def setup_upload_jobs(cidc_api) -> Tuple[int, int]:
"""
Insert two uploads into the database created by different users
and return their IDs.
"""
with cidc_api.app_context():
other_user = Users(email="*****@*****.**")
other_user.insert()
job1 = UploadJobs(
uploader_email=user_email,
trial_id=trial_id,
status=UploadJobStatus.STARTED.value,
metadata_patch={
"test": {
"upload_placeholder": "baz"
},
"test2": "foo"
},
upload_type="",
gcs_xlsx_uri="",
gcs_file_map={"bip": "baz"},
multifile=False,
)
job2 = UploadJobs(
uploader_email=other_user.email,
trial_id=trial_id,
status=UploadJobStatus.STARTED.value,
metadata_patch={
"array": [{
"upload_placeholder": "baz"
}, {
"test2": "foo"
}]
},
upload_type="",
gcs_xlsx_uri="",
gcs_file_map={"bip": "baz"},
multifile=False,
)
job1.insert()
job2.insert()
return job1.id, job2.id
def setup_data(cidc_api, clean_db):
user = Users(email="*****@*****.**", approval_date=datetime.now())
shipment = {
"courier": "FEDEX",
"ship_to": "",
"ship_from": "",
"assay_type": assay_type,
"manifest_id": manifest_id,
"date_shipped": "2020-06-10 00:00:00",
"date_received": "2020-06-11 00:00:00",
"account_number": "",
"assay_priority": "1",
"receiving_party": "MSSM_Rahman",
"tracking_number": "",
"shipping_condition": "Frozen_Dry_Ice",
"quality_of_shipment": "Specimen shipment received in good condition",
}
metadata = {
"protocol_identifier":
trial_id,
"shipments": [
# we get duplicate shipment uploads sometimes
shipment,
shipment,
],
"participants": [{
"cimac_participant_id":
f"CTTTPP{p}",
"participant_id":
"x",
"cohort_name":
"",
"samples": [{
"cimac_id": f"CTTTPP{p}SS.0{s}",
"sample_location": "",
"type_of_primary_container": "Other",
"type_of_sample": "Other",
"collection_event_name": "",
"parent_sample_id": "",
} for s in range(num_samples[p])],
} for p in range(num_participants)],
"allowed_cohort_names": [""],
"allowed_collection_event_names": [""],
}
trial = TrialMetadata(trial_id=trial_id, metadata_json=metadata)
upload_job = UploadJobs(
uploader_email=user.email,
trial_id=trial.trial_id,
upload_type="pbmc",
gcs_xlsx_uri="",
metadata_patch=metadata,
multifile=False,
)
upload_job._set_status_no_validation(UploadJobStatus.MERGE_COMPLETED.value)
with cidc_api.app_context():
user.insert()
trial.insert()
upload_job.insert()
clean_db.refresh(user)
clean_db.refresh(upload_job)
clean_db.refresh(trial)
return user, upload_job, trial