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https://github.com/galaxyproject/galaxy.git
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Nate Coraor
dfdbef9d36
permissions, user-side permissions settings on datasets, viewing associated datasets under the role page in the admin controler (is this even necessary?), filtering out roles by type. I haven't addressed tests, so the security-related functional tests will fail. I haven't looked at history sharing yet either. Cleanup to remove unused methods is needed in the admin controller. And the admin templates are a bit messy.
55 lines
2.1 KiB
Python
55 lines
2.1 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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base_dataset = out_data.items()[0][1]
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history = base_dataset.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.HistoryDatasetAssociation( create_dataset = True ) #This import should become a library
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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.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
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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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newdata.set_size()
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app.model.flush()
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