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https://github.com/galaxyproject/galaxy.git
synced 2026-09-22 06:16:50 +08:00
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?
147 lines
6.8 KiB
Python
147 lines
6.8 KiB
Python
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def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
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# FIXME: this function is duplicated in the DynamicOptions class. It is used here only to
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# set data.name in exec_after_process().
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microbe_info= {}
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orgs = {}
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filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
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for i, line in enumerate( open( filename ) ):
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ):
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fields = line.split( sep )
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#read each line, if not enough fields, go to next line
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try:
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info_type = fields.pop(0)
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if info_type.upper() == "ORG":
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#ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
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org_num = fields.pop(0)
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name = fields.pop(0)
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kingdom = fields.pop(0)
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group = fields.pop(0)
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chromosomes = fields.pop(0)
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info_url = fields.pop(0)
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link_site = fields.pop(0)
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if org_num not in orgs:
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orgs[ org_num ] = {}
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orgs[ org_num ][ 'chrs' ] = {}
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orgs[ org_num ][ 'name' ] = name
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orgs[ org_num ][ 'kingdom' ] = kingdom
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orgs[ org_num ][ 'group' ] = group
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orgs[ org_num ][ 'chromosomes' ] = chromosomes
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orgs[ org_num ][ 'info_url' ] = info_url
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orgs[ org_num ][ 'link_site' ] = link_site
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elif info_type.upper() == "CHR":
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#CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
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org_num = fields.pop(0)
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chr_acc = fields.pop(0)
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name = fields.pop(0)
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length = fields.pop(0)
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gi = fields.pop(0)
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gb = fields.pop(0)
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info_url = fields.pop(0)
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chr = {}
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chr[ 'name' ] = name
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chr[ 'length' ] = length
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chr[ 'gi' ] = gi
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chr[ 'gb' ] = gb
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chr[ 'info_url' ] = info_url
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if org_num not in orgs:
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orgs[ org_num ] = {}
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orgs[ org_num ][ 'chrs' ] = {}
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orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr
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elif info_type.upper() == "DATA":
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#DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
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uid = fields.pop(0)
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org_num = fields.pop(0)
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chr_acc = fields.pop(0)
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feature = fields.pop(0)
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filetype = fields.pop(0)
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path = fields.pop(0)
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data = {}
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data[ 'filetype' ] = filetype
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data[ 'path' ] = path
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data[ 'feature' ] = feature
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if org_num not in orgs:
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orgs[ org_num ] = {}
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orgs[ org_num ][ 'chrs' ] = {}
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if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]:
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orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {}
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orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data
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else: continue
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except: continue
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for org_num in orgs:
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org = orgs[ org_num ]
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if org[ 'kingdom' ] not in microbe_info:
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microbe_info[ org[ 'kingdom' ] ] = {}
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if org_num not in microbe_info[ org[ 'kingdom' ] ]:
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microbe_info[ org[ 'kingdom' ] ][org_num] = org
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return microbe_info
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#post processing, set build for data and add additional data to history
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from galaxy import datatypes, config, jobs
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from shutil import copyfile
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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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kingdom = param_dict.get( 'kingdom', None )
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#group = param_dict.get( 'group', None )
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org = param_dict.get( 'org', None )
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#if not (kingdom or group or org):
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if not (kingdom or org):
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print "Parameters are not available."
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GALAXY_DATA_INDEX_DIR = app.config.tool_data_path
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microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' )
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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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chr = fields[2]
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dbkey = fields[3]
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file_type = fields[4]
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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 + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")"
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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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chr = fields[2]
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dbkey = fields[3]
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filepath = fields[4]
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file_type = fields[5]
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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 + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
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newdata.flush()
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app.security_agent.set_dataset_permissions( newdata.dataset, base_dataset.dataset.groups )
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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.init_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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