Expose map–SCKAN node mappings; add a query and a test query.

mapserver/competency/flatmap.py

@@ -109,6 +109,7 @@ def anatomical_map_knowledge(map_uuid: str, competency_db: CompetencyKnowledge)
             'nerves': path_knowledge.get('node-nerves', []),
             'phenotypes': path_phenotypes.get(path_id, []),
             'references': path_evidence.get(path_id, []),
+            'node-mappings': path_knowledge.get('node-mappings', []),
         }
         if 'alert' in properties:
             knowledge_terms[path_id]['alert'] = properties['alert']

mapserver/competency/queries.d/query_27.yaml

@@ -0,0 +1,146 @@
+queries:
+  - id: 27
+    label: Node mapping from sckan to map
+    sql: >
+      WITH node_mappings AS (
+          SELECT DISTINCT
+              sckan.sckan_id,
+              sckan.path_id,
+              sckan.sckan_node_id,
+              map.source_id,
+              map.node_id
+          FROM (
+              SELECT
+                  source_id AS sckan_id,
+                  path_id,
+                  node_id AS sckan_node_id
+              FROM path_nodes
+              WHERE source_id IN (
+                  SELECT sckan_id
+                  FROM path_node_mappings
+                  WHERE %CONDITION_1%
+              )
+                AND %CONDITION_0%
+          ) AS sckan
+          LEFT JOIN (
+              SELECT
+                  source_id,
+                  path_id,
+                  node_id,
+                  sckan_id,
+                  sckan_node_id
+              FROM path_node_mappings
+              WHERE %CONDITION_1%
+                AND %CONDITION_0%
+          ) AS map
+          ON sckan.path_id = map.path_id
+            AND sckan.sckan_node_id = map.sckan_node_id
+      ),
+
+      sckan_labels AS (
+          SELECT
+              nm.sckan_id,
+              nm.sckan_node_id,
+              string_agg(pt.label, ', ' ORDER BY seq.pos) AS sckan_node_label
+          FROM node_mappings nm
+          JOIN path_node_features pnf
+            ON nm.sckan_id = pnf.source_id
+          AND nm.path_id = pnf.path_id
+          AND nm.sckan_node_id = pnf.node_id
+          JOIN feature_terms pt
+            ON pnf.source_id = pt.source_id
+          AND pnf.feature_id = pt.term_id
+          CROSS JOIN LATERAL (
+              SELECT pos
+              FROM (
+                  SELECT pnf.node_id::jsonb->>0 AS value, 1 AS pos
+                  UNION ALL
+                  SELECT value, ordinality + 1 AS pos
+                  FROM jsonb_array_elements_text(pnf.node_id::jsonb->1) WITH ORDINALITY
+              ) s
+              WHERE s.value = pt.term_id
+          ) AS seq
+          GROUP BY nm.sckan_id, nm.sckan_node_id
+      ),
+
+      map_labels AS (
+          SELECT
+              nm.source_id,
+              nm.node_id,
+              string_agg(pt.label, ', ' ORDER BY seq.pos) AS node_label
+          FROM node_mappings nm
+          JOIN path_node_features pnf
+            ON nm.source_id = pnf.source_id
+          AND nm.path_id = pnf.path_id
+          AND nm.node_id = pnf.node_id
+          JOIN feature_terms pt
+            ON pnf.source_id = pt.source_id
+          AND pnf.feature_id = pt.term_id
+          CROSS JOIN LATERAL (
+              SELECT pos
+              FROM (
+                  SELECT pnf.node_id::jsonb->>0 AS value, 1 AS pos
+                  UNION ALL
+                  SELECT value, ordinality + 1 AS pos
+                  FROM jsonb_array_elements_text(pnf.node_id::jsonb->1) WITH ORDINALITY
+              ) s
+              WHERE s.value = pt.term_id
+          ) AS seq
+          GROUP BY nm.source_id, nm.node_id
+      )
+
+      SELECT
+          nm.sckan_id,
+          nm.path_id,
+          nm.sckan_node_id,
+          UPPER(SUBSTRING(sl.sckan_node_label, 1, 1)) ||
+          SUBSTRING(sl.sckan_node_label, 2) AS sckan_node_label,
+          COALESCE(nm.source_id, '') AS source_id,
+          COALESCE(nm.node_id, '')   AS node_id,
+          COALESCE(UPPER(SUBSTRING(ml.node_label, 1, 1)) ||
+          SUBSTRING(ml.node_label, 2), '') AS node_label
+      FROM node_mappings nm
+      NATURAL JOIN sckan_labels sl
+      LEFT JOIN map_labels ml
+            ON nm.source_id = ml.source_id
+            AND nm.node_id   = ml.node_id;
+    parameters:
+    - id: path_id
+      column: path_id
+      label: Neuron population
+      type: string
+      multiple: true
+      condition: CONDITION_0
+    - id: source_id
+      column: source_id
+      label: Knowledge source
+      type: string
+      multiple: true
+      condition: CONDITION_1
+      default_msg: the latest source is used
+      default_sql: >
+        select source_id from knowledge_sources where source_id like 'sckan%'
+        order by source_id desc limit 1
+    order: ''
+    results:
+    - key: sckan_id
+      label: SKCAN Knowledge source
+      type: string
+    - key: path_id
+      label: Neuron population
+      type: string
+    - key: sckan_node_id
+      label: SKCAN Node ID
+      type: string
+    - key: sckan_node_label
+      label: SKCAN Node Label
+      type: string
+    - key: source_id
+      label: Knowledge source
+      type: string
+    - key: node_id
+      label: Map Node ID
+      type: string
+    - key: node_label
+      label: Map Node Label
+      type: string

