Fix multi-compare phenogrid (#725)

Closes #656 and #697 - Revert typer from 0.12.3 to 0.7 + typer-cli - Swap `object_best_matches` for `subject_best_matches` in `compareSetToSets` - Add Ancestor IC to cell hover info - Add `metric` parameter to phenogrid search and multi-compare URLs - Link to `phenogrid.md` from `CONTRIBUTING.md` - [x] Update phenogrid documentation about making iframes a little - [x] Add test for phenogrid content (@kevinschaper) - [ ] Change example in phenotype explore / testbed (another PR? this one?) --------- Co-authored-by: Kevin Schaper <kevinschaper@gmail.com>
monarch-initiative · May 31, 2024 · a9d9d64 · a9d9d64
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diff --git a/README.md b/README.md
@@ -2,9 +2,10 @@
 
 The Monarch Initiative is an extensive knowledge graph and ecosystem of tools made for the benefit of clinicians, researchers, and scientists. The knowledge graph consists of millions of entities – genes, diseases, phenotypes, and many more – imported from dozens of sources.
 
-We welcome the contributions of the community to help us maintain and improve the knowledge graph and the tools that use it. To help get started on contributing to the Monarch Initiative, please see our CONTRIBUTING.md file.
+We welcome the contributions of the community to help us maintain and improve the knowledge graph and the tools that use it. To help get started on contributing to the Monarch Initiative, please see our [CONTRIBUTING.md](./CONTRIBUTING.md) file.
 
 # Monarch App
+
 [![documentation](https://img.shields.io/badge/-Documentation-purple?logo=read-the-docs&logoColor=white&style=for-the-badge)](https://monarch-initiative.github.io/monarch-documentation/)  
 ![](https://github.com/monarch-initiative/monarch-app/actions/workflows/test-backend.yaml/badge.svg)
 ![](https://github.com/monarch-initiative/monarch-app/actions/workflows/test-frontend.yaml/badge.svg)
@@ -18,9 +19,11 @@ as well as `monarch-py`, a Python library for interacting with the Monarch Initi
 
 If you wish to run Monarch-App as a local web application, please install the requirements below and then follow on to the usage section to start the application. Refer to [Using Local Data](#using-local-data) to see how you can run the full Monarch website locally and use your own data store.
 
+The app also offers a widget called Phenogrid that can be embedded in any website.  
+For more information on how to use the Phenogrid widget, please refer to the [Phenogrid documentation](./frontend/PHENOGRID.md).
 
 ### For developers
 
 The monarch-app repository contains the code to run the Monarch Initiative website in the `frontend` and `backend` directories as well as documentation, helper scripts, Docker files and services to help set up a local environment for development and for deployment.
 
-To start development, please refer to the CONTRIBUTING.md document with this README. If you are planning to only develop the frontend or backend of the application you can refer directly to the README and CONTRIBUTING files in each of those sections.
+To start development, please refer to the [CONTRIBUTING.md](./CONTRIBUTING.md) document with this README. If you are planning to only develop the frontend or backend of the application you can refer directly to the README and CONTRIBUTING files in each of those sections.
diff --git a/backend/poetry.lock b/backend/poetry.lock
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
@@ -17,20 +17,22 @@ packages = [{ include = "monarch_py", from = "src" }]
 python = "^3.9"
 pydantic = "^2"
 curies = "<1"
-linkml = "^1.6"
+linkml = "^1.7.10"
 prefixmaps = "^0.2"
 bioregistry = "^0.10.57"
 oaklib = ">=0.6.6"
 
-docker = "^7.0.0"
-fastapi = "^0.111.0"
+docker = "^7.1.0"
+# fastapi = "^0.111.0"
+fastapi = "^0.103.1"
 gunicorn = "^22.0.0"
 loguru = "*"
 pystow = ">=0.5.4"
 requests = "^2.31.0"
 rich = "*"
-typer = "^0.12"
-# spacy = ">=3.7.5,<3.8.0"
+# typer = "^0.12"
+typer = "^0.7.0"
+typer-cli = "^0.0.13"
 spacy = { git = "https://github.com/explosion/spaCy.git", branch = "master" }
 beautifulsoup4 = "^4.12.3"
 

diff --git a/backend/src/monarch_py/api/middleware/logging_middleware.py b/backend/src/monarch_py/api/middleware/logging_middleware.py
@@ -1,4 +1,5 @@
 """Middleware to log requests."""
+
 from loguru import logger
 import logging
 
@@ -10,7 +11,6 @@
 
 
 class LoggingMiddleware(BaseHTTPMiddleware):
-
     """Middleware to log requests."""
 
