comparison TrustStoreGalaxyBrowse.py @ 45:31838e0ecf45 default tip

Fixes.

44:5589d367885e

                break
            os.write(file_handle, chunk)
        os.close(file_handle)
        gzipped_file.close()

        shutil.copy(uncompressed, outputFile)
        try:
            os.remove(uncompressed)
            os.remove(download)
        except OSError:
            pass
    else:
        shutil.copy(download, outputFile)

def construct_multi_filename(id, name, file_type):
    """ Implementation of *Number of Output datasets cannot be determined until
    tool run* from documentation_.
    .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
    From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py
    """
    filename = "%s_%s_%s_%s_%s" % ('primary', id, name, 'visible', file_type)
    return filename

def metadata_to_json(dataset_id, filename, name, extesion, ds_type='dataset', primary=False):
    """ Return line separated JSON
    From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py
    """
    meta_dict = dict(type=ds_type,
                     ext=extesion,
                     filename=filename,
                     name=name,
                     metadata={})
    if primary:
        meta_dict['base_dataset_id'] = dataset_id

                    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)

45:31838e0ecf45

                break
            os.write(file_handle, chunk)
        os.close(file_handle)
        gzipped_file.close()

        try:
            shutil.copy(uncompressed, outputFile)
        except shutil.Error:
            pass # If the file is already in the right location, move along.
        try:
            os.remove(uncompressed)
            os.remove(download)
        except OSError:
            pass
    else:
        try:
            shutil.copy(download, outputFile)
        except shutil.Error:
            pass # If the file is already in the right location, move along.

def construct_multi_filename(id, name, file_type):
    """ Implementation of *Number of Output datasets cannot be determined until
    tool run* from documentation_.
    .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
    From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py
    """
    filename = "%s_%s_%s_%s_%s" % ('primary', id, name, 'visible', file_type)
    return filename

def metadata_to_json(dataset_id, filename, name, extension, ds_type='dataset', primary=False):
    """ Return line separated JSON
    From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py
    """
    ext = extension
    if ext == 'fa':
        ext = 'fasta'
    meta_dict = dict(type=ds_type,
                     ext=ext,
                     filename=filename,
                     name=name,
                     metadata={})
    if primary:
        meta_dict['base_dataset_id'] = dataset_id

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