def handle(self, *args, **options):
required = ['username', 'title', 'file_name', 'source_column_index', 'data_file_column']
for arg in required:
if not options[arg]:
raise CommandError('%s was not provided.' % arg)
parser = SingleFileColumnParser()
parser.file_permanent = options['data_file_permanent']
parser.file_column_index = int( options['data_file_column'] )
parser.source_column_index = [int(x.strip()) for x in options['source_column_index'].split(",")]
parser.column_index_separator = "/"
parser.file_base_path = options['base_path']
if options['auxiliary_file_column'] is not None:
parser.auxiliary_file_column_index = int( options['auxiliary_file_column'] )
if options['species_column'] is not None:
parser.species_column_index = int( options['species_column'] )
if options['genome_build_column'] is not None:
parser.genome_build_column_index = int( options['genome_build_column'] )
if options['annotation_column'] is not None:
parser.annotation_column_index = int( options['annotation_column'] )
investigation = parser.run(options['file_name'])
investigation.title = options['title']
investigation.save()
create_dataset( investigation.uuid, options['username'], dataset_title=options['title'], slug=options['slug'], public=options['is_public'] )
def handle(self, *args, **options):
# set pre-defined options for the Refinery default tabular file format
options['source_column_index'] = "0" # source = filename
options['data_file_column'] = "1"
options['auxiliary_file_column'] = "2"
options['species_column'] = "3"
options['genome_build_column'] = "4"
options['annotation_column'] = "5"
options['data_file_permanent'] = True
required = ['username', 'title', 'file_name']
for arg in required:
if not options[arg]:
raise CommandError('%s was not provided.' % arg)
parser = SingleFileColumnParser()
parser.source_column_index = [
int(x.strip()) for x in options['source_column_index'].split(",")
]
parser.column_index_separator = "/"
parser.file_base_path = options['base_path']
# fixed settings
parser.file_column_index = int(options['data_file_column'])
parser.auxiliary_file_column_index = int(
options['auxiliary_file_column'])
parser.species_column_index = int(options['species_column'])
parser.genome_build_column_index = int(options['genome_build_column'])
parser.annotation_column_index = int(options['annotation_column'])
parser.file_permanent = options['data_file_permanent']
investigation = parser.run(options['file_name'])
investigation.title = options['title']
investigation.save()
create_dataset(investigation.uuid,
options['username'],
dataset_title=options['title'],
slug=options['slug'],
public=options['is_public'])
def handle(self, *args, **options):
# set pre-defined options for the Refinery default tabular file format
options["source_column_index"] = "0" # source = filename
options["data_file_column"] = "1"
options["auxiliary_file_column"] = "2"
options["species_column"] = "3"
options["genome_build_column"] = "4"
options["annotation_column"] = "5"
options["data_file_permanent"] = True
required = ["username", "title", "file_name"]
for arg in required:
if not options[arg]:
raise CommandError("%s was not provided." % arg)
parser = SingleFileColumnParser()
parser.source_column_index = [int(x.strip()) for x in options["source_column_index"].split(",")]
parser.column_index_separator = "/"
parser.file_base_path = options["base_path"]
# fixed settings
parser.file_column_index = int(options["data_file_column"])
parser.auxiliary_file_column_index = int(options["auxiliary_file_column"])
parser.species_column_index = int(options["species_column"])
parser.genome_build_column_index = int(options["genome_build_column"])
parser.annotation_column_index = int(options["annotation_column"])
parser.file_permanent = options["data_file_permanent"]
investigation = parser.run(options["file_name"])
investigation.title = options["title"]
investigation.save()
create_dataset(
investigation.uuid,
options["username"],
dataset_title=options["title"],
slug=options["slug"],
public=options["is_public"],
)
def process_metadata_table(username, title, metadata_file, source_columns,
data_file_column, auxiliary_file_column=None,
base_path="", data_file_permanent=False,
species_column=None, genome_build_column=None,
annotation_column=None, sample_column=None,
assay_column=None, slug=None, is_public=False):
"""Create a dataset given a metadata file object and its description
:param username: username
:type username: str
:param title: dataset name
:type title: str
:param metadata_file: metadata file in tab-delimited format
:type metadata_file: file
:param source_columns: a list of source column indices
:type source_columns: list of ints
:param data_file_column: data file column index
:type data_file_column: int
:param data_file_permanent: should data files be imported
:type data_file_permanent: bool
:param base_path: path to append to data file
:type base_path: str
:param auxiliary_file_column: auxiliary file column index
:type auxiliary_file_column: int
:param species_column: species column index
:type species_column: int
:param genome_build_column: genome build column index
:type genome_build_column: int
:param annotation_column: annotation column index
:type annotation_column: int
:param slug: dataset name shortcut
:type slug: str
:param is_public: is dataset available to public
:type is_public: bool
:returns: UUID of the new dataset
"""
try:
source_columns = [abs(int(x)) for x in source_columns]
except ValueError as exc:
logger.error(exc)
raise ValueError("source column indices must be integers")
try:
data_file_column = int(data_file_column)
except ValueError as exc:
logger.error(exc)
raise ValueError("data file column index must be an integer")
try:
auxiliary_file_column = int(auxiliary_file_column)
except (TypeError, ValueError):
auxiliary_file_column = None
try:
base_path = str(base_path)
except ValueError:
base_path = ""
try:
species_column = int(species_column)
except (TypeError, ValueError):
species_column = None
try:
genome_build_column = int(genome_build_column)
except (TypeError, ValueError):
genome_build_column = None
try:
annotation_column = int(annotation_column)
except (TypeError, ValueError):
annotation_column = None
try:
sample_column = int(sample_column)
except (TypeError, ValueError):
sample_column = None
try:
assay_column = int(assay_column)
except (TypeError, ValueError):
assay_column = None
try:
slug = str(slug)
except ValueError:
slug = None
data_file_permanent = bool(data_file_permanent)
is_public = bool(is_public)
file_source_translator = generate_file_source_translator(
username=username, base_path=base_path)
parser = SingleFileColumnParser(
metadata_file=metadata_file,
file_source_translator=file_source_translator,
source_column_index=source_columns,
data_file_column_index=data_file_column,
auxiliary_file_column_index=auxiliary_file_column,
file_base_path=base_path, data_file_permanent=data_file_permanent,
species_column_index=species_column,
genome_build_column_index=genome_build_column,
annotation_column_index=annotation_column,
sample_column_index=sample_column, assay_column_index=assay_column,
column_index_separator="/")
investigation = parser.run()
investigation.title = title
investigation.save()
return create_dataset(
investigation_uuid=investigation.uuid, username=username,
dataset_name=title, slug=slug, public=is_public)
def process_metadata_table(username,
title,
metadata_file,
source_columns,
data_file_column,
auxiliary_file_column=None,
base_path="",
data_file_permanent=False,
species_column=None,
genome_build_column=None,
annotation_column=None,
sample_column=None,
assay_column=None,
slug=None,
is_public=False,
delimiter="comma",
custom_delimiter_string=","):
"""Create a dataset given a metadata file object and its description
:param username: username
:type username: str
:param title: dataset name
:type title: str
:param metadata_file: metadata file in tab-delimited format
:type metadata_file: file
:param source_columns: a list of source column indices
:type source_columns: list of ints
:param data_file_column: data file column index
:type data_file_column: int
:param data_file_permanent: should data files be imported
:type data_file_permanent: bool
:param base_path: path to append to data file
:type base_path: str
:param auxiliary_file_column: auxiliary file column index
:type auxiliary_file_column: int
:param species_column: species column index
:type species_column: int
:param genome_build_column: genome build column index
:type genome_build_column: int
:param annotation_column: annotation column index
:type annotation_column: int
:param slug: dataset name shortcut
:type slug: str
:param is_public: is dataset available to public
:type is_public: bool
:returns: UUID of the new dataset
"""
try:
source_columns = [abs(int(x)) for x in source_columns]
except ValueError as exc:
logger.error(exc)
raise ValueError("source column indices must be integers")
try:
data_file_column = int(data_file_column)
except ValueError as exc:
logger.error(exc)
raise ValueError("data file column index must be an integer")
try:
auxiliary_file_column = int(auxiliary_file_column)
except (TypeError, ValueError):
auxiliary_file_column = None
try:
base_path = str(base_path)
except ValueError:
base_path = ""
try:
species_column = int(species_column)
except (TypeError, ValueError):
species_column = None
try:
genome_build_column = int(genome_build_column)
except (TypeError, ValueError):
genome_build_column = None
try:
annotation_column = int(annotation_column)
except (TypeError, ValueError):
annotation_column = None
try:
sample_column = int(sample_column)
except (TypeError, ValueError):
sample_column = None
try:
assay_column = int(assay_column)
except (TypeError, ValueError):
assay_column = None
try:
if slug:
slug = str(slug)
except ValueError:
slug = None
try:
delimiter = str(delimiter)
except ValueError:
delimiter = "comma"
try:
custom_delimiter_string = str(custom_delimiter_string)
except ValueError:
custom_delimiter_string = ","
data_file_permanent = bool(data_file_permanent)
is_public = bool(is_public)
file_source_translator = generate_file_source_translator(
username=username, base_path=base_path)
parser = SingleFileColumnParser(
metadata_file=metadata_file,
file_source_translator=file_source_translator,
source_column_index=source_columns,
data_file_column_index=data_file_column,
auxiliary_file_column_index=auxiliary_file_column,
file_base_path=base_path,
data_file_permanent=data_file_permanent,
species_column_index=species_column,
genome_build_column_index=genome_build_column,
annotation_column_index=annotation_column,
sample_column_index=sample_column,
assay_column_index=assay_column,
column_index_separator="/",
delimiter=delimiter,
custom_delimiter_string=custom_delimiter_string)
investigation = parser.run()
investigation.title = title
investigation.save()
return create_dataset(investigation_uuid=investigation.uuid,
username=username,
dataset_name=title,
slug=slug,
public=is_public)
