Merge pull request #9 from reactome/add-ci

Add ci
reactome · Feb 21, 2024 · eb1b596 · eb1b596
2 parents 262575c + 6e98796
commit eb1b596
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diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,7 @@
+.git
+.github
+
+.dockerignore
+.gitignore
+Dockerfile
+README.md
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,89 @@
+name: analysis core ci
+
+
+on:
+    workflow_dispatch:
+
+    pull_request:
+        types:
+            - opened
+            - synchronize
+
+    push:
+        branches:
+            - main
+
+
+permissions:
+    id-token: write
+    contents: read
+
+
+jobs:
+    lint:
+        if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+        runs-on: ubuntu-latest
+        env:
+            REPO_DIR : /opt/analysis-core
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Run lint
+              run: |
+                docker build --build-arg REPO_DIR="$REPO_DIR" --target setup-env -t lint-image .
+                docker run --name lint-container lint-image
+            
+            - name: Display lint errors
+              if: failure()
+              run: |
+                docker cp lint-container:"$REPO_DIR"/lint.log .
+                while IFS= read -r LINT_MSG; do echo "::warning::${LINT_MSG}"; done < lint.log
+                exit 1
+
+    docker-build:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+
+            - uses: docker/setup-buildx-action@v3
+
+            - uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: Dockerfile
+                tags: tmp-tag
+                outputs: type=docker,dest=/tmp/image.tar
+
+            - uses: actions/upload-artifact@v4
+              with:
+                name: image-artifact
+                path: /tmp/image.tar
+
+    docker-push:
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
+        needs: docker-build
+        runs-on: ubuntu-latest
+        steps:
+            - env:
+                AWS_REGION : us-east-1
+              uses: aws-actions/configure-aws-credentials@v4
+              with:
+                role-to-assume: ${{ vars.AWS_ROLE }}
+                aws-region: ${{ env.AWS_REGION }}
+
+            - id: login-ecr
+              uses: aws-actions/amazon-ecr-login@v2
+
+            - uses: actions/download-artifact@v4
+              with:
+                name: image-artifact
+                path: /tmp
+
+            - env:
+                AWS_REGISTRY : ${{ steps.login-ecr.outputs.registry }}
+                AWS_REPO : analysis-core
+                IMG_TAG : latest 
+              run: |
+                docker load --input /tmp/image.tar
+                docker image tag tmp-tag $AWS_REGISTRY/$AWS_REPO:$IMG_TAG
+                docker push $AWS_REGISTRY/$AWS_REPO:$IMG_TAG
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,39 @@
+ARG REPO_DIR=/opt/analysis-core
+
+
+# ===== stage 1 =====
+FROM maven:3.9.6-eclipse-temurin-11-focal AS setup-env
+
+ARG REPO_DIR
+
+WORKDIR ${REPO_DIR}
+
+COPY . .
+
+SHELL ["/bin/bash", "-c"]
+
+# run lint if container started
+ENTRYPOINT []
+
+CMD mvn -B -q checkstyle:check | \
+    grep -i --color=never '\.java\|failed to execute goal' > lint.log && \
+    exit 1 || \
+    exit 0
+
+
+# ===== stage 2 =====
+FROM setup-env AS build-jar
+
+RUN mvn clean package
+
+
+# ===== stage 3 =====
+FROM eclipse-temurin:11-jre-focal
+
+ARG REPO_DIR
+
+ARG JAR_FILE=target/analysis-core-exec.jar
+
+WORKDIR ${REPO_DIR}
+
+COPY --from=build-jar ${REPO_DIR}/${JAR_FILE} ./target/
diff --git a/checkstyle.xml b/checkstyle.xml
@@ -0,0 +1,9 @@
+<!DOCTYPE module PUBLIC
+        "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
+        "https://checkstyle.org/dtds/configuration_1_3.dtd">
+<module name="Checker">
+    <module name="LineLength">
+        <property name="max" value="150"/>
+    </module>
+    <!-- Add more modules as needed -->
+</module>
diff --git a/pom.xml b/pom.xml
@@ -11,6 +11,7 @@
     <description>The Reactome analysis-core extracts data from the graph-database to create the intermediate data format
         to be kept in memory and used for the analysis-service
     </description>
+
     <name>analysis-core</name>
 
     <organization>
@@ -37,6 +38,7 @@
     </parent>
 
     <properties>
+        <java.version>11</java.version>
         <start.class>org.reactome.server.analysis.core.Main</start.class>
     </properties>
 
