To close #169 by adding endpoint 'my_hpos' (#379)

* More tests for variants

* Add test for enabling a non-existing user

* Add my_hpos endpoint #169

tests/test_statistics.py

@@ -53,9 +53,21 @@ def test_my_variants(_demo_client):
     resp = _demo_client.get("/my_variants?limit=10000")
     assert len(resp.json) == 4099
     assert "'variant_id': [{'display': '14-95236097-C-A'" in str(resp.json)
+    resp = _demo_client.get("/my_variants?limit=100001")
+    assert resp.status_code == 400
+    assert resp.json == {"message": "The maximum page size for variants is 100000"}
 
 
 def test_my_genes(_demo_client):
     resp = _demo_client.get("/my_genes")
     assert len(resp.json) == 3
     assert "'percentage_gene_gc_content': 49.73" in str(resp.json)
+
+
+def test_my_hpos(_demo_client):
+    resp = _demo_client.get("/my_hpos")
+    assert len(resp.json) == 7
+    assert "'Abnormal retinal morphology'" in str(resp.json)
+    resp = _demo_client.get("/my_hpos?limit=100001")
+    assert resp.status_code == 400
+    assert resp.json == {"message": "The maximum page size for variants is 100000"}

tests/test_users.py

@@ -102,6 +102,9 @@ def test_enable_user(_admin):
     assert status == 400
     assert not response.json.get("success")
     assert response.json.get("message") == "Cannot change the status of Admin user!"
+    response, status = enable_user("abcdefxyz", "True")
+    assert status == 404
+    assert response.json.get("message") == "User not found"
 
 
 def test_bad_attempt_to_disable_user(_admin):

tests/test_variants.py

@@ -1,7 +1,7 @@
 import sys
 from io import StringIO
 from views.variant import _get_genotypes  # noqa: F401
-from views.variant import variant, variant_preview
+from views.variant import variant, variant_preview, _get_variants
 
 
 def test_get_genotypes_exception():
@@ -67,3 +67,8 @@ def test_variant_preview(_demo):
 def test_wrong_variant_preview(_demo):
     response = variant_preview("something-else")
     assert response.status_code == 400
+
+
+def test_get_variants(_demo):
+    response = _get_variants("wrong")
+    assert not response

views/hpo.py

@@ -3,10 +3,12 @@
 """
 from flask import session, jsonify
 from psycopg2 import sql
-from views import application
+from views import MAX_PAGE_SIZE, application
 from views.auth import requires_auth, USER
+from views.exceptions import PhenopolisException
+from views.individual import _get_authorized_individuals
 from views.postgres import get_db, session_scope
-from views.general import process_for_display, cache_on_browser
+from views.general import _get_pagination_parameters, process_for_display, cache_on_browser
 from db.helpers import cursor2dict, query_user_config
 
 
@@ -174,3 +176,33 @@ def _preview(cur, user, hpo_id):
         q = q1 + q2
     cur.execute(q, [user])
     return cur.rowcount
+
+
+@application.route("/my_hpos")
+@requires_auth
+def get_all_hpos():
+    with session_scope() as db_session:
+        individuals = _get_authorized_individuals(db_session)
+        sqlq_all_hpos = sql.SQL(
+            """
+            select distinct t.hpo_id, t."name" from phenopolis.individual_feature ife
+            join hpo.term t on t.id = ife.feature_id
+            where ife.individual_id = any(%s) and ife.type in ('observed')
+        """
+        )
+        try:
+            limit, offset = _get_pagination_parameters()
+            if limit > MAX_PAGE_SIZE:
+                return (
+                    jsonify(message="The maximum page size for variants is {}".format(MAX_PAGE_SIZE)),
+                    400,
+                )
+            sqlq = sqlq_all_hpos + sql.SQL("limit {} offset {}".format(limit, offset))
+            with get_db() as conn:
+                with conn.cursor() as cur:
+                    cur.execute(sqlq, [[x.id for x in individuals]])
+                    hpos = cursor2dict(cur)
+            process_for_display(db_session, hpos)
+        except PhenopolisException as e:
+            return jsonify(success=False, message=str(e)), e.http_status
+    return jsonify(hpos), 200

views/variant.py

@@ -75,7 +75,7 @@ def _get_variants(target: str):
             * variant_id (e.g '14-76156575-A-G') - and it will return the variant(s) dict for it
                 '12-7241974-C-T', e.g., returns 2 dicts because of 'phenopolis.individual_variant'
             * gene_id (e.g. 'ENSG00000144285') - and it will return all variants linked to that gene
-            * phenopolis_id (e.g. 'PH00008256') - aand it will return all variants linked to that patient
+            * phenopolis_id (e.g. 'PH00008256') - and it will return all variants linked to that patient
         input 'target' must obey its respective string format.
     Returns:
         List[dict variant]: empty ([]), one or more variants depending on input target