Skip to content

Commit

Permalink
Merge pull request wtsi-npg#190 from kjsanger/bugfix/update-multiplex…
Browse files Browse the repository at this point in the history 
…ed-ont-metadata

Bugfix: use annotate_results_collection to update metadata
  • Loading branch information
@kjsanger
kjsanger authored Sep 15, 2023
2 parents db184bb + 51c9fa5 commit 73132a1
Show file tree
Hide file tree
Showing 2 changed files with 51 additions and 19 deletions.
3 changes: 1 addition & 2 deletions src/npg_irods/ont.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -279,9 +279,8 @@ def ensure_secondary_metadata_updated(
)

component = Component(expt, slot, tag_id)
flowcells = find_flowcells_by_component(mlwh_session, component)

return _do_secondary_metadata_and_perms_update(item, flowcells)
return annotate_results_collection(item, component, mlwh_session=mlwh_session)


def find_recent_expt(sess: Session, since: datetime) -> list[str]:
Expand Down
67 changes: 50 additions & 17 deletions tests/test_ont.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,25 +17,26 @@
#
# @author Keith James <kdj@sanger.ac.uk>

from datetime import datetime

import pytest
from partisan.irods import AC, AVU, Collection, DataObject, Permission, format_timestamp

from pytest import mark as m

from datetime import datetime
from conftest import LATEST, history_in_meta, ont_tag_identifier, tests_have_admin
from npg_irods import ont
from conftest import LATEST, ont_tag_identifier, tests_have_admin, history_in_meta
from npg_irods.metadata.common import SeqConcept
from npg_irods.metadata.lims import (
TrackedSample,
TrackedStudy,
ensure_consent_withdrawn,
)
from npg_irods.metadata.common import SeqConcept

from npg_irods.ont import (
Component,
Instrument,
annotate_results_collection,
apply_metadata,
ensure_secondary_metadata_updated,
is_minknow_report,
)

Expand Down Expand Up @@ -158,7 +159,7 @@ def test_add_new_sample_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh):

path = ont_synthetic_irods / expt / "20190904_1514_GA10000_flowcell011_69126024"
c = Component(experiment_name=expt, instrument_slot=slot)
annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)
assert annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)

coll = Collection(path)
for avu in [
Expand Down Expand Up @@ -246,7 +247,7 @@ def test_add_new_plex_sample_metadata(


class TestONTMetadataUpdate(object):
@m.context("When ONT metadata are updated")
@m.context("When ONT metadata are applied")
@m.context("When the metadata are absent")
@m.it("Adds the metadata")
def test_updates_absent_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh):
Expand All @@ -256,15 +257,18 @@ def test_updates_absent_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh):
)
assert AVU(TrackedSample.NAME, "name1") not in coll.metadata()

apply_metadata(
num_found, num_updated, num_errors = apply_metadata(
experiment_name="simple_experiment_001",
instrument_slot=1,
mlwh_session=ont_synthetic_mlwh,
)

assert AVU(TrackedSample.NAME, "name1") in coll.metadata()
assert num_found == 1
assert num_updated == 1
assert num_errors == 0

@m.context("When ONT metadata are updated")
@m.context("When ONT metadata are applied")
@m.context("When correct metadata are already present")
@m.it("Leaves the metadata unchanged")
def test_updates_present_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh):
Expand All @@ -274,15 +278,18 @@ def test_updates_present_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh)
)
coll.add_metadata(AVU(TrackedSample.NAME, "name1"))

apply_metadata(
num_found, num_updated, num_errors = apply_metadata(
experiment_name="simple_experiment_001",
instrument_slot=1,
mlwh_session=ont_synthetic_mlwh,
)

assert AVU(TrackedSample.NAME, "name1") in coll.metadata()
assert num_found == 1
assert num_updated == 1
assert num_errors == 0

