Adding initial dashboard code

controller.py

@@ -8,6 +8,7 @@
 import services
 import json
 import jsonpickle
+import logging
 
 config = {
     "DEBUG": True,
@@ -66,6 +67,25 @@ def assertion_lookup(aid):
     return json.dumps(one_data)
 
 
+@app.route('/dashboard', strict_slashes=False)
+@cache.cached(timeout=30)
+def dashboard_page():
+    logging.info('starting')
+    # pmc, pmid = get_documents_counts(1)
+    pmc = 1159142
+    pmid = 2174169
+    logging.info('got document counts')
+    # assoc = {'a': 1, 'b': 2}
+    # asser = {'x': 100, 'y': 150}
+    assoc = get_association_counts()
+    logging.info(f'got association counts {assoc}')
+    asser = get_assertion_counts()
+    logging.info(f'got assertion counts {asser}')
+    return render_template('dashboard.html',
+                           pmc_count=pmc, pmid_count=pmid,
+                           records_dict=assoc, assertions_dict=asser)
+
+
 @app.route('/evidence/<evidence_id>', strict_slashes=False)
 @cache.cached(timeout=30)
 def evidence_page(evidence_id):
@@ -309,6 +329,8 @@ def get_edge_list(assertions, use_uniprot=False):
             for ev in assertion.evidence_list:
                 if ev.get_top_predicate() == predicate:
                     edge_list.append({
+                        "assertion_id": ev.assertion_id,
+                        "evidence_id": ev.evidence_id,
                         "document_pmid": ev.document_id,
                         "document_zone": ev.document_zone,
                         "document_year": ev.document_year_published,
@@ -386,6 +408,73 @@ def get_translated_options() -> (list, list):
     return subjects, objects
 
 
+def get_documents_counts(version=1) -> tuple[int, int]:
+    pmc_query = text("SELECT SUM(IF(docid LIKE 'PMC%', 1, 0)) AS PMC, SUM(IF(docid LIKE 'PMID%', 1, 0)) AS PMID FROM "
+                     "(SELECT DISTINCT(document_id) as docid "
+                     "FROM evidence JOIN evidence_version ON "
+                     "evidence.evidence_id = evidence_version.evidence_id "
+                     "WHERE evidence_version.version = :v) x")
+    # pmid_query = text("SELECT COUNT(DISTINCT(document_id)) "
+    #                  "FROM evidence JOIN evidence_version ON "
+    #                  "evidence.evidence_id = evidence_version.evidence_id "
+    #                  "WHERE evidence_version.version = :v AND document_id LIKE 'PMID%'")
+    s = Session()
+    logging.info('starting query')
+    row, = s.execute(pmc_query, {'v': version}).all()
+    pmc_count = row['PMC']
+    pmid_count = row['PMID']
+
+    # logging.info('starting query 2')
+    # pmid_count = s.execute(pmid_query, {'v': version}).scalar()
+    # document_query = text("SELECT DISTINCT(e.document_id) "
+    #                       "FROM evidence e INNER JOIN evidence_version ev ON e.evidence_id = ev.evidence_id "
+    #                       "WHERE version = :v")
+    # document_list = [doc_id for doc_id, in s.execute(document_query, {'v': version})]
+    logging.info('data retrieved')
+    # pmc_count = 0
+    # pmid_count = 0
+    # for document in document_list:
+    #     if document.startswith('PMC'):
+    #         pmc_count += 1
+    #     elif document.startswith('PMID'):
+    #         pmid_count += 1
+    # logging.info('counting complete')
+    return pmc_count, pmid_count
+
+def get_association_counts() -> dict[str, int]:
+    association_query = text("select assertion.association_curie, top_evidence_scores.predicate_curie, count(1) AS c "
+                             "from evidence "
+                             "join evidence_version on evidence.evidence_id = evidence_version.evidence_id "
+                             "join top_evidence_scores on evidence.evidence_id = top_evidence_scores.evidence_id "
+                             "join assertion on evidence.assertion_id = assertion.assertion_id "
+                             "where evidence_version.version = 1 "
+                             "group by assertion.association_curie, top_evidence_scores.predicate_curie")
+    # ass_query = text("SELECT association_curie, 'related_to' AS predicate_curie, 7 AS c FROM assertion LIMIT 1000")
+    s = Session()
+    association_count_dict = {}
+    for row in s.execute(association_query):
+        key = row['association_curie'] + '|' + row['predicate_curie']
+        value = row['c']
+        association_count_dict[key] = value
+    return association_count_dict
+
+
+def get_assertion_counts() -> dict[str, int]:
+    assertion_count_query = text("select assertion.association_curie, count(1) AS c "
+         "from assertion "
+         "join evidence on evidence.assertion_id = assertion.assertion_id "
+         "join evidence_version on evidence.evidence_id = evidence_version.evidence_id "
+         "where evidence_version.version = 2 "
+         "group by assertion.association_curie")
+    s = Session()
+    assertion_count_dict = {}
+    for row in s.execute(assertion_count_query):
+        key = row['association_curie']
+        value = row['c']
+        assertion_count_dict[key] = value
+    return assertion_count_dict
+
+
 @app.teardown_appcontext
 def shutdown_session(response_or_exc):
     Session.remove()
@@ -399,6 +488,8 @@ def shutdown_session(response_or_exc):
 assert secret_password
 models.init_db(username=username, password=secret_password)
 Session = scoped_session(models.Session)
+logging.basicConfig(format='%(asctime)s %(module)s:%(funcName)s:%(levelname)s: %(message)s', level=logging.INFO)
+logging.info('Starting Main')
 
