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Greg Von Kuster
6d80665988
alter table dataset add column file_size numeric(15,0) Also added new script update_dataset_size.py
53 lines
1.9 KiB
Python
53 lines
1.9 KiB
Python
import os, sys
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from galaxy import datatypes, config, jobs
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from shutil import copyfile
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#post processing, set build for data and add additional data to history
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def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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history = out_data.items()[0][1].history
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if history == None:
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print "unknown history!"
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return
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new_stdout = ""
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split_stdout = stdout.split("\n")
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basic_name = ""
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for line in split_stdout:
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fields = line.split("\t")
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if fields[0] == "#File1":
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description = fields[1]
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dbkey = fields[2]
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file_type = fields[3]
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name, data = out_data.items()[0]
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basic_name = data.name
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data.name = data.name + " (" + description + ")"
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data.dbkey = dbkey
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data.info = data.name
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data = app.datatypes_registry.change_datatype( data, file_type )
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data.init_meta()
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data.set_peek()
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data.set_size()
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app.model.flush()
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elif fields[0] == "#NewFile":
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description = fields[1]
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dbkey = fields[2]
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filepath = fields[3]
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file_type = fields[4]
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newdata = app.model.Dataset()
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newdata.extension = file_type
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newdata.name = basic_name + " (" + description + ")"
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history.add_dataset( newdata )
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app.model.flush()
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try:
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copyfile(filepath,newdata.file_name)
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newdata.info = newdata.name
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newdata.state = jobs.JOB_OK
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except:
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newdata.info = "The requested file is missing from the system."
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newdata.state = jobs.JOB_ERROR
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newdata.dbkey = dbkey
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newdata.set_meta()
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newdata.set_peek()
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new_data.set_size()
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app.model.flush()
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