Merge pull request #266 from RobokopU24/update/trapi-1-4

Parse TRAPI 1.4
RobokopU24 · Oct 23, 2023 · e1cec4c · e1cec4c
2 parents ed3b3ea + bc9a0b6
commit e1cec4c
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Showing 7 changed files with 3,266 additions and 3,844 deletions.
diff --git a/api_routes/sample-query-cache.json b/api_routes/sample-query-cache.json
diff --git a/src/pages/answer/resultsTable/AttributesTable.jsx b/src/pages/answer/resultsTable/AttributesTable.jsx
@@ -72,7 +72,7 @@ const PublicationLinkCell = ({ value }) => {
   );
 };
 
-const AttributesTable = ({ attributes }) => (
+const AttributesTable = ({ attributes, sources }) => (
   <Box style={{ maxHeight: 500, overflow: 'auto' }}>
     <Table size="small" aria-label="edge attributes table">
       <TableHead style={{ position: 'sticky', top: 0 }}>
@@ -96,6 +96,32 @@ const AttributesTable = ({ attributes }) => (
             }
           </TableRow>
         ))}
+        <TableRow>
+          <TableCell>
+            Sources
+          </TableCell>
+          <TableCell>
+            {Array.isArray(sources) && sources.map((source, i) => (
+              <section key={i}>
+                <p style={{ marginBottom: '0px', fontStyle: 'italic' }}>{source.resource_id}</p>
+                <p style={{ filter: 'opacity(0.75)', fontSize: '0.8em' }}>{source.resource_role}</p>
+                {Boolean(source.upstream_resource_ids) && Array.isArray(source.upstream_resource_ids) && (
+                  <>
+                    <p style={{ marginBottom: '0px' }}>Upstream resource ids:</p>
+                    <ul>
+                      {source.upstream_resource_ids.map((urid, j) => (
+                        <li key={j}>
+                          {urid}
+                        </li>
+                      ))}
+                    </ul>
+                  </>
+                )}
+                {i === sources.length - 1 ? null : <hr />}
+              </section>
+            ))}
+          </TableCell>
+        </TableRow>
       </StyledTableBody>
     </Table>
   </Box>

diff --git a/src/pages/answer/resultsTable/ResultExplorer.jsx b/src/pages/answer/resultsTable/ResultExplorer.jsx
@@ -163,6 +163,7 @@ export default function ResultExplorer({ answerStore }) {
       .map((key) => ({
         ...answerStore.selectedResult.edges[key],
         attributes: answerStore.resultJSON.knowledge_graph.edges[key].attributes,
+        sources: answerStore.resultJSON.knowledge_graph.edges[key].sources,
       }));
     // this is weird, but stops the simulation from throwing a
     // `d3 cannot create property 'vx' on string` error when trying to move edges
@@ -262,7 +263,7 @@ export default function ResultExplorer({ answerStore }) {
                 .attr('stroke', '#999');
             })
             .on('click', function (e) {
-              handleClickEdge(e, d3.select(this).datum().attributes);
+              handleClickEdge(e, d3.select(this).datum());
             }),
         (update) => update
           .call((e) => e.select('title')
@@ -313,10 +314,10 @@ export default function ResultExplorer({ answerStore }) {
     }
   }
 
-  const handleClickEdge = (event, attributes) => {
+  const handleClickEdge = (event, data) => {
     setPopoverPosition({ x: event.clientX, y: event.clientY });
 
-    setPopoverData(attributes);
+    setPopoverData(data);
     setPopoverOpen('edge');
   };
 
@@ -378,7 +379,7 @@ export default function ResultExplorer({ answerStore }) {
         anchorPosition={{ top: popoverPosition.y, left: popoverPosition.x }}
         above
       >
-        <AttributesTable attributes={popoverData} />
+        <AttributesTable attributes={popoverData.attributes} sources={popoverData.sources} />
       </Popover>
 
       <Popover

diff --git a/src/pages/answer/useAnswerStore.js b/src/pages/answer/useAnswerStore.js
@@ -29,6 +29,28 @@ export default function useAnswerStore() {
     setResultJSON({});
   }
 
