Add network visualization to concept page

pyproject.toml

@@ -43,6 +43,7 @@ web = [
     "flask",
     "bootstrap_flask",
     "neo4j",
+    "biomappings",
 ]
 
 

src/semra/api.py

@@ -469,13 +469,19 @@ def validate_mappings(mappings: list[Mapping]) -> None:
             raise ValueError(f"invalid object prefix: {mapping}.")
         if not bioregistry.is_valid_identifier(mapping.s.prefix, mapping.s.identifier):
             raise ValueError(
-                f"Invalid mapping subject.\n\nMapping:{mapping}.\n\nSubject: {mapping.s}\n\nUse regex {bioregistry.get_pattern(mapping.s.prefix)}"
+                f"Invalid mapping subject."
+                f"\n\nMapping:{mapping}."
+                f"\n\nSubject: {mapping.s}"
+                f"\n\nUse regex {bioregistry.get_pattern(mapping.s.prefix)}"
             )
         if ":" in mapping.s.identifier:
             raise ValueError(f"banana in mapping subject: {mapping}")
         if not bioregistry.is_valid_identifier(mapping.o.prefix, mapping.o.identifier):
             raise ValueError(
-                f"Invalid mapping object.\n\nMapping:{mapping}.\n\nObject: {mapping.o}\n\nUse regex {bioregistry.get_pattern(mapping.o.prefix)}"
+                f"Invalid mapping object."
+                f"\n\nMapping:{mapping}."
+                f"\n\nObject: {mapping.o}"
+                f"\n\nUse regex {bioregistry.get_pattern(mapping.o.prefix)}"
             )
         if ":" in mapping.o.identifier:
             raise ValueError(f"banana in mapping object: {mapping}")

src/semra/client.py

@@ -6,6 +6,8 @@
 from typing import Any, TypeAlias
 
 import neo4j
+import neo4j.graph
+import networkx as nx
 import pydantic
 from neo4j import Transaction, unit_of_work
 
@@ -217,13 +219,43 @@ def summarize_authors(self) -> Counter:
         return Counter(dict(self.read_query(query)))
 
     def get_highest_exact_matches(self, limit: int = 10) -> Counter:
-        query = "MATCH (a)-[:`skos:exactMatch`]-(b) WHERE a.priority RETURN a.curie, count(distinct b) as c ORDER BY c DESCENDING LIMIT $limit"
+        query = """\
+            MATCH (a)-[:`skos:exactMatch`]-(b)
+            WHERE a.priority RETURN a.curie, count(distinct b) as c
+            ORDER BY c DESCENDING
+            LIMIT $limit
+        """
         return Counter(dict(self.read_query(query, limit=limit)))
 
     def get_exact_matches(self, curie: str) -> dict[Reference, str]:
         query = "MATCH (a {curie: $curie})-[:`skos:exactMatch`]-(b) RETURN b"
         return {Reference.from_curie(node["curie"]): node["name"] for node, in self.read_query(query, curie=curie)}
 
+    def get_connected_component(self, curie: str) -> tuple[list[neo4j.graph.Node], list[neo4j.graph.Relationship]]:
+        query = """\
+        MATCH (:concept {curie: $curie})-[r *..3 {hasPrimary: true}]-(n:concept)
+        RETURN collect(DISTINCT n) AS nodes, collect(DISTINCT r) AS relations
+        """
+        res = self.read_query(query, curie=curie)
+        nodes = res[0][0]
+        relations = list({r for relations in res[0][1] for r in relations})
+        return nodes, relations
+
+    def get_connected_component_graph(self, curie: str) -> nx.MultiDiGraph:
+        nodes, relations = self.get_connected_component(curie)
+        g = nx.MultiDiGraph()
+        for node in nodes:
+            g.add_node(node["curie"], **node)
+        for relation in relations:
+            g.add_edge(
+                relation.nodes[0]["curie"],
+                relation.nodes[1]["curie"],
+                key=relation.element_id,
+                type=relation.type,
+                **relation,
+            )
+        return g
+
     def get_concept_name(self, curie: str) -> str:
         return _get_name_by_curie(curie)
 

