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109 lines
4.9 KiB
Python
109 lines
4.9 KiB
Python
#!/usr/bin/env python
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# Dan Blankenberg
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# Very simple example of using the API to run Data Managers
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# Script makes the naive assumption that dbkey==sequence id, which in many cases is not true nor desired
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# *** This script is not recommended for use as-is on a production server ***
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import os
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import sys
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import optparse
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import urlparse
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import time
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sys.path.insert( 0, os.path.dirname( __file__ ) )
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from common import post, get
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DEFAULT_SLEEP_TIME = 3
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FETCH_GENOME_TOOL_ID = 'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1'
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BUILD_INDEX_TOOLS_ID = [ 'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_index_builder_data_manager/0.0.1',
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'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_color_space_index_builder_data_manager/0.0.1' ]
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def run_tool( tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_time=None, **kwargs ):
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sleep_time = sleep_time or DEFAULT_SLEEP_TIME
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tools_url = urlparse.urljoin( galaxy_url, 'api/tools' )
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payload = {
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'tool_id' : tool_id,
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}
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if history_id:
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payload['history_id'] = history_id
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payload[ 'inputs' ] = params
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rval = post( api_key, tools_url, payload )
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if wait:
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outputs = list( rval['outputs'] )
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while outputs:
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finished_datasets = []
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for i, dataset_dict in enumerate( outputs ):
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if dataset_is_terminal( dataset_dict['id'], api_key=api_key, galaxy_url=galaxy_url ):
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finished_datasets.append( i )
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for i in reversed( finished_datasets ):
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outputs.pop( 0 )
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if wait and outputs:
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time.sleep( sleep_time )
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return rval
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def get_dataset_state( hda_id, api_key, galaxy_url ):
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datasets_url = urlparse.urljoin( galaxy_url, 'api/datasets/%s' % hda_id )
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dataset_info = get( api_key, datasets_url )
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return dataset_info['state']
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def dataset_is_terminal( hda_id, api_key, galaxy_url ):
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dataset_state = get_dataset_state( hda_id, api_key, galaxy_url )
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return dataset_state in [ 'ok', 'error' ]
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if __name__ == '__main__':
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parser = optparse.OptionParser()
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parser.add_option( '-k', '--key', dest='api_key', action='store', type="string", default=None, help='API Key.' )
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parser.add_option( '-u', '--url', dest='base_url', action='store', type="string", default='http://localhost:8080', help='Base URL of Galaxy Server' )
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parser.add_option( '-d', '--dbkey', dest='dbkeys', action='append', type="string", default=[], help='List of dbkeys to download and Index' )
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parser.add_option( '-s', '--sleep_time', dest='sleep_time', action='store', type="int", default=DEFAULT_SLEEP_TIME, help='How long to sleep between check loops' )
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(options, args) = parser.parse_args()
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# check options
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assert options.api_key is not None, ValueError( 'You must specify an API key.' )
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assert options.dbkeys, ValueError( 'You must specify at least one dbkey to use.' )
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# check user is admin
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configuration_options = get( options.api_key, urlparse.urljoin( options.base_url, 'api/configuration' ) )
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if 'library_import_dir' not in configuration_options: # hack to check if is admin user
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print "Warning: Data Managers are only available to admin users. The API Key provided does not appear to belong to an admin user. Will attempt to run anyway."
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# Fetch Genomes
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dbkeys = {}
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for dbkey in options.dbkeys:
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if dbkey not in dbkeys:
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dbkeys[ dbkey ] = run_tool( FETCH_GENOME_TOOL_ID, None, { 'dbkey': dbkey, 'reference_source|reference_source_selector': 'ucsc', 'reference_source|requested_dbkey': dbkey }, options.api_key, options.base_url, wait=False )
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else:
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"dbkey (%s) was specified more than once, skipping additional specification." % ( dbkey )
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print 'Genomes Queued for downloading.'
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# Start indexers
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indexing_tools = []
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while dbkeys:
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for dbkey, value in dbkeys.items():
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if dataset_is_terminal( value['outputs'][0]['id'], options.api_key, options.base_url ):
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del dbkeys[ dbkey ]
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for tool_id in BUILD_INDEX_TOOLS_ID:
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indexing_tools.append( run_tool( tool_id, None, { 'all_fasta_source': dbkey }, options.api_key, options.base_url, wait=False ) )
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if dbkeys:
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time.sleep( options.sleep_time )
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print 'All genomes downloaded and indexers now queued.'
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# Wait for indexers to finish
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while indexing_tools:
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for i, indexing_tool_value in enumerate( indexing_tools ):
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if dataset_is_terminal( indexing_tool_value['outputs'][0]['id'], options.api_key, options.base_url ):
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print 'Finished:', indexing_tool_value
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del indexing_tools[i]
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break
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if indexing_tools:
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time.sleep( options.sleep_time )
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print 'All indexers have been run, please check results.'
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