def refresh_materialized_view(schema_name, view_name, db: DatabaseSession):
"""
Refresh materialized view <schema>.<view> in ID3C.
"""
LOG.info(f"Refreshing materialized view «{schema_name}.{view_name}»")
db.cursor().execute(
"""
select refresh_materialized_view(%s, %s)
""", (schema_name, view_name))
LOG.info("Successfully refreshed materialized view")
def ls():
"""List users."""
session = DatabaseSession()
with session.cursor() as cursor:
cursor.execute("""
select usename as name,
pg_catalog.shobj_description(usesysid, 'pg_authid') as description,
coalesce(array_agg(groname order by groname) filter (where groname is not null), '{}') as roles
from pg_catalog.pg_user
left join pg_catalog.pg_group on (grolist @> array[usesysid])
where usename not in ('postgres', 'rdsadmin')
group by name, usesysid
order by name
""")
users = list(cursor)
# Line up name + description nicely into a column
def maxlen(attr):
return max(map(len, filter(None, map(attrgetter(attr), users))),
default=0)
template = "{:<%d}" % (maxlen("name") + 3)
for user in users:
click.secho(template.format(user.name), bold=True, nl=False)
click.echo(", ".join(user.roles))
def insert_dets(db: DatabaseSession, project: Project, offers: List[dict]):
"""
Inserts synthethic DETs into ``receiving.redcap_det`` for the REDCap record
*offers* made for *project*.
"""
dets = [(Json(det(project, offer, TESTING_INSTRUMENT)), )
for offer in offers]
LOG.info(f"Inserting {len(dets):,} synthetic REDCap DETs for {project}")
with db.cursor() as cursor:
execute_values(
cursor, """
insert into receiving.redcap_det (document) values %s
""", dets)
def etl_fhir(*, db: DatabaseSession):
LOG.debug(f"Starting the FHIR ETL routine, revision {REVISION}")
# Fetch and iterate over FHIR documents that aren't processed
#
# Use a server-side cursor by providing a name and limit to one fetched
# record at a time, to limit local process size.
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same FHIR documents.
LOG.debug("Fetching unprocessed FHIR documents")
fhir_documents = db.cursor("fhir")
fhir_documents.itersize = 1
fhir_documents.execute(
"""
select fhir_id as id, document
from receiving.fhir
where not processing_log @> %s
order by id
for update
""", (Json([{
"etl": ETL_NAME,
"revision": REVISION
}]), ))
for record in fhir_documents:
with db.savepoint(f"FHIR document {record.id}"):
LOG.info(f"Processing FHIR document {record.id}")
assert_bundle_collection(record.document)
bundle = Bundle(record.document)
resources = extract_resources(bundle)
# Loop over every Resource the Bundle entry, processing what is
# needed along the way.
try:
assert_required_resource_types_present(resources)
process_bundle_entries(db, bundle)
except SkipBundleError as error:
LOG.warning(
f"Skipping bundle in FHIR document «{record.id}»: {error}")
mark_skipped(db, record.id)
continue
mark_processed(db, record.id, {"status": "processed"})
LOG.info(f"Finished processing FHIR document {record.id}")
def upsert_encounter_location(db: DatabaseSession, encounter_id: int,
relation: str, location_id: int) -> Any:
"""
Upserts an encounter location by its *encounter_id* and *relation*.
"""
LOG.debug(f"Upserting encounter {relation} location")
with db.cursor() as cursor:
cursor.execute(
"""
insert into warehouse.encounter_location (encounter_id, relation, location_id)
values (%s, %s, %s)
on conflict (encounter_id, relation) do update
set location_id = excluded.location_id
""", (encounter_id, relation, location_id))
assert cursor.rowcount == 1, "Upsert affected no rows!"
def mark_processed(db: DatabaseSession, det_id: int, entry = {}) -> None:
LOG.debug(f"Appending to processing log of REDCap DET record {det_id}")
data = {
"det_id": det_id,
"log_entry": Json({
**entry,
"timestamp": datetime.now(timezone.utc),
}),
}
with db.cursor() as cursor:
cursor.execute("""
update receiving.redcap_det
set processing_log = processing_log || %(log_entry)s
where redcap_det_id = %(det_id)s
""", data)
def set_ls():
"""List identifier sets."""
session = DatabaseSession()
with session.cursor() as cursor:
cursor.execute("""
select name, description
from warehouse.identifier_set
order by lower(name)
""")
sets = list(cursor)
# Line up names nicely into a column
template = "{:<%d}" % (max(len(s.name) for s in sets) + 3)
for set in sets:
click.secho(template.format(set.name), bold = True, nl = False)
click.echo(set.description)
def labels(filename, layout: str='default'):
"""
Make barcode labels for an existing batch of identifiers.
A PDF of printable barcode labels is generated using the Lab Labels¹
instance <https://backoffice.seattleflu.org/labels/>. An alternative
instance may be used by setting the LABEL_API environment variable to the
instance URL.
The batch of identifiers to make labels for is selected interactively based
on the identifier set and time of original generation.
If --layout is requested, the printable barcode labels will use the given
version of the layout, if available.