@@ -111,6 +113,7 @@
             <groupId>commons-fileupload</groupId>
             <artifactId>commons-fileupload</artifactId>
         </dependency>
+
         <dependency>
             <groupId>commons-codec</groupId>
             <artifactId>commons-codec</artifactId>
@@ -119,24 +122,28 @@
 
     <build>
         <finalName>analysis-core</finalName>
+
         <resources>
             <resource>
                 <directory>src/main/resources</directory>
                 <filtering>true</filtering>
             </resource>
         </resources>
+
         <testResources>
             <testResource>
                 <directory>src/test/resources</directory>
                 <filtering>true</filtering>
             </testResource>
         </testResources>
+
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-resources-plugin</artifactId>
                 <version>${maven.resources.version}</version>
             </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
@@ -208,6 +215,34 @@
                     </execution>
                 </executions>
             </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                <version>3.1.1</version>
+                <dependencies>
+                    <!-- This dependency allows Checkstyle to understand Java 11 syntax -->
+                    <dependency>
+                        <groupId>com.puppycrawl.tools</groupId>
+                        <artifactId>checkstyle</artifactId>
+                        <version>8.44</version>
+                    </dependency>
+                </dependencies>
+                <executions>
+                    <execution>
+                        <id>checkstyle-check</id>
+                        <goals>
+                            <goal>check</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <configLocation>checkstyle.xml</configLocation>
+                    <!-- Optional: Set encoding -->
+                    <encoding>UTF-8</encoding>
+                </configuration>
+            </plugin>
+
         </plugins>
     </build>
 
@@ -224,6 +259,7 @@
                 <enabled>false</enabled>
             </snapshots>
         </repository>
+
         <!-- EBI SNAPSHOT repo -->
         <repository>
             <id>nexus-ebi-snapshot-repo</id>
@@ -237,5 +273,4 @@
             </snapshots>
         </repository>
     </repositories>
-
 </project>
diff --git a/src/main/java/org/reactome/server/analysis/core/Main.java b/src/main/java/org/reactome/server/analysis/core/Main.java
@@ -32,14 +32,15 @@ public static void main(String[] args) throws JSAPException {
 
         // Program Arguments -h, -p, -u, -k
         SimpleJSAP jsap = new SimpleJSAP(Main.class.getName(), "Connect to Reactome Graph Database",
-                new Parameter[]{
-                        new FlaggedOption("host", JSAP.STRING_PARSER, "bolt://localhost:7687", JSAP.NOT_REQUIRED, 'h', "host", "The neo4j host")
-                        , new FlaggedOption("user", JSAP.STRING_PARSER, "neo4j", JSAP.NOT_REQUIRED, 'u', "user", "The neo4j user")
-                        , new FlaggedOption("password", JSAP.STRING_PARSER, "neo4jj", JSAP.REQUIRED, 'k', "password", "The neo4j password")
-                        , new FlaggedOption("output", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'o', "output", "The file where the results are written to")
-                        , new QualifiedSwitch("test", JSAP.BOOLEAN_PARSER, null, JSAP.NOT_REQUIRED, 't', "test", "Test main species")
-                        , new QualifiedSwitch("verbose", JSAP.BOOLEAN_PARSER, null, JSAP.NOT_REQUIRED, 'v', "verbose",  "Requests verbose output")
-                }
+            new Parameter[]{
+                new FlaggedOption("host", JSAP.STRING_PARSER, "bolt://localhost:7687", JSAP.NOT_REQUIRED, 'h', "host", "The neo4j host")
+                , new FlaggedOption("user", JSAP.STRING_PARSER, "neo4j", JSAP.NOT_REQUIRED, 'u', "user", "The neo4j user")
+                , new FlaggedOption("password", JSAP.STRING_PARSER, "neo4jj", JSAP.REQUIRED, 'k', "password", "The neo4j password")
+                , new FlaggedOption("output", JSAP.STRING_PARSER, JSAP.NO_DEFAULT,
+                                    JSAP.REQUIRED, 'o', "output", "The file where the results are written to")
+                , new QualifiedSwitch("test", JSAP.BOOLEAN_PARSER, null, JSAP.NOT_REQUIRED, 't', "test", "Test main species")
+                , new QualifiedSwitch("verbose", JSAP.BOOLEAN_PARSER, null, JSAP.NOT_REQUIRED, 'v', "verbose",  "Requests verbose output")
+            }
         );
 
         JSAPResult config = jsap.parse(args);
@@ -132,4 +133,4 @@ private static void calculateNumbersInHierarchyNodesForMainResources(HierarchyBu
     }
 
