comparison TrustStoreGalaxyBrowse.py @ 14:c7287129f37f

And again.

13:da8958ad788e

import os
import json
import operator
import urlparse
from py_ts import TrustStoreClient, utils
import galaxy.model # need to import model before sniff to resolve a circular import dependency
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)

                    download = truststore.getFile(store, location)
                    if download is None:
                        print("File %s not found." % location.name)
                        sys.exit(4)
                    ungzip(download, target_output_filename)
                    ext = sniff.handle_uploaded_dataset_file(filename, datatypes_registry, ext=ext)
                    print("Guessed file type: " + ext)
                    metadata_file.write(
                        metadata_to_json(dataset_id, target_output_filename, name, ext, data_type))
    else:
        print("Store is damaged or we don't have sufficient access.")
        sys.exit(4)

14:c7287129f37f

import os
import json
import operator
import urlparse
from py_ts import TrustStoreClient, utils
# import galaxy.model # need to import model before sniff to resolve a circular import dependency
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)

                    download = truststore.getFile(store, location)
                    if download is None:
                        print("File %s not found." % location.name)
                        sys.exit(4)
                    ungzip(download, target_output_filename)
                    # ext = sniff.handle_uploaded_dataset_file(target_output_filename, datatypes_registry, ext=ext)
                    # print("Guessed file type: " + ext)
                    print("in file: " + properties_file)
                    metadata_file.write(
                        metadata_to_json(dataset_id, target_output_filename, name, extension, data_type))
    else:
        print("Store is damaged or we don't have sufficient access.")
        sys.exit(4)