| Next changeset 1:6524e573d9c2 (2018-01-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d |
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added:
README data_manager/data_manager_manual.py data_manager/data_manager_manual.xml data_manager_conf.xml tool_data_table_conf.xml.sample |
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| 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 |
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| @@ -0,0 +1,1 @@ +This tool manually builds local data and populates tool data tables. |
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| 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 |
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| b'@@ -0,0 +1,172 @@\n+#!/usr/bin/env python\n+# Dan Blankenberg\n+\n+import json\n+import logging\n+import optparse\n+import os\n+import shutil\n+import tempfile\n+import urllib2\n+\n+from xml.etree.ElementTree import tostring\n+try:\n+ # For Python 3.0 and later\n+ from shutil import unpack_archive\n+except ImportError:\n+ # Fall back to Python 2 import\n+ from setuptools.archive_util import unpack_archive\n+\n+try:\n+ # For Python 3.0 and later\n+ from urllib.request import urlretrieve\n+except ImportError:\n+ # Fall back to Python 2 imports\n+ from urllib import urlretrieve\n+\n+_log_name = __name__\n+if _log_name == \'__builtin__\':\n+ _log_name = \'toolshed.installed.manual.data.manager\'\n+log = logging.getLogger( _log_name )\n+\n+\n+# --- These methods are called by/within the Galaxy Application\n+def exec_before_job( app, inp_data, out_data, param_dict, tool=None, **kwd ):\n+ # Look for any data tables that haven\'t been defined for this data manager before and dynamically add them to Galaxy\n+ param_dict = dict( **param_dict )\n+ data_tables_param = param_dict.get( \'data_tables\', [] )\n+ if not isinstance( data_tables_param, list ):\n+ data_tables_param = [data_tables_param]\n+ if tool:\n+ tool_shed_repository = tool.tool_shed_repository\n+ else:\n+ tool_shed_repository = None\n+ tdtm = None\n+ data_manager = app.data_managers.get_manager( tool.data_manager_id, None )\n+ for data_table_param in data_tables_param:\n+ data_table_name = data_table_param.get( \'data_table_name\', None )\n+ if data_table_name:\n+ # get data table managed by this data Manager\n+ data_table = app.tool_data_tables.get_tables().get( str( data_table_name ), None )\n+ if data_table:\n+ data_table_filename = data_table.get_filename_for_source( data_manager, None )\n+ if not data_table_filename:\n+ if tdtm is None:\n+ from tool_shed.tools import data_table_manager\n+ tdtm = data_table_manager.ToolDataTableManager( app )\n+ target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir( tool_shed_repository )\n+ # Dynamically add this data table\n+ log.debug( "Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name )\n+ repo_info = tdtm.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=None )\n+ if repo_info is not None:\n+ repo_info = tostring( repo_info )\n+ tmp_file = tempfile.NamedTemporaryFile()\n+ tmp_file.write( __get_new_xml_definition( app, data_table, data_manager, repo_info, target_dir ) )\n+ tmp_file.flush()\n+ app.tool_data_tables.add_new_entries_from_config_file( tmp_file.name, None, app.config.shed_tool_data_table_config, persist=True )\n+ tmp_file.close()\n+\n+\n+def __get_new_xml_definition( app, data_table, data_manager, repo_info=None, location_file_dir=None ):\n+ sub_dict = { \'table_name\': data_table.name, \'comment_char\': \'\', \'columns\': \'\', \'file_path\': \'\' }\n+ sub_dict.update( data_manager.get_tool_shed_repository_info_dict() )\n+ if data_table.comment_char:\n+ sub_dict[\'comment_char\'] = \'comment_char="%s"\' % ( data_table.comment_char )\n+ for i, name in enumerate( data_table.get_column_name_list() ):\n+ if name is not None:\n+ sub_dict[\'columns\'] = "%s\\n%s" % ( sub_dict[\'columns\'], \'<column name="%s" index="%s" />\' % ( name, i ) )\n+ location_file_dir = location_file_dir or app.config.galaxy_data_manager_data_path\n+ for filename in data_table.filenames.keys():\n+ sub_dict[\'file_path\'] = os.path.basename( filename )\n+ sub_dict[\'file_path\'] = os.path.join( location_file_dir, sub_dict[\'file_path\'] ) # os.path.abspath?