# HG changeset patch
# User iuc
# Date 1515941536 18000
# Node ID 81ed42c0721a2c13c172b41b061decc38bf4c7cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
diff -r 000000000000 -r 81ed42c0721a README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Sun Jan 14 09:52:16 2018 -0500
@@ -0,0 +1,1 @@
+This tool manually builds local data and populates tool data tables.
diff -r 000000000000 -r 81ed42c0721a data_manager/data_manager_manual.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_manual.py Sun Jan 14 09:52:16 2018 -0500
@@ -0,0 +1,172 @@
+#!/usr/bin/env python
+# Dan Blankenberg
+
+import json
+import logging
+import optparse
+import os
+import shutil
+import tempfile
+import urllib2
+
+from xml.etree.ElementTree import tostring
+try:
+ # For Python 3.0 and later
+ from shutil import unpack_archive
+except ImportError:
+ # Fall back to Python 2 import
+ from setuptools.archive_util import unpack_archive
+
+try:
+ # For Python 3.0 and later
+ from urllib.request import urlretrieve
+except ImportError:
+ # Fall back to Python 2 imports
+ from urllib import urlretrieve
+
+_log_name = __name__
+if _log_name == '__builtin__':
+ _log_name = 'toolshed.installed.manual.data.manager'
+log = logging.getLogger( _log_name )
+
+
+# --- These methods are called by/within the Galaxy Application
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None, **kwd ):
+ # Look for any data tables that haven't been defined for this data manager before and dynamically add them to Galaxy
+ param_dict = dict( **param_dict )
+ data_tables_param = param_dict.get( 'data_tables', [] )
+ if not isinstance( data_tables_param, list ):
+ data_tables_param = [data_tables_param]
+ if tool:
+ tool_shed_repository = tool.tool_shed_repository
+ else:
+ tool_shed_repository = None
+ tdtm = None
+ data_manager = app.data_managers.get_manager( tool.data_manager_id, None )
+ for data_table_param in data_tables_param:
+ data_table_name = data_table_param.get( 'data_table_name', None )
+ if data_table_name:
+ # get data table managed by this data Manager
+ data_table = app.tool_data_tables.get_tables().get( str( data_table_name ), None )
+ if data_table:
+ data_table_filename = data_table.get_filename_for_source( data_manager, None )
+ if not data_table_filename:
+ if tdtm is None:
+ from tool_shed.tools import data_table_manager
+ tdtm = data_table_manager.ToolDataTableManager( app )
+ target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir( tool_shed_repository )
+ # Dynamically add this data table
+ log.debug( "Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name )
+ repo_info = tdtm.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=None )
+ if repo_info is not None:
+ repo_info = tostring( repo_info )
+ tmp_file = tempfile.NamedTemporaryFile()
+ tmp_file.write( __get_new_xml_definition( app, data_table, data_manager, repo_info, target_dir ) )
+ tmp_file.flush()
+ app.tool_data_tables.add_new_entries_from_config_file( tmp_file.name, None, app.config.shed_tool_data_table_config, persist=True )
+ tmp_file.close()
+
+
+def __get_new_xml_definition( app, data_table, data_manager, repo_info=None, location_file_dir=None ):
+ sub_dict = { 'table_name': data_table.name, 'comment_char': '', 'columns': '', 'file_path': '' }
+ sub_dict.update( data_manager.get_tool_shed_repository_info_dict() )
+ if data_table.comment_char:
+ sub_dict['comment_char'] = 'comment_char="%s"' % ( data_table.comment_char )
+ for i, name in enumerate( data_table.get_column_name_list() ):
+ if name is not None:
+ sub_dict['columns'] = "%s\n%s" % ( sub_dict['columns'], '' % ( name, i ) )
+ location_file_dir = location_file_dir or app.config.galaxy_data_manager_data_path
+ for filename in data_table.filenames.keys():
+ sub_dict['file_path'] = os.path.basename( filename )
+ sub_dict['file_path'] = os.path.join( location_file_dir, sub_dict['file_path'] ) # os.path.abspath?