tests/test_query_27.py

@@ -0,0 +1,67 @@
+import pytest
+from utility import cq_request, assert_valid_query_response, MALE_UUID, FEMALE_UUID, RAT_UUID
+
+base_query = {
+    'query_id': '27',
+    'parameters': [
+        {'column': 'path_id','value': 'ilxtr:neuron-type-bolew-unbranched-15'}
+    ]
+}
+
+expected_sckan_node_ids = [
+    '["ILX:0738293", []]',
+    '["ILX:0738305", ["UBERON:0001532"]]',
+    '["ILX:0793621", []]',
+    '["UBERON:0001989", []]',
+    '["UBERON:0003708", []]'
+]
+expected_node_ids = [
+    '["ILX:0738293", []]',
+    '["ILX:0738305", []]',
+    '["ILX:0793621", []]',
+    '["UBERON:0001989", []]',
+    '["UBERON:0003708", []]'
+]
+
+def test_human_male_map():
+    query = {**base_query, 'parameters': base_query['parameters'] + [{'column': 'source_id', 'value': MALE_UUID}]}
+    response = cq_request(query)
+
+    assert_valid_query_response(
+        response,
+        expected_num_keys=7,
+        expected_num_values=5,
+        expected_column_values={
+            'sckan_node_id': expected_sckan_node_ids,
+            'node_id': expected_node_ids
+        }
+    )
+
+def test_human_female_map():
+    query = {**base_query, 'parameters': base_query['parameters'] + [{'column': 'source_id', 'value': FEMALE_UUID}]}
+    response = cq_request(query)
+
+    assert_valid_query_response(
+        response,
+        expected_num_keys=7,
+        expected_num_values=5,
+        expected_column_values={
+            'sckan_node_id': expected_sckan_node_ids,
+            'node_id': expected_node_ids
+        }
+    )
+
+def test_human_rat_map():
+    query = {**base_query, 'parameters': base_query['parameters'] + [{'column': 'source_id', 'value': RAT_UUID}]}
+    response = cq_request(query)
+
+    assert_valid_query_response(
+        response,
+        expected_num_keys=7,
+        expected_num_values=5,
+        expected_column_values={
+            'sckan_node_id': expected_sckan_node_ids,
+            'node_id': expected_node_ids
+        }
+    )
+#===============================================================================

tests/utility.py

@@ -1,15 +1,28 @@
 import requests
+from tools.portal_maps import ENDPOINTS, latest_maps
 
-END_POINT = 'https://mapcore-demo.org/devel/flatmap/v4/competency/query'
+END_POINT = ENDPOINTS['development']
+CQ_END_POINT = f'{END_POINT}/competency/query'
 HEADERS = {'Content-Type': 'application/json'}
 
-MALE_UUID = '2b76d336-5c56-55e3-ab1e-795d6c63f9c1'
-FEMALE_UUID = '91359a0f-9e32-5309-b365-145d9956817d'
-RAT_UUID = 'fb6d0345-cb70-5c7e-893c-d744a6313c95'
+# latest flatmap UUIDs for testing obtained dynamically
+maps = latest_maps(END_POINT)
+MALE_UUID = (
+    maps.get(('NCBITaxon:9606', 'PATO:0000384'), {}).get('uuid')
+    or "2b76d336-5c56-55e3-ab1e-795d6c63f9c1"
+)
+FEMALE_UUID = (
+    maps.get(('NCBITaxon:9606', 'PATO:0000383'), {}).get('uuid')
+    or "91359a0f-9e32-5309-b365-145d9956817d"
+)
+RAT_UUID = (
+    maps.get(('NCBITaxon:10114', None), {}).get('uuid')
+    or "fb6d0345-cb70-5c7e-893c-d744a6313c95"
+)
 SCKAN_VERSION = 'sckan-2024-09-21'
 
 def cq_request(query: dict):
-    response = requests.post(END_POINT, json=query, headers=HEADERS)
+    response = requests.post(CQ_END_POINT, json=query, headers=HEADERS)
     return response
 
 def assert_valid_query_response(