update spring boot to match cbioportal - spring boot 3, spring 6, spr…

…ing batch 5
genome-nexus · Feb 26, 2024 · 3169800 · 3169800
1 parent d217c2d
commit 3169800
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Showing 10 changed files with 28 additions and 50 deletions.
diff --git a/annotationPipeline/src/main/java/org/cbioportal/annotation/pipeline/BatchConfiguration.java b/annotationPipeline/src/main/java/org/cbioportal/annotation/pipeline/BatchConfiguration.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center.
+ * Copyright (c) 2016 - 2024 Memorial Sloan-Kettering Cancer Center.
  *
  * This library is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
@@ -36,37 +36,33 @@
 import org.cbioportal.models.AnnotatedRecord;
 
 import org.springframework.batch.core.*;
-import org.springframework.batch.item.*;
 import org.springframework.batch.core.configuration.annotation.*;
-import org.springframework.context.annotation.*;
+import org.springframework.batch.core.job.builder.JobBuilder;
+import org.springframework.batch.core.repository.JobRepository;
+import org.springframework.batch.core.step.builder.StepBuilder;
+import org.springframework.batch.item.*;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.batch.core.configuration.annotation.StepScope;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.*;
+import org.springframework.transaction.PlatformTransactionManager;
 
 /**
  * @author Zachary Heins
  */
 @Configuration
-@EnableBatchProcessing
 @ComponentScan(basePackages="org.cbioportal.annotator")
 public class BatchConfiguration
 {
     public static final String ANNOTATION_JOB = "annotationJob";
 
-    @Autowired
-    public JobBuilderFactory jobBuilderFactory;
-
-    @Autowired
-    public StepBuilderFactory stepBuilderFactory;
-
     @Value("${chunk:1000000}")
-    private String chunk;
+    private String chunkSize;
 
     @Bean
-    public Job annotationJob()
+    public Job annotationJob(JobRepository jobRepository, Step step)
     {
-        return jobBuilderFactory.get(ANNOTATION_JOB)
-            .start(step())
+        return new JobBuilder(ANNOTATION_JOB, jobRepository)
+            .start(step)
             .build();
     }
 
@@ -76,10 +72,10 @@ public AnnotationUtil annotationUtil() {
     }
 
     @Bean
-    public Step step()
+    public Step step(JobRepository jobRepository, PlatformTransactionManager transactionManager)
     {
-        return stepBuilderFactory.get("step")
-            .<AnnotatedRecord, String> chunk(Integer.parseInt(chunk))
+        return new StepBuilder("step", jobRepository)
+            .<AnnotatedRecord, String> chunk(Integer.parseInt(chunkSize), transactionManager)
             .reader(reader())
             .processor(processor())
             .writer(writer())

diff --git a/...tationPipeline/src/main/java/org/cbioportal/annotation/pipeline/MutationRecordReader.java b/...tationPipeline/src/main/java/org/cbioportal/annotation/pipeline/MutationRecordReader.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2016 - 2020 Memorial Sloan-Kettering Cancer Center.
+ * Copyright (c) 2016 - 2024 Memorial Sloan-Kettering Cancer Center.
  *
  * This library is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS

diff --git a/...tationPipeline/src/main/java/org/cbioportal/annotation/pipeline/MutationRecordWriter.java b/...tationPipeline/src/main/java/org/cbioportal/annotation/pipeline/MutationRecordWriter.java
@@ -98,7 +98,7 @@ public void close() throws ItemStreamException {
     }
 
     @Override
-    public void write(List<? extends String> items) throws Exception {
+    public void write(Chunk<? extends String> items) throws Exception {
         if (recordsToWriteCount > 0) {
             flatFileItemWriter.write(items);
         }