+ if not os.path.exists( sub_dict['file_path'] ):
+ # Create empty file
+ log.debug( "Attempting to create a missing location file %s." % sub_dict['file_path'] )
+ open( sub_dict['file_path'], 'wb+' ).close()
+ break
+ sub_dict[ 'repo_info' ] = repo_info or ''
+ return """
+
+ %(columns)s
+
+ %(repo_info)s
+
+ """ % sub_dict
+
+
+def galaxy_code_get_available_data_tables( trans ):
+ # list of data tables
+ return [ ( x, x, False ) for x in trans.app.tool_data_tables.get_tables().keys() ]
+
+
+def galaxy_code_get_available_data_table_columns( trans, data_table_name ):
+ return [ ( x, x, True ) for x in trans.app.tool_data_tables.get( data_table_name ).get_column_name_list() ]
+# --- End Galaxy called Methods ---
+
+
+def get_data_table_entries( params, galaxy_data_manager_data_path ):
+ rval = {}
+ data_tables = params.get( 'data_tables', [] )
+ for data_table in data_tables:
+ entry_dict = {}
+ for column in data_table.get( 'columns', [] ):
+ value = column.get( 'data_table_column_value', '' )
+ if column.get( 'is_path', {} ).get( 'is_path_selector', None ) == 'yes' and column.get( 'is_path', {} ).get( 'abspath', None ) == 'abspath':
+ value = os.path.abspath( os.path.join( galaxy_data_manager_data_path, value ) )
+ entry_dict[ column.get( 'data_table_column_name', '' ) ] = value
+ data_table_name = data_table['data_table_name']
+ rval[ data_table_name ] = rval.get( data_table_name, [] )
+ rval[ data_table_name ].append( entry_dict )
+ return rval
+
+
+def get_file_content( params, target_directory ):
+ directory_content = params.get( 'directory_content', [] )
+ for content in directory_content:
+ target_path = os.path.join( target_directory, content.get( 'subdir', '' ) )
+ try:
+ os.makedirs( target_path )
+ except OSError:
+ pass
+ if content.get( 'file_source', {}).get( 'file_source_selector', None ) == 'URL':
+ ( filename, headers ) = urlretrieve( content.get( 'file_source', {}).get( 'file_URL', None ) )
+ try:
+ bname = headers['Content-Disposition']
+ except KeyError:
+ bname = os.path.basename( urllib2.urlparse.urlsplit( content.get( 'file_source', {}).get( 'file_URL', None ) ).path )
+ else:
+ filename = content.get( 'file_source', {}).get( 'file_history', None )
+ bname = os.path.basename( filename )
+ file_action = content.get( 'file_action', {}).get( 'file_action_selector', None )
+ if file_action == 'unpack':
+ unpack_archive( filename, target_path )
+ else:
+ filename_override = content.get( 'file_action', {}).get( 'filename_override', None )
+ if filename_override:
+ target_path = os.path.join( target_path, filename_override )
+ else:
+ target_path = os.path.join( target_path, bname )
+ shutil.copyfile( filename, target_path )
+ return len( directory_content )
+
+
+def main():
+ parser = optparse.OptionParser()
+ parser.add_option( '', '--galaxy_data_manager_data_path', dest='galaxy_data_manager_data_path', default='', help='Root path for galaxy_data_manager_data_path' )
+ (options, args) = parser.parse_args()
+
+ filename = args[0]
+
+ params = json.loads( open( filename ).read() )
+ target_directory = params[ 'output_data' ][0]['extra_files_path']
+
+ data_table_entries = get_data_table_entries( params['param_dict'], options.galaxy_data_manager_data_path )
+
+ # save info to json file
+ open( filename, 'wb' ).write( json.dumps( { "data_tables": data_table_entries} ) )
+
+ get_file_content( params['param_dict'], target_directory )
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 81ed42c0721a data_manager/data_manager_manual.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_manual.xml Sun Jan 14 09:52:16 2018 -0500
@@ -0,0 +1,69 @@
+
+
+ Entry Builder
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool allows manually specifying data table entries and optionally providing filesystem contents.
+
+
+