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Add go indexer #1312

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@adamgibs adamgibs requested a review from a team as a code owner April 25, 2025 15:27
devopsagr
devopsagr reviewed Apr 25, 2025
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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

checkstyle

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> reported by reviewdog 🐶
Indent must use tab characters

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 57 in 90c857a

SearchResponse<GOSearchResultDocument> response = goApi.findSearchResult(Integer.valueOf(page), indexerConfig.getBufferSize(), params);

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> reported by reviewdog 🐶
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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 58 in 90c857a

if (response == null || CollectionUtils.isEmpty(response.getResults())) {

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

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return;

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> reported by reviewdog 🐶
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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 60 in 90c857a

}

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 61 in 90c857a

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> reported by reviewdog 🐶
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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 62 in 90c857a

indexDocuments(response.getResults());

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

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} catch (Exception e) {

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 64 in 90c857a

log.error("Error while indexing...", e);

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 65 in 90c857a

System.exit(-1);

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

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return;

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 67 in 90c857a

}

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 68 in 90c857a

}

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

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}

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 71 in 90c857a

@Override

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

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protected ObjectMapper customizeObjectMapper(ObjectMapper objectMapper) {

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 73 in 90c857a

return RestConfig.config.getJacksonObjectMapperFactory().createObjectMapper();

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agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java

Line 74 in 90c857a

}

oblodgett
oblodgett reviewed Apr 25, 2025
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agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java Outdated
@@ -34,6 +35,7 @@ public enum IndexerConfig {
ReleaseInfoIndexer("release", ReleaseInfoIndexer.class, 1, 1, 1, 1, 1),
DiseaseSummaryIndexer("diseaseSummary", DiseaseSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1),
GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 1500, 1500, 8, 1),
GOCurationIndexer("goCuration", GOSearchResultCurationIndexer.class, 4, 1500, 1500, 8, 1),
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To be consistant like the gene this should be called goSearchResult

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@adamgibs sorry I think thinking more of the text name vs Enum name. As in its text name is still "goCuration"

@adamgibs adamgibs requested a review from oblodgett April 25, 2025 15:42
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@oblodgett oblodgett Awaiting requested review from oblodgett

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@adamgibs @oblodgett @devopsagr