¹ https://github.com/MullinsLab/Lab-Labels
"""
session = DatabaseSession()
# Fetch batches of identifiers
with session.cursor() as cursor:
cursor.execute("""
select identifier_set.name as set_name,
to_char(generated, 'FMDD Mon YYYY') as generated_date,
generated,
count(*)
from warehouse.identifier
join warehouse.identifier_set using (identifier_set_id)
group by generated, identifier_set.name
order by generated, identifier_set.name
""")
batches = list(cursor)
# Print batches for selection
click.echo("\nThe following batches of identifiers exist:\n")
for index, batch in enumerate(batches, 1):
click.secho(f"{index:2d}) ", bold = True, nl = False)
click.echo(f"{batch.generated_date:>11} — {batch.count:>5,} {batch.set_name}")
# Which batch do we want?
choice = click.prompt(
"\nFor which batch would you like to make labels",
prompt_suffix = "? ",
type = click.IntRange(1, len(batches)),
default = str(len(batches)))
chosen_batch = batches[int(choice) - 1]
# Fetch identifiers for the chosen batch
with session.cursor() as cursor:
cursor.execute("""
select uuid, barcode
from warehouse.identifier
join warehouse.identifier_set using (identifier_set_id)
where identifier_set.name = %s
and generated = %s
""", (chosen_batch.set_name, chosen_batch.generated))
identifiers = list(cursor)
assert len(identifiers) == chosen_batch.count
label_layout = labelmaker.layout_identifiers(chosen_batch.set_name, identifiers, layout)
pdf = labelmaker.generate_pdf(label_layout)
filename.write(pdf)
def etl_longitudinal(*, db: DatabaseSession):
LOG.debug(f"Starting the longitudinal ETL routine, revision {REVISION}")
# Fetch and iterate over longitudinal records that aren't processed
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same longitudinal records.
LOG.debug("Fetching unprocessed longitudinal records")
longitudinal = db.cursor("longitudinal")
longitudinal.execute(
"""
select longitudinal_id as id, document
from receiving.longitudinal
where not processing_log @> %s
order by id
for update
""", (Json([{
"revision": REVISION
}]), ))
for record in longitudinal:
with db.savepoint(f"longitudinal record {record.id}"):
LOG.info(f"Processing longitudinal record {record.id}")
# Check validity of barcode
received_sample_identifier = sample_identifier(db, record.document)
# Check sample exists in database
if received_sample_identifier:
sample = find_sample(db, identifier=received_sample_identifier)
else:
sample = None
# Most of the time we expect to see existing sites so a
# select-first approach makes the most sense to avoid useless
# updates.
site = find_or_create_site(
db,
identifier=site_identifier(record.document),
details={"type": record.document['type']})
# Most of the time we expect to see existing individuals and new
# encounters.
# Encounters we see more than once are presumed to be
# corrections.
individual = find_or_create_individual(
db,
identifier=record.document["individual"],
sex=sex(record.document))
encounter = upsert_encounter(
db,
identifier=record.document["identifier"],
encountered=record.document["encountered"],
individual_id=individual.id,
site_id=site.id,
age=age(record.document),
details=encounter_details(record.document))
if sample:
sample = update_sample(db,
sample=sample,
encounter_id=encounter.id)
# Link encounter to a Census tract, if we have it
tract_identifier = record.document.get("census_tract")
if tract_identifier:
tract = find_location(db, "tract", str(tract_identifier))
assert tract, f"Tract «{tract_identifier}» is unknown"
upsert_encounter_location(db,
encounter_id=encounter.id,
relation="residence",
location_id=tract.id)
mark_processed(db, record.id, {"status": "processed"})
LOG.info(f"Finished processing longitudinal record {record.id}")
def etl_manifest(*, db: DatabaseSession):
LOG.debug(f"Starting the manifest ETL routine, revision {REVISION}")
# XXX TODO: Stop hardcoding valid identifier sets. Instead, accept them as
# an option or config (and validate option choices against what's actually
# in the database). We won't want to validate using click.option(),
# because that would necessitate a database connection simply to run
# bin/id3c at all.
# -trs, 13 May 2019
expected_identifier_sets = {
"samples": {"samples"},
"collections": {
"collections-environmental",
"collections-fluathome.org",
"collections-household-intervention",
"collections-household-intervention-asymptomatic",
"collections-household-observation",
"collections-household-observation-asymptomatic",
"collections-kiosks",
"collections-kiosks-asymptomatic",
"collections-seattleflu.org",
"collections-swab&send",
"collections-swab&send-asymptomatic",
"collections-self-test",
"collections-scan",
"collections-haarvi",
"samples-haarvi",
},
"rdt": {"collections-fluathome.org"}
}
# Fetch and iterate over samples that aren't processed
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same samples.
LOG.debug("Fetching unprocessed manifest records")
manifest = db.cursor("manifest")
manifest.execute("""
select manifest_id as id, document
from receiving.manifest
where not processing_log @> %s
order by id
for update
""", (Json([{ "etl": ETL_NAME, "revision": REVISION }]),))
for manifest_record in manifest:
with db.savepoint(f"manifest record {manifest_record.id}"):
LOG.info(f"Processing record {manifest_record.id}")
# Convert sample barcode to full identifier, ensuring it's
# known and from the correct identifier set.
sample_barcode = manifest_record.document.pop("sample")
sample_identifier = find_identifier(db, sample_barcode)
if not sample_identifier:
LOG.warning(f"Skipping sample with unknown sample barcode «{sample_barcode}»")
mark_skipped(db, manifest_record.id)
continue
if (manifest_record.document.get("sample_type") and
manifest_record.document["sample_type"] == "rdt"):
assert sample_identifier.set_name in expected_identifier_sets["rdt"], \
(f"Sample identifier found in set «{sample_identifier.set_name}», " +
f"not {expected_identifier_sets['rdt']}")
else:
assert sample_identifier.set_name in expected_identifier_sets["samples"], \
(f"Sample identifier found in set «{sample_identifier.set_name}», " +
f"not {expected_identifier_sets['samples']}")
# Optionally, convert the collection barcode to full
# identifier, ensuring it's known and from the correct
# identifier set.
collection_barcode = manifest_record.document.pop("collection", None)
collection_identifier = find_identifier(db, collection_barcode) if collection_barcode else None
if collection_barcode and not collection_identifier:
LOG.warning(f"Skipping sample with unknown collection barcode «{collection_barcode}»")
mark_skipped(db, manifest_record.id)
continue
assert not collection_identifier \
or collection_identifier.set_name in expected_identifier_sets["collections"], \
f"Collection identifier found in set «{collection_identifier.set_name}», not {expected_identifier_sets['collections']}" # type: ignore
# Sample collection date
collection_date = manifest_record.document.get("date")
# Upsert sample cooperatively with enrollments ETL routine
#
# The details document was intentionally modified by two pop()s
# earlier to remove barcodes that were looked up. The
# rationale is that we want just one clear place in the
# warehouse for each piece of information.
sample, status = upsert_sample(db,
identifier = sample_identifier.uuid,
collection_identifier = collection_identifier.uuid if collection_identifier else None,
collection_date = collection_date,
additional_details = manifest_record.document)
mark_loaded(db, manifest_record.id,
status = status,
sample_id = sample.id)
LOG.info(f"Finished processing manifest record {manifest_record.id}")
def upsert_sample(db: DatabaseSession,
identifier: str,
collection_identifier: Optional[str],
collection_date: Optional[str],
additional_details: dict) -> Tuple[Any, str]:
"""
Upsert sample by its *identifier* and/or *collection_identifier*.