src/semra/pipeline.py

@@ -94,7 +94,8 @@ class Configuration(BaseModel):
     remove_imprecise: bool = True
     validate_raw: bool = Field(
         default=False,
-        description="Should the raw mappings be validated against Bioregistry prefixes and local unique identifier regular expressions (when available)?",
+        description="Should the raw mappings be validated against Bioregistry "
+        "prefixes and local unique identifier regular expressions (when available)?",
     )
 
     raw_pickle_path: Path | None = None

src/semra/templates/base.html

@@ -29,8 +29,10 @@
     </style>
     {% endblock %}
 
+    <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
+            integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo"
+            crossorigin="anonymous"></script>
     <script src="https://kit.fontawesome.com/4c86883252.js" crossorigin="anonymous"></script>
-
     <title>{% block title %}{% endblock %}</title>
     {% endblock %}
 </head>
@@ -46,5 +48,6 @@
     </p>
 </footer>
 
+{% block scripts %}{% endblock %}
 </body>
 </html>

src/semra/templates/concept.html

@@ -4,6 +4,75 @@
 
 {% block title %}SeMRA{% endblock %}
 
+{% block head %}
+{{ super() }}
+<style>
+    #cy {
+        width: 100%;
+        height: 500px;
+        display: block;
+    }
+</style>
+<script src="https://code.jquery.com/jquery-3.1.1.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.26.0/cytoscape.min.js"></script>
+{% endblock %}
+
+{% block scripts %}
+<script>
+    let edgeLabel = {
+        'oboinowl:hasDbXref': 'xref',
+        'skos:exactMatch': 'exact'
+    };
+    $.getJSON("/api/cytoscape/{{ curie }}", function (data) {
+        // console.log(data);
+        var cy = cytoscape({
+            container: document.getElementById('cy'),
+            elements: data,
+            style: [
+                {
+                    selector: 'node',
+                    style: {
+                        'label': function (node) {
+                            return `${node.data("name")}\n${node.data("curie")})`
+                        },
+                        'width': '30px',
+                        'height': '30px',
+                        'color': 'blue',
+                        'background-fit': 'contain',
+                        'background-clip': 'none',
+                        'text-wrap': 'wrap'
+                    }
+                },
+                {
+                    selector: 'edge',
+                    style: {
+                        'label': function (edge) {
+                            return `${edgeLabel[edge.data("type")]}`
+                        },
+                        "curve-style": "bezier",
+                        'text-background-color': 'yellow',
+                        'text-background-opacity': 0.4,
+                        'width': '4px',
+                        'target-arrow-shape': 'triangle',
+                        'control-point-step-size': '140px',
+                        autorotate: true
+                    }
+                }
+            ],
+            layout: {
+                name: 'cose',
+                animate: true,
+                padding: 100,
+            }
+        });
+
+        var layout = cy.layout({ name: 'cose' });
+        layout.run();
+
+layout.run();
+    });
+</script>
+{% endblock %}
 
 {% block content %}
 <div class="container" style="margin-top: 50px; margin-bottom: 50px">
@@ -49,6 +118,7 @@ <h6>Exact Matches</h6>
                 {% endfor %}
                 </tbody>
             </table>
+            <div id="cy"></div>
         </div>
     </div>
 </div>

src/semra/wsgi.py

@@ -4,8 +4,10 @@
 
 import fastapi
 import flask
+import networkx as nx
 from curies import Reference
 from fastapi import Path
+from fastapi.responses import JSONResponse
 from flask import Flask, render_template
 from flask_bootstrap import Bootstrap5
 from starlette.middleware.wsgi import WSGIMiddleware
@@ -14,25 +16,24 @@
 from semra.client import Neo4jClient
 
 try:
-    import biomappings.utils as biomappings_utils
+    import biomappings.utils
 except ImportError:
-    biomappings_utils = None
+    BIOMAPPINGS_GIT_HASH = None
+else:
+    BIOMAPPINGS_GIT_HASH = biomappings.utils.get_git_hash()
 
 client = Neo4jClient()
 
-api_router = fastapi.APIRouter()
+api_router = fastapi.APIRouter(prefix="/api")
 
 flask_app = Flask(__name__)
 flask_app.secret_key = os.urandom(8)
 Bootstrap5(flask_app)
 
