-
Notifications
You must be signed in to change notification settings - Fork 25
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
David Stirling
authored
Nov 3, 2020
1 parent
4f0a525
commit 2520c42
Showing
1 changed file
with
155 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,155 @@ | ||
| import json | ||
| import boto3 | ||
| import string | ||
| import os | ||
| import posixpath | ||
| class JobQueue(): | ||
|
|
||
| def __init__(self,name=None): | ||
| self.sqs = boto3.resource('sqs') | ||
| self.queue = self.sqs.get_queue_by_name(QueueName=name+'Queue') | ||
| self.inProcess = -1 | ||
| self.pending = -1 | ||
|
|
||
| def scheduleBatch(self, data): | ||
| msg = json.dumps(data) | ||
| response = self.queue.send_message(MessageBody=msg) | ||
| print 'Batch sent. Message ID:',response.get('MessageId') | ||
|
|
||
| #project specific stuff | ||
| topdirname='' #PROJECTNAME | ||
| projectname='' #PROJECTNAME | ||
| batchsuffix='' #BATCHNAME | ||
| rows=list(string.ascii_uppercase)[0:8] | ||
| columns=range(1,13) | ||
| sites=range(1,18) | ||
| platelist=[] # PLATEFOLDERNAMES | ||
| illumpipename='illum.cppipe' | ||
| qcpipename='qc.cppipe' | ||
| analysispipename='analysis.cppipe' | ||
| batchpipenameillum='Batch_data_illum.h5' | ||
| batchpipename='Batch_data.h5' | ||
|
|
||
| #not project specific, unless you deviate from the structure | ||
| startpath=posixpath.join('projects',topdirname) | ||
| pipelinepath=posixpath.join(startpath,os.path.join('workspace/pipelines',batchsuffix)) | ||
| illumoutpath=posixpath.join(startpath,os.path.join(batchsuffix,'illum')) | ||
| QCoutpath=posixpath.join(startpath,os.path.join('workspace/qc',os.path.join(batchsuffix,'results'))) | ||
| analysisoutpath=posixpath.join(startpath,os.path.join('workspace/analysis',batchsuffix)) | ||
| inputpath=posixpath.join(startpath,os.path.join('workspace/qc',os.path.join(batchsuffix,'rules'))) | ||
| datafilepath=posixpath.join(startpath,os.path.join('workspace/load_data_csv',batchsuffix)) | ||
| anlysisoutputstructure="Metadata_Plate/analysis/Metadata_Plate-Metadata_Well-Metadata_Site" | ||
| batchpath=posixpath.join(startpath,os.path.join('workspace/batchfiles',batchsuffix)) | ||
|
|
||
| def MakeIllumJobs(mode='repurp'): | ||
| illumqueue = JobQueue(projectname+'_Illum') | ||
| for toillum in platelist: | ||
| if mode=='repurp': | ||
| templateMessage_illum = {'Metadata': 'Metadata_Plate='+toillum, | ||
| 'pipeline': posixpath.join(pipelinepath,illumpipename),'output': illumoutpath, | ||
| 'input': inputpath, 'data_file':posixpath.join(datafilepath,toillum+'.csv')} | ||
| elif mode=='batch': | ||
| templateMessage_illum = {'Metadata': 'Metadata_Plate='+toillum, | ||
| 'pipeline': posixpath.join(batchpath,batchpipenameillum), | ||
| 'output': illumoutpath, | ||
| 'input':inputpath, | ||
| 'data_file': posixpath.join(batchpath,batchpipenameillum) | ||
| } | ||
| else: | ||
| templateMessage_illum = {'Metadata': 'Metadata_Plate='+toillum, | ||
| 'pipeline': posixpath.join(pipelinepath,illumpipename),'output': illumoutpath, | ||
| 'input': inputpath, 'data_file':posixpath.join(datafilepath,untruncatedplatedict[toillum],'load_data.csv')} | ||
|
|
||
| illumqueue.scheduleBatch(templateMessage_illum) | ||
|
|
||
| print 'Illum job submitted. Check your queue' | ||
|
|
||
| def MakeQCJobs(repurp=False): | ||
| qcqueue = JobQueue(projectname+'_QC') | ||
| for toqc in platelist: | ||
| for eachrow in rows: | ||
| for eachcol in columns: | ||
| if repurp==False: | ||
| templateMessage_qc = {'Metadata': 'Metadata_Plate='+toqc+',Metadata_Well='+eachrow+'%02d' %eachcol, | ||