An existing sample has its *identifier*, *collection_identifier*,
*collection_date* updated, and the provided *additional_details* are
merged (at the top-level only) into the existing sample details, if any.
Raises an exception if there is more than one matching sample.
"""
data = {
"identifier": identifier,
"collection_identifier": collection_identifier,
"collection_date": collection_date,
"additional_details": Json(additional_details),
}
# Look for existing sample(s)
with db.cursor() as cursor:
cursor.execute("""
select sample_id as id, identifier, collection_identifier, encounter_id
from warehouse.sample
where identifier = %(identifier)s
or collection_identifier = %(collection_identifier)s
for update
""", data)
samples = list(cursor)
# Nothing found → create
if not samples:
LOG.info("Creating new sample")
status = 'created'
sample = db.fetch_row("""
insert into warehouse.sample (identifier, collection_identifier, collected, details)
values (%(identifier)s,
%(collection_identifier)s,
date_or_null(%(collection_date)s),
%(additional_details)s)
returning sample_id as id, identifier, collection_identifier, encounter_id
""", data)
# One found → update
elif len(samples) == 1:
status = 'updated'
sample = samples[0]
LOG.info(f"Updating existing sample {sample.id}")
sample = db.fetch_row("""
update warehouse.sample
set identifier = %(identifier)s,
collection_identifier = %(collection_identifier)s,
collected = date_or_null(%(collection_date)s),
details = coalesce(details, '{}') || %(additional_details)s
where sample_id = %(sample_id)s
returning sample_id as id, identifier, collection_identifier, encounter_id
""",
{ **data, "sample_id": sample.id })
assert sample.id, "Update affected no rows!"
# More than one found → error
else:
raise Exception(f"More than one sample matching sample and/or collection barcodes: {samples}")
return sample, status
def kit_enrollments(*, db: DatabaseSession):
LOG.debug(
f"Starting the kit enrollments ETL routine, revision {ENROLLMENTS_REVISION}"
)
expected_barcode_types = {"ScannedSelfSwab", "ManualSelfSwab"}
LOG.debug("Fetching unprocessed enrollments")
enrollments = db.cursor("enrollments")
enrollments.execute(
"""
select enrollment_id as id, document
from receiving.enrollment
where not processing_log @> %s
order by id
for update
""", (Json([{
"etl": ETL_NAME,
"revision": ENROLLMENTS_REVISION
}]), ))
for enrollment in enrollments:
with db.savepoint(f"enrollment {enrollment.id}"):
LOG.info(f"Processing enrollment {enrollment.id}")
# Find encounter that should have been created
# from this enrollment record through etl enrollments
encounter = find_encounter(db, enrollment.document["id"])
# Error out the kit etl process if no encounter found
# The kit etl process can try again starting with this record
# next time with the idea that the encounter will be
# created by then.
if not encounter:
raise EncounterNotFoundError(
f"No encounter with identifier «{enrollment.document['id']}» found"
)
# Skip and mark the enrollment document as processed if the
# encounter found is linked to a site that is not self-test
if encounter.site != "self-test":
LOG.debug(
f"Found encounter {encounter.id} «{encounter.identifier}»"
+ f"linked to site «{encounter.site}», not 'self-test'")
mark_enrollment_processed(db, enrollment.id)
continue
for code in enrollment.document["sampleCodes"]:
barcode = code.get("code")
# Kit must have a barcode
if not barcode:
LOG.warning(f"No barcode found in sampleCodes {code}")
continue
# Barcode must be of expected barcode type
if code["type"] not in expected_barcode_types:
LOG.debug(f"Skipping barcode with type {code['type']}")
continue
# Convert kit barcode to full identifier
kit_identifier = find_identifier(db, barcode)
if not kit_identifier:
LOG.warning(
f"Skipping kit with unknown barcode «{barcode}»")
continue
if kit_identifier.set_name not in expected_identifier_sets[
"kits"]:
LOG.warning(
f"Skipping kit with identifier found in " +
f"set «{kit_identifier.set_name}» not {expected_identifier_sets['kits']}"
)
continue
details = {"type": code["type"]}
kit, status = upsert_kit_with_encounter(
db,
identifier=kit_identifier.uuid,
encounter_id=encounter.id,
additional_details=details)
if status == "updated":
update_kit_samples(db, kit)
mark_enrollment_processed(db, enrollment.id)
LOG.info(f"Finished processing enrollment {enrollment.id}")
def kit_manifests(*, db: DatabaseSession):
LOG.debug(
f"Starting the kits manifests ETL routine, revision {MANIFEST_REVISION}"
)
LOG.debug("Fetching unprocessed manifest records")
manifest = db.cursor("manifest")
manifest.execute(
"""
select manifest_id as id, document
from receiving.manifest
where not processing_log @> %s
order by id
for update
""", (Json([{
"etl": ETL_NAME,
"revision": MANIFEST_REVISION
}]), ))
for manifest_record in manifest:
with db.savepoint(f"manifest record {manifest_record.id}"):
LOG.info(f"Processing record {manifest_record.id}")
# Mark record as skipped
# if it does not contain a kit related sample
if "kit" not in manifest_record.document:
LOG.info(
f"Skipping manifest record {manifest_record.id} without kit data"
)
mark_skipped(db, manifest_record.id)
continue
sample_barcode = manifest_record.document.pop("sample")
sample_identifier = find_identifier(db, sample_barcode)
# Mark record as skipped
# if it has an unknown sample barcode
if not sample_identifier:
LOG.warning(
f"Skipping manifest record with unknown sample barcode «{sample_barcode}»"
)
mark_skipped(db, manifest_record.id)
continue
# Mark record as skipped sample identifier set is unexpected
if sample_identifier.set_name not in expected_identifier_sets[
"samples"]:
LOG.warning(
f"Skipping manifest record with sample identifier found in "
+
f"set «{sample_identifier.set_name}», not {expected_identifier_sets['samples']}"
)
mark_skipped(db, manifest_record.id)
continue
# Find sample that should have been created from this
# manifest record via etl manifest
sample = find_sample(db, sample_identifier.uuid)
