Mercurial > repos > cathywise > truststore_browse
changeset 9:3e8bd0d01725
Attempt to guess data type.
| author | Wise, Catherine (Digital, Acton) <Catherine.Wise@csiro.au> |
|---|---|
| date | Thu, 25 Jun 2015 08:26:34 +1000 |
| parents | 278e80313c7f |
| children | 7301c2e96fce |
| files | TrustStoreGalaxyBrowse.py |
| diffstat | 1 files changed, 10 insertions(+), 1 deletions(-) [+] |
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--- a/TrustStoreGalaxyBrowse.py Wed Jun 24 14:16:51 2015 +1000 +++ b/TrustStoreGalaxyBrowse.py Thu Jun 25 08:26:34 2015 +1000 @@ -10,6 +10,8 @@ import urlparse from py_ts import TrustStoreClient, utils from galaxy.datatypes.checkers import util +from galaxy.datatypes import sniff +from galaxy.datatypes.registry import Registry # Tell urllib3 to use pyOpenSSL because we are on old Python stdlib. # import urllib3.contrib.pyopenssl @@ -119,6 +121,12 @@ operator.itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0]) extra_files_path = json_params['__new_file_path__'] + datatypes_registry = Registry() + datatypes_registry.load_datatypes( + root_dir=all_params['job_config']['GALAXY_ROOT_DIR'], + config=all_params['job_config']['GALAXY_DATATYPES_CONF_FILE'] + ) + url_params = urlparse.unquote(json_params['URL']).split(";") if len(url_params) < 3: print("The url we got back is malformed: "+ json_params['URL']) @@ -184,8 +192,9 @@ first = False else: target_output_filename = os.path.normpath(os.path.join(extra_files_path, name)) + ext = sniff.handle_uploaded_dataset_file(filename, datatypes_registry, ext=ext) metadata_file.write( - metadata_to_json(dataset_id, target_output_filename, name, extension, data_type)) + metadata_to_json(dataset_id, target_output_filename, name, ext, data_type)) download = truststore.getFile(store, location) if download is None: print("File %s not found." % location.name)