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https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Greg Von Kuster
e190e6e2b0
We're still supporting the current dynamic_options functionality. This is a first pass and will be cleaned up as we continue to evolve more tools to use this new approach. Within tool configs, SelectToolParameter types now include a <select_options> tag set. Several tools have been altered to use this new approach. Other tools we enhanced to use the ColumnListParameter type.
54 lines
1.9 KiB
Python
54 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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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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newdata.flush()
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history.add_dataset( newdata )
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newdata.flush()
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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.init_meta()
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newdata.set_peek()
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#
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app.model.flush()
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