diff --git a/client-api/pom.xml b/client-api/pom.xml index 3ac127ed..bd533e67 100644 --- a/client-api/pom.xml +++ b/client-api/pom.xml @@ -17,8 +17,6 @@ UTF-8 - 1.7 - 1.7 diff --git a/data/pom.xml b/data/pom.xml index 85c96dad..e905b45c 100644 --- a/data/pom.xml +++ b/data/pom.xml @@ -11,6 +11,8 @@ data data + + diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMeta.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMeta.java index d0aebb36..189a22be 100644 --- a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMeta.java +++ b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMeta.java @@ -1,16 +1,5 @@ package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; -import lombok.Builder; -import lombok.Value; -import lombok.extern.jackson.Jacksonized; - -@Jacksonized -@Value -@Builder -public class InfoColumnMeta { - - String key, description; - boolean continuous; - Float min, max; +public record InfoColumnMeta(String key, String description, boolean continuous, Float min, Float max) { } diff --git a/genomic-processor/pom.xml b/genomic-processor/pom.xml index 4ffabd57..8b82278d 100644 --- a/genomic-processor/pom.xml +++ b/genomic-processor/pom.xml @@ -12,8 +12,6 @@ genomic-processor - 18 - 18 UTF-8 diff --git a/pom.xml b/pom.xml index a19ec9fc..a25477aa 100644 --- a/pom.xml +++ b/pom.xml @@ -26,6 +26,8 @@ war + 21 + 21 UTF-8 1.4.10 2.20.153 @@ -118,7 +120,8 @@ maven-compiler-plugin 3.8.0 - 11 + + 21 diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java index f1cb8ca1..68e0140b 100644 --- a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java +++ b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java @@ -389,13 +389,13 @@ public Set getInfoStoreValues(String conceptPath) { @Override public List getInfoColumnMeta() { return getInfoStoreColumns().stream().map(infoStores::get) - .map(fileBackedByteIndexedInfoStore -> InfoColumnMeta.builder() - .key(fileBackedByteIndexedInfoStore.column_key) - .description(fileBackedByteIndexedInfoStore.description) - .continuous(fileBackedByteIndexedInfoStore.isContinuous) - .min(fileBackedByteIndexedInfoStore.min) - .max(fileBackedByteIndexedInfoStore.max) - .build() + .map(fileBackedByteIndexedInfoStore -> new InfoColumnMeta( + fileBackedByteIndexedInfoStore.column_key, + fileBackedByteIndexedInfoStore.description, + fileBackedByteIndexedInfoStore.isContinuous, + fileBackedByteIndexedInfoStore.min, + fileBackedByteIndexedInfoStore.max + ) ) .collect(Collectors.toList()); } diff --git a/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java b/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java index 5ded227e..ff24f62f 100644 --- a/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java +++ b/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java @@ -56,7 +56,7 @@ public void getInfoStoreValues() { public void getInfoColumnMeta() { List infoColumnMeta = genomicProcessorRestClient.getInfoColumnMeta(); for (InfoColumnMeta columnMeta : infoColumnMeta) { - if (columnMeta.getKey().equals("Variant_consequence_calculated")) { + if (columnMeta.key().equals("Variant_consequence_calculated")) { return; } } diff --git a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java index 1d0f8c2e..04e5863f 100644 --- a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java +++ b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java @@ -155,12 +155,12 @@ public SearchResults search(@RequestBody QueryRequest searchJson) { //FileBackedByteIndexedInfoStore store = abstractProcessor.getInfoStore(infoColumn); String query = searchJson.getQuery().toString(); String lowerCase = query.toLowerCase(); - boolean storeIsNumeric = infoColumnMeta.isContinuous(); - if (infoColumnMeta.getDescription().toLowerCase().contains(lowerCase) - || infoColumnMeta.getKey().toLowerCase().contains(lowerCase)) { - infoResults.put(infoColumnMeta.getKey(), - ImmutableMap.of("description", infoColumnMeta.getDescription(), "values", - storeIsNumeric ? new ArrayList() : abstractProcessor.searchInfoConceptValues(infoColumnMeta.getKey(), ""), "continuous", + boolean storeIsNumeric = infoColumnMeta.continuous(); + if (infoColumnMeta.description().toLowerCase().contains(lowerCase) + || infoColumnMeta.key().toLowerCase().contains(lowerCase)) { + infoResults.put(infoColumnMeta.key(), + ImmutableMap.of("description", infoColumnMeta.description(), "values", + storeIsNumeric ? new ArrayList() : abstractProcessor.searchInfoConceptValues(infoColumnMeta.key(), ""), "continuous", storeIsNumeric)); } });