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108 lines
4.8 KiB
Python
108 lines
4.8 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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from __future__ import print_function
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import optparse
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import time
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from six.moves.urllib.parse import urljoin
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from common import get, post # noqa: I100,I202
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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 = 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 = 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, 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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