| 'pipeline': posixpath.join(pipelinepath,qcpipename), | ||
| 'output': QCoutpath, | ||
| 'input': inputpath, | ||
| 'data_file': posixpath.join(datafilepath,toqc+'.csv') | ||
| } | ||
| else: | ||
| templateMessage_qc = {'Metadata': 'Metadata_Plate='+toqc+',Metadata_Well='+eachrow+'%02d' %eachcol, | ||
| 'pipeline': posixpath.join(pipelinepath,qcpipename), | ||
| 'output': QCoutpath, | ||
| 'input': inputpath, | ||
| 'data_file': posixpath.join(datafilepath,untruncatedplatedict[toqc],'load_data.csv') | ||
| } | ||
| qcqueue.scheduleBatch(templateMessage_qc) | ||
|
|
||
| print 'QC job submitted. Check your queue' | ||
|
|
||
| def MakeQCJobs_persite(repurp=False): | ||
| qcqueue = JobQueue(projectname+'_QC') | ||
| for toqc in platelist: | ||
| for eachrow in rows: | ||
| for eachcol in columns: | ||
| for eachsite in sites: | ||
| if repurp==False: | ||
| templateMessage_qc = {'Metadata': 'Metadata_Plate='+toqc+',Metadata_Well='+eachrow+'%02d' %eachcol+',Metadata_Site='+str(eachsite), | ||
| 'pipeline': posixpath.join(pipelinepath,qcpipename), | ||
| 'output': QCoutpath, | ||
| 'input': inputpath, | ||
| 'data_file': posixpath.join(datafilepath,toqc+'.csv') | ||
| } | ||
| else: | ||
| templateMessage_qc = {'Metadata': 'Metadata_Plate='+toqc+',Metadata_Well='+eachrow+'%02d' %eachcol+',Metadata_Site='+str(eachsite), | ||
| 'pipeline': posixpath.join(pipelinepath,qcpipename), | ||
| 'output': QCoutpath, | ||
| 'input': inputpath, | ||
| 'data_file': posixpath.join(datafilepath,untruncatedplatedict[toqc],'load_data.csv') | ||
| } | ||
|
|
||
| qcqueue.scheduleBatch(templateMessage_qc) | ||
|
|
||
| print 'QC job submitted. Check your queue' | ||
|
|
||
|
|
||
| def MakeAnalysisJobs(mode='repurp'): | ||
| analysisqueue = JobQueue(projectname+'_Analysis') | ||
| for toanalyze in platelist: | ||
| for eachrow in rows: | ||
| for eachcol in columns: | ||
| for eachsite in sites: | ||
| if mode=='repurp': | ||
| templateMessage_analysis = {'Metadata': 'Metadata_Plate='+toanalyze+',Metadata_Well='+eachrow+'%02d' %eachcol+',Metadata_Site='+str(eachsite), | ||
| 'pipeline': posixpath.join(pipelinepath,analysispipename), | ||
| 'output': analysisoutpath, | ||
| 'output_structure':anlysisoutputstructure, | ||
| 'input':inputpath, | ||
| 'data_file': posixpath.join(datafilepath,toanalyze+'_with_illum.csv') | ||
| } | ||
| elif mode=='batch': | ||
| templateMessage_analysis = {'Metadata': 'Metadata_Plate='+toanalyze+',Metadata_Well='+eachrow+'%02d' %eachcol+',Metadata_Site='+str(eachsite), | ||
| 'pipeline': posixpath.join(batchpath,batchpipename), | ||
| 'output': analysisoutpath, | ||
| 'output_structure':anlysisoutputstructure, | ||
| 'input':inputpath, | ||
| 'data_file': posixpath.join(batchpath,batchpipename) | ||
| } | ||
| else: | ||
| templateMessage_analysis = {'Metadata': 'Metadata_Plate='+toanalyze+',Metadata_Well='+eachrow+'%02d' %eachcol+',Metadata_Site='+str(eachsite), | ||
| 'pipeline': posixpath.join(pipelinepath,analysispipename), | ||
| 'output': analysisoutpath, | ||
| 'output_structure':anlysisoutputstructure, | ||
| 'input':inputpath, | ||
| 'data_file': posixpath.join(datafilepath,untruncatedplatedict[toanalyze],'load_data_with_illum.csv') | ||
| } | ||
|
|
||
| analysisqueue.scheduleBatch(templateMessage_analysis) | ||
|
|
||
| print 'Analysis job submitted. Check your queue' | ||
|
|
||
| #MakeIllumJobs(mode='batch') | ||
| #MakeQCJobs(repurp=True) | ||
| #MakeQCJobs_persite(repurp=True) | ||
| #MakeAnalysisJobs(mode='batch') | ||
|
|