Email parser job descriptions
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info ( "Down job starting: %s " % path ) # Read the file inputFile = job. If the range is larger than a threshold N the range is divided recursively and a follow on job is then created which merges back the results else the file is sorted and placed in the output. Next let’s look at the job that begins the actual workflow, setup.ĭef down ( job, inputFileStoreID, N, path, downCheckpoints, options, memory = sortMemory ): """ Input is a file, a subdivision size N, and a path in the hierarchy of jobs. Sorted file from the job store back into “userland”. When the workflowĮnds we capture its output (the sorted file’s fileID) and use that in () to move the That we have to check whether or not the workflow is restarting so that we don’t import the file more than once.įinally we can kick off the workflow by calling () on the job setup.
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'file://' as per the documentation for () when staging a file that is stored locally. We create a path to the input file prepended with If this option isn’t given, it’s here that we make our own file with the call toįinally we come to the context manager that initializes the workflow. The option -fileToSort allows you to specify a file
Email parser job descriptions verification#
Next we do a little bit of verification of the input arguments. Should give you a pretty good idea of what they can do. The help message listed with the arguments The command line arguments unique to this workflow, and parse the input. It’s important that we add theĬall to () to initialize our parser with all of Toil’s default options.
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exportFile ( sortedFileID, sortedFileURL )įirst we make a parser to process command line arguments using the argparse module. downCheckpoints, options = options, memory = sortMemory )) else : sortedFileID = workflow. wrapJobFn ( setup, sortFileID, int ( options. importFile ( sortFileURL ) sortedFileID = workflow. abspath ( fileName ) sortFileID = workflow. abspath ( sortedFileName ) if not workflow. N ) # Now we are ready to run with Toil ( options ) as workflow : sortedFileURL = 'file://' + os. N ) <= 0 : raise RuntimeError ( "Invalid value of N: %s " % options. fileToSort ): raise RuntimeError ( "File to sort does not exist: %s " % options. ' ) makeFileToSort ( fileName = fileName, lines = options. exists ( sortedFileName ): print ( f 'Output file. outputFile or "sortedFile.txt" if not options. mergeMemory = sortMemory # do some input verification sortedFileName = options. sortMemory = sortMemory if not hasattr ( options, "mergeMemory" ) or not options. parse_args () if not hasattr ( options, "sortMemory" ) or not options. add_argument ( "-mergeMemory", dest = "mergeMemory", help = "Memory for jobs that collate results.", default = None ) options = parser. add_argument ( "-sortMemory", dest = "sortMemory", help = "Memory for jobs that sort chunks of the file.", default = None ) parser. add_argument ( '-downCheckpoints', action = 'store_true', help = 'If this option is set, the workflow will make checkpoints on its way through' 'the recursive "down" part of the sort' ) parser. " "All lines must of length less than or equal to N or program will fail", default = 10000 ) parser.
Email parser job descriptions serial#
add_argument ( "-N", dest = "N", help = "The threshold below which a serial sort function is used to sort file. add_argument ( "-overwriteOutput", help = "Write over the output file if it already exists.", default = True ) parser. add_argument ( "-outputFile", help = "Where the sorted output will go" ) parser. add_argument ( "-fileToSort", help = "The file you wish to sort" ) parser. add_argument ( '-lineLength', default = defaultLineLen, help = 'Length of lines in file to sort.', type = int ) parser.
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add_argument ( '-numLines', default = defaultLines, help = 'Number of lines in file to sort.', type = int ) parser. Def main ( options = None ): if not options : # deal with command line arguments parser = ArgumentParser () Job.