TranQL query optimization, loading error/state improvements, variable view color fix #325
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -74,12 +74,15 @@ export const ConceptModalBody = ({ result }) => { | ||
| const { context } = useEnvironment(); | ||
| const [currentTab, _setCurrentTab] = useState('overview') | ||
| const { query, setSelectedResult, fetchKnowledgeGraphs, fetchVariablesForConceptId, fetchCDEs, studySources } = useHelxSearch() | ||
| const [graphs, setGraphs] = useState(undefined) | ||
| const [studies, setStudies] = useState(undefined) | ||
| const [cdes, setCdes] = useState(undefined) | ||
| const [cdeRelatedConcepts, setCdeRelatedConcepts] = useState(null) | ||
| const [cdeRelatedStudies, setCdeRelatedStudies] = useState(null) | ||
|
|
||
| const [cdesLoading, cdesError] = useMemo(() => ([ cdes === undefined, cdes === null ]), [cdes]) | ||
| const [graphsLoading, graphsError] = useMemo(() => ([ graphs === undefined, graphs === null ]), [graphs]) | ||
| const [studiesLoading, studiesError] = useMemo(() => ([ studies === undefined, studies === null ]), [studies]) | ||
|
|
||
| /** Abort controllers */ | ||
| const fetchVarsController = useRef() | ||
| @@ -113,7 +116,7 @@ export const ConceptModalBody = ({ result }) => { | ||
| 'studies': { | ||
| title: studyTitle, | ||
| icon: <StudiesIcon />, | ||
| content: <StudiesTab studies={ studies } loading={ studiesLoading } error={ studiesError } />, | ||
| tooltip: <div> | ||
| The Studies tab displays studies referencing or researching the concept. | ||
| Studies are grouped into { studySources.length } categories: | ||
| @@ -132,7 +135,7 @@ export const ConceptModalBody = ({ result }) => { | ||
| 'cdes': { | ||
| title: cdeTitle, | ||
| icon: <CdesIcon />, | ||
| content: <CdesTab cdes={ cdes } cdeRelatedConcepts={ cdeRelatedConcepts } cdeRelatedStudies={cdeRelatedStudies} loading={ cdesLoading } error={ cdesError } />, | ||
| tooltip: <div> | ||
| The CDEs tab displays{ context.brand === "heal" ? " HEAL-approved" : "" } common data elements (CDEs) | ||
| associated with the concept. A CDE is a standardized question used across studies and clinical | ||
| @@ -147,10 +150,10 @@ export const ConceptModalBody = ({ result }) => { | ||
| 'kgs': { | ||
| title: 'Knowledge Graphs', | ||
| icon: <KnowledgeGraphsIcon />, | ||
| content: <KnowledgeGraphsTab graphs={ graphs } loading={ graphsLoading } error={ graphsError } />, | ||
| tooltip: <div> | ||
| The Knowledge Graphs tab displays relevant edges from the <a href="https://robokop.renci.org/" target="_blank" rel="noopener noreferrer">ROBOKOP Knowledge Graph</a> | ||
| portion connected to the concept and containing your search terms. This section highlights | ||
| potential interesting knowledge graph relationships and shows terms (e.g., synonyms) that | ||
| would be returned as related concepts. | ||
| </div> | ||
| @@ -214,13 +217,14 @@ export const ConceptModalBody = ({ result }) => { | ||
| return studies | ||
| }, {})) | ||
| } catch (e) { | ||
| if (e.name !== "CanceledError") { | ||
| console.warning(e) | ||
| setStudies(null) | ||
| } | ||
| } | ||
| } | ||
| const getCdes = async () => { | ||
| try { | ||
| fetchCdesController.current?.abort() | ||
| fetchCdesController.current = new AbortController() | ||
| fetchCdesTranqlController.current.forEach((controller) => controller.abort()) | ||
| @@ -229,90 +233,51 @@ export const ConceptModalBody = ({ result }) => { | ||
| const cdeData = await fetchCDEs(result.id, query, { | ||
| signal: fetchCdesController.current.signal | ||
| }) | ||
| const loadRelatedConceptsAndStudies = async (cdeId) => { | ||
| const getNodeAttribute = (node, attrName) => { | ||
| return node.attributes.find((attr) => attr.name === attrName) | ||
| } | ||
| const tranqlUrl = context.tranql_url | ||
| const controller = new AbortController() | ||
| fetchCdesTranqlController.current.push(controller) | ||
|
|
||
| const res = await fetch( | ||
| `${tranqlUrl}tranql/query`, | ||
| { | ||
| headers: { 'Content-Type': 'text/plain' }, | ||
| method: 'POST', | ||
| body: `SELECT publication->named_thing FROM "redis:" WHERE publication="${cdeId}"`, | ||
|