# Error out the kit etl process if no sample found
# The kit etl process can try again starting with this record
# next time with the idea that the sample will be
# created by then.
if not sample:
raise SampleNotFoundError(
f"No sample with «{sample_identifier.uuid}» found")
# Mark record as skipped if the sample does not have a
# sample type (utm or rdt)
if sample.type not in {"utm", "rdt"}:
LOG.info(f"Skipping manifest record {manifest_record.id} " +
f"with unknown sample type {sample.type}")
mark_skipped(db, manifest_record.id)
continue
kit_barcode = manifest_record.document.pop("kit")
kit_identifier = find_identifier(db, kit_barcode)
# Mark record as skipped if it has an unknown kit barcode
if not kit_identifier:
LOG.warning(
f"Skipping kit with unknown barcode «{kit_barcode}»")
mark_skipped(db, manifest_record.id)
continue
# Mark record as skipped if kit identifier set is unexpected
if kit_identifier.set_name not in expected_identifier_sets["kits"]:
LOG.warning(
f"Skipping kit with identifier found in " +
f"set «{kit_identifier.set_name}» not {expected_identifier_sets['kits']}"
)
mark_skipped(db, manifest_record.id)
continue
# List of extra data not needed for kit record that can
# be removed before adding manifest document to kit details
extra_data = [
"collection", "sample_type", "aliquot_date", "aliquots",
"racks"
]
for key in extra_data:
manifest_record.document.pop(key, None)
# Try to find identifier for the test-strip barcode for rdt samples
if sample.type == "rdt":
update_test_strip(db, manifest_record.document)
kit, status = upsert_kit_with_sample(
db,
identifier=kit_identifier.uuid,
sample=sample,
additional_details=manifest_record.document)
if status == "updated":
update_sample(db, sample, kit.encounter_id)
mark_loaded(db, manifest_record.id, status, kit.id)
def etl_presence_absence(*, db: DatabaseSession):
LOG.debug(
f"Starting the presence_absence ETL routine, revision {REVISION}")
# Fetch and iterate over presence-absence tests that aren't processed
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same presence-absence tests.
LOG.debug("Fetching unprocessed presence-absence tests")
presence_absence = db.cursor("presence_absence")
presence_absence.itersize = 1
presence_absence.execute(
"""
select presence_absence_id as id, document,
received::date as received_date
from receiving.presence_absence
where not processing_log @> %s
order by id
for update
""", (Json([{
"revision": REVISION
}]), ))
for group in presence_absence:
with db.savepoint(f"presence_absence group {group.id}"):
LOG.info(f"Processing presence_absence group {group.id}")
# Samplify will now send documents with a top level key
# "samples". The new format also includes a "chip" key for each
# sample which is then included in the unique identifier for
# each presence/absence result
# -Jover, 14 Nov 2019
try:
received_samples = group.document["samples"]
except KeyError as error:
# Skip documents in the old format because they do not
# include the "chip" key which is needed for the
# unique identifier for each result.
# -Jover, 14 Nov 2019
# Also skip old format to avoid ingesting wrong data from
# plate swapped data! This will lead to 188 samples with the
# wrong nwgc_id associated with them.
# -Jover, 06 Dec 2019
if (group.document.get("store") is not None
or group.document.get("Update") is not None):
LOG.info(
"Skipping presence_absence record that is in old format"
)
mark_processed(db, group.id)
continue
else:
raise error from None
for received_sample in received_samples:
received_sample_barcode = received_sample.get("investigatorId")
if not received_sample_barcode:
LOG.info(
f"Skipping sample «{received_sample['sampleId']}» without SFS barcode"
)
continue
# Don't go any further if the sample is marked as Failed
sample_failed = received_sample.get("sampleFailed")
if sample_failed is True:
LOG.info(
f"Skipping sample «{received_sample_barcode}» that has been failed"
)
continue
# Don't go any further if there are no results to import.
test_results = received_sample["targetResults"]
if not test_results:
LOG.warning(
f"Skipping sample «{received_sample_barcode}» without any results"
)
continue
received_sample_id = str(received_sample["sampleId"])
chip = received_sample.get("chip")
extraction_date = received_sample.get("extractionDate")
assay_name = received_sample.get("assayName")
assay_date = received_sample.get("assayDate")
