From 3d226d57f16a684f2089af662bdc50902ff82915 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Wed, 28 Aug 2024 15:06:15 -0400 Subject: [PATCH 01/15] adds verifier code --- pom.xml | 34 +++- .../release/orthopairs/verifier/Verifier.java | 169 ++++++++++++++++++ 2 files changed, 202 insertions(+), 1 deletion(-) create mode 100644 src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java diff --git a/pom.xml b/pom.xml index b0d5815..77321c9 100644 --- a/pom.xml +++ b/pom.xml @@ -61,9 +61,27 @@ org.apache.logging.log4j log4j-core - 2.11.0 + 2.17.0 + + + org.apache.logging.log4j + log4j-api + 2.17.0 + + + + org.jcommander + jcommander + 1.83 + + org.reactome.release.verifier + verifier-lib + 1.0-SNAPSHOT + + + junit @@ -165,4 +183,18 @@ + + + + + oss.sonatype.org-snapshot + http://oss.sonatype.org/content/repositories/snapshots + + false + + + true + + + diff --git a/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java new file mode 100644 index 0000000..d59c48e --- /dev/null +++ b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java @@ -0,0 +1,169 @@ +package org.reactome.release.orthopairs.verifier; + +import com.beust.jcommander.JCommander; +import com.beust.jcommander.Parameter; + +import org.reactome.release.verifier.Results; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.List; +import java.util.stream.Collectors; + +import static org.reactome.release.verifier.CountUtils.greaterThanOrEqualTo5PercentDrop; +import static org.reactome.release.verifier.FileUtils.*; + +/** + * @author Joel Weiser (joel.weiser@oicr.on.ca) + * Created 8/15/2024 + */ +public class Verifier { + @Parameter(names = "-release", description = "Current Reactome Release number", required = true) + private int releaseNumber; + + public static void main(String[] args) throws IOException { + Verifier verifier = new Verifier(); + JCommander.newBuilder() + .addObject(verifier) + .build() + .parse(args); + + verifier.run(); + } + + private void run() throws IOException { + Results results = compareCurrentAndPreviousOrthopairFiles(); + + results.report(); + if (results.hasErrors()) { + results.reportErrors(); + System.exit(1); + } + } + + private Results compareCurrentAndPreviousOrthopairFiles() throws IOException { + Results overallResults = new Results(); + + List previousOrthopairFilePaths = getPreviousOrthopairFilePaths(); + for (Path currentOrthopairFilePath : getCurrentOrthopairFilePaths()) { + Path previousOrthopairFilePath = + getAnalgousPreviousOrthopairFile(currentOrthopairFilePath, previousOrthopairFilePaths); + + if (previousOrthopairFilePath != null) { + Results lineCountResults = checkLineCount(currentOrthopairFilePath, previousOrthopairFilePath); + Results fileSizeResults = checkFileSize(currentOrthopairFilePath, previousOrthopairFilePath); + + overallResults.addInfoMessages(lineCountResults.getInfoMessages()); + overallResults.addInfoMessages(fileSizeResults.getInfoMessages()); + overallResults.addErrorMessages(lineCountResults.getErrorMessages()); + overallResults.addErrorMessages(fileSizeResults.getErrorMessages()); + } + } + + return overallResults; + } + + private List getCurrentOrthopairFilePaths() throws IOException { + return Files.list(Paths.get(String.valueOf(releaseNumber))).collect(Collectors.toList()); + } + + private List getPreviousOrthopairFilePaths() throws IOException { + String folderName = downloadPreviousOrthopairFiles(); + Files.list(Paths.get(folderName)).filter(file -> file.getFileName().toString().endsWith(".gz")).forEach(file -> { + try { + gunzipFile(file); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + return Files.list(Paths.get(folderName)).filter(file -> file.getFileName().toString().endsWith(".tsv")).collect(Collectors.toList()); + } + + private Path getAnalgousPreviousOrthopairFile( + Path currentOrthopairFilePath, List previousOrthopairFilePaths) { + + return previousOrthopairFilePaths + .stream() + .filter(previousOrthopairFilePath -> + previousOrthopairFilePath.getFileName().toString() + .equals(currentOrthopairFilePath.getFileName().toString()) + ) + .findFirst() + .orElse(null); + } + + private Results checkLineCount(Path currentOrthopairFilePath, Path previousOrthopairFilePath) + throws IOException { + + Results lineCountResults = new Results(); + + int currentLineCount = (int) Files.lines(currentOrthopairFilePath).count(); + int previousLineCount = (int) Files.lines(previousOrthopairFilePath).count(); + + if (greaterThanOrEqualTo5PercentDrop(currentLineCount, previousLineCount)) { + lineCountResults.addErrorMessage( + String.format("%s has significantly fewer lines than %s (%d vs. %d) - Difference: %d lines", + currentOrthopairFilePath, previousOrthopairFilePath, currentLineCount, previousLineCount, + (previousLineCount - currentLineCount)) + ); + } else { + lineCountResults.addInfoMessage( + String.format("%s (%d lines) vs. %s (%d lines) - Difference: %d lines", + currentOrthopairFilePath, currentLineCount, previousOrthopairFilePath, previousLineCount, + (currentLineCount - previousLineCount)) + ); + } + + return lineCountResults; + } + + private Results checkFileSize(Path currentOrthopairFilePath, Path previousOrthopairFilePath) throws IOException { + + Results fileSizeResults = new Results(); + + int currentFileSize = (int) Files.size(currentOrthopairFilePath); + int previousFileSize = (int) Files.size(previousOrthopairFilePath); + + if (greaterThanOrEqualTo5PercentDrop(currentFileSize, previousFileSize)) { + fileSizeResults.addErrorMessage( + String.format("%s has significantly smaller size than %s (%d bytes vs. %d bytes) - Difference: %d bytes", + currentOrthopairFilePath, previousOrthopairFilePath, currentFileSize, previousFileSize, + (previousFileSize - currentFileSize)) + ); + } else { + fileSizeResults.addInfoMessage( + String.format("%s (%d bytes) vs. %s (%d bytes) - Difference: %d bytes", + currentOrthopairFilePath, currentFileSize, previousOrthopairFilePath, previousFileSize, + (currentFileSize - previousFileSize)) + ); + } + + return fileSizeResults; + } + + + private String downloadPreviousOrthopairFiles() throws IOException { + deleteDirectory(getPreviousReleaseNumberDirectory()); + downloadFolderFromS3("reactome", getS3FolderPath()); + return renameFolderToPreviousReleaseVersionNumber().toString(); + } + + private Path renameFolderToPreviousReleaseVersionNumber() throws IOException { + Files.move(Paths.get(getS3FolderPath()).getFileName(), getPreviousReleaseNumberDirectory()); + return getPreviousReleaseNumberDirectory(); + } + + private String getS3FolderPath() { + return String.format("private/releases/%d/orthopairs/data/orthopairs/", getPreviousReleaseNumber()); + } + + private Path getPreviousReleaseNumberDirectory() { + return Paths.get(String.valueOf(getPreviousReleaseNumber())); + } + + private int getPreviousReleaseNumber() { + return this.releaseNumber - 1; + } +} From 8428b535bf2539c574edb0dc02701fcdd7741a9a Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Tue, 3 Dec 2024 19:37:53 -0500 Subject: [PATCH 02/15] updates Jenkinsfile to run verifier jar --- Jenkinsfile | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 9508bfb..bbcbfb8 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -40,11 +40,21 @@ pipeline{ dir ('orthopairs') { // The credentials used here are a config file uploaded to Jenkins. withCredentials([file(credentialsId: 'Config', variable: 'ConfigFile')]) { - sh "java -jar target/orthopairs-${env.ORTHOPAIRS_VERSION}-jar-with-dependencies.jar $ConfigFile" + sh "java -jar target/orthopairs-jar-with-dependencies.jar $ConfigFile" } } } } } + + // This stage verifies orthopairs have correct size by comparing against the previous releases' files + stage('Post: Verify Orthopairs files have correct size') { + steps { + script { + def currentRelease = (pwd() =~ /Releases\/(\d+)\//)[0][1]; + sh "java -jar target/orthopairs-verifier-jar-with-dependencies.jar -release $currentRelease" + } + } + } } } From 26ac174f09b0fbfb6197616295e6089c409cc130 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Tue, 3 Dec 2024 19:38:52 -0500 Subject: [PATCH 03/15] adds executions for main and verifier jar builds --- pom.xml | 73 +++++++++++++++++++++++++++++++++++++-------------------- 1 file changed, 48 insertions(+), 25 deletions(-) diff --git a/pom.xml b/pom.xml index 77321c9..81fa38f 100644 --- a/pom.xml +++ b/pom.xml @@ -103,6 +103,20 @@ + + + + oss.sonatype.org-snapshot + http://oss.sonatype.org/content/repositories/snapshots + + false + + + true + + + + @@ -125,23 +139,46 @@ org.apache.maven.plugins maven-assembly-plugin 3.2.0 - - - - org.reactome.release.orthopairs.Main - - - - jar-with-dependencies - - - make-assembly + main-build + package + + single + + + + + + true + org.reactome.release.orthopairs.Main + + + + jar-with-dependencies + + orthopairs + + + + verifier-build package single + + + + + true + org.reactome.release.orthopairs.verifier.Verifier + + + + jar-with-dependencies + + orthopairs-verifier + @@ -183,18 +220,4 @@ - - - - - oss.sonatype.org-snapshot - http://oss.sonatype.org/content/repositories/snapshots - - false - - - true - - - From f58eab84b10749f458d5ce712c7e6f81bbafdfd2 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 18:01:16 -0500 Subject: [PATCH 04/15] updates Jenkinsfile to build with "mvn clean package" --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index bbcbfb8..4401f10 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -28,7 +28,7 @@ pipeline{ steps { script { dir ('orthopairs') { - sh "mvn clean compile assembly:single" + sh "mvn clean package" } } } From cab7bf2edbcf7ad773fd80f5aaf4df3a865b3c06 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 18:17:30 -0500 Subject: [PATCH 05/15] changes build to use "mvn clean package" --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index ff06af5..97ae130 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -48,7 +48,7 @@ pipeline{ stage('Setup: Build jar file') { steps { script { - utils.buildJarFile() + utils.buildJarFileWithPackage() } } } From 036163201bb27cba1894d97fdae1e7be8a4e9390 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 18:18:12 -0500 Subject: [PATCH 06/15] updates results call to use reportInfoMessages method --- .../java/org/reactome/release/orthopairs/verifier/Verifier.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java index d59c48e..88d7998 100644 --- a/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java +++ b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java @@ -36,7 +36,7 @@ public static void main(String[] args) throws IOException { private void run() throws IOException { Results results = compareCurrentAndPreviousOrthopairFiles(); - results.report(); + results.reportInfoMessages(); if (results.hasErrors()) { results.reportErrors(); System.exit(1); From 27aced945497d3ab19061612c5c3e927a280c390 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 18:23:47 -0500 Subject: [PATCH 07/15] updates pom.xml to restore ebi repo --- pom.xml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/pom.xml b/pom.xml index af350f4..ca69965 100644 --- a/pom.xml +++ b/pom.xml @@ -126,6 +126,18 @@ true + + + nexus-ebi-repo + The EBI internal repository + https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ + + true + + + false + + From ac722cfe1b82868c86fbb2b539d02f1b138a70c0 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 18:35:31 -0500 Subject: [PATCH 08/15] updates pom.xml to remove newline --- pom.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/pom.xml b/pom.xml index ca69965..b85b55a 100644 --- a/pom.xml +++ b/pom.xml @@ -162,7 +162,6 @@ org.apache.maven.plugins maven-assembly-plugin 3.2.0 - main-build From 68aca786a0c12ea1c31bb3d9c505a63759dbca4e Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 18:39:16 -0500 Subject: [PATCH 09/15] adds skip tests to mvn clean package --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 97ae130..280c318 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -48,7 +48,7 @@ pipeline{ stage('Setup: Build jar file') { steps { script { - utils.buildJarFileWithPackage() + sh "mvn clean package -DskipTests" } } } From ccbfc7617105bd61b1b5e7acbdcf6332066eaab6 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 19:27:21 -0500 Subject: [PATCH 10/15] updates verifier to use 10% drop as threshold for error --- .../release/orthopairs/verifier/Verifier.java | 33 ++++++++++++------- 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java index 88d7998..8bee947 100644 --- a/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java +++ b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java @@ -13,6 +13,7 @@ import java.util.stream.Collectors; import static org.reactome.release.verifier.CountUtils.greaterThanOrEqualTo5PercentDrop; +import static org.reactome.release.verifier.CountUtils.greaterThanOrEqualToXPercentDrop; import static org.reactome.release.verifier.FileUtils.