def run_prefix( # pylint: disable=too-many-arguments
project_id, prefix, metadata_json, status, host, email, password, api_key
): # pylint: disable=C0301
"""Assign all uploads from Gencove prefix to a project. Optionally add
metadata to the samples. Uploads can also be filtered through status.
Examples:
Assign uploads to a project:
gencove projects run-prefix 06a5d04b-526a-4471-83ba-fb54e0941758 gncv://my-project/path
Assign uploads to a project with metadata:
gencove projects run-prefix 06a5d04b-526a-4471-83ba-fb54e0941758 gncv://my-project/path --metadata-json='{"batch": "batch1"}'
Assign uploads filtered by status to a project:
gencove projects run-prefix 06a5d04b-526a-4471-83ba-fb54e0941758 gncv://my-project/path --status assigned
""" # noqa: E501
RunPrefix(
project_id,
prefix,
Credentials(email=email, password=password, api_key=api_key),
RunPrefixOptionals(
host=host, metadata_json=metadata_json, status=status
),
).run()
def test_login_mfa(mocker):
"""Test that the the login function in APIClient asks for the one time
password token.
"""
api_client = APIClient()
credentials = Credentials(email="*****@*****.**",
password="******",
api_key="")
def _request(
endpoint,
params,
*args, # pylint: disable=unused-argument
**kwargs, # pylint: disable=unused-argument
):
if endpoint == ApiEndpoints.GET_JWT.value:
if "otp_token" not in params:
raise APIClientError(
{"otp_token": ["Please enter your OTP token."]}, 401)
return {"access": "access", "refresh": "refresh"}
return {}
mocked_request = mocker.patch.object(APIClient,
"_request",
side_effect=_request)
mocked_prompt = mocker.patch("gencove.utils.click.prompt",
return_value="token")
login(api_client, credentials)
assert mocked_request.call_count == 2
mocked_prompt.assert_called_once_with("One time password",
type=str,
err=True)
def create_project_batch( # pylint: disable=too-many-arguments
project_id,
batch_type,
batch_name,
sample_ids,
host,
email,
password,
api_key,
):
"""Create a batch in a project."""
if sample_ids:
sample_ids = [s_id.strip() for s_id in sample_ids.split(",")]
echo_debug("Sample ids translation: {}".format(sample_ids))
else:
sample_ids = []
CreateBatch(
project_id,
batch_type,
batch_name,
sample_ids,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def create( # pylint: disable=too-many-arguments
project_id,
identifier,
metadata_json,
host,
email,
password,
api_key,
): # pylint: disable=line-too-long
"""Sets up periodic import of BaseSpace projects (their Biosamples) whose name contain the identifer
to a project in Gencove. Optionally assign metadata to the samples to be added when the automatic
import job runs.
Examples:
Set up automatic import of BaseSpace projects' samples that contain the identifier to a project:
gencove basespace autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 identifier-in-basespace-project-name
Set up automatic import of BaseSpace projects' samples that contain the identifier to a project with metadata:
gencove basespace autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 identifier-in-basespace-project-name --metadata-json='{"batch": "batch1"}'
""" # noqa: E501
BaseSpaceAutoImport(
project_id,
identifier,
Credentials(email=email, password=password, api_key=api_key),
BaseSpaceAutoImportOptionals(host=host, metadata_json=metadata_json),
).run()
def s3_import( # pylint: disable=too-many-arguments
s3_uri,
project_id,
metadata_json,
host,
email,
password,
api_key,
): # pylint: disable=line-too-long
"""Import all samples from a S3 URI to a project. Optionally add
metadata to the samples.
Examples:
Import samples to a project:
gencove s3 import s3://bucket/path/ 06a5d04b-526a-4471-83ba-fb54e0941758
Import samples to a project:
gencove s3 import s3://bucket/path/ 06a5d04b-526a-4471-83ba-fb54e0941758 --metadata-json='{"batch": "batch1"}'
""" # noqa: E501
S3Import(
s3_uri,
project_id,
Credentials(email=email, password=password, api_key=api_key),
S3ImportOptionals(host=host, metadata_json=metadata_json),
).run()
def biosamples_list(
basespace_project_id,
host,
email,
password,
api_key,
):
"""List all Biosamples from BaseSpace project.
Examples:
List Biosamples of a BaseSpace project:
gencove basespace biosamples list 12345678
List Biosamples of a BaseSpace projects:
gencove basespace biosamples list 12345678,87654321
"""
BiosamplesList(
basespace_project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def list_project_batch_types(project_id, host, email, password, api_key):
"""List batch types that are available for a project."""
