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missed fixing some unit tests affected by a change, ended up refactor…
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…ing the tests to test more clearly
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@SeriousHorncat
SeriousHorncat committed Sep 26, 2024
1 parent 27f6ff3 commit c5119f7
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Showing 2 changed files with 26 additions and 46 deletions.
14 changes: 7 additions & 7 deletions backend/src/repository/genomic_unit_collection.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ def add_transcript_to_genomic_unit(self, genomic_unit, transcript_id):
{'$addToSet': {'transcripts': {'transcript_id': transcript_id, 'annotations': []}}},
)

def __update_genomic_unit_by_mongo_id(self, genomic_unit_document):
def update_genomic_unit_by_mongo_id(self, genomic_unit_document):
""" Takes a genomic unit and overwrites the existing object based on the object's id """
genomic_unit_id = genomic_unit_document['_id']

Expand Down Expand Up @@ -180,7 +180,7 @@ def annotate_genomic_unit(self, genomic_unit, genomic_annotation):
genomic_unit_json = self.find_genomic_unit(genomic_unit)
self.__add_to_annotations_from_document(genomic_unit_json['annotations'], dataset_name, genomic_annotation)

updated_document = self.__update_genomic_unit_by_mongo_id(genomic_unit_json)
updated_document = self.update_genomic_unit_by_mongo_id(genomic_unit_json)

return updated_document

Expand All @@ -197,7 +197,7 @@ def __annotate_transcript_dataset(self, genomic_unit, transcript_id: str, genomi
if transcript["transcript_id"] == transcript_id:
self.__add_to_annotations_from_document(transcript['annotations'], dataset_name, genomic_annotation)

return self.__update_genomic_unit_by_mongo_id(genomic_unit_document)
return self.update_genomic_unit_by_mongo_id(genomic_unit_document)

def __add_to_annotations_from_document(self, list_of_annotations, dataset_name, genomic_annotation):
new_dataset_entry, annotation_entry = create_annotation_entry(dataset_name, genomic_annotation)
Expand All @@ -219,7 +219,7 @@ def annotate_genomic_unit_with_file(self, genomic_unit, genomic_annotation):
for annotation in genomic_unit_document['annotations']:
if data_set in annotation:
annotation[data_set][0]['value'].append(genomic_annotation['value'])
return self.__update_genomic_unit_by_mongo_id(genomic_unit_document)
return self.update_genomic_unit_by_mongo_id(genomic_unit_document)

annotation_data_set = {
genomic_annotation['data_set']: [{
Expand All @@ -230,7 +230,7 @@ def annotate_genomic_unit_with_file(self, genomic_unit, genomic_annotation):
}

genomic_unit_document['annotations'].append(annotation_data_set)
return self.__update_genomic_unit_by_mongo_id(genomic_unit_document)
return self.update_genomic_unit_by_mongo_id(genomic_unit_document)

def update_genomic_unit_file_annotation(self, genomic_unit, data_set, annotation_value, file_id_old):
""" Replaces existing annotation image with new image """
Expand All @@ -245,7 +245,7 @@ def update_genomic_unit_file_annotation(self, genomic_unit, data_set, annotation
annotation[data_set][0]['value'].append(annotation_value)
break

self.__update_genomic_unit_by_mongo_id(genomic_unit_document)
self.update_genomic_unit_by_mongo_id(genomic_unit_document)

return

Expand All @@ -261,7 +261,7 @@ def remove_genomic_unit_file_annotation(self, genomic_unit, data_set, file_id):
annotation[data_set][0]['value'].pop(i)
break

return self.__update_genomic_unit_by_mongo_id(genomic_unit_document)
return self.update_genomic_unit_by_mongo_id(genomic_unit_document)

def create_genomic_unit(self, genomic_unit):
"""
Expand Down
58 changes: 19 additions & 39 deletions backend/tests/unit/repository/test_genomic_unit_collection.py
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
""" Manages the genomic unit collection. Including reading, writing, fetching various genomic units. """
from unittest.mock import Mock
import copy
from pymongo import ReturnDocument
import pytest

from bson import ObjectId
Expand Down Expand Up @@ -121,25 +120,6 @@ def test_add_transcript_to_genomic_unit(genomic_unit_collection):
)


def test_update_genomic_unit_annotation_by_mongo_id(genomic_unit_collection):
"""
Verifies that the update genomic unit with mongo id function makes the pymongo call with the correct params
"""
genomic_unit_document = {
"_id": ObjectId('62fbfa5f616a9799131174c8'),
"hgvs_variant": "NM_001017980.3:c.164G>T",
"transcripts": [],
"annotations": {},
}

