mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
Nicola Soranzo
a353b2e88f
using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ```
93 lines
3.2 KiB
Python
93 lines
3.2 KiB
Python
#!/usr/bin/env python
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"""
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Build index for full-text whoosh search of files in data libraries.
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Requires configuration settings in galaxy.ini. See the whoosh settings in the
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data library search section for more details.
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Run from the ~/scripts/data_libraries directory:
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%sh build_whoosh_index.sh
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"""
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from __future__ import print_function
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import os
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import sys
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from six import text_type
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from six.moves import configparser
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
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# Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether search is enabled.
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try:
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from whoosh.filedb.filestore import FileStorage
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from whoosh.fields import Schema, STORED, TEXT
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whoosh_search_enabled = True
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schema = Schema(id=STORED, name=TEXT, info=TEXT, dbkey=TEXT, message=TEXT)
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import galaxy.model.mapping
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from galaxy import config, model
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except ImportError:
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whoosh_search_enabled = False
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schema = None
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def build_index(sa_session, whoosh_index_dir):
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storage = FileStorage(whoosh_index_dir)
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index = storage.create_index(schema)
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writer = index.writer()
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def to_unicode(a_basestr):
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if not isinstance(a_basestr, text_type):
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return text_type(a_basestr, 'utf-8')
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else:
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return a_basestr
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lddas_indexed = 0
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for id, name, info, dbkey, message in get_lddas(sa_session):
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writer.add_document(id=id,
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name=to_unicode(name),
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info=to_unicode(info),
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dbkey=to_unicode(dbkey),
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message=to_unicode(message))
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lddas_indexed += 1
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writer.commit()
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print("Number of active library datasets indexed: ", lddas_indexed)
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def get_lddas(sa_session):
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for ldda in sa_session.query(model.LibraryDatasetDatasetAssociation).filter_by(deleted=False):
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id = ldda.id
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name = ldda.name
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info = ldda.library_dataset.get_info()
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if info and not info.startswith('upload'):
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info = info.replace('no info', '')
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else:
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info = ''
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dbkey = ldda.metadata.dbkey
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if ldda.message:
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message = ldda.message
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else:
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message = ''
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yield id, name, info, dbkey, message
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def get_sa_session_and_needed_config_settings(ini_file):
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conf_parser = configparser.ConfigParser({'here': os.getcwd()})
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conf_parser.read(ini_file)
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kwds = dict()
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for key, value in conf_parser.items("app:main"):
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kwds[key] = value
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config_settings = config.Configuration(**kwds)
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db_con = config_settings.database_connection
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if not db_con:
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db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config_settings.database
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model = galaxy.model.mapping.init(config_settings.file_path, db_con, engine_options={}, create_tables=False)
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return model.context.current, config_settings
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if __name__ == "__main__":
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if whoosh_search_enabled:
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ini_file = sys.argv[1]
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sa_session, config_settings = get_sa_session_and_needed_config_settings(ini_file)
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whoosh_index_dir = config_settings.whoosh_index_dir
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build_index(sa_session, whoosh_index_dir)
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