# The assayType field will be removed after Samplify starts
# sending us OpenArray results with target.clinicalStatus.
#
# kfay, 28 Dec 2020
assay_type = received_sample.get("assayType")
# Guard against empty chip values
assert chip or "chip" not in received_sample, "Received bogus chip id"
# Must be current results
LOG.info(f"Processing sample «{received_sample_barcode}»")
if not received_sample.get("isCurrentExpressionResult"):
LOG.warning(
f"Skipping out-of-date results for sample «{received_sample_barcode}»"
)
continue
# Barcode must match a known identifier
received_sample_identifier = sample_identifier(
db, received_sample_barcode)
if not received_sample_identifier:
LOG.warning(
f"Skipping results for sample without a known identifier «{received_sample_barcode}»"
)
continue
# Track Samplify's internal ids for our samples, which is
# unfortunately necessary for linking genomic data NWGC also
# sends.
sample = update_sample(
db,
identifier=received_sample_identifier,
additional_details=sample_details(received_sample))
# Finally, process all results.
for test_result in test_results:
test_result_target_id = test_result["geneTarget"]
LOG.debug(
f"Processing target «{test_result_target_id}» for \
sample «{received_sample_barcode}»")
# Skip this result if it's actually a non-result
present = target_present(test_result)
if present is ...:
LOG.debug(
f"No test result for «{test_result_target_id}», skipping"
)
continue
# Most of the time we expect to see existing targets so a
# select-first approach makes the most sense to avoid useless
# updates.
target = find_or_create_target(
db,
identifier=test_result_target_id,
control=target_control(test_result["controlStatus"]))
# The unique identifier for each result. If chip is
# applicable, then it's included to differentiate the same
# sample being run on multiple chips (uncommon, but it
# happens).
if chip:
identifier = f"NWGC/{received_sample_id}/{target.identifier}/{chip}"
else:
identifier = f"NWGC/{received_sample_id}/{target.identifier}"
# Most of the time we expect to see new samples and new
# presence_absence tests, so an insert-first approach makes more sense.
# Presence-absence tests we see more than once are presumed to be
# corrections.
upsert_presence_absence(db,
identifier=identifier,
sample_id=sample.id,
target_id=target.id,
present=present,
details=presence_absence_details(
test_result,
group.received_date, chip,
extraction_date, assay_name,
assay_date, assay_type))
mark_processed(db, group.id)
LOG.info(f"Finished processing presence_absence group {group.id}")
def etl_manifest(*, db: DatabaseSession):
LOG.debug(f"Starting the manifest ETL routine, revision {REVISION}")
# XXX TODO: Stop hardcoding valid identifier sets. Instead, accept them as
# an option or config (and validate option choices against what's actually
# in the database). We won't want to validate using click.option(),
# because that would necessitate a database connection simply to run
# bin/id3c at all.
# -trs, 13 May 2019
expected_identifier_sets = {
"samples": {"samples"},
"collections": {
"collections-environmental",
"collections-fluathome.org",
"collections-household-intervention",
"collections-household-intervention-asymptomatic",
"collections-household-observation",
"collections-household-observation-asymptomatic",
"collections-kiosks",
"collections-kiosks-asymptomatic",
"collections-seattleflu.org",
"collections-swab&send",
"collections-swab&send-asymptomatic",
"collections-self-test",
"collections-scan",
"collections-scan-kiosks",
"collections-haarvi",
"samples-haarvi",
"collections-validation",
"collections-uw-home",
"collections-uw-observed",
"collections-household-general",
"collections-childcare",
"collections-school-testing-home",
"collections-school-testing-observed",
"collections-apple-respiratory",
"collections-apple-respiratory-serial",
"collections-adult-family-home-outbreak",
"collections-workplace-outbreak",
},
"rdt": {"collections-fluathome.org"}
}
# Fetch and iterate over samples that aren't processed
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same samples.
LOG.debug("Fetching unprocessed manifest records")
manifest = db.cursor("manifest")
manifest.execute(
"""
select manifest_id as id, document
from receiving.manifest
where not processing_log @> %s
order by id
for update
""", (Json([{
"etl": ETL_NAME,
"revision": REVISION
}]), ))
for manifest_record in manifest:
with db.savepoint(f"manifest record {manifest_record.id}"):
LOG.info(f"Processing record {manifest_record.id}")
# When updating an existing row, update the identifiers
# only if the record has both the 'sample' and
# 'collection' keys.
should_update_identifiers = "sample" in manifest_record.document \
and "collection" in manifest_record.document
# Sample collection date
# Don't pop this entry off the document. For backwards
# compatibility reasons, keep it in the document so that 'date'
# also gets written to the 'details' column in warehouse.sample.
collected_date = manifest_record.document.get("date", None)
# Attempt to find barcodes and their related identifiers
sample_barcode = manifest_record.document.pop("sample", None)
sample_identifier = find_identifier(
db, sample_barcode) if sample_barcode else None
collection_barcode = manifest_record.document.pop(
"collection", None)
collection_identifier = find_identifier(
db, collection_barcode) if collection_barcode else None
# Skip a record if it has no associated barcodes
if not sample_barcode and not collection_barcode:
LOG.warning(
f"Skipping record «{manifest_record.id}» because it has neither a sample "
"barcode nor a collection barcode")
mark_skipped(db, manifest_record.id)
continue
# Skip a record if it has a sample barcode but the barcode doesn't match an identifier
if sample_barcode and not sample_identifier:
LOG.warning(
f"Skipping sample with unknown sample barcode «{sample_barcode}»"
)
mark_skipped(db, manifest_record.id)
continue
# Skip a record if it has a collection barcode but the barcode doesn't match an identifier
if collection_barcode and not collection_identifier:
LOG.warning(
f"Skipping sample with unknown collection barcode «{collection_barcode}»"
)
mark_skipped(db, manifest_record.id)
continue
# Skip a record if the collection identifier is from an unexpected set
if collection_identifier and collection_identifier.set_name not in expected_identifier_sets[
"collections"]:
LOG.warning(
f"Skipping sample because collection identifier found in set «{collection_identifier.set_name}», not \
{expected_identifier_sets['collections']}")
mark_skipped(db, manifest_record.id)
continue
# Validate the sample identifer and assert if a record fails
if sample_identifier:
if (manifest_record.document.get("sample_type")
and manifest_record.document["sample_type"] == "rdt"):
assert sample_identifier.set_name in expected_identifier_sets["rdt"], \
(f"Sample identifier found in set «{sample_identifier.set_name}»," +
f"not {expected_identifier_sets['rdt']}")
else:
assert sample_identifier.set_name in expected_identifier_sets["samples"], \
(f"Sample identifier found in set «{sample_identifier.set_name}», " +
f"not {expected_identifier_sets['samples']}")
# Upsert sample cooperatively with enrollments ETL routine
#
# The details document was intentionally modified by two pop()s
# earlier to remove barcodes that were looked up.
# The rationale is that we want just one clear place in the
# warehouse for each piece of information.
sample, status = upsert_sample(
db,
update_identifiers=should_update_identifiers,
identifier=sample_identifier.uuid
if sample_identifier else None,
collection_identifier=collection_identifier.uuid
if collection_identifier else None,
collection_date=collected_date,
additional_details=manifest_record.document)
mark_loaded(db,
manifest_record.id,
status=status,
sample_id=sample.id)
LOG.info(
f"Finished processing manifest record {manifest_record.id}")
def etl_consensus_genome(*, db: DatabaseSession):
LOG.debug(
f"Starting the consensus genome ETL routine, revision {REVISION}")
# Fetch and iterate over consensus genome records that aren't processed
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same consensus genome records.