genomic_unit_collection.update_genomic_unit_annotation_by_mongo_id(genomic_unit_document)

genomic_unit_collection.collection.find_one_and_update.assert_called_once_with({
'_id': ObjectId('62fbfa5f616a9799131174c8')
}, {'$set': genomic_unit_document},
return_document=ReturnDocument.AFTER)


def test_annotate_transcript_genomic_unit(genomic_unit_collection):
""" Verifies that a transcript annotates a genomic unit properly """
genomic_unit = {'unit': 'NM_001017980.3:c.164G>T', 'type': GenomicUnitType.HGVS_VARIANT}
Expand All @@ -160,19 +140,18 @@ def test_annotate_transcript_genomic_unit(genomic_unit_collection):
}
)

expected_genomic_unit = {
"_id": ObjectId("62fbfa5f616a9799131174ca"),
"hgvs_variant": "NM_001017980.3:c.164G>T",
"transcripts": [{'transcript_id': 'NM_001363810.1', 'annotations': []}],
"annotations": {},
}

genomic_unit_collection.annotate_genomic_unit(genomic_unit, transcript_annotation_unit)

genomic_unit_collection.collection.find_one_and_update.assert_called_once_with({
'_id': ObjectId("62fbfa5f616a9799131174ca")
}, {
'$set': {
"_id": ObjectId("62fbfa5f616a9799131174ca"),
"hgvs_variant": "NM_001017980.3:c.164G>T",
"transcripts": [{'transcript_id': 'NM_001363810.1', 'annotations': []}],
"annotations": {},
}
},
return_document=ReturnDocument.AFTER)
genomic_unit_collection.collection.find_one_and_update.assert_called_once()
actual_updated_genomic_unit = genomic_unit_collection.collection.find_one_and_update.call_args_list[0][0][1]['$set']
assert actual_updated_genomic_unit == expected_genomic_unit


@pytest.mark.parametrize(
Expand Down Expand Up @@ -231,11 +210,12 @@ def test_annotation_genomic_unit_with_file(genomic_unit_collection, get_annotati
expected_genomic_unit['annotations'].append(expected_annotation_update)

genomic_unit_collection.collection.find_one.return_value = genomic_unit
genomic_unit_collection.update_genomic_unit_annotation_by_mongo_id = Mock()

genomic_unit_collection.annotate_genomic_unit_with_file(incoming_genomic_unit, annotation_unit)

genomic_unit_collection.update_genomic_unit_annotation_by_mongo_id.assert_called_once_with(expected_genomic_unit)
genomic_unit_collection.collection.find_one_and_update.assert_called_once()
actual_updated_genomic_unit = genomic_unit_collection.collection.find_one_and_update.call_args_list[0][0][1]['$set']
assert actual_updated_genomic_unit == expected_genomic_unit


def test_update_existing_genomic_unit_file_annotation(genomic_unit_collection, get_annotation_json):
Expand Down Expand Up @@ -266,13 +246,13 @@ def test_update_existing_genomic_unit_file_annotation(genomic_unit_collection, g

expected_genomic_unit['annotations'].append(expected_annotation_update)

genomic_unit_collection.update_genomic_unit_annotation_by_mongo_id = Mock()

genomic_unit_collection.update_genomic_unit_file_annotation(
incoming_genomic_unit, data_set, annotation_unit_value, file_id_old
)

genomic_unit_collection.update_genomic_unit_annotation_by_mongo_id.assert_called_once_with(expected_genomic_unit)
genomic_unit_collection.collection.find_one_and_update.assert_called_once()
actual_updated_genomic_unit = genomic_unit_collection.collection.find_one_and_update.call_args_list[0][0][1]['$set']
assert actual_updated_genomic_unit == expected_genomic_unit


def test_remove_existing_genomic_unit_file_annotation(genomic_unit_collection, get_annotation_json):
Expand All @@ -299,11 +279,11 @@ def test_remove_existing_genomic_unit_file_annotation(genomic_unit_collection, g
}]
})

genomic_unit_collection.update_genomic_unit_annotation_by_mongo_id = Mock()

genomic_unit_collection.remove_genomic_unit_file_annotation(incoming_genomic_unit, data_set, file_id)

genomic_unit_collection.update_genomic_unit_annotation_by_mongo_id.assert_called_once_with(expected_genomic_unit)
genomic_unit_collection.collection.find_one_and_update.assert_called_once()
actual_updated_genomic_unit = genomic_unit_collection.collection.find_one_and_update.call_args_list[0][0][1]['$set']
assert actual_updated_genomic_unit == expected_genomic_unit


@pytest.fixture(name="prepare_test_annotate", scope="function")
Expand Down

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