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Merge pull request #43 from napakalas/issue-#42
Expose map–SCKAN node mappings; add a query and a test query.
2 parents b65b830 + 33637e7 commit dbb0ef4

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Lines changed: 233 additions & 5 deletions

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‎mapserver/competency/flatmap.py‎

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

‎mapserver/competency/queries.d/query_27.yaml‎

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

‎tests/test_query_27.py‎

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

‎tests/utility.py‎

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@@ -1,15 +1,29 @@
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import requests
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from tools.portal_maps import ENDPOINTS, latest_maps
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END_POINT = 'https://mapcore-demo.org/devel/flatmap/v4/competency/query'
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END_POINT = ENDPOINTS['development']
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CQ_END_POINT = f'{END_POINT}/competency/query'
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HEADERS = {'Content-Type': 'application/json'}
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MALE_UUID = '2b76d336-5c56-55e3-ab1e-795d6c63f9c1'
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FEMALE_UUID = '91359a0f-9e32-5309-b365-145d9956817d'
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RAT_UUID = 'fb6d0345-cb70-5c7e-893c-d744a6313c95'
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# latest flatmap UUIDs for testing obtained dynamically
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maps = latest_maps(END_POINT)
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MALE_KEY = ('NCBITaxon:9606', 'PATO:0000384')
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FEMALE_KEY = ('NCBITaxon:9606', 'PATO:0000383')
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RAT_KEY = ('NCBITaxon:10114', None)
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MALE_FALLBACK_UUID = '2b76d336-5c56-55e3-ab1e-795d6c63f9c1'
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FEMALE_FALLBACK_UUID = '91359a0f-9e32-5309-b365-145d9956817d'
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RAT_FALLBACK_UUID = 'fb6d0345-cb70-5c7e-893c-d744a6313c95'
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MALE_UUID = maps.get(MALE_KEY, {}).get('uuid', MALE_FALLBACK_UUID)
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FEMALE_UUID = maps.get(FEMALE_KEY, {}).get('uuid', FEMALE_FALLBACK_UUID)
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RAT_UUID = maps.get(RAT_KEY, {}).get('uuid', RAT_FALLBACK_UUID)
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SCKAN_VERSION = 'sckan-2024-09-21'
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def cq_request(query: dict):
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response = requests.post(END_POINT, json=query, headers=HEADERS)
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response = requests.post(CQ_END_POINT, json=query, headers=HEADERS)
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return response
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def assert_valid_query_response(

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