ListBatchTypes(
project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def create( # pylint: disable=too-many-arguments
project_id,
s3_uri,
metadata_json,
host,
email,
password,
api_key,
): # pylint: disable=line-too-long
"""Sets up automatic import from S3 URI to a project in Gencove. Optionally assign metadata to the samples to be added when the automatic
import job runs.
Examples:
Set up automatic import from S3 to a project:
gencove s3 autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 s3://bucket/path/to/project
Set up automatic import from S3 to a project with metadata:
gencove s3 autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 s3://bucket/path/to/project --metadata-json='{"batch": "batch1"}'
""" # noqa: E501
S3AutoImport(
project_id,
s3_uri,
Credentials(email=email, password=password, api_key=api_key),
S3AutoImportOptionals(host=host, metadata_json=metadata_json),
).run()
def list_uploads( # pylint: disable=E0012,C0330,R0913
search, status, host, email, password, api_key
):
"""List user uploads."""
ListSampleSheet(
Credentials(email=email, password=password, api_key=api_key),
UploadsOptions(host=host, status=status, search=search),
).run()
def get_batch(batch_id, output_filename, host, email, password, api_key,
no_progress):
"""Get batch that is available for a project."""
GetBatch(
batch_id,
output_filename,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
no_progress,
).run()
def upload( # pylint: disable=E0012,C0330,R0913
source,
destination,
host,
email,
password,
api_key,
run_project_id,
output,
no_progress,
metadata,
): # noqa: D301
"""Upload FASTQ files to Gencove's system.
SOURCE: folder that contains fastq files to be uploaded (acceptable file
extensions are .fastq.gz, .fastq.bgz, .fq.gz, .fq.bgz), or .fastq-map.csv
file with the mapping of R1/R2 files to related sample by client_id
DESTINATION (optional): gncv://[folder], where the folder is the location
on Gencove systems
Examples:
Upload directory contents:
gencove upload test_dataset gncv://test
\f
Args:
source (.fastq.gz, .fastq.bgz, .fq.gz, .fq.bgz):
folder that contains fastq files to be uploaded
OR .fastq-map.csv file
destination (str, optional): 'gncv://' notated folder
on Gencove's system, where the files will be uploaded to.
run_project_id (UUID, optional): ID of a project to which all files
in this upload will be assigned to and then immediately analyzed.
output (str, optional): must be used with run_project_id. "-"
redirects the JSON to STDOUT, and a name redirects the output to
a file.
no_progress (bool, optional, default False): do not show progress
bar.
metadata (str, optional): JSON metadata to be applied to all samples
"""
Upload(
source,
destination,
Credentials(email=email, password=password, api_key=api_key),
UploadOptions(
host=host, project_id=run_project_id, metadata=metadata
),
output,
no_progress,
).run()
def status_merged_vcf(
project_id,
host,
email,
password,
api_key,
):
"""Get status of merge VCF files job in a project."""
StatusMergedVCF(
project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def create_merged_vcf(
project_id,
host,
email,
password,
api_key,
):
"""Merge VCF files in a project."""
CreateMergedVCF(
project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def list_project_samples( # pylint: disable=E0012,C0330,R0913
project_id, search, status, archive_status, host, email, password,
api_key):
"""List samples in a project."""
ListSamples(
project_id,
Credentials(email=email, password=password, api_key=api_key),
SamplesOptions(
host=host,
status=status,
archive_status=archive_status,
search=search,
),
).run()
def get_metadata(
sample_id,
output_filename,
host,
email,
password,
api_key,
):
"""Get sample metadata."""
GetMetadata(
sample_id,
output_filename,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def set_metadata(
sample_id,
json,
host,
email,
password,
api_key,
):
"""Set sample metadata."""
SetMetadata(
sample_id,
json,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def get_merged_vcf(
project_id,
output_filename,
host,
email,
password,
api_key,
no_progress,
):
"""Download merged VCF file in a project."""
GetMergedVCF(
project_id,
output_filename,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
no_progress,
).run()
def delete_project_samples( # pylint: disable=too-many-arguments
project_id,
sample_ids,
host,
email,
password,
api_key,
):
"""Delete samples in a project."""
sample_ids = ([s_id.strip()
for s_id in sample_ids.split(",")] if sample_ids else [])
echo_debug("Sample ids translation: {}".format(sample_ids))
DeleteSamples(
project_id,
sample_ids,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def basespace_list(
host,
email,
password,
api_key,
):
"""List all BaseSpace projects.
Examples:
Import Biosamples to a project:
gencove basespace projects list
"""
BaseSpaceList(
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def autoimport_list(
host,
email,
password,
api_key,
):
"""Lists S3 automatic import jobs.
Examples:
List S3 automatic import jobs:
gencove s3 autoimports list
""" # noqa: E501
S3AutoImportList(
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def basespace_import( # pylint: disable=too-many-arguments
basespace_project_ids,
project_id,
metadata_json,
host,
email,
password,
api_key,
): # pylint: disable=line-too-long
"""Import all Biosamples from BaseSpace projects to a project. Optionally add
metadata to the samples.
