# HG changeset patch # User dfornika # Date 1558725545 14400 # Node ID d51005ef511cd0089bb066e7995512030f3868dc planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit 77f160b9d557a33ee830c2aff93d423ce2d6b815-dirty diff -r 000000000000 -r d51005ef511c data_manager/mob_suite_build_database.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/mob_suite_build_database.py Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,84 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import json +import os +import string +import subprocess +import sys + + +DATA_TABLE_NAME = "mob_suite_databases" + + +def mob_suite_build_database_mob_init(mob_suite_args, target_directory, data_table_name=DATA_TABLE_NAME): + + now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") + + database_value = "_".join([ + ]) + + database_name = " ".join([ + ]) + + database_path = database_value + + args = [ + ] + + run(['mob_init'] + args, target_directory) + + data_table_entry = { + "data_tables": { + data_table_name: [ + { + "value": database_value, + "name": database_name, + "path": database_path, + } + ] + } + } + + return data_table_entry + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('data_manager_json') + parser.add_argument( '--threads', dest='threads', default=1, help='threads' ) + parser.add_argument( '--mode', dest='mode', default=1, help='database construction mode' ) + args = parser.parse_args() + + data_manager_input = json.loads(open(args.data_manager_json).read()) + + target_directory = data_manager_input['output_data'][0]['extra_files_path'] + + try: + os.mkdir( target_directory ) + except OSError as exc: + if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): + pass + else: + raise + + data_manager_output = {} + + if str(args.mode) == 'mob_init': + mob_suite_args = {} + data_manager_output = mob_suite_build_database_mob_init( + mob_suite_args, + target_directory, + ) + else: + sys.exit("Invalid database construction mode") + + open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) + + +if __name__ == "__main__": + main() diff -r 000000000000 -r d51005ef511c data_manager/mob_suite_build_database.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/mob_suite_build_database.xml Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,33 @@ + + + database builder + + mob_suite + + echo '1.4.9.1' + + + + + + + + + + + + + + + + + + + 10.1099/mgen.0.000206 + + diff -r 000000000000 -r d51005ef511c data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,18 @@ + + + + + + + + + ${path} + mob_suite_databases/${path} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/mob_suite_databases/${path} + abspath + + + + + diff -r 000000000000 -r d51005ef511c tool-data/mob_suite_databases.loc.sample diff -r 000000000000 -r d51005ef511c tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+