LOG.debug("Fetching unprocessed consensus genome records")
consensus_genome = db.cursor("consensus genome")
consensus_genome.execute(
"""
select consensus_genome_id as id, document, received
from receiving.consensus_genome
where not processing_log @> %s
order by id
for update
""", (Json([{
"revision": REVISION
}]), ))
for record in consensus_genome:
with db.savepoint(f"consensus genome record {record.id}"):
LOG.info(f"Processing consensus genome record {record.id}")
# Verify sample identifier is in the database
sample = find_sample(db,
record.document["sample_identifier"],
for_update=False)
assert sample, f"No sample found with identifier «{record.document['sample_identifier']}»"
# Most of the time we expect to see existing sequence read sets,
# but we also want to update the details log. However, the
# only unique constraint on the sequence_read_set table is
# defined within a trigger function, as Postgres does not allow
# unique constraints on array columns. Therefore, perform a
# find-or-create followed by an update to the details column to
# avoid conflict.
sequence_read_set = find_or_create_sequence_read_set(
db, record.document, sample)
status = record.document.get("status")
# Find the matching organism within the warehouse for the
# reference organism
organism_name = get_lineage(db, record.document)
organism = find_organism(db, organism_name)
assert organism, f"No organism found with name «{organism_name}»"
# Only upsert genome and genomic sequences if the assembly job
# was marked as complete.
if status == 'complete':
# Most of the time we expect to see new sequences, so an
# insert-first approach makes the most sense to avoid useless
# queries.
genome = upsert_genome(db,
sequence_read_set=sequence_read_set,
organism=organism,
document=record.document)
for masked_consensus in record.document['masked_consensus']:
genomic_sequence = upsert_genomic_sequence(
db, genome=genome, masked_consensus=masked_consensus)
update_sequence_read_set_details(db, sequence_read_set.id,
organism, status)
mark_processed(db, record.id, {"status": "processed"})
LOG.info(
f"Finished processing consensus genome record {record.id}")
def notify(*, action: str):
LOG.debug(f"Starting the reportable conditions notification routine, revision {REVISION}")
db = DatabaseSession()
def webhook(suffix):
return os.environ.get("SLACK_WEBHOOK_ALERTS_TEST") \
or os.environ[f"SLACK_WEBHOOK_REPORTING_{suffix}"]
slack_webhooks = {
"ncov-reporting": webhook("HCOV19"),
}
projects = [
{
"collection_sets": {"collections-childcare"},
"slack_channel_name": "ncov-reporting-childcare",
"slack_webhook": webhook("HCOV19_CHILDCARE"),
},
{
"collection_sets": {"collections-apple-respiratory"},
"slack_channel_name": "ncov-reporting-apple",
"slack_webhook": webhook("HCOV19_APPLE"),
},
{
"collection_sets": {"collections-school-testing-home",
"collections-school-testing-observed",
"collections-radxup-yakima-schools-home",
"collections-radxup-yakima-schools-observed"},
"slack_channel_name": "ncov-reporting-schools",
"slack_webhook": webhook("HCOV19_SCHOOLS"),
},
{
"collection_sets": {"collections-adult-family-home-outbreak"},
"slack_channel_name": "ncov-reporting-afh",
"slack_webhook": webhook("HCOV19_AFH"),
},
{
"collection_sets": {"collections-workplace-outbreak"},
"slack_channel_name": "ncov-reporting-workplace",
"slack_webhook": webhook("HCOV19_WORKPLACE"),
}
]
# Fetch and iterate over reportable condition records that aren't processed
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same reportable condition records.
LOG.debug("Fetching unprocessed reportable conditions records")
reportable_conditions = db.cursor("reportable_conditions")
reportable_conditions.execute("""
select reportable_condition_v1.*, presence_absence_id as id
from shipping.reportable_condition_v1
join warehouse.presence_absence using (presence_absence_id)
where details @> %s is not true
order by id
for update of presence_absence;
""", (Json({"reporting_log":[{ "revision": REVISION }]}),))
processed_without_error = None
try:
for record in reportable_conditions:
with db.savepoint(f"reportable condition presence_absence_id {record.id}"):
LOG.info(f"Processing reportable condition, presence_absence_id «{record.id}»")
if not record.site:
LOG.info(f"No site found for presence_absence_id «{record.id}». " +
"Inferring site from manifest data.")
responses = {'ncov-reporting': send_slack_post_request(record, slack_webhooks['ncov-reporting'])}
# Also send study-specific results to their respective channels
for project in projects:
if (record.collection_set_name in project['collection_sets']):
responses[project['slack_channel_name']] = send_slack_post_request(
record, project['slack_webhook'])
# Check all POSTs to Slack were successful to mark as processed
# This does mean that if one fails but others succeed, there
# will be duplicate POSTs to the already succeeded channels.
# The chance of this happening is pretty small, but we can
# revisit this if it becomes a common problem
# -Jover, 21 October 2020
if all(response.status_code == 200 for response in responses.values()):
mark_processed(db, record.id, {"status": "sent Slack notification"})
LOG.info(f"Finished processing presence_absence_id «{record.id}»")
else:
for channel, response in responses.items():
if response.status_code != 200:
LOG.error(("Error: A Slack notification could not " \
f"be sent to the channel «{channel}» for "
f"presence_absence_id «{record.id}».\n" \
f"Slack API returned status code {response.status_code}: "\
f"{response.text}"))
except Exception as error:
processed_without_error = False
LOG.error(f"Aborting with error")
raise error from None
else:
processed_without_error = True
finally:
if action == "prompt":
ask_to_commit = \
"Commit all changes?" if processed_without_error else \
"Commit successfully processed reportable condition records up to this point?"
