opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

remove another abspath; use optparse;

Browse Source
This commit is contained in:
Martin Cech
2015-04-14 11:31:44 -04:00
parent 66e61271b1
commit dc736c73f2
1 changed files with 20 additions and 16 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/tool_shed/build_ts_whoosh_index.py
+20 -16
View File
@@ -1,8 +1,8 @@
"""
Build indexes for searching the TS.
Run this script from the galaxy folder, example:
Run this script from the Tool Shed folder, example:
$ python scripts/tool_shed/build_ts_whoosh_index_test.py config/tool_shed.ini
$ python scripts/tool_shed/build_ts_whoosh_index_test.py -c config/tool_shed.ini -r database/community_files
Make sure you adjusted your config to:
* turn on searching via toolshed_search_on
@@ -11,6 +11,7 @@ Make sure you adjusted your config to:
import sys
import os
import ConfigParser
from optparse import OptionParser
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
@@ -18,7 +19,9 @@ sys.path = new_path
from galaxy.util import pretty_print_time_interval
import galaxy.webapps.tool_shed.model.mapping
from galaxy.webapps.tool_shed import config, model
from galaxy.webapps.tool_shed import config
from galaxy.webapps.tool_shed import model
from galaxy.tools.loader_directory import load_tool_elements_from_path
from galaxy import eggs
eggs.require( "SQLAlchemy" )
@@ -50,7 +53,7 @@ tool_schema = Schema(
repo_id=STORED )
def build_index( sa_session, toolshed_whoosh_index_dir ):
def build_index( sa_session, toolshed_whoosh_index_dir, path_to_repositories ):
"""
Build the search indexes. One for repositories and another for tools within.
"""
@@ -76,7 +79,7 @@ def build_index( sa_session, toolshed_whoosh_index_dir ):
repos_indexed = 0
tools_indexed = 0
for repo in get_repos( sa_session ):
for repo in get_repos( sa_session, path_to_repositories ):
repo_index_writer.add_document( id=repo.get( 'id' ),
name=to_unicode( repo.get( 'name' ) ),
@@ -112,7 +115,7 @@ def build_index( sa_session, toolshed_whoosh_index_dir ):
print "TOTAL tools indexed: ", tools_indexed
def get_repos( sa_session ):
def get_repos( sa_session, path_to_repositories ):
"""
Load repos from DB and included tools from .xml configs.
"""
@@ -147,12 +150,8 @@ def get_repos( sa_session ):
# Parse all the tools within repo for separate index.
tools_list = []
from galaxy.webapps.tool_shed.model import directory_hash_id
path = '/srv/toolshed/test/var/data/repos'
# path = os.path.join( os.getcwd(), 'database/community_files' )
path = os.path.join( path, *directory_hash_id( repo.id ))
path = os.path.join( path_to_repositories, *model.directory_hash_id( repo.id ))
path = os.path.join( path, "repo_%d" % repo.id )
from galaxy.tools.loader_directory import load_tool_elements_from_path
if os.path.exists(path):
tool_elems = load_tool_elements_from_path(path)
if tool_elems:
@@ -185,9 +184,9 @@ def get_repos( sa_session ):
return results
def get_sa_session_and_needed_config_settings( ini_file ):
def get_sa_session_and_needed_config_settings( path_to_tool_shed_config ):
conf_parser = ConfigParser.ConfigParser( { 'here' : os.getcwd() } )
conf_parser.read( ini_file )
conf_parser.read( path_to_tool_shed_config )
kwds = dict()
for key, value in conf_parser.items( "app:main" ):
kwds[ key ] = value
@@ -199,7 +198,12 @@ def get_sa_session_and_needed_config_settings( ini_file ):
return model.context.current, config_settings
if __name__ == "__main__":
ini_file = sys.argv[ 1 ]
sa_session, config_settings = get_sa_session_and_needed_config_settings( ini_file )
parser = OptionParser()
parser.add_option("-c", "--config", dest="path_to_tool_shed_config", default="config/tool_shed.ini", help="specify tool_shed.ini location")
parser.add_option("-r", "--repos", dest="path_to_repositories", default="database/community_files", help="specify path to folder with repositories")
(options, args) = parser.parse_args()
path_to_tool_shed_config = options.path_to_tool_shed_config
path_to_repositories = options.path_to_repositories
sa_session, config_settings = get_sa_session_and_needed_config_settings( path_to_tool_shed_config )
toolshed_whoosh_index_dir = config_settings.get( 'toolshed_whoosh_index_dir', None )
build_index( sa_session, toolshed_whoosh_index_dir )
build_index( sa_session, toolshed_whoosh_index_dir, path_to_repositories )