Merge pull request #190 from haohangyan/search_ui

Search UI

src/indra_cogex/apps/search/__init__.py

@@ -0,0 +1,6 @@
+
+from .search import search_blueprint
+
+__all__ = [
+    "search_blueprint",
+]

src/indra_cogex/apps/search/search.py

@@ -0,0 +1,134 @@
+import json
+
+from flask import Blueprint, render_template, request, jsonify, redirect, url_for
+from flask_jwt_extended import jwt_required
+from flask_wtf import FlaskForm
+from indra.statements import get_all_descendants, Statement
+from wtforms import StringField, SubmitField
+from wtforms.fields.simple import BooleanField
+from wtforms.validators import DataRequired
+
+from indra_cogex.apps.utils import render_statements, format_stmts
+from indra_cogex.client.queries import *
+__all__ = ["search_blueprint"]
+
+search_blueprint = Blueprint("search", __name__, url_prefix="/search")
+
+class SearchForm(FlaskForm):
+    agent_name = StringField("Agent Name", validators=[DataRequired()])
+    agent_role = StringField("Agent Role")
+    other_agent = StringField("Other Agent")
+    other_agent_role = StringField("Other Agent Role")
+    source_type = StringField("Source Type")
+    rel_type = StringField("Relationship Type")
+    left_arrow = BooleanField("⇐")
+    right_arrow = BooleanField("➔")
+    both_arrow = BooleanField("⇔")
+    paper_id = StringField("Paper ID")
+    mesh_terms = StringField("MeSH Terms")
+    submit = SubmitField("Search")
+
+
+@search_blueprint.route("/", methods=['GET','POST'])
+@jwt_required(optional=True)
+def search():
+    stmt_types = {c.__name__ for c in get_all_descendants(Statement)}
+    stmt_types -= {"Influence", "Event", "Unresolved"}
+    stmt_types_json = json.dumps(sorted(list(stmt_types)))
+
+    form = SearchForm()
+
+    # POST Request: Generate a sharable link with query parameters
+    if form.validate_on_submit():
+        query_params = {
+            "agent": form.agent_name.data,
+            "agent_tuple": request.form.get("agent_tuple"),
+            "other_agent": form.other_agent.data,
+            "other_agent_tuple": request.form.get("other_agent_tuple"),
+            "source_type": form.source_type.data,
+            "rel_types": json.loads(form.rel_type.data) if form.rel_type.data else None,
+            "agent_role": form.agent_role.data,
+            "other_role": form.other_agent_role.data,
+            "paper_id": form.paper_id.data,
+            "mesh_terms": form.mesh_terms.data,
+            "mesh_tuple": request.form.get("mesh_tuple"),
+        }
+        query_params = {k: v for k, v in query_params.items() if v}
+        return redirect(url_for("search.search", **query_params))
+
+    # GET Request: Extract query parameters and fetch statements
+    agent = request.args.get("agent")
+    agent_tuple = request.args.get("agent_tuple")
+    if agent_tuple:
+        source_db, source_id = json.loads(agent_tuple)
+        agent = (source_db, source_id)
+
+    other_agent = request.args.get("other_agent")
+    other_agent_tuple = request.args.get("other_agent_tuple")
+    if other_agent_tuple:
+        source_db, source_id = json.loads(other_agent_tuple)
+        other_agent = (source_db, source_id)
+
+    source_type = request.args.get("source_type")
+    rel_types = request.args.getlist("rel_types")
+
+    agent_role = request.args.get("agent_role")
+    other_role = request.args.get("other_role")
+    paper_id = request.args.get("paper_id")
+    mesh_terms = request.args.get("mesh_terms")
+    mesh_tuple = request.args.get("mesh_tuple")
+    if mesh_tuple:
+        source_db, source_id = json.loads(mesh_tuple)
+        mesh_terms = (source_db, source_id)
+
+    # Fetch and display statements
+    if agent or other_agent or rel_types:
+        statements, evidence_count = get_statements(
+            agent=agent,
+            agent_role=agent_role,
+            other_agent=other_agent,
+            other_role=other_role,
+            stmt_sources=source_type,
+            rel_types=rel_types,
+            paper_term=paper_id,
+            mesh_term=mesh_terms,
+            limit=1000,
+            evidence_limit=1000,
+            return_evidence_counts=True,
+        )
+        return render_statements(stmts=statements, evidence_count=evidence_count)
+
+    # Render the form page
+    return render_template(
+        "search/search_page.html",
+        form=form,
+        stmt_types_json=stmt_types_json,
+    )
+
+from flask import current_app
+
+@search_blueprint.route("/gilda_ground", methods=["GET","POST"])
+@jwt_required(optional=True)
+def gilda_ground_endpoint():
+    data = request.get_json()
+    current_app.logger.info(f"Received payload: {data}")
+    agent_text = data.get("agent")
+    if not agent_text:
+        return {"error": "Agent text is required."}, 400
+
+    try:
+        gilda_list = gilda_ground(agent_text)
+        return jsonify(gilda_list)
+    except Exception as e:
+        return {"error": str(e)}, 500
+
+def gilda_ground(agent_text):
+    try:
+        from gilda.api import ground
+        return [r.to_json() for r in ground(agent_text)]
+    except ImportError:
+        import requests
+        res = requests.post('http://grounding.indra.bio/ground', json={'text': agent_text})
+        return res.json()
+    except Exception as e:
+        return {"error": f"Grounding failed: {str(e)}"}