commit = click.confirm(ask_to_commit)
else:
commit = action == "commit"
if commit:
LOG.info(
"Committing all changes" if processed_without_error else \
"Committing successfully processed reportable condition records up to this point")
db.commit()
else:
LOG.info("Rolling back all changes; the database will not be modified")
db.rollback()
def decorated(*args, db: DatabaseSession, log_output: bool, **kwargs):
LOG.debug(
f"Starting the REDCap DET ETL routine {name}, revision {revision}"
)
redcap_det = db.cursor(f"redcap-det {name}")
redcap_det.execute(
"""
select redcap_det_id as id, document
from receiving.redcap_det
where not processing_log @> %s
and document::jsonb @> %s
order by id
for update
""", (Json([etl_id]), Json(det_contains)))
with pickled_cache(CACHE_FILE) as cache:
for det in redcap_det:
with db.savepoint(f"redcap_det {det.id}"):
LOG.info(f"Processing REDCap DET {det.id}")
instrument = det.document['instrument']
# Only pull REDCap record if
# `include_incomplete` flag was not included and
# the current instrument is complete
if not include_incomplete and not is_complete(
instrument, det.document):
LOG.debug(
f"Skipping incomplete or unverified REDCap DET {det.id}"
)
mark_skipped(db, det.id, etl_id)
continue
redcap_record = get_redcap_record_from_det(
det.document, raw_coded_values)
if not redcap_record:
LOG.debug(
f"REDCap record is missing or invalid. Skipping REDCap DET {det.id}"
)
mark_skipped(db, det.id, etl_id)
continue
# Only process REDCap record if all required instruments are complete
incomplete_instruments = {
instrument
for instrument in required_instruments
if not is_complete(instrument, redcap_record)
}
if incomplete_instruments:
LOG.debug(f"The following required instruments «{incomplete_instruments}» are not yet marked complete. " + \
f"Skipping REDCap DET {det.id}")
mark_skipped(db, det.id, etl_id)
continue
bundle = routine(db=db,
cache=cache,
det=det,
redcap_record=redcap_record)
if not bundle:
mark_skipped(db, det.id, etl_id)
continue
if log_output:
print(as_json(bundle))
insert_fhir_bundle(db, bundle)
mark_loaded(db, det.id, etl_id, bundle['id'])
def etl_enrollments(*, db: DatabaseSession):
LOG.debug(f"Starting the enrollment ETL routine, revision {REVISION}")
# Fetch and iterate over enrollments that aren't processed
#
# Use a server-side cursor by providing a name. This ensures we limit how
# much data we fetch at once, to limit local process size. Each enrollment
# document is ~10 KB and the default fetch size (cursor.itersize) is 2,000,
# thus we'll get ~20 MB on each fetch of 2,000 enrollments.
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same enrollments.
LOG.debug("Fetching unprocessed enrollments")
enrollments = db.cursor("enrollments")
enrollments.execute(
"""
select enrollment_id as id, document
from receiving.enrollment
where not processing_log @> %s
order by id
for update
""", (Json([{
"etl": ETL_NAME,
"revision": REVISION
}]), ))
for enrollment in enrollments:
with db.savepoint(f"enrollment {enrollment.id}"):
LOG.info(f"Processing enrollment {enrollment.id}")
# Out of an abundance of caution, fail when the schema version
# of the enrollment document changes. This ensures manual
# intervention happens on document structure changes. After
# seeing how versions are handled over time, this restriction
# may be toned down a bit.
known_versions = {"1.1.0", "1.0.0"}
assert enrollment.document["schemaVersion"] in known_versions, \
f"Document schema version {enrollment.document['schemaVersion']} is not in {known_versions}"
# Most of the time we expect to see existing sites so a
# select-first approach makes the most sense to avoid useless
# updates.
site = find_or_create_site(
db,
identifier=enrollment.document["site"]["name"],
details=site_details(enrollment.document["site"]))
# Most of the time we expect to see new individuals and new
# encounters, so an insert-first approach makes more sense.
# Encounters we see more than once are presumed to be
# corrections.
individual = upsert_individual(
db,
identifier=enrollment.document["participant"],
sex=assigned_sex(enrollment.document))
encounter = upsert_encounter(
db,
identifier=enrollment.document["id"],
encountered=enrollment.document["startTimestamp"],
individual_id=individual.id,
site_id=site.id,
age=age(enrollment.document),
details=encounter_details(enrollment.document))
process_samples(db, encounter.id, enrollment.document)
process_locations(db, encounter.id, enrollment.document)
mark_processed(db, enrollment.id)
LOG.info(f"Finished processing enrollment {enrollment.id}")
def etl_clinical(*, db: DatabaseSession):
LOG.debug(f"Starting the clinical ETL routine, revision {REVISION}")
