# 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 @@
+
+
+
+
+
+
+
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 @@
+
+
+
+
+