Mercurial > repos > fabio > gdcwebapp
changeset 10:c0be9583df97 draft
Uploaded 20170525
| author | fabio |
|---|---|
| date | Thu, 25 May 2017 17:58:15 -0400 |
| parents | 61989e353d24 |
| children | 9d24947d4335 |
| files | ._gdcwebapp.xml ._json_data_source_mod.py gdcwebapp.xml json_data_source_mod.py tool_dependencies.xml |
| diffstat | 5 files changed, 23 insertions(+), 32 deletions(-) [+] |
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--- a/gdcwebapp.xml Thu May 25 15:49:07 2017 -0400 +++ b/gdcwebapp.xml Thu May 25 17:58:15 2017 -0400 @@ -1,25 +1,24 @@ <?xml version="1.0"?> <tool name="GDCWebApp" id="data_source_gdcwebapp" tool_type="data_source" hidden="False" display_interface="False" version="1.0.0" force_history_refresh="True"> <description>an intuitive interface to filter, extract, and convert Genomic Data Commons experiments</description> - <requirements> - <requirement type="package" version="2.7.10">python</requirement> - <!--<requirement type="package" version="1.0.0">galaxy_json_data_source</requirement>--> - </requirements> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> - <!--<version_command>json_data_source.py --version</version_command>--> - <!--<command>json_data_source.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "."</command>--> - <command interpreter="python">json_data_source_mod.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "." --appdata "${tool.name}"</command> + <command> + <![CDATA[ + mkdir -p ${tool.name}_tmp && + python ${__tool_directory__}/json_data_source_mod.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "." --appdata "${tool.name}_tmp" + ]]> + </command> <inputs check_values="False" action="http://bioinf.iasi.cnr.it/gdcwebapp/app.php" > <display>Go to GDCWebApp service $GALAXY_URL</display> <param name="URL" type="hidden" value="" /> </inputs> <outputs> - <data name="output1" format="auto" /> - <collection name="list_output" type="list:list" label="${tool.name} output"> - <discover_datasets pattern="(?P<archive_name>.*)_(?P<file_name>.*)\..*" ext="auto" visible="True" directory="${tool.name}" /> + <data name="output1" format="auto" visible="False" /> + <collection name="list_output" type="list:list" label="${tool.name} Output Collection"> + <discover_datasets pattern="(?P<archive_name>.*)_(?P<file_name>.*)\..*" ext="auto" visible="True" directory="${tool.name}_tmp" /> </collection> </outputs> <options sanitize="False" refresh="True" />
--- a/json_data_source_mod.py Thu May 25 15:49:07 2017 -0400 +++ b/json_data_source_mod.py Thu May 25 17:58:15 2017 -0400 @@ -145,6 +145,7 @@ extra_files_path = ''.join( [ target_output_filename, 'files' ] ) download_extra_data( extra_data, extra_files_path ) + """ the following code handles archives and decompress them in a collection """ check_ext = "" if ( fname.endswith( "gz" ) ): check_ext = "r:gz" @@ -157,25 +158,25 @@ for entry in tf: fileobj = tf.extractfile( entry ) if entry.isfile(): - """ - dataset_url, output_filename, \ - extra_files_path, file_name, \ - ext, out_data_name, \ - hda_id, dataset_id = set_up_config_values(json_params) - """ + + #dataset_url, output_filename, \ + # extra_files_path, file_name, \ + # ext, out_data_name, \ + # hda_id, dataset_id = set_up_config_values(json_params) + filename = os.path.basename( entry.name ) extension = splitext( filename ) extra_data = None #target_output_filename = output_filename - """ (?P<archive_name>.*)_(?P<file_name>.*)\..* """ + # (?P<archive_name>.*)_(?P<file_name>.*)\..* filename_with_collection_prefix = query_item.get( 'name' ) + "_" + filename target_output_filename = os.path.join(appdata_path, filename_with_collection_prefix) - """ - metadata_parameter_file.write( metadata_to_json_for_archive_entry( dataset_id, extension, - filename, target_output_filename, - ds_type='dataset', - primary=primary) ) - """ + + #metadata_parameter_file.write( metadata_to_json_for_archive_entry( dataset_id, extension, + # filename, target_output_filename, + # ds_type='dataset', + # primary=primary) ) + store_file_from_archive( fileobj, target_output_filename ) return True
--- a/tool_dependencies.xml Thu May 25 15:49:07 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="python" version="2.7.10"> - <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <!--<package name="galaxy_json_data_source" version="1.0.0"> - <repository changeset_revision="5ea54764a6b9" name="package_galaxy_json_data_source" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package>--> -</tool_dependency>