.startswith("p_"), condRows.dtype.names)
extrasDict = {}
for col in extraCols:
extrasDict[col] = list(n.unique(condRows[col]))
extrasJSON = simplejson.dumps(extrasDict)
extractBy = ["( %s )" % e for e in n.unique(condRows["ExtractBy"])]
extractByString = " | ".join(extractBy)
condObj = Condition(
name=cond,
extractBy=extractByString,
extrasDict=extrasJSON,
project=project,
status=enums.getChoice(enums.CONDITION_STATUS, "INSTANTIATED"),
)
condObj.save()
# Add secondary jobs to condition object
condObj.secondaryJob.add(*jobs)
conditionObjects.append(condObj)
return conditionObjects
project = createProject(projectDict)
jobs = createSecondaryJobs()
createConditions(jobs, project)
return MProject(project)
def validateProjectDefinition(definition):
validator = ExperimentDefinitionValidator(definition)
definition = validator.getExperimentDefinition()
isValid, validMsg = validator.validateDefinition()
return (isValid, validMsg)
