diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 00000000..671af8a9 --- /dev/null +++ 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 new file mode 100644 index 00000000..d41242ab --- /dev/null +++ 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 new file mode 100644 index 00000000..826f5887 --- /dev/null +++ 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 new file mode 100644 index 00000000..8506a80e --- /dev/null +++ b/checkstyle.xml @@ -0,0 +1,9 @@ + + + + + + + diff --git a/pom.xml b/pom.xml index 05d3f644..bbaa8569 100644 --- a/pom.xml +++ b/pom.xml @@ -11,6 +11,7 @@ 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 + analysis-core @@ -37,6 +38,7 @@ + 11 org.reactome.server.analysis.core.Main @@ -111,6 +113,7 @@ commons-fileupload commons-fileupload + commons-codec commons-codec @@ -119,24 +122,28 @@ analysis-core + src/main/resources true + src/test/resources true + org.apache.maven.plugins maven-resources-plugin ${maven.resources.version} + org.apache.maven.plugins maven-compiler-plugin @@ -208,6 +215,34 @@ + + + org.apache.maven.plugins + maven-checkstyle-plugin + 3.1.1 + + + + com.puppycrawl.tools + checkstyle + 8.44 + + + + + checkstyle-check + + check + + + + + checkstyle.xml + + UTF-8 + + + @@ -224,6 +259,7 @@ false + nexus-ebi-snapshot-repo @@ -237,5 +273,4 @@ - diff --git a/src/main/java/org/reactome/server/analysis/core/Main.java b/src/main/java/org/reactome/server/analysis/core/Main.java index 7a4a0b1f..9805f843 100644 --- 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 } -} \ No newline at end of file +} 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 index b022d2f1..54c7d955 100644 --- 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 index bc4aef5b..949918a9 100644 --- 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 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:$taxId})<-[:species]-(:Pathway)-[:hasEvent]->(rle:ReactionLikeEvent), " + + " (rle)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|" + + "diseaseEntity|regulatedBy|regulator|hasComponent|hasMember|hasCandidate|repeatedUnit|proteinMarker|RNAMarker*]->(pe:PhysicalEntity) " + + "WHERE (pe)-[:referenceEntity]->() " + + "WITH DISTINCT pe " + + "MATCH (pe)-[:referenceEntity]->(re:ReferenceEntity) " + + "OPTIONAL MATCH (re)-[:referenceGene]->(re2:ReferenceEntity)-[:referenceDatabase]->(rd:ReferenceDatabase) " + + "OPTIONAL MATCH (pe)-[:referenceEntity|crossReference*]->(dbi:DatabaseIdentifier) " + + "WITH DISTINCT re, " + + "COLLECT(DISTINCT rd.displayName + \":\" + re2.identifier) AS reIdentifiers, " + + "COLLECT(DISTINCT CASE dbi WHEN NULL THEN NULL ELSE {databaseName: dbi.databaseName, identifier: dbi.identifier} END) AS dbis, " + + "COUNT(DISTINCT dbi) AS n " + + "RETURN re.dbId AS referenceEntity, " + + " re.secondaryIdentifier AS secondaryIdentifiers, " + + " re.geneName AS geneNames, " + + " reIdentifiers + re.otherIdentifier AS otherIdentifiers, " + + " [{databaseName: re.databaseName, " + + " identifier: CASE WHEN re.variantIdentifier IS NOT NULL THEN re.variantIdentifier ELSE re.identifier END " + " }] + CASE WHEN n = 0 THEN [] ELSE dbis END AS xrefs"; Map xrefMap = new HashMap<>(); @@ -82,17 +85,21 @@ public void build(Map speciesMap) { if (Main.VERBOSE) System.out.print(msgPrefix + speciesPrefix + " >> retrieving participants..."); //language=Cypher - query = "MATCH (:Species{taxId:$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 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 paramsMap = new HashMap<>(); Collection orthologyResults; @@ -201,4 +212,4 @@ public EntitiesContainer getEntitiesContainer() { public IdentifiersMap getEntitiesMap() { return entitiesMap; } -} \ No newline at end of file +} diff --git a/src/main/java/org/reactome/server/analysis/core/importer/InteractorsBuilder.java b/src/main/java/org/reactome/server/analysis/core/importer/InteractorsBuilder.java index 6c01ad46..17ad17cc 100644 --- a/src/main/java/org/reactome/server/analysis/core/importer/InteractorsBuilder.java +++ b/src/main/java/org/reactome/server/analysis/core/importer/InteractorsBuilder.java @@ -49,17 +49,20 @@ public void build(Set speciesNodes, EntitiesContainer entities, Int paramsMap.put("taxId", species.getTaxID()); String speciesPrefix = "'" + species.getName() + "' (" + (++s) + "/" + st + ")"; - if (Main.VERBOSE) System.out.print("\rCreating the interactors container for " + speciesPrefix + " >> retrieving targets for interactors..."); - - query = "MATCH (:Species{taxId:$taxId})<-[:species]-(p:Pathway)-[:hasEvent]->(rle:ReactionLikeEvent), " + - " (rle)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|diseaseEntity|regulatedBy|regulator*]->(pe:PhysicalEntity)-[:referenceEntity]->(re:ReferenceEntity) " + - "WHERE (p:TopLevelPathway) OR (:TopLevelPathway)-[:hasEvent*]->(p) " + - //" AND NOT (pe)-[:hasModifiedResidue]->(:TranslationalModification) " + - "WITH DISTINCT p, re, COLLECT(DISTINCT {dbId: rle.dbId, stId: rle.stId}) AS rles " + - "RETURN DISTINCT re.databaseName AS databaseName, " + - " CASE WHEN re.variantIdentifier IS NOT NULL THEN re.variantIdentifier ELSE re.identifier END AS identifier, " + - " p.dbId AS pathway, " + - " rles AS reactions"; + if (Main.VERBOSE) System.out.print("\rCreating interactors container for " + speciesPrefix + " >> retrieving targets..."); + + + query = "" + + "MATCH (:Species{taxId:$taxId})<-[:species]-(p:Pathway)-[:hasEvent]->(rle:ReactionLikeEvent), " + + " (rle)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|diseaseEntity|" + + "regulatedBy|regulator*]->(pe:PhysicalEntity)-[:referenceEntity]->(re:ReferenceEntity) " + + "WHERE (p:TopLevelPathway) OR (:TopLevelPathway)-[:hasEvent*]->(p) " + + //" AND NOT (pe)-[:hasModifiedResidue]->(:TranslationalModification) " + + "WITH DISTINCT p, re, COLLECT(DISTINCT {dbId: rle.dbId, stId: rle.stId}) AS rles " + + "RETURN DISTINCT re.databaseName AS databaseName, " + + " CASE WHEN re.variantIdentifier IS NOT NULL THEN re.variantIdentifier ELSE re.identifier END AS identifier, " + + " p.dbId AS pathway, " + + " rles AS reactions"; Collection its; try { @@ -148,7 +151,7 @@ private InteractorNode getOrCreate(Resource resource, String identifier) { } else { //Using IdentifiersMap causes this "oddity" here, but is a minor inconvenient if (interactors.size() > 1) - logger.error("Interactors duplication. There should not be more than one interactor for " + identifier + " [" + resource.getName() + "]"); + logger.error("Duplicate interactors found for " + identifier + " [" + resource.getName() + "]"); return interactors.iterator().next(); } } diff --git a/src/main/java/org/reactome/server/analysis/core/importer/psimod/PsiModRetrieval.java b/src/main/java/org/reactome/server/analysis/core/importer/psimod/PsiModRetrieval.java index ae30714e..b112f296 100755 --- a/src/main/java/org/reactome/server/analysis/core/importer/psimod/PsiModRetrieval.java +++ b/src/main/java/org/reactome/server/analysis/core/importer/psimod/PsiModRetrieval.java @@ -38,7 +38,16 @@ class PsiModRetrieval { public enum Relations { - self, parents, hierarchicalParents, hierarchicalAncestors, ancestors, children, hierarchicalChildren, hierarchicalDescendants, descendants, jstree + self, + parents, + hierarchicalParents, + hierarchicalAncestors, + ancestors, + children, + hierarchicalChildren, + hierarchicalDescendants, + descendants, + jstree } private static final int ONTOLOGY_SIZE = 20; @@ -91,7 +100,8 @@ private static BufferedReader getContentBufferedReader(String uri) { } /** - * Consults the web service at the Onthology Lookup Service (http://www.ebi.ac.uk/ols/docs/api) to get the other PSIMOD terms with the specified relation + * Consults the web service at the Onthology Lookup Service (http://www.ebi.ac.uk/ols/docs/api) + * to get the other PSIMOD terms with the specified relation * * @param id The PSIMOD id for the term. Ex. "00046" * @param relation Any value of the enum {@link Relations} Ex. "parents", "children", "hierarchicalChildren", "hierarchicalAncestors" @@ -158,7 +168,8 @@ private static String createUri(String ontologyName) { } private static String createUri(String ontologyName, String term, Relations relation) { - return "http://www.ebi.ac.uk/ols/api/ontologies/" + ontologyName + "/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMOD_" + term + "/" + relation + "?size=" + ONTOLOGY_SIZE; + return "http://www.ebi.ac.uk/ols/api/ontologies/" + ontologyName + + "/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMOD_" + term + "/" + relation + "?size=" + ONTOLOGY_SIZE; } private static int getOntologySize(String onthologyName) { diff --git a/src/main/java/org/reactome/server/analysis/core/methods/EnrichmentAnalysis.java b/src/main/java/org/reactome/server/analysis/core/methods/EnrichmentAnalysis.java index c5411bcc..aefb54e2 100644 --- a/src/main/java/org/reactome/server/analysis/core/methods/EnrichmentAnalysis.java +++ b/src/main/java/org/reactome/server/analysis/core/methods/EnrichmentAnalysis.java @@ -57,8 +57,10 @@ private void analyse(HierarchiesData hierarchies, Set identi IdentifiersMap entitiesMap = analysisData.getEntitiesMap(); IdentifiersMap interactorsMap = analysisData.getInteractorsMap(); - logger.trace("Analysing: " + originalSampleSize + " identifier(s). Including interactors: " + includeInteractors + ". Project to species: " + (speciesNode == null ? false : speciesNode.getName())); - long start = System.currentTimeMillis(); + logger.trace("Analysing: {} identifier(s). Including interactors: {}. Project to species: {}", + originalSampleSize, includeInteractors, (speciesNode == null ? false : speciesNode.getName())); + + long start = System.currentTimeMillis(); Set newSample = new HashSet<>(); for (AnalysisIdentifier identifier : identifiers) { @@ -126,7 +128,9 @@ private void analyse(HierarchiesData hierarchies, Set identi logger.trace("Final sample size is " + finalSampleSize + " identifier(s)"); hierarchies.setResultStatistics(sampleSizePerResource, hierarchies.getNotFound().size(), includeInteractors); long end = System.currentTimeMillis(); - logger.info("Analysis for " + originalSampleSize + " identifier(s) (" + finalSampleSize + " when expanded) performed in " + (end - start) + " ms"); + logger.info("Analysis for {} identifier(s) ({} when expanded) performed in {} ms", + originalSampleSize, finalSampleSize, (end - start)); + } private void decreaseCounter() { diff --git a/src/main/java/org/reactome/server/analysis/core/methods/IdentifiersMapping.java b/src/main/java/org/reactome/server/analysis/core/methods/IdentifiersMapping.java index 7e30e924..6e0b498c 100644 --- a/src/main/java/org/reactome/server/analysis/core/methods/IdentifiersMapping.java +++ b/src/main/java/org/reactome/server/analysis/core/methods/IdentifiersMapping.java @@ -1,6 +1,5 @@ package org.reactome.server.analysis.core.methods; - import org.reactome.server.analysis.core.data.AnalysisData; import org.reactome.server.analysis.core.model.EntityNode; import org.reactome.server.analysis.core.model.IdentifiersMap; @@ -58,7 +57,9 @@ private MapSet getMapping(Set identifiers, Spe MapSet rtn = new MapSet<>(); final int originalSampleSize = identifiers.size(); - logger.trace("Mapping: " + originalSampleSize + " identifier(s). Including interactors: " + includeInteractors + ". Project to species: " + (speciesNode == null ? false : speciesNode.getName())); + logger.trace("Mapping: {} identifier(s). Including interactors: {}. Project to species: {}", + originalSampleSize, includeInteractors, (speciesNode == null ? false : speciesNode.getName())); + long start = System.currentTimeMillis(); IdentifiersMap entitiesMap = analysisData.getEntitiesMap(); @@ -78,7 +79,7 @@ private MapSet getMapping(Set identifiers, Spe MapSet interactors = interactorsMap.get(identifier); for (Resource resource : interactors.keySet()) { for (InteractorNode interactorNode : interactors.getElements(resource)) { - Set interactsWith = interactorNode.getInteractsWith(); //InteractorHelper.getInteractsWith(speciesNode, entitiesMap, interactorNode); + Set interactsWith = interactorNode.getInteractsWith(); rtn.add(identifier, new MappedIdentifier(resource, interactorNode.getAccession(), interactsWith)); } } @@ -91,8 +92,6 @@ private MapSet getMapping(Set identifiers, Spe return rtn; } - - private void decreaseCounter() { synchronized (MAPPING_SEMAPHORE) { if (--MAPPING_COUNT == 0) { diff --git a/src/main/java/org/reactome/server/analysis/core/model/PathwayNodeData.java b/src/main/java/org/reactome/server/analysis/core/model/PathwayNodeData.java index 66134132..ff646b93 100644 --- a/src/main/java/org/reactome/server/analysis/core/model/PathwayNodeData.java +++ b/src/main/java/org/reactome/server/analysis/core/model/PathwayNodeData.java @@ -220,7 +220,9 @@ public Set getFoundEntities(MainResource resource) { return rtn; } - private List> groupEntitiesExpressionValues(Collection identifiers, Collection interactors) { + private List> groupEntitiesExpressionValues( + Collection identifiers, + Collection interactors) { List> evss = new LinkedList<>(); Collection aggregation = new HashSet<>(); aggregation.addAll(identifiers); @@ -662,4 +664,4 @@ private Counter getOrCreateCounter(MainResource mainResource){ } return counter; } -} \ No newline at end of file +} diff --git a/src/main/java/org/reactome/server/analysis/core/result/AnalysisStoredResult.java b/src/main/java/org/reactome/server/analysis/core/result/AnalysisStoredResult.java index 9431c523..b87ed0bd 100644 --- a/src/main/java/org/reactome/server/analysis/core/result/AnalysisStoredResult.java +++ b/src/main/java/org/reactome/server/analysis/core/result/AnalysisStoredResult.java @@ -307,7 +307,8 @@ public AnalysisStoredResult filterPathways(String resource, Double pValue, boole return filterPathways(null, resource, pValue, includeDisease, min, max); } - public AnalysisStoredResult filterPathways(List species, String resource, Double pValue, boolean includeDisease, Integer min, Integer max) { + public AnalysisStoredResult filterPathways(List species, String resource, Double pValue, + boolean includeDisease, Integer min, Integer max) { final boolean includeInteractors = summary.isInteractors(); MainResource mr = ResourceFactory.getMainResource(resource); List pathways = new LinkedList<>(); diff --git a/src/main/java/org/reactome/server/analysis/core/result/model/AnalysisSummary.java b/src/main/java/org/reactome/server/analysis/core/result/model/AnalysisSummary.java index a006b4b0..02e49d41 100644 --- a/src/main/java/org/reactome/server/analysis/core/result/model/AnalysisSummary.java +++ b/src/main/java/org/reactome/server/analysis/core/result/model/AnalysisSummary.java @@ -22,7 +22,10 @@ public class AnalysisSummary { private String gsaToken; private String gsaMethod; - AnalysisSummary(String token, Boolean projection, Boolean interactors, String sampleName, AnalysisType type, String server, Boolean includeDisease, String gsaToken, String gsaMethod) { + AnalysisSummary(String token, Boolean projection, Boolean interactors, + String sampleName, AnalysisType type, String server, + Boolean includeDisease, String gsaToken, String gsaMethod) { + this.token = token; this.type = type.toString(); this.sampleName = sampleName; @@ -34,24 +37,32 @@ public class AnalysisSummary { this.gsaMethod = gsaMethod; } - public AnalysisSummary(String token, Boolean projection, Boolean interactors, String sampleName, AnalysisType type, String fileName, String server, Boolean includeDisease) { + public AnalysisSummary(String token, Boolean projection, Boolean interactors, + String sampleName, AnalysisType type, String fileName, + String server, Boolean includeDisease) { this(token, projection, interactors, sampleName, type, server, includeDisease, null, null); this.fileName = fileName; if(this.fileName!=null) this.fileName = this.fileName.split("\\?")[0]; } - public AnalysisSummary(String token, Boolean projection, Boolean interactors, String sampleName, AnalysisType type, Long species, String server, Boolean includeDisease) { + public AnalysisSummary(String token, Boolean projection, Boolean interactors, + String sampleName, AnalysisType type, Long species, + String server, Boolean includeDisease) { this(token, projection, interactors, sampleName, type, server, includeDisease, null, null); this.species = species; } - public AnalysisSummary(String token, Boolean projection, Boolean interactors, String sampleName, AnalysisType type, boolean text, String server, Boolean