 if __name__ == "__main__":
     app.run(debug=True, host="0.0.0.0", port=int(os.environ.get("PORT", 8080)))

templates/dashboard.html

@@ -0,0 +1,20 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+	<meta charset="utf-8">
+	<meta name="viewport" content="width=device-width, initial-scale=1">
+	<meta name="description" content="">
+	<meta name="author" content="">
+	<title>{{ title }}</title>
+	<link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-F3w7mX95PdgyTmZZMECAngseQB83DfGTowi0iMjiWaeVhAn4FJkqJByhZMI3AhiU" crossorigin="anonymous">
+	<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-/bQdsTh/da6pkI1MST/rWKFNjaCP5gBSY4sEBT38Q/9RBh9AH40zEOg7Hlq2THRZ" crossorigin="anonymous"></script>
+	<script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
+	<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.css">
+</head>
+<body>
+<p>Unique PMC documents that support at least one assertion: {{ pmc_count }}</p>
+<p>Unique PubMed documents that support at least one assertion: {{ pmid_count }}</p>
+<p>Record counts by association type: {{ records_dict }}</p>
+<p>Assertion count by type: {{ assertions_dict }}</p>
+</body>
+</html>

templates/freetext_search.html

@@ -112,7 +112,11 @@ <h6 class="card-subtitle mb-2 text-muted" id="queryResultsCount">The number of r
 				let sentenceHTML = spliceStrings(item.sentence, spliceList);
 				let evidenceHTML = '<a target="_blank" href="https://pubmed.ncbi.nlm.nih.gov/' + item.document_pmid.split(':')[1] + '/">'
 					+ item.document_pmid + '<small><i class="bi bi-box-arrow-up-right"></i></small></a> ' + item.document_year + ' ' + item.document_zone
-					+ ' (Confidence - ' + item.confidence_score + ') [' + item.predicate_curie + '] : <br>';
+					+ ' (Confidence - ' + item.confidence_score + ') [' + item.predicate_curie + ']'
+					+ '<a target="_blank" href="https://tmui.text-mining-kp.org/assertion/' + item.assertion_id + '">'
+					+ 'Assertion Feedback<small><i class="bi bi-box-arrow-up-right"></i></small></a>'
+					+ '<a target="_blank" href="https://tmui.text-mining-kp.org/evidence/' + item.evidence_id + '">'
+					+ 'Evidence Feedback<small><i class="bi bi-box-arrow-up-right"></i></small></a>: <br>';
 				listElement = document.createElement('li');
 				listElement.className = 'list-group-item';
 				listElement.innerHTML = evidenceHTML + sentenceHTML;