Updated code for better caching and reruning the indexer in place #1226
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| @@ -23,6 +23,9 @@ public interface VocabularyRESTInterface { | |||
| @POST | |||
| @Path("/find") | |||
| @JsonView({View.FieldsAndLists.class}) | |||
| SearchResponse<VocabularyTerm> find(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params); | |||
| SearchResponse<VocabularyTerm> find( | |||
| @DefaultValue("0") @QueryParam("page") Integer page, | |||
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| SearchResponse<VocabularyTerm> find(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params); | ||
| SearchResponse<VocabularyTerm> find( | ||
| @DefaultValue("0") @QueryParam("page") Integer page, | ||
| @DefaultValue("10") @QueryParam("limit") Integer limit, |
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| @@ -168,6 +168,10 @@ public <D extends ESDocument> void indexDocuments(Iterable<D> docs, Class<?> vie | |||
| } else { | |||
| json = om.writeValueAsString(doc); | |||
| } | |||
| if(json.length() > 19_000_000) { | |||
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'if' is not followed by whitespace.
| @@ -30,7 +30,9 @@ public void index() { | |||
| log.info("Pulling All Terms Finished"); | |||
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| Iterable<SearchableItemDocument> docs = goTrans.translateEntities(terms); | |||
| docs.forEach(doc -> doc.setPopularity(popularityScore.get(doc.getPrimaryKey()))); | |||
| for(SearchableItemDocument doc: docs) { | |||
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| @@ -337,14 +364,15 @@ public Map<String, Map<String, Set<Allele>>> getAllAllelesCache() { | |||
| } | |||
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| public void fixupAllelesWithVariants(Set<Allele> allAlleles, Set<Allele> allelesWithVariants) { | |||
| allelesWithVariants.forEach(allele -> { | |||
| getTranscriptWithExonInfo(); | |||
| for(Allele allele: allelesWithVariants) { | |||
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| alleleSynonymMap = new HashMap<>(); | ||
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| for(Allele a: alleleSynonymsIter) { |
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| alleleCrossReferenceMap = new HashMap<>(); | ||
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| for(Allele a: alleleCrossReferenceIter) { |
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'for' is not followed by whitespace.
| for (Allele a : allelesWithVariants) { | ||
| if(alleleSynonymMap.containsKey(a.getPrimaryKey())) { |
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'if' is not followed by whitespace.
| if(alleleSynonymMap.containsKey(a.getPrimaryKey())) { | ||
| a.setSynonyms(alleleSynonymMap.get(a.getPrimaryKey())); | ||
| } | ||
| if(alleleCrossReferenceMap.containsKey(a.getPrimaryKey())) { |
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| if (a.getVariants() != null && a.getVariants().size() > 0) { | ||
| for (Variant v : a.getVariants()) { | ||
| if(variantSOTermMap.containsKey(v.getPrimaryKey())) { |
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'if' is not followed by whitespace.
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