There was a problem hiding this comment. Be careful that this could pick up (1) things that aren't concepts, or (2) concepts that we haven't loaded. For example, when I tried running this locally, I found the related concept "Rheum", which we haven't actually loaded, so trying to select it (via "Open") resulted in a I prefer the approach we were using previously, which is to limit this query to certain types ( There was a problem hiding this comment. Hmm, good point. I considered that it could possibly lead to unindexed concepts from unrestricting the types, but I didn't find in an example of such a thing happening during my testing. There was a problem hiding this comment. I'll note that querying against these specific types in tranql isn't going to fix the issue of getting results back that aren't indexed in dug. This can be done by checking the concept returned by tranql is linked to a study variable, but this also isn't particularly practical. There was a bug with the concept lookup mechanism (used here) which I've fixed now, so you shouldn't be seeing that error anymore. Really, what needs to happen is the addition of a new Dug endpoint that let's you pull any documents out of the concept index by ID. Then we could do a subsequent lookup against the results returned by tranql and filter out any that aren't indexed. It's just that this feature isn't particularly prominent so the work hasn't been done. |
||
| signal: controller.signal | ||
| } | ||
| ) | ||
| const message = await res.json() | ||
| const kg = message.message.knowledge_graph | ||
| const cdeOutEdges = Object.values(kg.edges).filter((edge) => edge.subject === cdeId) | ||
| return cdeOutEdges.map(({ object }) => kg.nodes[object]) | ||
| .reduce((acc, node) => { | ||
| const [relatedConceptNodes, relatedStudyNodes] = acc | ||
| const types = getNodeAttribute(node, "category") | ||
| const url = getNodeAttribute(node, "url") | ||
| if (url && types && types.value.includes("biolink:Study")) relatedStudyNodes.push({ | ||
| c_id: node.id, | ||
| c_name: node.name, | ||
| c_link: url.value | ||
| }) | ||
| else relatedConceptNodes.push(node) | ||
| return [relatedConceptNodes, relatedStudyNodes] | ||
| }, [[], []]) | ||
| } | ||
| const relatedConcepts = {} | ||
| const relatedStudies = {} | ||
| if (cdeData) { | ||
| const cdeIds = cdeData.elements.map((cde) => cde.id) | ||
| await Promise.all(cdeIds.map(async (cdeId, i) => { | ||
| try { | ||
| const [relatedConceptsRaw, relatedStudiesRaw] = await loadRelatedConceptsAndStudies(cdeId) | ||
| // Counterproductive to suggest the concept the user is actively viewing as "related" | ||
| relatedConcepts[cdeId] = relatedConceptsRaw.filter((c) => c.id !== result.id) | ||
| relatedStudies[cdeId] = relatedStudiesRaw | ||
| } catch (e) { | ||
| // Here, we explicitly want to halt execution and forward this error to the outer handler | ||
| // if a related concept request was aborted, because we now have stale data and don't want to | ||
| @@ -321,25 +286,17 @@ export const ConceptModalBody = ({ result }) => { | ||
| relatedConcepts[cdeId] = null | ||
| } | ||
| })) | ||
| } | ||
| setCdes(cdeData) | ||
| /** Note that relatedConcepts are *TranQL* concepts/nodes, not DUG concepts. Both have the top level fields `id` and `name`. */ | ||
| setCdeRelatedConcepts(relatedConcepts) | ||
| setCdeRelatedStudies(relatedStudies) | ||
| } catch (e) { | ||
| // Check both because this function uses both Fetch API & Axios | ||
| if (e.name !== "CanceledError" && e.name !== "AbortError") { | ||
| console.warning(e) | ||
| setCdes(null) | ||
| } | ||
| } | ||
| } | ||
| const getKgs = async () => { | ||
| @@ -352,19 +309,22 @@ export const ConceptModalBody = ({ result }) => { | ||
| }) | ||
| setGraphs(kgs) | ||
| } catch (e) { | ||
| if (e.name !== "CanceledError") { | ||
| console.warning(e) | ||
| setGraphs(null) | ||
| } | ||
| } | ||
| } | ||
| if (!result.loading && !result.failed) { | ||
| setStudies(undefined) | ||
| setGraphs(undefined) | ||
| setCdes(undefined) | ||
| setCdeRelatedConcepts(null) | ||
| setCdeRelatedStudies(null) | ||
|
|
||
| getVars() | ||
| getKgs() | ||
| getCdes() | ||
| } | ||
| }, [fetchKnowledgeGraphs, fetchVariablesForConceptId, fetchCDEs, result, query]) | ||
|
|
||
| @@ -395,25 +355,29 @@ export const ConceptModalBody = ({ result }) => { | ||
| ]} | ||
| className="concept-modal-failed-result" | ||
| > | ||
| { result.suggestions && ( | ||
| <Fragment> | ||
| <Paragraph style={{ marginBottom: 0 }}> | ||
| <Text strong style={{ fontSize: 16 }}>Related concepts</Text> | ||
| </Paragraph> | ||
| <div> | ||
| { | ||
| result.suggestions | ||
| .slice(0, 8) | ||
| .map((suggestedResult) => ( | ||
| <a | ||
| key={ suggestedResult.id } | ||
| role="button" | ||
| style={{ display: "inline", marginRight: "12px", lineHeight: "36px" }} | ||
| onClick={() => setSelectedResult(suggestedResult)} | ||
| > | ||
| {suggestedResult.name} | ||
| </a> | ||
| )) | ||
| } | ||
| </div> | ||
| </Fragment> | ||
| ) } | ||
| </Result> | ||
| ) | ||
| return ( | ||
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Would it be useful to propagate the exception?
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Not in this scenario. The exception is "implicitly" handled by setting the state to null, indicating an error state.