+  /**
+   * Takes a TRAPI message and average the analysis scores for each
+   * result, and places that average in a new key called `score` on
+   * each result object.
+   * @param {object} msg - TRAPI message
+   */
+  function averageAnalysesScores(msg) {
+    const resultsWithScore = msg.results.map((result) => {
+      // get average score of all analyses
+      const score = result.analyses.reduce((sum, analysis) => sum + analysis.score, 0) / result.analyses.length;
+      return {
+        ...result,
+        score,
+      };
+    });
+
+    return {
+      ...msg,
+      results: resultsWithScore,
+    };
+  }
+
   /**
    * Initialize the answer store with a message
    *
@@ -37,7 +59,7 @@ export default function useAnswerStore() {
    * @param {object} msg - TRAPI message
    */
   function initialize(msg, updateDisplayState) {
-    setMessage(msg);
+    setMessage(averageAnalysesScores(msg));
     if (msg.knowledge_graph && msg.results) {
       setKgNodes(kgUtils.makeDisplayNodes(msg, hierarchies));
       updateDisplayState({ type: 'toggle', payload: { component: 'kg', show: true } });
@@ -94,35 +116,37 @@ export default function useAnswerStore() {
           }
         });
       });
+
       const edges = {};
       const edgesJSON = {};
-      Object.values(row.edge_bindings).forEach((value) => {
-        value.forEach((kgObject) => {
-          const kgEdge = message.knowledge_graph.edges[kgObject.id];
-          edgesJSON[kgObject.id] = kgEdge || 'Unknown';
-          if (kgEdge) {
-            const graphEdge = {
-              id: kgObject.id,
-              source: kgEdge.subject,
-              target: kgEdge.object,
-              predicate: kgEdge.predicate,
-            };
-            edges[kgObject.id] = graphEdge;
-            if (kgEdge.subject in nodes) {
-              nodes[kgEdge.subject].score += 1;
+      row.analyses.forEach((analysis) => {
+        Object.values(analysis.edge_bindings).forEach((edgeBindings) => {
+          edgeBindings.forEach((binding) => {
+            const kgEdge = message.knowledge_graph.edges[binding.id];
+            edgesJSON[binding.id] = kgEdge || 'Unknown';
+            if (kgEdge) {
+              const graphEdge = {
+                id: binding.id,
+                source: kgEdge.subject,
+                target: kgEdge.object,
+                predicate: kgEdge.predicate,
+              };
+              edges[binding.id] = graphEdge;
+              if (kgEdge.subject in nodes) {
+                nodes[kgEdge.subject].score += 1;
+              }
+              if (kgEdge.object in nodes) {
+                nodes[kgEdge.object].score += 1;
+              }
+              const subjectNode = message.knowledge_graph.nodes[kgEdge.subject];
+              const objectNode = message.knowledge_graph.nodes[kgEdge.object];
+              const edgeKey = `${subjectNode.name || kgEdge.subject} ${stringUtils.displayPredicate(kgEdge.predicate)} ${objectNode.name || kgEdge.object}`;
+              publications[edgeKey] = resultsUtils.getPublications(kgEdge);
             }
-            if (kgEdge.object in nodes) {
-              nodes[kgEdge.object].score += 1;
-            }
-
-            const subjectNode = message.knowledge_graph.nodes[kgEdge.subject];
-            const objectNode = message.knowledge_graph.nodes[kgEdge.object];
-            const edgeKey = `${subjectNode.name || kgEdge.subject} ${stringUtils.displayPredicate(kgEdge.predicate)} ${objectNode.name || kgEdge.object}`;
-
-            publications[edgeKey] = resultsUtils.getPublications(kgEdge);
-          }
+          });
         });
       });
+
       setSelectedResult({ nodes, edges });
       setSelectedRowId(rowId);
       setMetaData(publications);

diff --git a/src/utils/fetchCuries.js b/src/utils/fetchCuries.js
@@ -8,7 +8,11 @@ export default async function fetchCuries(entity, displayAlert, cancel) {
       'Failed to contact name resolver to search curies. Please try again later.');
     return [];
   }
-  const curieResponse = Object.keys(response);
+
+  if (!Array.isArray(response)) {
+    return [];
+  }
+  const curieResponse = response.map((node) => node.curie);
   if (!curieResponse.length) {
     return [];
   }

diff --git a/src/utils/trapi.js b/src/utils/trapi.js
@@ -78,10 +78,10 @@ function validateResults(results) {
       errors.push('Results node_bindings is not a valid JSON object');
     }
 
-    if (!('edge_bindings' in results[i])) {
-      errors.push('No edge_bindings in result object');
-    } else if (results[i].edge_bindings.constructor !== Object) {
-      errors.push('Results edge_bindings is not a valid JSON object');
+    if (!('analyses' in results[i])) {
+      errors.push('No analyses in result object');
+    } else if (!Array.isArray(results[i].analyses)) {
+      errors.push('Results analyses is not an array');
     }
     if (errors.length) {
       break;

diff --git a/tests/common/test_message.json b/tests/common/test_message.json
@@ -44,9 +44,13 @@
           "n0": [{ "id": "1" }],
           "n1": [{ "id": "2" }]
         },
-        "edge_bindings": {
-          "e0": [{ "id": "1" }]
-        }
+        "analyses": [
+          {
+            "edge_bindings": {
+              "e0": [{ "id": "1" }]
+            }
+          }
+        ]
       }
     ]
   }