Examples:
Import Biosamples to a project:
gencove basespace projects import 12345678 06a5d04b-526a-4471-83ba-fb54e0941758
Import Biosamples from multiple BaseSpace projects to a project:
gencove basespace projects import 12345678,87654321 06a5d04b-526a-4471-83ba-fb54e0941758
Import Biosamples to a project with metadata:
gencove basespace projects import 12345678 06a5d04b-526a-4471-83ba-fb54e0941758 --metadata-json='{"batch": "batch1"}'
""" # noqa: E501
basespace_project_ids = [
basespace_project_id.strip()
for basespace_project_id in basespace_project_ids.split(",")
]
echo_debug(
"BaseSpace project ids translation: {}".format(basespace_project_ids))
BaseSpaceImport(
basespace_project_ids,
project_id,
Credentials(email=email, password=password, api_key=api_key),
BaseSpaceImportOptionals(host=host, metadata_json=metadata_json),
).run()
def download( # pylint: disable=E0012,C0330,R0913
destination,
project_id,
sample_ids,
file_types,
skip_existing,
download_urls,
download_template,
host,
email,
password,
api_key,
no_progress,
): # noqa: D413,D301,D412 # pylint: disable=C0301
"""Download deliverables of a project.
Must specify either project id or sample ids.
Examples:
Download all samples results:
gencove download ./results --project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db
Download some samples:
gencove download ./results --sample-ids 59f5c1fd-cce0-4c4c-90e2-0b6c6c525d71,7edee497-12b5-4a1d-951f-34dc8dce1c1d
Download specific deliverables:
gencove download ./results --project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db --file-types alignment-bam,impute-vcf,fastq-r1,fastq-r2
Skip download entirely and print out the deliverables as a JSON:
gencove download - --project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db --download-urls
\f
Args:
destination (str): path/to/save/deliverables/to.
project_id (str): project id in Gencove's system.
sample_ids (list(str), optional): specific samples for which
to download the results. if not specified, download deliverables
for all samples.
file_types (list(str), optional): specific deliverables to download
results for. if not specified, all file types will be downloaded.
skip_existing (bool, optional, default True): skip downloading existing
files.
download_urls (bool, optional): output the files available for a
download. if the destination parameter is "-", it goes to the
stdout.
no_progress (bool, optional, default False): do not show progress
bar.
""" # noqa: E501
s_ids = tuple()
if sample_ids:
s_ids = tuple(s_id.strip() for s_id in sample_ids.split(","))
echo_debug("Sample ids translation: {}".format(s_ids))
f_types = tuple()
if file_types:
f_types = tuple(f_type.strip() for f_type in file_types.split(","))
echo_debug("File types translation: {}".format(f_types))
Download(
destination,
DownloadFilters(project_id=project_id,
sample_ids=s_ids,
file_types=f_types),
Credentials(email=email, password=password, api_key=api_key),
DownloadOptions(
host=host,
skip_existing=skip_existing,
download_template=download_template,
),
download_urls,
no_progress,
).run()
def download_file(
sample_id,
file_type,
destination,
host,
email,
password,
api_key,
no_progress,
): # noqa: D413,D301,D412 # pylint: disable=C0301
"""Download sample file metadata.
SAMPLE_ID specific sample for which to download the results
FILE_TYPE specific deliverable to download results for
DESTINATION path/to/file
Examples:
Download sample:
gencove samples download-file e6b45af7-07c5-4a6d-9f97-6e1efbf3e215 ancestry-json ancestry.json
Download and print to stdout then compress using gzip:
gencove samples download-file e6b45af7-07c5-4a6d-9f97-6e1efbf3e215 ancestry-json - | gzip > ancestry.json.gz
\f
Args:
sample_id (str): specific sample for which
to download the results.
file_type (str): specific deliverable to download
results for.
destination (str): path/to/file.
no_progress (bool, optional, default False): do not show progress
bar.
""" # noqa: E501
if destination in ("-", "/dev/stdout"):
DownloadFile(
sample_id,
file_type,
sys.stdout.buffer,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
no_progress,
).run()
else:
try:
with open(destination, "wb") as destination_file:
DownloadFile(
sample_id,
file_type,
destination_file,
Credentials(email=email,
password=password,
api_key=api_key),
Optionals(host=host),
no_progress,
).run()
except IsADirectoryError:
echo_error("Please specify a file path (not directory path)"
" for DESTINATION")
raise click.Abort() # pylint: disable=raise-missing-from
def list_projects(host, email, password, api_key):
"""List your projects."""
List(
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()