def donor(rec_id):
"""
Backports a huma-donor record belonging to
https://www.encodeproject.org/profiles/human_donor.json.
The record will be checked for existence in Pulsar by doing a search on the field
`donor.upstread_identifer`` using as a query value the record's accession on the ENCODE Portal,
and also its aliases alias.
Args:
rec_id: `str`. An identifier (alias or uuid) for a human-donor record on the ENCODE Portal.
Returns:
`dict`: The JSON representation of the existing Donor if it already exists in
in Pulsar, otherwise the POST response.
"""
rec = ENC_CONN.get(rec_id, ignore404=False)
accession = rec[ACCESSION_PROP]
aliases = rec[ALIASES_PROP]
# Check if upstream exists already in Pulsar:
pulsar_rec = models.Donor.find_by({UPSTREAM_PROP: [accession, *aliases]})
if pulsar_rec:
return pulsar_rec
payload = {}
AGE_PROP = "age"
if AGE_PROP in rec:
payload[AGE_PROP] = rec[AGE_PROP]
GENDER_PROP = "sex"
if GENDER_PROP in rec:
payload["gender"] = rec[GENDER_PROP]
payload[UPSTREAM_PROP] = accession
try:
payload["name"] = euu.strip_alias_prefix(aliases[0])
except IndexError:
payload["name"] = rec_id
return models.Donor.post(payload)
def test_strip_alias_prefix(self):
"""Tests the function ``strip_alias_prefix()`` for success.
"""
alias = "michael-snyder:B-167"
self.assertEqual(utils.strip_alias_prefix(alias), "B-167")
def treatment(rec_id, patch=False):
"""
Backports a treatement record belonging to
https://www.encodeproject.org/profiles/treatment.json.
The required properties in the ENCODE Portal are:
1. treatment_term_name,
2. treatment_type.
An example on the Portal: https://www.encodeproject.org/treatments/933a1ff2-43a2-4a54-9c87-aad228d0033e/.
Identifying properties on the Portal are 'aliases' and 'uuid'.
Args:
rec_id: `str`. An identifier (alias or uuid) for a treatment record on the ENCODE Portal.
Returns:
`dict`: The JSON representation of the existing Treatment if it already exists in
in Pulsar, otherwise the POST response.
"""
rec = ENC_CONN.get(rec_id, ignore404=False)
aliases = rec[ALIASES_PROP]
#check if upstream exists already in Pulsar:
pulsar_rec = models.Treatment.find_by(
{UPSTREAM_PROP: [*aliases, rec[UUID_PROP], rec["@id"]]})
if pulsar_rec and not patch:
return pulsar_rec
payload = {}
payload["aliases"] = aliases
pulsar_document_ids = []
for doc_id in rec["documents"]:
pulsar_document_ids.append(document(doc_id))
payload["document_ids"] = pulsar_document_ids
payload[UPSTREAM_PROP] = rec[UUID_PROP]
payload["concentration"] = rec["amount"]
amount_units = rec["amount_units"]
pulsar_amount_units_rec = models.ConcentrationUnit.find_by(
payload={"name": amount_units})
if not pulsar_amount_units_rec:
raise Exception(
"ConcentrationUnit '{}' couldn't be found.".format(amount_units))
pulsar_amount_units_rec = pulsar_amount_units_rec["concentration_unit"]
payload["concentration_unit_id"] = pulsar_amount_units_rec["id"]
payload["duration"] = rec["duration"]
payload["duration_units"] = rec["duration_units"]
temp_prop_name = "temperature"
if temp_prop_name in rec:
temp = rec[temp_prop_name]
temp_units = rec["temperature_units"]
if temp_units == "Kelvin":
temp = pulsarpy.utils.kelvin_to_celsius(temp)
elif temp_units == "Fahrenheit":
temp = pulsarpy.utils.fahrenheit_to_celsius(temp)
payload[temp_prop_name] = rec[temp_prop_name]
ttn = rec["treatment_term_name"]
tti = rec["treatment_term_id"]
#Create new TreatmentTermName if not found in Pulsar.
pulsar_ttn_rec = treatment_term_name(ttn, tti)["treatment_term_name"]
payload["treatment_term_name_id"] = pulsar_ttn_rec["id"]
payload["treatment_type"] = rec["treatment_type"]
#The Portal's treatment model doesn't include a name prop or a description prop.
# Thus, 'name' shall be set to be equal to 'upstream_identifier'.
payload["name"] = euu.strip_alias_prefix(upstream)
if not pulsar_rec:
return models.Treatment.post(payload)
else:
pulsar_obj = models.Treatment(pulsar_rec["id"])
return pulsar_obj.patch(payload)