includeDisease) { + public AnalysisSummary(String token, Boolean projection, Boolean interactors, + String sampleName, AnalysisType type, boolean text, + String server, Boolean includeDisease) { this(token, projection, interactors, sampleName, type, server, includeDisease, null, null); this.text = text; } public AnalysisSummary(String token, ExternalAnalysisSummary summary) { - this(token, summary.getProjection(), summary.getInteractors(), summary.getSampleName(), summary.getType(), summary.getServer(), summary.getIncludeDisease(), summary.getGsaToken(), summary.getGsaMethod()); + this(token, summary.getProjection(), summary.getInteractors(), summary.getSampleName(), + summary.getType(), summary.getServer(), summary.getIncludeDisease(), + summary.getGsaToken(), summary.getGsaMethod()); } public String getToken() { diff --git a/src/main/java/org/reactome/server/analysis/core/result/model/FoundEntities.java b/src/main/java/org/reactome/server/analysis/core/result/model/FoundEntities.java index fdaa73b9..b2e0d47a 100644 --- a/src/main/java/org/reactome/server/analysis/core/result/model/FoundEntities.java +++ b/src/main/java/org/reactome/server/analysis/core/result/model/FoundEntities.java @@ -20,7 +20,8 @@ public class FoundEntities { private Integer totalEntitiesCount; private Map resourceToMappedEntitiesCount; - private FoundEntities(List identifiers, Set resources, List expNames, Integer found, Integer totalEntitiesCount, Map resourceToMappedEntitiesCount) { + private FoundEntities(List identifiers, Set resources, List expNames, + Integer found, Integer totalEntitiesCount, Map resourceToMappedEntitiesCount) { this.identifiers = identifiers; this.resources = resources; this.expNames = expNames; @@ -91,8 +92,16 @@ public Integer getTotalEntitiesCount() { public Map getResourceToMappedEntitiesCount() { if (resourceToMappedEntitiesCount == null) { Map> resourceToIds = new HashMap<>(); - identifiers.forEach(foundEntity -> foundEntity.getMapsTo().forEach(identifierMap -> resourceToIds.computeIfAbsent(identifierMap.getResource(), s -> new HashSet<>()).addAll(identifierMap.getIds()))); - resourceToMappedEntitiesCount = resourceToIds.keySet().stream().collect(Collectors.toMap(resource -> resource, resource -> resourceToIds.get(resource).size())); + identifiers.forEach(foundEntity -> + foundEntity.getMapsTo().forEach(identifierMap -> + resourceToIds.computeIfAbsent(identifierMap.getResource(), s -> new HashSet<>()) + .addAll(identifierMap.getIds()))); + resourceToMappedEntitiesCount = resourceToIds.keySet().stream() + .collect(Collectors.toMap( + resource -> resource, + resource -> resourceToIds.get(resource).size() + )); + } return resourceToMappedEntitiesCount; } @@ -116,7 +125,12 @@ public FoundEntities filter(String resource) { } else { identifiers = filterByResource(resource.toUpperCase()); } - return new FoundEntities(identifiers, resources, expNames, identifiers.size(), this.getTotalEntitiesCount(), this.getResourceToMappedEntitiesCount()); + return new FoundEntities(identifiers, + resources, + expNames, + identifiers.size(), + this.getTotalEntitiesCount(), + this.getResourceToMappedEntitiesCount()); } public FoundEntities filter(String resource, Integer pageSize, Integer page) { @@ -140,7 +154,12 @@ public FoundEntities filter(String resource, Integer pageSize, Integer page) { int to = from + pageSize; to = to > identifiers.size() ? identifiers.size() : to; Set resources = resource.equals("TOTAL") ? this.resources : new HashSet<>(Arrays.asList(resource)); - return new FoundEntities(identifiers.subList(from, to), resources, this.expNames, identifiers.size(), this.getTotalEntitiesCount(), this.getResourceToMappedEntitiesCount()); + return new FoundEntities(identifiers.subList(from, to), + resources, + this.expNames, + identifiers.size(), + this.getTotalEntitiesCount(), + this.getResourceToMappedEntitiesCount()); } else { return null; } diff --git a/src/main/java/org/reactome/server/analysis/core/result/model/FoundInteractors.java b/src/main/java/org/reactome/server/analysis/core/result/model/FoundInteractors.java index 7928ed99..01256dfe 100644 --- a/src/main/java/org/reactome/server/analysis/core/result/model/FoundInteractors.java +++ b/src/main/java/org/reactome/server/analysis/core/result/model/FoundInteractors.java @@ -50,7 +50,10 @@ public FoundInteractors(PathwayNodeSummary nodeSummary, List expNames) { for (Resource resource : summaries.keySet()) { for (IdentifierSummary identifier : summaries.getElements(resource)) { - identifiers.add(new FoundInteractor(identifier, mapsTo.getElements(identifier), new IdentifierMap(resource.getName(), interactsWith.getElements(identifier)))); + identifiers.add(new FoundInteractor(identifier, + mapsTo.getElements(identifier), + new IdentifierMap(resource.getName(), + interactsWith.getElements(identifier)))); } } diff --git a/src/main/java/org/reactome/server/analysis/core/result/utils/ExternalAnalysisResultCheck.java b/src/main/java/org/reactome/server/analysis/core/result/utils/ExternalAnalysisResultCheck.java index b64d7871..e2111613 100644 --- a/src/main/java/org/reactome/server/analysis/core/result/utils/ExternalAnalysisResultCheck.java +++ b/src/main/java/org/reactome/server/analysis/core/result/utils/ExternalAnalysisResultCheck.java @@ -85,7 +85,8 @@ private void checkExpressionSummary(ExternalExpressionSummary expressionSummary, } } - private void checkPathways(List pathways, ExternalExpressionSummary expressionSummary, final List messages) { + private void checkPathways(List pathways, + ExternalExpressionSummary expressionSummary, final List messages) { if (pathways == null) return; for (int i = 1; i <= pathways.size(); i++) { @@ -107,7 +108,8 @@ private void checkPathways(List pathways, ExternalEx } } - private void checkPathwayNodeData(ExternalPathwayNodeData data, ExternalExpressionSummary expressionSummary, final int i, final List messages) { + private void checkPathwayNodeData(ExternalPathwayNodeData data, ExternalExpressionSummary expressionSummary, + final int i, final List messages) { //Statistics check if (data.getStatistics() == null || data.getStatistics().isEmpty()) { messages.add(String.format("'statistics' not found for pathway %d", i)); @@ -148,7 +150,8 @@ private void checkPathwayNodeData(ExternalPathwayNodeData data, ExternalExpressi } else { int aux = (exp == null) ? 0 : exp.size(); if (aux != expValues) { - messages.add(String.format("'exp' field contains %d values but it must contain %d values in the entity %d for pathway %d", aux, expValues, j, i)); + messages.add(String.format("'exp' field contains %d values but it must contain %d" + + " values in the entity %d for pathway %d", aux, expValues, j, i)); } else { for (int k = 1; j <= exp.size(); j++) { final Double value = exp.get(k - 1); @@ -156,7 +159,8 @@ private void checkPathwayNodeData(ExternalPathwayNodeData data, ExternalExpressi messages.add(String.format("The value in position %d in 'exp' field is null in entity %d for pathway %d", k, j, i)); } else if (!expressionSummary.isValid(value)) { - messages.add(String.format("The value in position %d in 'exp' field is not between the specified boundaries in of entity %d for pathway %d", + messages.add(String.format("The value in position %d in 'exp' field is not between the specified" + + " boundaries in of entity %d for pathway %d", k, j, i)); } } @@ -197,7 +201,8 @@ private void checkPathwayNodeData(ExternalPathwayNodeData data, ExternalExpressi } else { int aux = (exp == null) ? 0 : exp.size(); if (aux != expValues) { - messages.add(String.format("'exp' field contains %d values but it must contain %d values in the interactor %d for pathway %d", aux, expValues, j, i)); + messages.add(String.format("'exp' field contains %d values but it must contain %d" + + " values in the interactor %d for pathway %d", aux, expValues, j, i)); } else { for (int k = 1; j <= exp.size(); j++) { final Double value = exp.get(k - 1); @@ -205,7 +210,8 @@ private void checkPathwayNodeData(ExternalPathwayNodeData data, ExternalExpressi messages.add(String.format("The value in position %d in 'exp' field is null in interactor %d for pathway %d", k, j, i)); } else if (!expressionSummary.isValid(value)) { - messages.add(String.format("The value