-#  Could group this in a function later
-app = fastapi.FastAPI()
-app.include_router(api_router)
-api_router.mount("/", WSGIMiddleware(flask_app))
 
+EXAMPLE_CONCEPTS = ["efo:0002142"]
 EXAMPLE_MAPPINGS = ["25b67912bc720127a43a06ce4688b672", "5a56bf7ac409d8de84c3382a99e17715"]
-BIOMAPPINGS_GIT_HASH = biomappings_utils is not None and biomappings_utils.get_git_hash()
+
 
 PREDICATE_COUNTER = client.summarize_predicates()
 MAPPING_SET_COUNTER = client.summarize_mapping_sets()
@@ -48,15 +49,15 @@
 
 
 def _figure_number(n: int):
-    if n > 1_000_000:
+    if n > 1_000_000:  # noqa:PLR2004
         lead = n / 1_000_000
-        if lead < 10:
+        if lead < 10:  # noqa:PLR2004
             return round(lead, 1), "M"
         else:
             return round(lead), "M"
-    if n > 1_000:
+    if n > 1_000:  # noqa:PLR2004
         lead = n / 1_000
-        if lead < 10:
+        if lead < 10:  # noqa:PLR2004
             return round(lead, 1), "K"
         else:
             return round(lead), "K"
@@ -99,7 +100,6 @@ def view_concept(curie: str):
     name = client.get_concept_name(curie)
     exact_matches = client.get_exact_matches(curie)
     # TODO when showing equivalence between two entities from same namespace, suggest curating a replaced by relation
-
     return render_template(
         "concept.html",
         reference=reference,
@@ -152,12 +152,22 @@ def view_mapping_set(curie: str):
     return render_template("mapping_set.html", mapping_set=m)
 
 
-@api_router.get("/api/evidence/{curie}", response_model=Evidence)
+@api_router.get("/evidence/{curie}", response_model=Evidence)
 def get_evidence(curie: str = Path(description="An evidence's MD5 hex digest.")):  # noqa:B008
     return client.get_evidence(curie)
 
 
-@api_router.get("/api/mapping/{mapping}", response_model=Mapping)
+@api_router.get("/cytoscape/{curie}")
+def get_concept_cytoscape(
+    curie: str = Path(description="the compact URI (CURIE) for a concept", examples=EXAMPLE_CONCEPTS)  # noqa:B008
+):
+    """Get the mapping graph surrounding the concept as a Cytoscape.js JSON object."""
+    graph = client.get_connected_component_graph(curie)
+    cytoscape_json = nx.cytoscape_data(graph)["elements"]
+    return JSONResponse(cytoscape_json)
+
+
+@api_router.get("/mapping/{mapping}", response_model=Mapping)
 def get_mapping(
     mapping: str = Path(  # noqa:B008
         description="A mapping's MD5 hex digest.",
@@ -167,7 +177,7 @@ def get_mapping(
     return client.get_mapping(mapping)
 
 
-@api_router.get("/api/mapping_set/{mapping_set}", response_model=MappingSet)
+@api_router.get("/mapping_set/{mapping_set}", response_model=MappingSet)
 def get_mapping_set(
     mapping_set: str = Path(  # noqa:B008
         description="A mapping set's MD5 hex digest.", examples=["7831d5bc95698099fb6471667e5282cd"]
@@ -176,12 +186,22 @@ def get_mapping_set(
     return client.get_mapping_set(mapping_set)
 
 
-@api_router.get("/api/mapping_set/", response_model=list[MappingSet])
+@api_router.get("/mapping_set/", response_model=list[MappingSet])
 def get_mapping_sets():
     return client.get_mapping_sets()
 
 
+def get_app():
+    app = fastapi.FastAPI(
+        title="Semantic Reasoning Assembler",
+        description="A web app to access a SeMRA Neo4j database",
+    )
+    app.include_router(api_router)
+    app.mount("/", WSGIMiddleware(flask_app))
+    return app
+
+
 if __name__ == "__main__":
     import uvicorn
 
-    uvicorn.run(api_router, port=5000, host="0.0.0.0")  # noqa:S104
+    uvicorn.run(get_app(), port=5000, host="0.0.0.0")  # noqa:S104