*; /** @@ -49,7 +50,7 @@ private Results compareCurrentAndPreviousOrthopairFiles() throws IOException { List previousOrthopairFilePaths = getPreviousOrthopairFilePaths(); for (Path currentOrthopairFilePath : getCurrentOrthopairFilePaths()) { Path previousOrthopairFilePath = - getAnalgousPreviousOrthopairFile(currentOrthopairFilePath, previousOrthopairFilePaths); + getAnalogousPreviousOrthopairFile(currentOrthopairFilePath, previousOrthopairFilePaths); if (previousOrthopairFilePath != null) { Results lineCountResults = checkLineCount(currentOrthopairFilePath, previousOrthopairFilePath); @@ -81,7 +82,7 @@ private List getPreviousOrthopairFilePaths() throws IOException { return Files.list(Paths.get(folderName)).filter(file -> file.getFileName().toString().endsWith(".tsv")).collect(Collectors.toList()); } - private Path getAnalgousPreviousOrthopairFile( + private Path getAnalogousPreviousOrthopairFile( Path currentOrthopairFilePath, List previousOrthopairFilePaths) { return previousOrthopairFilePaths @@ -102,17 +103,21 @@ private Results checkLineCount(Path currentOrthopairFilePath, Path previousOrtho int currentLineCount = (int) Files.lines(currentOrthopairFilePath).count(); int previousLineCount = (int) Files.lines(previousOrthopairFilePath).count(); - if (greaterThanOrEqualTo5PercentDrop(currentLineCount, previousLineCount)) { + if (greaterThanOrEqualToXPercentDrop(currentLineCount, previousLineCount, 10)) { lineCountResults.addErrorMessage( - String.format("%s has significantly fewer lines than %s (%d vs. %d) - Difference: %d lines", + String.format("%s has significantly fewer lines than %s (%d vs. %d) - Difference: %d lines (%.2f%%)", currentOrthopairFilePath, previousOrthopairFilePath, currentLineCount, previousLineCount, - (previousLineCount - currentLineCount)) + (previousLineCount - currentLineCount), + (float) (previousLineCount - currentLineCount) / previousLineCount + ) ); } else { lineCountResults.addInfoMessage( - String.format("%s (%d lines) vs. %s (%d lines) - Difference: %d lines", + String.format("%s (%d lines) vs. %s (%d lines) - Difference: %d lines (%.2f%%)", currentOrthopairFilePath, currentLineCount, previousOrthopairFilePath, previousLineCount, - (currentLineCount - previousLineCount)) + (currentLineCount - previousLineCount), + (float) (previousLineCount - currentLineCount) / previousLineCount + ) ); } @@ -126,17 +131,21 @@ private Results checkFileSize(Path currentOrthopairFilePath, Path previousOrthop int currentFileSize = (int) Files.size(currentOrthopairFilePath); int previousFileSize = (int) Files.size(previousOrthopairFilePath); - if (greaterThanOrEqualTo5PercentDrop(currentFileSize, previousFileSize)) { + if (greaterThanOrEqualToXPercentDrop(currentFileSize, previousFileSize, 10)) { fileSizeResults.addErrorMessage( - String.format("%s has significantly smaller size than %s (%d bytes vs. %d bytes) - Difference: %d bytes", + String.format("%s has significantly smaller size than %s (%d bytes vs. %d bytes) - Difference: %d bytes (%.2f%%)", currentOrthopairFilePath, previousOrthopairFilePath, currentFileSize, previousFileSize, - (previousFileSize - currentFileSize)) + (previousFileSize - currentFileSize), + (float) (previousFileSize - currentFileSize) / previousFileSize + ) ); } else { fileSizeResults.addInfoMessage( - String.format("%s (%d bytes) vs. %s (%d bytes) - Difference: %d bytes", + String.format("%s (%d bytes) vs. %s (%d bytes) - Difference: %d bytes (%.2f%%)", currentOrthopairFilePath, currentFileSize, previousOrthopairFilePath, previousFileSize, - (currentFileSize - previousFileSize)) + (currentFileSize - previousFileSize), + (float) (currentFileSize - previousFileSize) / previousFileSize + ) ); } From 5911f0697e8c1d24189affd7f2e2332affc9eca9 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 22:31:04 -0500 Subject: [PATCH 11/15] adds check for verification failure --- Jenkinsfile | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 280c318..c2d3e72 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -70,7 +70,19 @@ pipeline{ steps { script { def currentRelease = (pwd() =~ /Releases\/(\d+)\//)[0][1]; - sh "java -jar target/orthopairs-verifier-jar-with-dependencies.jar -release $currentRelease" + try { + sh "java -jar target/orthopairs-verifier-jar-with-dependencies.jar -release $currentRelease" + } catch (Exception e) { + def userInput = input( + id: 'userInput', message: "Orthopairs has errors - do you want to continue the orthopair pipeline", + parameters: [ + [$class: 'BooleanParameterDefinition', defaultValue: true, name: 'response'] + ] + ) + if (!userInput) { + error('Please manually address the orthopair error messages before continuing'); + } + } } } } From 8e9dab2412e92d8eec71088357019933fc8bbb5e Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 22:36:08 -0500 Subject: [PATCH 12/15] fixes percentage change display --- .../reactome/release/orthopairs/verifier/Verifier.