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Nate Coraor
3802816b69
both permitted_actions and groups are set appropriately on datasets. Somewhat tested and mostly working, but needs more testing. Greg: If a userless session has a history, if that user logs in, the DefaultHistoryGroupAssociation for the current history as well as the datasets in that history are supposed to be updated with the permissions in DefaultUserGroupAssociation, but this isn't happening. Possibly because the default permissions on userless histories create datasets in the public group with only the DATASET_ACCESS permission (or possibly for another reason). What are the implications of giving public users DATASET_MANAGE_PERMISSIONS?
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.set_dataset_permissions( newdata.dataset, base_dataset.dataset.groups )
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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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