diff --git a/annotationPipeline/src/test/java/org/cbioportal/annotation/SpringBatchIntegrationTest.java b/annotationPipeline/src/test/java/org/cbioportal/annotation/SpringBatchIntegrationTest.java
@@ -70,7 +70,6 @@ public void check_if_maf_file_still_the_same_when_annotating_with_uniprot_transc
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -87,7 +86,6 @@ public void check_if_maf_file_still_the_same_when_annotating_with_mskcc_transcri
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -104,7 +102,6 @@ public void check_if_minimal_example_maf_file_still_the_same_when_annotating_wit
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -121,7 +118,6 @@ public void check_if_corner_cases_example_maf_file_still_the_same_when_annotatin
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -138,7 +134,6 @@ public void check_if_corner_cases_example_maf_file_still_the_same_when_annotatin
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -155,7 +150,6 @@ public void check_if_corner_cases_example_maf_file_still_the_same_when_annotatin
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -172,7 +166,6 @@ public void check_if_corner_cases_example_maf_file_still_the_same_when_annotatin
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -194,7 +187,6 @@ public void run_vcf2maf_test_case_mskcc() throws Exception {
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -216,7 +208,6 @@ public void run_vcf2maf_test_case_uniprot() throws Exception {
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -233,7 +224,6 @@ public void check_if_my_variant_info_provides_gnomad_annotations() throws Except
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -250,7 +240,6 @@ public void check_if_nucleotide_context_provides_Ref_Tri_and_Var_Tri_columns() t
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
     }
@@ -268,7 +257,6 @@ public void test_output_format_extended() throws Exception {
                 .addString("outputFormat", "extended")
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .addString("postIntervalSize", String.valueOf(-1))
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
@@ -287,7 +275,6 @@ public void test_output_format_minimal() throws Exception {
                 .addString("outputFormat", "minimal")
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .addString("postIntervalSize", String.valueOf(-1))
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
@@ -310,7 +297,6 @@ public void test_output_format_with_formatFileHeaders() throws Exception {
                 .addString("outputFormat", "Hugo_Symbol,Entrez_Gene_Id,Center,NCBI_Build,Chromosome,Annotation_Status")
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "uniprot")
-                .addString("errorReportLocation", null)
                 .addString("postIntervalSize", String.valueOf(-1))
                 .toJobParameters();
         testWith(jobParameters, expectedFile, actualFile);
@@ -328,7 +314,6 @@ public void test_if_output_contains_original_genomic_location() throws Exception
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .addString("postIntervalSize", String.valueOf(-1))
                 .addString("addOriginalGenomicLocation", String.valueOf(true))
                 .toJobParameters();
@@ -347,7 +332,6 @@ public void test_strip_off_first_matching_base() throws Exception {
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .addString("postIntervalSize", String.valueOf(-1))
                 .addString("stripMatchingBases", "first")
                 .toJobParameters();
@@ -366,7 +350,6 @@ public void test_no_strip_off_matching_bases() throws Exception {
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .addString("postIntervalSize", String.valueOf(-1))
                 .addString("stripMatchingBases", "none")
                 .toJobParameters();
@@ -385,7 +368,6 @@ public void test_ignore_original_genomic_location_in_input() throws Exception {
                 .addString("outputFilename", actualFile)
                 .addString("replace", String.valueOf(true))
                 .addString("isoformOverride", "mskcc")
-                .addString("errorReportLocation", null)
                 .addString("postIntervalSize", String.valueOf(-1))
                 .addString("stripMatchingBases", "none")
                 .addString("ignoreOriginalGenomicLocation", String.valueOf(true))
@@ -404,4 +386,4 @@ private void testWith(JobParameters jobParameters, String expectedPath, String a
         assertEquals("COMPLETED", actualJobExitStatus.getExitCode());
         AssertFile.assertFileEquals(expectedResult, actualResult);
     }
-}
+}
diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2016 - 2020 Memorial Sloan-Kettering Cancer Center.
+ * Copyright (c) 2016 - 2024 Memorial Sloan-Kettering Cancer Center.
  *
  * This library is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
@@ -67,7 +67,7 @@
  *
  */
 
-@Configuration
+@Configuration(enforceUniqueMethods=false)
 public class GenomeNexusImpl implements Annotator {
 
     @Value("${genomenexus.base:https://www.genomenexus.org}")

diff --git a/annotator/src/test/java/org/cbioportal/annotator/MockGenomeNexusImpl.java b/annotator/src/test/java/org/cbioportal/annotator/MockGenomeNexusImpl.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 - 2020 Memorial Sloan-Kettering Cancer Center.
+ * Copyright (c) 2018 - 2024 Memorial Sloan-Kettering Cancer Center.
  *
  * This library is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
@@ -64,7 +64,7 @@
  *
  * @author ochoaa
  */
-@Configuration
+@Configuration(enforceUniqueMethods=false)
 public class MockGenomeNexusImpl extends GenomeNexusImpl {
 
     private final boolean REPLACE = false;

diff --git a/databaseAnnotator/pom.xml b/databaseAnnotator/pom.xml
@@ -25,6 +25,7 @@
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-web</artifactId>
+      <version>${spring.version}</version>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>

diff --git a/databaseAnnotator/src/main/java/org/cbioportal/database/annotator/AnnotateRecordsWriter.java b/databaseAnnotator/src/main/java/org/cbioportal/database/annotator/AnnotateRecordsWriter.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2017 Memorial Sloan-Kettering Cancer Center.
+ * Copyright (c) 2017-2024 Memorial Sloan-Kettering Cancer Center.
  *
  * This library is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
@@ -75,8 +75,8 @@ public void close() throws ItemStreamException {
     }
 
     @Override
-    public void write(List<? extends MutationEvent> list) throws Exception {
-        for (MutationEvent event : list) {
+    public void write(Chunk<? extends MutationEvent> chunk) throws Exception {
+        for (MutationEvent event : chunk) {
             updateMutationEventInDb(event);
         }
     }

diff --git a/databaseAnnotator/src/main/java/org/cbioportal/database/annotator/BatchConfiguration.java b/databaseAnnotator/src/main/java/org/cbioportal/database/annotator/BatchConfiguration.java
@@ -47,7 +47,6 @@
  */
 
 @Configuration
-@EnableBatchProcessing
 @ComponentScan(basePackages="org.cbioportal.annotator")
 public class BatchConfiguration {
 

diff --git a/pom.xml b/pom.xml
@@ -21,14 +21,14 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.7.18</version>
+    <version>3.1.4</version>
   </parent>
 
   <properties>
     <java.version>21</java.version>
     <slf4j.version>1.7.30</slf4j.version>
-    <spring.version>5.3.31</spring.version>
-    <jackson.version>2.11.2</jackson.version>
+    <spring.version>6.0.12</spring.version>
+    <jackson.version>2.14.3</jackson.version>
     <mockito.version>5.10.0</mockito.version>
   </properties>