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https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 10:51:34 +08:00
Daniel Blankenberg
7b7453366f
Additional effort is needed to abstract more previously existing functionality out of web controllers. Add script that is able to create a sequencer configuration for the sample tracking system using API.
46 lines
2.3 KiB
Python
Executable File
46 lines
2.3 KiB
Python
Executable File
#!/usr/bin/env python
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import os, sys#, traceback
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sys.path.insert( 0, os.path.dirname( __file__ ) )
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from common import submit, get
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def create_sequencer_configuration( key, base_url, request_form_filename, sample_form_filename, request_type_filename, email_addresses, return_formatted=True ):
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#create request_form
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data = {}
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data[ 'xml_text' ] = open( request_form_filename ).read()
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request_form = submit( key, "%sforms" % base_url, data, return_formatted=False )[0]
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#create sample_form
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data = {}
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data[ 'xml_text' ] = open( sample_form_filename ).read()
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sample_form = submit( key, "%sforms" % base_url, data, return_formatted=False )[0]
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#get user ids
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user_ids = [ user['id'] for user in get( key, "%susers" % base_url ) if user['email'] in email_addresses ]
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#create role, assign to user
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data = {}
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data[ 'name' ] = "request_type_role_%s_%s_%s name" % ( request_form['id'], sample_form['id'], '_'.join( email_addresses ) )
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data[ 'description' ] = "request_type_role_%s_%s_%s description" % ( request_form['id'], sample_form['id'], '_'.join( email_addresses ) )
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data[ 'user_ids' ] = user_ids
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role_ids = [ role[ 'id' ] for role in submit( key, "%sroles" % base_url, data, return_formatted=False ) ]
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#create request_type
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data = {}
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data[ 'request_form_id' ] = request_form[ 'id' ]
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data[ 'sample_form_id' ] = sample_form[ 'id' ]
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data[ 'role_ids' ] = role_ids
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data[ 'xml_text' ] = open( request_type_filename ).read()
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return submit( key, "%srequest_types" % base_url, data, return_formatted=return_formatted ) #create and print out results for request type
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def main():
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try:
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key = sys.argv[1]
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base_url = sys.argv[2]
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request_form_filename = sys.argv[3]
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sample_form_filename = sys.argv[4]
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request_type_filename = sys.argv[5]
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email_addresses = sys.argv[6].split( ',' )
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except IndexError:
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print 'usage: %s key base_url request_form_xml_description_file sample_form_xml_description_file request_type_xml_description_file email_address1[,email_address2]' % os.path.basename( sys.argv[0] )
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sys.exit( 1 )
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return create_sequencer_configuration( key, base_url, request_form_filename, sample_form_filename, request_type_filename, email_addresses, return_formatted=True )
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if __name__ == "__main__":
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main()
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