\n+ if not os.path.exists( sub_dict[\'f'..b'e empty file\n+ log.debug( "Attempting to create a missing location file %s." % sub_dict[\'file_path\'] )\n+ open( sub_dict[\'file_path\'], \'wb+\' ).close()\n+ break\n+ sub_dict[ \'repo_info\' ] = repo_info or \'\'\n+ return """\n+ <tables><table name="%(table_name)s" %(comment_char)s>\n+ %(columns)s\n+ <file path="%(file_path)s" />\n+ %(repo_info)s\n+ </table></tables>\n+ """ % sub_dict\n+\n+\n+def galaxy_code_get_available_data_tables( trans ):\n+ # list of data tables\n+ return [ ( x, x, False ) for x in trans.app.tool_data_tables.get_tables().keys() ]\n+\n+\n+def galaxy_code_get_available_data_table_columns( trans, data_table_name ):\n+ return [ ( x, x, True ) for x in trans.app.tool_data_tables.get( data_table_name ).get_column_name_list() ]\n+# --- End Galaxy called Methods ---\n+\n+\n+def get_data_table_entries( params, galaxy_data_manager_data_path ):\n+ rval = {}\n+ data_tables = params.get( \'data_tables\', [] )\n+ for data_table in data_tables:\n+ entry_dict = {}\n+ for column in data_table.get( \'columns\', [] ):\n+ value = column.get( \'data_table_column_value\', \'\' )\n+ if column.get( \'is_path\', {} ).get( \'is_path_selector\', None ) == \'yes\' and column.get( \'is_path\', {} ).get( \'abspath\', None ) == \'abspath\':\n+ value = os.path.abspath( os.path.join( galaxy_data_manager_data_path, value ) )\n+ entry_dict[ column.get( \'data_table_column_name\', \'\' ) ] = value\n+ data_table_name = data_table[\'data_table_name\']\n+ rval[ data_table_name ] = rval.get( data_table_name, [] )\n+ rval[ data_table_name ].append( entry_dict )\n+ return rval\n+\n+\n+def get_file_content( params, target_directory ):\n+ directory_content = params.get( \'directory_content\', [] )\n+ for content in directory_content:\n+ target_path = os.path.join( target_directory, content.get( \'subdir\', \'\' ) )\n+ try:\n+ os.makedirs( target_path )\n+ except OSError:\n+ pass\n+ if content.get( \'file_source\', {}).get( \'file_source_selector\', None ) == \'URL\':\n+ ( filename, headers ) = urlretrieve( content.get( \'file_source\', {}).get( \'file_URL\', None ) )\n+ try:\n+ bname = headers[\'Content-Disposition\']\n+ except KeyError:\n+ bname = os.path.basename( urllib2.urlparse.urlsplit( content.get( \'file_source\', {}).get( \'file_URL\', None ) ).path )\n+ else:\n+ filename = content.get( \'file_source\', {}).get( \'file_history\', None )\n+ bname = os.path.basename( filename )\n+ file_action = content.get( \'file_action\', {}).get( \'file_action_selector\', None )\n+ if file_action == \'unpack\':\n+ unpack_archive( filename, target_path )\n+ else:\n+ filename_override = content.get( \'file_action\', {}).get( \'filename_override\', None )\n+ if filename_override:\n+ target_path = os.path.join( target_path, filename_override )\n+ else:\n+ target_path = os.path.join( target_path, bname )\n+ shutil.copyfile( filename, target_path )\n+ return len( directory_content )\n+\n+\n+def main():\n+ parser = optparse.OptionParser()\n+ parser.add_option( \'\', \'--galaxy_data_manager_data_path\', dest=\'galaxy_data_manager_data_path\', default=\'\', help=\'Root path for galaxy_data_manager_data_path\' )\n+ (options, args) = parser.parse_args()\n+\n+ filename = args[0]\n+\n+ params = json.loads( open( filename ).read() )\n+ target_directory = params[ \'output_data\' ][0][\'extra_files_path\']\n+\n+ data_table_entries = get_data_table_entries( params[\'param_dict\'], options.galaxy_data_manager_data_path )\n+\n+ # save info to json file\n+ open( filename, \'wb\' ).write( json.dumps( { "data_tables": data_table_entries} ) )\n+\n+ get_file_content( params[\'param_dict\'], target_directory )\n+\n+\n+if __name__ == "__main__":\n+ main()\n' |
