Trm 30823 uniparc proteome redundant fasta #524
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# Conflicts: # uniparc-rest/src/test/java/org/uniprot/api/uniparc/controller/UniParcGetIdControllerIT.java
# Conflicts: # common-rest/src/main/java/org/uniprot/api/rest/output/converter/JsonMessageConverter.java
# Conflicts: # idmapping-common/src/main/java/org/uniprot/api/idmapping/common/response/converter/uniparc/UniParcEntryPairFastaMessageConverter.java # uniparc-common/src/main/java/org/uniprot/api/uniparc/common/service/UniParcQueryService.java # uniparc-rest/src/main/java/org/uniprot/api/uniparc/controller/UniParcController.java # uniparc-rest/src/test/java/org/uniprot/api/uniparc/controller/AbstractGetSingleUniParcByIdTest.java # uniparc-rest/src/test/java/org/uniprot/api/uniparc/controller/UniParcGetByProteomeIdIT.java
# Conflicts: # uniparc-common/src/main/java/org/uniprot/api/uniparc/common/service/UniParcEntryService.java # uniparc-common/src/main/java/org/uniprot/api/uniparc/common/service/filter/UniParcCrossReferenceTaxonomyFilter.java # uniparc-common/src/main/java/org/uniprot/api/uniparc/common/service/filter/UniParcDatabaseFilter.java # uniparc-common/src/test/java/org/uniprot/api/uniparc/common/service/filter/UniParcCrossReferenceTaxonomyFilterTest.java # uniparc-common/src/test/java/org/uniprot/api/uniparc/common/service/filter/UniParcDatabaseFilterTest.java # uniparc-common/src/test/java/org/uniprot/api/uniparc/common/service/filter/UniParcDatabaseStatusFilterTest.java
# Conflicts: # common-rest/src/main/java/org/uniprot/api/rest/openapi/OpenAPIConstants.java # uniparc-common/src/main/java/org/uniprot/api/uniparc/common/repository/UniParcStreamConfig.java # uniparc-common/src/main/java/org/uniprot/api/uniparc/common/service/UniParcEntryService.java # uniparc-rest/src/main/java/org/uniprot/api/uniparc/controller/UniParcEntryLightController.java
ahmadshadab
reviewed
Dec 11, 2024
uniparc-common/src/main/java/org/uniprot/api/uniparc/common/service/UniParcEntryService.java
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| .documentIdStream(uniParcTupleStreamDocumentIdStream) | ||
| .build(); | ||
| } | ||
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Do we need to update k8s meta cm with any new config?
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Already added in k8s module.
...a/org/uniprot/api/uniparc/common/repository/store/stream/UniParcFastaBatchStoreIterable.java
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...a/org/uniprot/api/uniparc/common/repository/store/stream/UniParcFastaBatchStoreIterable.java
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| MessageConverterContext<UniParcEntry> context, OutputStream outputStream) { | ||
| TL_ENTITY_ONLY.set(context.isEntityOnly()); | ||
| } | ||
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Which API will set this isEntityOnly flag? I can only see in UniSave
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This parser can be used for 2 scenarios, and we need entityOnly to distinguishes it.
- /uniparc/{upi} (entityOnly is true) -> and we should use the simple fastaParser
- /uniparc/proteome use cases (entityOnly is false) for the more complex proteomeFastaParser.
PS2: We change entity only "context.setEntityOnly(true)" at BasicSearchController.getEntityResponse for every getById request (Entry request).
PS1: For uniparc search and stream we have another UniParcLightFastaMessageConverter for the light object.
...mon/src/main/java/org/uniprot/api/uniparc/common/service/filter/UniParcProteomeIdFilter.java
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| @Parameter(description = FIELDS_UNIPARC_DESCRIPTION, example = FIELDS_UNIPARC_EXAMPLE) | ||
| @ValidReturnFields(uniProtDataType = UniProtDataType.UNIPARC) | ||
| private String fields; | ||
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Do we need fields in fasta format?
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I created a Jira for it: TRM-32296
| @@ -37,4 +61,88 @@ static UniParcDocument.UniParcDocumentBuilder getUniParcDocument(UniParcEntry en | |||
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| return builder; | |||
| } | |||
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thank you for moving the code to common place
| "$.messages[0]", | ||
| containsString( | ||
| "Invalid request received. Requested media type/format not accepted: 'application/json'."))); | ||
| } |
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Nice to have multivalues test for devs. Sometime, we miss unit tests.
ahmadshadab
approved these changes
Jan 9, 2025
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