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java index 8bee947..f1049ce 100644 --- a/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java +++ b/src/main/java/org/reactome/release/orthopairs/verifier/Verifier.java @@ -108,7 +108,7 @@ private Results checkLineCount(Path currentOrthopairFilePath, Path previousOrtho String.format("%s has significantly fewer lines than %s (%d vs. %d) - Difference: %d lines (%.2f%%)", currentOrthopairFilePath, previousOrthopairFilePath, currentLineCount, previousLineCount, (previousLineCount - currentLineCount), - (float) (previousLineCount - currentLineCount) / previousLineCount + ((float) (previousLineCount - currentLineCount) / previousLineCount) * 100.0 ) ); } else { @@ -116,7 +116,7 @@ private Results checkLineCount(Path currentOrthopairFilePath, Path previousOrtho String.format("%s (%d lines) vs. %s (%d lines) - Difference: %d lines (%.2f%%)", currentOrthopairFilePath, currentLineCount, previousOrthopairFilePath, previousLineCount, (currentLineCount - previousLineCount), - (float) (previousLineCount - currentLineCount) / previousLineCount + ((float) (previousLineCount - currentLineCount) / previousLineCount) * 100.0 ) ); } @@ -136,7 +136,7 @@ private Results checkFileSize(Path currentOrthopairFilePath, Path previousOrthop String.format("%s has significantly smaller size than %s (%d bytes vs. %d bytes) - Difference: %d bytes (%.2f%%)", currentOrthopairFilePath, previousOrthopairFilePath, currentFileSize, previousFileSize, (previousFileSize - currentFileSize), - (float) (previousFileSize - currentFileSize) / previousFileSize + ((float) (previousFileSize - currentFileSize) / previousFileSize) * 100.0 ) ); } else { @@ -144,7 +144,7 @@ private Results checkFileSize(Path currentOrthopairFilePath, Path previousOrthop String.format("%s (%d bytes) vs. %s (%d bytes) - Difference: %d bytes (%.2f%%)", currentOrthopairFilePath, currentFileSize, previousOrthopairFilePath, previousFileSize, (currentFileSize - previousFileSize), - (float) (currentFileSize - previousFileSize) / previousFileSize + ((float) (currentFileSize - previousFileSize) / previousFileSize) * 100.0 ) ); } From 9ff0f6fa4ebb699e6af8fe8b90de3016776c4808 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 3 Mar 2025 22:45:47 -0500 Subject: [PATCH 13/15] removes file line count check from Jenkinsfile --- Jenkinsfile | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index c2d3e72..1f243de 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -87,22 +87,6 @@ pipeline{ } } - // This stage compares the line counts of the orthopairs files generated between the current and previous release. - // An intelligible output should be visible at the console logs for the build. - stage('Post: Orthopairs file line counts') { - steps { - script { - def releaseVersion = utils.getReleaseVersion() - def previousReleaseVersion = utils.getPreviousReleaseVersion() - def currentDir = pwd() - sh "mkdir -p ${previousReleaseVersion}/" - sh "aws s3 --recursive --no-progress cp s3://reactome/private/releases/${previousReleaseVersion}/orthopairs/data/orthopairs/ ${previousReleaseVersion}/" - sh "gunzip -q ${previousReleaseVersion}/*" - utils.outputLineCountsOfFilesBetweenFolders("$releaseVersion", "$previousReleaseVersion", "$currentDir") - sh "rm -r ${previousReleaseVersion}" - } - } - } // Logs and data files generated by this step are archived in the Reactome S3 bucket. // All files are then deleted on server. stage('Post: Archive Outputs'){ From 17cfc32b4b69c6251238f90a150667e54da042bf Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Tue, 4 Mar 2025 11:10:20 -0500 Subject: [PATCH 14/15] Update checkstyle.xml --- checkstyle.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/checkstyle.xml b/checkstyle.xml index 8506a80..c9d5dc6 100644 --- a/checkstyle.xml +++ b/checkstyle.xml @@ -3,7 +3,7 @@ "https://checkstyle.org/dtds/configuration_1_3.dtd"> - + From 91b0ab51a44d48f782f8cdc0c4cb95d620c7fd73 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Tue, 4 Mar 2025 11:12:15 -0500 Subject: [PATCH 15/15] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2c0f414..08ef07f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,7 @@ CMD mvn -B -q checkstyle:check | \ # ===== stage 2 ===== FROM setup-env AS build-jar -RUN mvn clean compile assembly:single +RUN mvn clean package -DskipTests # ===== stage 3 ===== @@ -32,7 +32,7 @@ FROM eclipse-temurin:11-jre-focal ARG REPO_DIR -ARG JAR_FILE=target/orthopairs-*-jar-with-dependencies.jar +ARG JAR_FILE=target/orthopairs-jar-with-dependencies.jar WORKDIR ${REPO_DIR}