     async def dispatch(self, request: Request, call_next):

diff --git a/backend/src/monarch_py/api/semsim.py b/backend/src/monarch_py/api/semsim.py
@@ -81,9 +81,9 @@ def _post_compare(request: SemsimCompareRequest):
         Example: <br>
     <pre>
     {
-      "subjects": ["MP:0010771","MP:0002169","MP:0005391","MP:0005389","MP:0005367"],
-      "objects": ["HP:0004325","HP:0000093","MP:0006144"],
-      "metric": "ancestor_information_content"
+        "subjects": ["MP:0010771", "MP:0002169"],
+        "objects": ["HP:0004325"]
+        "metric": "ancestor_information_content"
     }
     </pre>
     """
@@ -94,30 +94,27 @@ def _post_compare(request: SemsimCompareRequest):
 @router.post("/multicompare")
 def _post_multicompare(request: SemsimMultiCompareRequest):
     """
-            Pairwise similarity between two sets of terms <br>
-            <br>
-            Example: <br>
-        <pre>
+        Pairwise similarity between two sets of terms <br>
+        <br>
+        Example: <br>
+    <pre>
     {
-      "metric": "ancestor_information_content",
-      "subjects": [ "HP:0002616", "HP:0001763", "HP:0004944", "HP:0010749", "HP:0001533", "HP:0002020", "HP:0012450", "HP:0003394", "HP:0003771", "HP:0012378", "HP:0001278", "HP:0002827",
-    "HP:0002829", "HP:0002999", "HP:0003010"],
-      "object_sets": [
-        {
-          "id": "MGI:97486",
-          "label": "Pax2",
-          "phenotypes": [ "MP:0003675", "MP:0003675", "MP:0003675", "MP:0011382", "MP:0011366", "MP:0010097", "MP:0012536", "MP:0003558", "MP:0004729", "MP:0009113", "MP:0006090", "MP:0001325", "MP:0001325", "MP:0006309",
-    "MP:0004017", "MP:0012533", "MP:0004505", "MP:0004505", "MP:0004505"]
-        },
-        {
-          "id": "MGI:95819",
-          "label": "Grin1",
-          "phenotypes": ["MP:0001435", "MP:0001405", "MP:0002797", "MP:0001386", "MP:0001901", "MP:0001901", "MP:0001901", "MP:0001901", "MP:0001901", "MP:0002906", "MP:0004811", "MP:0001900",
-    "MP:0009748", "MP:0008428", "MP:0008428", "MP:0008428"]
-        }
-      ]
+        "metric": "ancestor_information_content",
+        "subjects": ["HP:0002616","HP:0001763","HP:0004944","HP:0010749","HP:0001533","HP:0002020","HP:0012450"],
+        "object_sets": [
+            {
+            "id": "MGI:2441732",
+            "label": "Adgrg7",
+            "phenotypes": ["MP:0011965","MP:0002834","MP:0003731","MP:0011962","MP:0011960","MP:0008489","MP:0003291","MP:0001262"]
+            },
+            {
+            "id": "MGI:87909",
+            "label": "Acta2",
+            "phenotypes": ["MP:0002834","MP:0003070","MP:0004022","MP:0004021","MP:0003026","MP:0006264","MP:0000230","MP:0000233","MP:0000272","MP:0009862"]
+            }
+        ]
     }
-        </pre>
+    </pre>
     """
     return semsimian().multi_compare(request)
 

diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py
@@ -450,12 +450,12 @@ def get_association_facets(
             offset=0,
             total=query_result.response.num_found,
             items=[],
-            facet_fields=convert_facet_fields(query_result.facet_counts.facet_fields)
-            if query_result.facet_counts
-            else [],
-            facet_queries=convert_facet_queries(query_result.facet_counts.facet_queries)
-            if query_result.facet_counts
-            else [],
+            facet_fields=(
+                convert_facet_fields(query_result.facet_counts.facet_fields) if query_result.facet_counts else []
+            ),
+            facet_queries=(
+                convert_facet_queries(query_result.facet_counts.facet_queries) if query_result.facet_counts else []
+            ),
         )
 
     def get_association_table(
@@ -505,9 +505,9 @@ def get_mappings(
             subject_id=[subject_id] if isinstance(subject_id, str) else subject_id,
             predicate_id=[p.value for p in predicate_id] if predicate_id else None,
             object_id=[object_id] if isinstance(object_id, str) else object_id,
-            mapping_justification=[mapping_justification]
-            if isinstance(mapping_justification, str)
-            else mapping_justification,
+            mapping_justification=(
+                [mapping_justification] if isinstance(mapping_justification, str) else mapping_justification
+            ),
             offset=offset,
             limit=limit,
         )

diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py
@@ -5,8 +5,8 @@
 def association_counts():
     return {
         "items": [
-            {"label": "Phenotypes", "count": 3859, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"},
-            {"label": "Causal Genes", "count": 119, "category": "biolink:CausalGeneToDiseaseAssociation"},
-            {"label": "Correlated Genes", "count": 139, "category": "biolink:CorrelatedGeneToDiseaseAssociation"},
+            {"label": "Phenotypes", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"},
+            {"label": "Causal Genes", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"},
+            {"label": "Correlated Genes", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"},
         ]
     }