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Adds a full entity to the semsim search response #504

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merged 5 commits into from
Dec 13, 2023
Merged

Adds a full entity to the semsim search response #504

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e9c188e
Adds a full entity to the semsim search response
kevinschaper Dec 13, 2023
7704d4c
Merge branch 'main' into semsim-search-add-entity
glass-ships Dec 13, 2023
aef5525
merge main, format
glass-ships Dec 13, 2023
bcdfd43
remove id, keep subject
glass-ships Dec 13, 2023
89d0469
manually edit model.ts, similarity fields are numbers
glass-ships Dec 13, 2023
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6 changes: 5 additions & 1 deletion backend/src/monarch_py/api/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,8 +92,12 @@ def search(self, termset: List[str], prefix: str, limit: int):
response = rq.get(url=url)
data = response.json()
results = [
SemsimSearchResult(score=i[0], similarity=self.convert_tsps_data(i[1]), subject_id=i[2]) for i in data
SemsimSearchResult(
subject=solr().get_entity(i[2], extra=False), score=i[0], similarity=self.convert_tsps_data(i[1])
)
for i in data
]

return results


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2 changes: 1 addition & 1 deletion backend/src/monarch_py/datamodels/model.py
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Expand Up @@ -646,7 +646,7 @@ class BestMatch(ConfiguredBaseModel):

class SemsimSearchResult(ConfiguredBaseModel):

subject_id: str = Field(...)
subject: Entity = Field(...)
score: Optional[float] = Field(None)
similarity: Optional[TermSetPairwiseSimilarity] = Field(None)

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6 changes: 5 additions & 1 deletion backend/src/monarch_py/datamodels/similarity.yaml
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Expand Up @@ -80,9 +80,13 @@ classes:

SemsimSearchResult:
slots:
- subject_id
- subject
- score
- similarity
slot_usage:
subject:
range: Entity
inlined: true

types:
ZeroToOne:
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2 changes: 1 addition & 1 deletion backend/tests/fixtures/association_response.py
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Expand Up @@ -5,7 +5,7 @@
def association_response():
return {
"responseHeader": {
"QTime": 0,
"QTime": 1,
"params": {
"mm": "100%",
"q": "*:*",
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2 changes: 1 addition & 1 deletion backend/tests/fixtures/autocomplete_response.py
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Expand Up @@ -5,7 +5,7 @@
def autocomplete_response():
return {
"responseHeader": {
"QTime": 1,
"QTime": 0,
"params": {
"mm": "100%",
"q": "fanc",
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2 changes: 1 addition & 1 deletion backend/tests/fixtures/histopheno_response.py
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Expand Up @@ -5,7 +5,7 @@
def histopheno_response():
return {
"responseHeader": {
"QTime": 2,
"QTime": 1,
"params": {
"facet.query": [
'object_closure:"HP:0000924"',
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12 changes: 6 additions & 6 deletions backend/tests/fixtures/phenotype_explorer_compare.py
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Expand Up @@ -5,8 +5,8 @@
def phenotype_explorer_compare():
return {
"subject_termset": {
"MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"},
"MP:0002169": {"id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)"},
"MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"},
},
"object_termset": {"HP:0004325": {"id": "HP:0004325", "label": "Decreased body weight (HPO)"}},
"subject_best_matches": {
Expand Down Expand Up @@ -69,16 +69,16 @@ def phenotype_explorer_compare():
"HP:0004325": {
"match_source": "HP:0004325",
"match_source_label": "Decreased body weight (HPO)",
"match_target": "MP:0010771",
"match_target_label": "integument phenotype (MPO)",
"match_target": "MP:0002169",
"match_target_label": "no abnormal phenotype detected (MPO)",
"score": 1.5540019332516637,
"match_subsumer": None,
"match_subsumer_label": None,
"similarity": {
"subject_id": "HP:0004325",
"subject_label": None,
"subject_source": None,
"object_id": "MP:0010771",
"object_id": "MP:0002169",
"object_label": None,
"object_source": None,
"ancestor_id": "UPHENO:0001003",
Expand All @@ -87,10 +87,10 @@ def phenotype_explorer_compare():
"object_information_content": None,
"subject_information_content": None,
"ancestor_information_content": 1.5540019332516637,
"jaccard_similarity": 0.24,
"jaccard_similarity": 0.23076923076923078,
"cosine_similarity": None,
"dice_similarity": None,
"phenodigm_score": 0.61070489107293,
"phenodigm_score": 0.5988454147360435,
},
}
},
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