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| 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 |
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| @@ -0,0 +1,69 @@ +<tool id="data_manager_manual" name="Manual Data Manager" version="0.0.1" tool_type="manage_data"> + <options sanitize="False" /> + <description>Entry Builder</description> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/data_manager_manual.py' + '${out_file}' + --galaxy_data_manager_data_path '${__app__.config.galaxy_data_manager_data_path}' + ]]></command> + <inputs> + <repeat name="data_tables" title="Data Table to define" min="1"> + <param name="data_table_name" type="select" multiple="False" optional="False" label="Choose Desired Data Table" + dynamic_options="galaxy_code_get_available_data_tables( __trans__ )" refresh_on_change="True"/> + <repeat name="columns" title="Table Columns" min="1"> + <param name="data_table_column_name" type="select" multiple="False" optional="False" label="Column Name" + dynamic_options="galaxy_code_get_available_data_table_columns( __trans__, data_table_name )" /> + <!-- <param name="data_table_column_name" type="text" label="Column Name"/> --> + <param name="data_table_column_value" type="text" label="Value to use for data table column"/> + <conditional name="is_path"> + <param name="is_path_selector" type="select" label="Value is a path"> + <option value="yes">Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="abspath" type="boolean" label="Apply abspath" checked="True" truevalue="abspath" falsevalue="" /> + </when> + <when value="no"/> + </conditional> + </repeat> + </repeat> + <repeat name="directory_content" title="Directory Content"> + <param name="subdir" type="text" label="Place in Subdirectory" value=""/> + <conditional name="file_source"> + <param name="file_source_selector" type="select" label="File Content Source"> + <option value="history">History Item</option> + <option value="URL" selected="True">URL</option> + </param> + <when value="history"> + <param name="file_history" type="data" multiple="false" optional="false" format="data" label="File from history" /> + </when> + <when value="URL"> + <param name="file_URL" type="text" label="Fetch from URL" value=""/> + </when> + </conditional> + <conditional name="file_action"> + <param name="file_action_selector" type="select" label="File Actions"> + <option value="unpack">Extract Archive</option> + <option value="None" selected="True">None</option> + </param> + <when value="None"> + <param name="filename_override" type="text" label="Override with Filename" value=""/> + </when> + <when value="unpack"> + </when> + </conditional> + </repeat> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" dbkey="dbkey"/> + </outputs> + <tests> + </tests> + <help> +**What it does** + +This tool allows manually specifying data table entries and optionally providing filesystem contents. + + </help> + <code file="data_manager_manual.py" /> +</tool> |
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| diff -r 000000000000 -r 81ed42c0721a data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Sun Jan 14 09:52:16 2018 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_manual.xml" id="data_manager_manual" version="0.0.1" undeclared_tables="True" /> +</data_managers> |
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| diff -r 000000000000 -r 81ed42c0721a tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Jan 14 09:52:16 2018 -0500 |
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| @@ -0,0 +1,2 @@ +<tables> +</tables> |