Example #1
0
    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)
Example #2
0
 def validateProjectDefinition(definition):
     validator = ExperimentDefinitionValidator(definition)
     definition = validator.getExperimentDefinition()
     isValid, validMsg = validator.validateDefinition()
     return (isValid, validMsg)