# Fetch and iterate over clinical records that aren't processed
#
# Rows we fetch are locked for update so that two instances of this
# command don't try to process the same clinical records.
LOG.debug("Fetching unprocessed clinical records")
clinical = db.cursor("clinical")
clinical.execute("""
select clinical_id as id, document
from receiving.clinical
where not processing_log @> %s
order by id
for update
""", (Json([{ "revision": REVISION }]),))
for record in clinical:
with db.savepoint(f"clinical record {record.id}"):
LOG.info(f"Processing clinical record {record.id}")
# Check validity of barcode
received_sample_identifier = sample_identifier(db,
record.document["barcode"])
# Skip row if no matching identifier found
if received_sample_identifier is None:
LOG.info("Skipping due to unknown barcode " + \
f"{record.document['barcode']}")
mark_skipped(db, record.id)
continue
# Check sample exists in database
sample = find_sample(db,
identifier = received_sample_identifier)
# Skip row if sample does not exist
if sample is None:
LOG.info("Skipping due to missing sample with identifier " + \
f"{received_sample_identifier}")
mark_skipped(db, record.id)
continue
# Most of the time we expect to see existing sites so a
# select-first approach makes the most sense to avoid useless
# updates.
site = find_or_create_site(db,
identifier = site_identifier(record.document["site"]),
details = {"type": "retrospective"})
# Most of the time we expect to see new individuals and new
# encounters, so an insert-first approach makes more sense.
# Encounters we see more than once are presumed to be
# corrections.
individual = upsert_individual(db,
identifier = record.document["individual"],
sex = sex(record.document["AssignedSex"]))
encounter = upsert_encounter(db,
identifier = record.document["identifier"],
encountered = record.document["encountered"],
individual_id = individual.id,
site_id = site.id,
age = age(record.document),
details = encounter_details(record.document))
sample = update_sample(db,
sample = sample,
encounter_id = encounter.id)
# Link encounter to a Census tract, if we have it
tract_identifier = record.document.get("census_tract")
if tract_identifier:
# Special-case float-like identifiers in earlier date
tract_identifier = re.sub(r'\.0$', '', str(tract_identifier))
tract = find_location(db, "tract", tract_identifier)
assert tract, f"Tract «{tract_identifier}» is unknown"
upsert_encounter_location(db,
encounter_id = encounter.id,
relation = "residence",
location_id = tract.id)
mark_processed(db, record.id, {"status": "processed"})
LOG.info(f"Finished processing clinical record {record.id}")
def decorated(*args,
db: DatabaseSession,
log_output: bool,
det_limit: int = None,
redcap_api_batch_size: int,
geocoding_cache: str = None,
**kwargs):
LOG.debug(
f"Starting the REDCap DET ETL routine {name}, revision {revision}"
)
project = Project(redcap_url, project_id)
if det_limit:
LOG.debug(f"Processing up to {det_limit:,} pending DETs")
limit = sql.Literal(det_limit)
else:
LOG.debug(f"Processing all pending DETs")
limit = sql.SQL("all")
redcap_det = db.cursor(f"redcap-det {name}")
redcap_det.execute(
sql.SQL("""
select redcap_det_id as id, document
from receiving.redcap_det
where not processing_log @> %s
and document::jsonb @> %s
order by id
limit {}
for update
""").format(limit), (Json([etl_id]), Json(det_contains)))
# First loop of the DETs to determine how to process each one.
# Uses `first_complete_dets` to keep track of which DET to
# use to process a unique REDCap record.
# Uses `all_dets` to keep track of the status for each DET record
# so that they can be processed in order of `redcap_det_id` later.
# --Jover, 21 May 2020
first_complete_dets: Dict[str, Any] = {}
all_dets: List[Dict[str, str]] = []
for det in redcap_det:
instrument = det.document['instrument']
record_id = det.document['record']
# Assume we are loading all DETs
# Status will be updated to "skip" if DET does not need to be processed
det_record = {"id": det.id, "status": "load"}
# Only pull REDCap record if
# `include_incomplete` flag was not included and
# the current instrument is complete
if not include_incomplete and not is_complete(
instrument, det.document):
det_record.update({
"status": "skip",
"reason": "incomplete/unverified DET"
})
# Check if this is record has an older DET
# Skip latest DET in favor of the first DET
# This is done to continue our first-in-first-out
# semantics of our receiving tables
elif first_complete_dets.get(record_id):
det_record.update({
"status": "skip",
"reason": "repeat REDCap record"
})
else:
first_complete_dets[record_id] = det
det_record["record_id"] = record_id
all_dets.append(det_record)
if not first_complete_dets:
LOG.info("No new complete DETs found.")
else:
# Batch request records from REDCap
LOG.info(f"Fetching REDCap project {project_id}")
record_ids = list(first_complete_dets.keys())
LOG.info(
f"Fetching {len(record_ids):,} REDCap records from project {project.id}"
)
# Convert list of REDCap records to a dict so that
# records can be looked up by record id.
# Records with repeating instruments or longitudinal
# events will have multiple entries in the list.
redcap_records: DefaultDict[str,
List[dict]] = defaultdict(list)
batches = list(chunked(record_ids, redcap_api_batch_size))
for i, batch in enumerate(batches, 1):
LOG.info(
f"Fetching REDCap record batch {i:,}/{len(batches):,} of size {len(batch):,}"
)
for record in project.records(ids=batch,
raw=raw_coded_values):
redcap_records[record.id].append(record)
# Process all DETs in order of redcap_det_id
with pickled_cache(geocoding_cache) as cache:
for det in all_dets:
with db.savepoint(f"redcap_det {det['id']}"):
LOG.info(f"Processing REDCap DET {det['id']}")
if det["status"] == "skip":
LOG.debug(
f"Skipping REDCap DET {det['id']} due to {det['reason']}"
)
mark_skipped(db, det["id"], etl_id, det["reason"])
continue
received_det = first_complete_dets.pop(
det["record_id"])
redcap_record_instances = redcap_records.get(
received_det.document["record"])
if not redcap_record_instances:
LOG.debug(
f"REDCap record is missing or invalid. Skipping REDCap DET {received_det.id}"
)
mark_skipped(db, received_det.id, etl_id,
"invalid REDCap record")
continue
bundle = routine(
db=db,
cache=cache,
det=received_det,
redcap_record_instances=redcap_record_instances)
if not bundle:
LOG.debug(
f"Skipping REDCap DET {received_det.id} due to insufficient data in REDCap record."
)
mark_skipped(db, received_det.id, etl_id,
"insufficient data in record")
continue
if log_output:
print(as_json(bundle))
insert_fhir_bundle(db, bundle)
mark_loaded(db, received_det.id, etl_id, bundle['id'])
