comparison TrustStoreGalaxyBrowse.py @ 9:3e8bd0d01725

Attempt to guess data type.

8:278e80313c7f

import json
import operator
import urlparse
from py_ts import TrustStoreClient, utils
from galaxy.datatypes.checkers import util

# Tell urllib3 to use pyOpenSSL because we are on old Python stdlib.
# import urllib3.contrib.pyopenssl
# urllib3.contrib.pyopenssl.inject_into_urllib3()
# 

    output_data = all_params.get('output_data')
    extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
      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__']

    url_params = urlparse.unquote(json_params['URL']).split(";")
    if len(url_params) < 3:
        print("The url we got back is malformed: "+ json_params['URL'])
        sys.exit(5)
    short_url = url_params[0]

                        target_output_filename = file_name
                        dataset = "new_primary_dataset"
                        first = False
                    else:
                        target_output_filename = os.path.normpath(os.path.join(extra_files_path, name))
                    metadata_file.write(
                        metadata_to_json(dataset_id, target_output_filename, name, extension, data_type))
                    download = truststore.getFile(store, location)
                    if download is None:
                        print("File %s not found." % location.name)
                        sys.exit(4)
                    ungzip(download, target_output_filename)

9:3e8bd0d01725

import json
import operator
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
# urllib3.contrib.pyopenssl.inject_into_urllib3()
# 

    output_data = all_params.get('output_data')
    extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
      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'])
        sys.exit(5)
    short_url = url_params[0]

                        target_output_filename = file_name
                        dataset = "new_primary_dataset"
                        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, ext, data_type))
                    download = truststore.getFile(store, location)
                    if download is None:
                        print("File %s not found." % location.name)
                        sys.exit(4)
                    ungzip(download, target_output_filename)