 
-}
+}
diff --git a/src/main/java/org/reactome/server/analysis/core/data/HierarchiesDataProducer.java b/src/main/java/org/reactome/server/analysis/core/data/HierarchiesDataProducer.java
@@ -36,7 +36,7 @@ static void initializeProducer(DataContainer data) {
         if (producer == null) {
             producer = new HierarchiesDataProducer(data);
         } else {
-            logger.warn("Already initialized. Please ensure you do not use two data containers or you do not initialise this object with the same twice.");
+	    logger.warn("Already initialized. Ensure you do not use two data containers or you do not initialise this object with the same twice.");
         }
     }
 

diff --git a/src/main/java/org/reactome/server/analysis/core/importer/EntitiesBuilder.java b/src/main/java/org/reactome/server/analysis/core/importer/EntitiesBuilder.java
@@ -52,22 +52,25 @@ public void build(Map<String, SpeciesNode> speciesMap) {
             if (Main.VERBOSE) System.out.print(msgPrefix + speciesPrefix + " >> retrieving xrefs...");
 
             //language=Cypher
-            query = "MATCH (:Species{taxId:$taxId})<-[:species]-(:Pathway)-[:hasEvent]->(rle:ReactionLikeEvent), " +
-                    "      (rle)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|diseaseEntity|regulatedBy|regulator|hasComponent|hasMember|hasCandidate|repeatedUnit|proteinMarker|RNAMarker*]->(pe:PhysicalEntity) " +
-                    "WHERE (pe)-[:referenceEntity]->() " +
-                    "WITH DISTINCT pe " +
-                    "MATCH (pe)-[:referenceEntity]->(re:ReferenceEntity) " +
-                    "OPTIONAL MATCH (re)-[:referenceGene]->(re2:ReferenceEntity)-[:referenceDatabase]->(rd:ReferenceDatabase) " +
-                    "OPTIONAL MATCH (pe)-[:referenceEntity|crossReference*]->(dbi:DatabaseIdentifier) " +
-                    "WITH DISTINCT re, " +
-                    "COLLECT(DISTINCT rd.displayName + \":\" + re2.identifier) AS reIdentifiers, " +
-                    "COLLECT(DISTINCT CASE dbi WHEN NULL THEN NULL ELSE {databaseName: dbi.databaseName, identifier: dbi.identifier} END) AS dbis, COUNT(DISTINCT dbi) AS n " +
-                    "RETURN re.dbId AS referenceEntity, " +
-                    "       re.secondaryIdentifier AS  secondaryIdentifiers, " +
-                    "       re.geneName AS geneNames, " +
-                    "       reIdentifiers + re.otherIdentifier AS otherIdentifiers, " +
-                    "       [{databaseName: re.databaseName, " +
-                    "         identifier: CASE WHEN re.variantIdentifier IS NOT NULL THEN re.variantIdentifier ELSE re.identifier END " +
+            query = "" +
+              "MATCH (:Species{taxId:$taxId})<-[:species]-(:Pathway)-[:hasEvent]->(rle:ReactionLikeEvent), " +
+              "      (rle)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|" +
+              "diseaseEntity|regulatedBy|regulator|hasComponent|hasMember|hasCandidate|repeatedUnit|proteinMarker|RNAMarker*]->(pe:PhysicalEntity) " +
+              "WHERE (pe)-[:referenceEntity]->() " +
+              "WITH DISTINCT pe " +
+              "MATCH (pe)-[:referenceEntity]->(re:ReferenceEntity) " +
+              "OPTIONAL MATCH (re)-[:referenceGene]->(re2:ReferenceEntity)-[:referenceDatabase]->(rd:ReferenceDatabase) " +
+              "OPTIONAL MATCH (pe)-[:referenceEntity|crossReference*]->(dbi:DatabaseIdentifier) " +
+              "WITH DISTINCT re, " +
+              "COLLECT(DISTINCT rd.displayName + \":\" + re2.identifier) AS reIdentifiers, " +
+              "COLLECT(DISTINCT CASE dbi WHEN NULL THEN NULL ELSE {databaseName: dbi.databaseName, identifier: dbi.identifier} END) AS dbis, " +
+              "COUNT(DISTINCT dbi) AS n " +
+              "RETURN re.dbId AS referenceEntity, " +
+              "       re.secondaryIdentifier AS  secondaryIdentifiers, " +
+              "       re.geneName AS geneNames, " +
+              "       reIdentifiers + re.otherIdentifier AS otherIdentifiers, " +
+              "       [{databaseName: re.databaseName, " +
+              "         identifier: CASE WHEN re.variantIdentifier IS NOT NULL THEN re.variantIdentifier ELSE re.identifier END " +
                     "         }] + CASE WHEN n = 0 THEN [] ELSE dbis END AS xrefs";
 