in position %d in 'exp' field is not between the specified boundaries in of interactor %d for pathway %d", + messages.add(String.format("The value in position %d in 'exp' field is not between the specified" + + " boundaries in of interactor %d for pathway %d", k, j, i)); } } @@ -221,15 +227,18 @@ private void checkPathwayNodeData(ExternalPathwayNodeData data, ExternalExpressi messages.add(String.format("Identifier 'null' for the mapping %d of interactor %d for pathway %d", k, j, i)); } if (in.getInteractsWith() == null || in.getInteractsWith().isEmpty()) { - messages.add(String.format("No interacts with provided for mapping %d in the interactor %d for pathway %d", k, j, i)); + messages.add(String.format("No interacts with provided for mapping %d" + + " in the interactor %d for pathway %d", k, j, i)); } else { for (int l = 1; l <= in.getInteractsWith().size(); l++) { ExternalMainIdentifier mi = in.getInteractsWith().get(l - 1); if (mi.getId() == null || mi.getId().isEmpty()) { - messages.add(String.format("Identifier 'null' for the interactsWith %d of the maps to %d of entity %d for pathway %d", l, k, j, i)); + messages.add(String.format("Identifier 'null' for the interactsWith %d of the maps to %d " + + "of entity %d for pathway %d", l, k, j, i)); } if (!isValidResource(mi.getResource())) { - messages.add(String.format("'%s' for the interactsWith %d of the maps to %d of interactor %d for pathway %d is not a valid MainResource", mi.getResource(), l, k, j, i)); + messages.add(String.format("'%s' for the interactsWith %d of the maps to %d of interactor %d " + + "for pathway %d is not a valid MainResource", mi.getResource(), l, k, j, i)); } } } @@ -312,7 +321,8 @@ private void checkPathwayNodeStatistics(ExternalStatistics statistic, ExternalEx messages.add(String.format("The value in position %d in 'exp' field is null in the statics (resource:%s) for pathway %d", j, statistic.getResource(), i)); } else if (!expressionSummary.isValid(value)) { - messages.add(String.format("The value in position %d in 'exp' field is not between the specified boundaries in the statics (resource:%s) for pathway %d", + messages.add(String.format("The value in position %d in 'exp' field is not between the specified " + + "boundaries in the statics (resource:%s) for pathway %d", j, statistic.getResource(), i)); } } @@ -362,7 +372,8 @@ private void checkNotFound(List notFound, ExternalExpression if (value == null) { messages.add(String.format("The value in position %d in 'exp' field is null in not found entity %d", j, i)); } else if (!expressionSummary.isValid(value)) { - messages.add(String.format("The value in position %d in 'exp' field is not between the specified boundaries in the not found entity %d", j, i)); + messages.add(String.format("The value in position %d in 'exp' field is not between " + + "the specified boundaries in the not found entity %d", j, i)); } } } @@ -382,4 +393,4 @@ public void setAnalysisData(AnalysisData analysisData) { this.analysisData = analysisData; } -} \ No newline at end of file +} diff --git a/src/main/java/org/reactome/server/analysis/core/result/utils/TokenUtils.java b/src/main/java/org/reactome/server/analysis/core/result/utils/TokenUtils.java index 2c93663f..605ead6d 100644 --- a/src/main/java/org/reactome/server/analysis/core/result/utils/TokenUtils.java +++ b/src/main/java/org/reactome/server/analysis/core/result/utils/TokenUtils.java @@ -48,7 +48,8 @@ public AnalysisStoredResult getFromToken(String token) { throw new ResourceNotFoundException(); } - public AnalysisSummary getAnalysisSummary(String token, Boolean projection, Boolean interactors, String sampleName, AnalysisType type, String userFileName, String serverName, boolean includeDisease) { + public AnalysisSummary getAnalysisSummary(String token, Boolean projection, Boolean interactors, String sampleName, + AnalysisType type, String userFileName, String serverName, boolean includeDisease) { if (userFileName != null && !userFileName.isEmpty()) { return new AnalysisSummary(token, projection, interactors, sampleName, type, userFileName, serverName, includeDisease); } else {