comparison TrustStoreGalaxyBrowse.py @ 43:174df9815ecd

Fix data types.

42:1ca5aa0a4d6b

import os
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]

    root = truststore.listDirectory(store)

    first = True

    print("Preparing the following for downloading: " + str(paths))

    if root is not None:
        with open(metadata_path, 'wb') as metadata_file:
            for path in paths:
                locations = utils.Navigation.files_at_path(root, path)

                    filename = "".join(c in SAFE_CHARS and c or '-' for c in location.name)
                    extension = os.path.splitext(filename)[1].strip(".")
                    name = construct_multi_filename(hda_id, filename, extension)
                    target_output_filename = None
                    data_type = "new_primary_dataset"
                    if first:
                        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)
    else:
        print("Store is damaged or we don't have sufficient access.")
        sys.exit(4)

43:174df9815ecd

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)
    short_url = url_params[0]

    root = truststore.listDirectory(store)

    first = True

    print("Preparing the following for downloading: " + str(paths))

    # Empty parameter file.
    open(file_name, 'w' ).close()

    if root is not None:
        with open(metadata_path, 'wb') as metadata_file:
            for path in paths:
                locations = utils.Navigation.files_at_path(root, path)

                    filename = "".join(c in SAFE_CHARS and c or '-' for c in location.name)
                    extension = os.path.splitext(filename)[1].strip(".")
                    name = construct_multi_filename(hda_id, filename, extension)
                    target_output_filename = None
                    data_type = "new_primary_dataset"
                    # if first:
                    #     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))
                    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)