'kive') # don't do this in practice, store your password somewhere safe
efd_name = "ExternalFiles" # make an ExternalFileDirectory with this name
efd_path = "" # fill this in with your own path
external_path = "external_file.dat"
external_file_contents = "foo"
with open(os.path.join(efd_path, external_path), "wb") as f:
f.write(external_file_contents)
# Upload data
try:
ext_ds = kive.add_dataset('ExternalDatasetFile',
'External copy of 1234A_R1',
None,
None,
None, ["Everyone"],
externalfiledirectory=efd_name,
external_path=external_path)
except KiveMalformedDataException:
ext_ds = kive.find_datasets(name='ExternalDatasetFile')[0]
# Now get the file and check that the results make sense.
retrieved_ext_ds = kive.get_dataset(ext_ds.dataset_id)
print(retrieved_ext_ds.__dict__)
assert retrieved_ext_ds.dataset_id == ext_ds.dataset_id
assert retrieved_ext_ds.filename == ext_ds.filename
assert retrieved_ext_ds.name == "ExternalDatasetFile"
assert retrieved_ext_ds.cdt.cdt_id == "__raw__"
efd_name = "ExternalFiles" # make an ExternalFileDirectory with this name
efd_path = "" # fill this in with your own path
external_path = "external_file.dat"
external_file_contents = "foo"
with open(os.path.join(efd_path, external_path), "wb") as f:
f.write(external_file_contents)
# Upload data
try:
ext_ds = kive.add_dataset(
'ExternalDatasetFile',
'External copy of 1234A_R1',
None,
None,
None,
["Everyone"],
externalfiledirectory=efd_name,
external_path=external_path
)
except KiveMalformedDataException:
ext_ds = kive.find_datasets(name='ExternalDatasetFile')[0]
# Now get the file and check that the results make sense.
retrieved_ext_ds = kive.get_dataset(ext_ds.dataset_id)
print(retrieved_ext_ds.__dict__)
assert retrieved_ext_ds.dataset_id == ext_ds.dataset_id
assert retrieved_ext_ds.filename == ext_ds.filename
assert retrieved_ext_ds.name == "ExternalDatasetFile"
from kiveapi import KiveAPI, KiveMalformedDataException
# This assumes you have a Kive instance listening on port 8000, running
# the demo fixture. In production, you wouldn't put your authentication
# information in source code.
KiveAPI.SERVER_URL = 'http://localhost:8000'
kive = KiveAPI()
kive.login('kive', 'kive')
# Upload data
try:
fastq1 = kive.add_dataset('New fastq file 1', 'None', open('exfastq1.fastq', 'r'), None, None, ["Everyone"])
except KiveMalformedDataException:
fastq1 = kive.find_datasets(name='New fastq file 1')[0]
try:
fastq2 = kive.add_dataset('New fastq file 2', 'None', open('exfastq2.fastq', 'r'), None, None, ["Everyone"])
except KiveMalformedDataException:
fastq2 = kive.find_datasets(name='New fastq file 2')[0]
# Get the pipeline by family ID
pipeline_family = kive.get_pipeline_family(2)
print('Using data:')
print(fastq1, fastq2)
print('With pipeline:')
print(pipeline_family.published_or_latest())
# Create a RunBatch.
rb = kive.create_run_batch(
from kiveapi import KiveAPI, KiveMalformedDataException
# This assumes you have a Kive instance listening on port 8000, running
# the demo fixture. In production, you wouldn't put your authentication
# information in source code.
KiveAPI.SERVER_URL = 'http://localhost:8000'
kive = KiveAPI()
kive.login('kive', 'kive')
# Upload data
try:
fastq1 = kive.add_dataset('New fastq file 1', 'None',
open('exfastq1.fastq', 'r'), None, None,
["Everyone"])
except KiveMalformedDataException:
fastq1 = kive.find_datasets(name='New fastq file 1')[0]
try:
fastq2 = kive.add_dataset('New fastq file 2', 'None',
open('exfastq2.fastq', 'r'), None, None,
["Everyone"])
except KiveMalformedDataException:
fastq2 = kive.find_datasets(name='New fastq file 2')[0]
# Get the pipeline by family ID
pipeline_family = kive.get_pipeline_family(2)
print('Using data:')
print(fastq1, fastq2)
print('With pipeline:')