diff --git a/pom.xml b/pom.xml index 416673f..07a0539 100755 --- a/pom.xml +++ b/pom.xml @@ -50,6 +50,7 @@ org.reactome.server.graph graph-core + 2.0.9-SNAPSHOT @@ -61,6 +62,7 @@ org.reactome.server.interactors interactor-core + 1.1.6-SNAPSHOT org.xerial @@ -73,6 +75,12 @@ + + uk.ac.ebi.enfin.mi.cluster + micluster + 1.9.0-SNAPSHOT + + org.reactome.server.tools diff --git a/src/main/java/org/reactome/server/service/manager/CustomInteractorManager.java b/src/main/java/org/reactome/server/service/manager/CustomInteractorManager.java index 216428b..9e90314 100644 --- a/src/main/java/org/reactome/server/service/manager/CustomInteractorManager.java +++ b/src/main/java/org/reactome/server/service/manager/CustomInteractorManager.java @@ -214,11 +214,14 @@ private List convertCustomInteraction(String searchTerm, Set> interact interactor.setAcc(interaction.getInteractorB().getAcc()); interactor.setScore(interaction.getIntactScore()); interactor.setAlias(interaction.getInteractorB().getAliasWithoutSpecies(true)); + interactor.setType(interaction.getInteractorB().getType()); // Set Id as auto increment interactor.setId(count++); diff --git a/src/main/java/org/reactome/server/service/model/interactors/Interactor.java b/src/main/java/org/reactome/server/service/model/interactors/Interactor.java index b3ebc34..5c06380 100755 --- a/src/main/java/org/reactome/server/service/model/interactors/Interactor.java +++ b/src/main/java/org/reactome/server/service/model/interactors/Interactor.java @@ -32,6 +32,9 @@ public class Interactor { @Schema(description = "This represents the URL for the given interactions identifiers.") private String evidencesURL; + @Schema(description = "This represents the type for given interaction") + private String type; + public Interactor() { } @@ -58,6 +61,11 @@ public Interactor(Interaction interaction) { this.score = interaction.getScore(); + this.type = re.getMoleculeType(); + + if (re.getName() != null && !re.getName().isEmpty()) this.alias = re.getName().get(0); + + if (re instanceof ReferenceSequence) { ReferenceSequence rs = (ReferenceSequence) re; if (rs.getGeneName() != null && !rs.getGeneName().isEmpty()) this.alias = rs.getGeneName().get(0); @@ -119,4 +127,12 @@ public String getEvidencesURL() { public void setEvidencesURL(String evidencesURL) { this.evidencesURL = evidencesURL; } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } } diff --git a/src/test/java/org/reactome/server/service/controller/interactors/TokenControllerTest.java b/src/test/java/org/reactome/server/service/controller/interactors/TokenControllerTest.java index f7dc049..117b71f 100644 --- a/src/test/java/org/reactome/server/service/controller/interactors/TokenControllerTest.java +++ b/src/test/java/org/reactome/server/service/controller/interactors/TokenControllerTest.java @@ -19,7 +19,7 @@ public class TokenControllerTest extends BaseTest { @Test public void getInteractors() throws Exception { - String token = getTokenFromLastestPSIFile(tokenFolder); + String token = getTokenFromLatestPSIFile(tokenFolder); /* To test it, you will need a valid token, which can be generated when running the CustomPsicquicControllerTest. @@ -31,7 +31,7 @@ The token (PSI--XXXXX.bin) will be written in the file system based on the