             Map<Long, ReferenceEntityIdentifiers> xrefMap = new HashMap<>();
@@ -82,17 +85,21 @@ public void build(Map<String, SpeciesNode> speciesMap) {
             if (Main.VERBOSE) System.out.print(msgPrefix + speciesPrefix + " >> retrieving participants...");
 
             //language=Cypher
-            query = "MATCH (:Species{taxId:$taxId})<-[:species]-(p:Pathway)-[:hasEvent]->(rle:ReactionLikeEvent), " +
-                    "      (rle)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|diseaseEntity|regulatedBy|regulator|hasComponent|hasMember|hasCandidate|repeatedUnit|proteinMarker|RNAMarker*]->(pe:PhysicalEntity)-[:referenceEntity]->(re:ReferenceEntity) " +
-                    "WITH DISTINCT p, pe, re, COLLECT(DISTINCT {dbId: rle.dbId, stId: rle.stId}) AS rles " +
-                    "OPTIONAL MATCH (pe)-[:hasModifiedResidue]->(tm:TranslationalModification)-[:psiMod]->(mod:PsiMod) " +
-                    "WITH DISTINCT p, pe, re, rles, COLLECT(DISTINCT {coordinate: tm.coordinate, mod: mod.identifier}) AS tmods, COUNT(DISTINCT mod) AS n " +
-                    "RETURN p.dbId AS pathway, " +
-                    "       pe.dbId AS physicalEntity, " +
-                    "       pe.speciesName AS speciesName, " +
-                    "       re.dbId as referenceEntity, " +
-                    "       rles AS reactions, " +
-                    "       CASE WHEN n = 0 THEN [] ELSE tmods END AS mods";
+            query = "" +
+              "MATCH (:Species{taxId:$taxId})<-[:species]-(p:Pathway)-[:hasEvent]->(rle:ReactionLikeEvent), " +
+              "      (rle)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|diseaseEntity|" +
+              "regulatedBy|regulator|hasComponent|hasMember|hasCandidate|repeatedUnit|proteinMarker|RNAMarker*]" +
+              "->(pe:PhysicalEntity)-[:referenceEntity]->(re:ReferenceEntity) " +
+              "WITH DISTINCT p, pe, re, COLLECT(DISTINCT {dbId: rle.dbId, stId: rle.stId}) AS rles " +
+              "OPTIONAL MATCH (pe)-[:hasModifiedResidue]->(tm:TranslationalModification)-[:psiMod]->(mod:PsiMod) " +
+              "WITH DISTINCT p, pe, re, rles, " +
+              "       COLLECT(DISTINCT {coordinate: tm.coordinate, mod: mod.identifier}) AS tmods, COUNT(DISTINCT mod) AS n " +
+              "RETURN p.dbId AS pathway, " +
+              "       pe.dbId AS physicalEntity, " +
+              "       pe.speciesName AS speciesName, " +
+              "       re.dbId as referenceEntity, " +
+              "       rles AS reactions, " +
+              "       CASE WHEN n = 0 THEN [] ELSE tmods END AS mods";
 
             Collection<EntitiesQueryResult> result;
             try {
@@ -157,8 +164,12 @@ public void setOrthologous() {
         if (Main.VERBOSE) System.out.print(msgPrefix + " retrieving relationships...");
 
         String query = "" +
-                "MATCH (re1:ReferenceEntity)<-[:referenceEntity]-(:PhysicalEntity)-[:inferredTo]->(:PhysicalEntity)-[:referenceEntity]->(re2:ReferenceEntity) " +
-                "RETURN DISTINCT re1.databaseName AS originDatabaseName, re1.identifier AS originIdentifier, re2.databaseName AS inferredToDatabaseName, re2.identifier AS inferredToIdentifier";
+          "MATCH (re1:ReferenceEntity)<-[:referenceEntity]-(:PhysicalEntity)" +
+                "-[:inferredTo]->(:PhysicalEntity)-[:referenceEntity]->(re2:ReferenceEntity) " +
+          "RETURN DISTINCT re1.databaseName AS originDatabaseName, " +
+          "re1.identifier AS originIdentifier, " +
+          "re2.databaseName AS inferredToDatabaseName, "+
+          "re2.identifier AS inferredToIdentifier";
         Map<String, Object> paramsMap = new HashMap<>();
 
         Collection<OrthologyResult> orthologyResults;
@@ -201,4 +212,4 @@ public EntitiesContainer getEntitiesContainer() {
     public IdentifiersMap<EntityNode> getEntitiesMap() {
         return entitiesMap;
     }
-}
+}