@m.context("When ONT metadata are updated")
@m.context("When ONT metadata are applied")
@m.context("When incorrect metadata are present")
@m.it("Changes the metadata and adds history metadata")
def test_updates_changed_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh):
Expand All @@ -292,7 +299,7 @@ def test_updates_changed_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh)
)
coll.add_metadata(AVU(TrackedSample.NAME, "name0"))

apply_metadata(
num_found, num_updated, num_errors = apply_metadata(
experiment_name="simple_experiment_001",
instrument_slot=1,
mlwh_session=ont_synthetic_mlwh,
Expand All @@ -303,8 +310,11 @@ def test_updates_changed_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh)
assert history_in_meta(
AVU.history(AVU(TrackedSample.NAME, "name0")), coll.metadata()
)
assert num_found == 1
assert num_updated == 1
assert num_errors == 0

@m.context("When ONT metadata are updated")
@m.context("When ONT metadata are applied")
@m.context("When an attribute has multiple incorrect values")
@m.it("Groups those values in the history metadata")
def test_updates_multiple_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh):
Expand All @@ -315,11 +325,12 @@ def test_updates_multiple_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh
coll.add_metadata(AVU(TrackedStudy.NAME, "Study A"))
coll.add_metadata(AVU(TrackedStudy.NAME, "Study B"))

apply_metadata(
num_found, num_updated, num_errors = apply_metadata(
experiment_name="simple_experiment_001",
instrument_slot=1,
mlwh_session=ont_synthetic_mlwh,
)

assert AVU(TrackedStudy.NAME, "Study Y") in coll.metadata()
assert AVU(TrackedStudy.NAME, "Study A") not in coll.metadata()
assert AVU(TrackedStudy.NAME, "Study B") not in coll.metadata()
Expand All @@ -330,6 +341,28 @@ def test_updates_multiple_metadata(self, ont_synthetic_irods, ont_synthetic_mlwh
),
coll.metadata(),
)
assert num_found == 1
assert num_updated == 1
assert num_errors == 0

@m.context("When ONT metadata are updated")
@m.context("When an iRODS path has metadata identifying its run component")
@m.it("Updates the metadata")
def test_updates_annotated_collection(
self, ont_synthetic_irods, ont_synthetic_mlwh
):
coll = Collection(
ont_synthetic_irods
/ "simple_experiment_001/20190904_1514_G100000_flowcell011_69126024"
)
coll.add_metadata(
AVU(Instrument.EXPERIMENT_NAME, "simple_experiment_001"),
AVU(Instrument.INSTRUMENT_SLOT, 1),
)

assert AVU(TrackedSample.NAME, "name1") not in coll.metadata()
assert ensure_secondary_metadata_updated(coll, mlwh_session=ont_synthetic_mlwh)
assert AVU(TrackedSample.NAME, "name1") in coll.metadata()


class TestONTPermissionsUpdate:
Expand All @@ -347,7 +380,7 @@ def test_public_read_reports(self, ont_synthetic_irods, ont_synthetic_mlwh):
AC("public", Permission.READ, zone="testZone"),
]

annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)
assert annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)

for ext in ["html", "md", "json.gz"]:
assert (
Expand All @@ -372,7 +405,7 @@ def test_retains_consent_withdrawn(self, ont_synthetic_irods, ont_synthetic_mlwh
assert ensure_consent_withdrawn(coll)
assert coll.acl() == expected_acl

annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)
assert annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)

assert coll.acl() == expected_acl, f"ACL of {coll} is {expected_acl}"
for item in coll.contents(acl=True, recurse=True):
Expand Down Expand Up @@ -421,7 +454,7 @@ def test_retains_consent_withdrawn_mx(
item.acl() == expected_acl
), f"ACL of barcode collection member {item} is {expected_acl}"

annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)
assert annotate_results_collection(path, c, mlwh_session=ont_synthetic_mlwh)

for bc_coll in bc_colls:
assert bc_coll.acl() == expected_acl, f"ACL of {c} is {expected_acl}"
Expand Down

0 comments on commit 73132a1

Please sign in to comment.