diff --git a/jami-batch/pom.xml b/jami-batch/pom.xml index b4b43bdc82..239f6afa1b 100644 --- a/jami-batch/pom.xml +++ b/jami-batch/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-batch diff --git a/jami-bridges/bridges-core/pom.xml b/jami-bridges/bridges-core/pom.xml index de4afc2c5b..63e9a7ee21 100644 --- a/jami-bridges/bridges-core/pom.xml +++ b/jami-bridges/bridges-core/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT bridges-core diff --git a/jami-bridges/jami-chebi/pom.xml b/jami-bridges/jami-chebi/pom.xml index 326bf087c8..b4465b11b1 100644 --- a/jami-bridges/jami-chebi/pom.xml +++ b/jami-bridges/jami-chebi/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-chebi diff --git a/jami-bridges/jami-ensembl/pom.xml b/jami-bridges/jami-ensembl/pom.xml index 5aee9cd465..4ce6abb8c1 100644 --- a/jami-bridges/jami-ensembl/pom.xml +++ b/jami-bridges/jami-ensembl/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-ensembl diff --git a/jami-bridges/jami-europubmedcentral/pom.xml b/jami-bridges/jami-europubmedcentral/pom.xml index 8e095fe882..31e41d18d2 100644 --- a/jami-bridges/jami-europubmedcentral/pom.xml +++ b/jami-bridges/jami-europubmedcentral/pom.xml @@ -4,7 +4,7 @@ jami-bridges psidev.psi.mi.jami.bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-europubmedcentral diff --git a/jami-bridges/jami-imexcentral/pom.xml b/jami-bridges/jami-imexcentral/pom.xml index 60dcd7d0d1..e9346998cb 100644 --- a/jami-bridges/jami-imexcentral/pom.xml +++ b/jami-bridges/jami-imexcentral/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-imexcentral diff --git a/jami-bridges/jami-obo/pom.xml b/jami-bridges/jami-obo/pom.xml index 1352bc6db8..da40696739 100644 --- a/jami-bridges/jami-obo/pom.xml +++ b/jami-bridges/jami-obo/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-obo diff --git a/jami-bridges/jami-ols/pom.xml b/jami-bridges/jami-ols/pom.xml index b7710b3e96..2b15220378 100644 --- a/jami-bridges/jami-ols/pom.xml +++ b/jami-bridges/jami-ols/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-ols diff --git a/jami-bridges/jami-ontology-manager/pom.xml b/jami-bridges/jami-ontology-manager/pom.xml index e7c8a8b8c9..abbd459176 100644 --- a/jami-bridges/jami-ontology-manager/pom.xml +++ b/jami-bridges/jami-ontology-manager/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-ontology-manager diff --git a/jami-bridges/jami-rna-central/pom.xml b/jami-bridges/jami-rna-central/pom.xml index c654545e31..28b236ae1f 100644 --- a/jami-bridges/jami-rna-central/pom.xml +++ b/jami-bridges/jami-rna-central/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-rna-central diff --git a/jami-bridges/jami-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcher.java b/jami-bridges/jami-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcher.java index 5d301ae8ae..f9a85ead7d 100644 --- a/jami-bridges/jami-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcher.java +++ b/jami-bridges/jami-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcher.java @@ -11,6 +11,7 @@ import psidev.psi.mi.jami.model.Organism; import psidev.psi.mi.jami.model.Xref; import psidev.psi.mi.jami.model.impl.*; +import psidev.psi.mi.jami.utils.XrefUtils; import java.io.IOException; import java.net.URL; @@ -88,6 +89,7 @@ private void addXRefs(NucleicAcid nucleicAcid, String pureIdentifier, Organism o private void extractXrefsAndAliases(NucleicAcid nucleicAcid, ApiXrefs.Result result) { Collection xrefs = nucleicAcid.getXrefs(); + Collection identifiers = nucleicAcid.getIdentifiers(); XrefType xrefType = XrefType.getByDatabase(result.getDatabase()); @@ -100,7 +102,13 @@ private void extractXrefsAndAliases(NucleicAcid nucleicAcid, ApiXrefs.Result res .map(PartialCvTerm::complete) .findFirst().orElse(OLSUtils.secondaryAcCV); - xrefs.add(new DefaultXref(database, result.getAccession().getExternalId(), qualifier)); + Xref newXref = new DefaultXref(database, result.getAccession().getExternalId(), qualifier); + + if (XrefUtils.isXrefAnIdentifier(newXref)) { + identifiers.add(newXref); + } else { + xrefs.add(newXref); + } xrefType.extraReferenceBuilders.stream() .map(builder -> builder.apply(result)) @@ -108,7 +116,13 @@ private void extractXrefsAndAliases(NucleicAcid nucleicAcid, ApiXrefs.Result res PartialXref.builder() .database(PartialCvTerm.from(database)) .build())) - .forEach(xrefs::add); + .forEach(xref -> { + if (XrefUtils.isXrefAnIdentifier(xref)) { + identifiers.add(xref); + } else { + xrefs.add(xref); + } + }); } xrefType.aliasBuilders.stream() diff --git a/jami-bridges/jami-uniprot-protein-api/pom.xml b/jami-bridges/jami-uniprot-protein-api/pom.xml index 0435eef046..3da511a0e1 100644 --- a/jami-bridges/jami-uniprot-protein-api/pom.xml +++ b/jami-bridges/jami-uniprot-protein-api/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-uniprot-protein-api diff --git a/jami-bridges/jami-uniprot-taxonomy/pom.xml b/jami-bridges/jami-uniprot-taxonomy/pom.xml index c3c2b8d713..495c5e7dc0 100644 --- a/jami-bridges/jami-uniprot-taxonomy/pom.xml +++ b/jami-bridges/jami-uniprot-taxonomy/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-uniprot-taxonomy diff --git a/jami-bridges/jami-uniprot/pom.xml b/jami-bridges/jami-uniprot/pom.xml index 521db678f3..4c87e2349a 100644 --- a/jami-bridges/jami-uniprot/pom.xml +++ b/jami-bridges/jami-uniprot/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-uniprot diff --git a/jami-bridges/jami-unisave/pom.xml b/jami-bridges/jami-unisave/pom.xml index 1a21ac6019..f79e75a040 100644 --- a/jami-bridges/jami-unisave/pom.xml +++ b/jami-bridges/jami-unisave/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami.bridges jami-bridges - 3.5.0 + 3.5.1-SNAPSHOT jami-unisave diff --git a/jami-bridges/pom.xml b/jami-bridges/pom.xml index 01b4b41f51..8b7d6099ff 100644 --- a/jami-bridges/pom.xml +++ b/jami-bridges/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT psidev.psi.mi.jami.bridges diff --git a/jami-commons/pom.xml b/jami-commons/pom.xml index 36579b8ba8..a4bd7be0dd 100644 --- a/jami-commons/pom.xml +++ b/jami-commons/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-commons diff --git a/jami-core/pom.xml b/jami-core/pom.xml index faa1379873..67ad332daa 100644 --- a/jami-core/pom.xml +++ b/jami-core/pom.xml @@ -5,7 +5,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-core diff --git a/jami-core/src/main/java/psidev/psi/mi/jami/model/NucleicAcid.java b/jami-core/src/main/java/psidev/psi/mi/jami/model/NucleicAcid.java index 65597ba8a9..aa6d340460 100644 --- a/jami-core/src/main/java/psidev/psi/mi/jami/model/NucleicAcid.java +++ b/jami-core/src/main/java/psidev/psi/mi/jami/model/NucleicAcid.java @@ -13,6 +13,10 @@ public interface NucleicAcid extends Polymer { public static final String NULCEIC_ACID="nucleic acid"; /** Constant NULCEIC_ACID_MI="MI:0318" */ public static final String NULCEIC_ACID_MI="MI:0318"; + public static final String MRNA = "mrna"; + public static final String MRNA_MI = "MI:0324"; + public static final String MIRNA = "mirna"; + public static final String MIRNA_MI = "MI:2204"; /** * The unique DDBJ/EMBL/GemBank identifier which identifies the nucleic acid. diff --git a/jami-core/src/main/resources/interactorDatabase.properties b/jami-core/src/main/resources/interactorDatabase.properties index 6645dfc4d8..53828ad0b7 100644 --- a/jami-core/src/main/resources/interactorDatabase.properties +++ b/jami-core/src/main/resources/interactorDatabase.properties @@ -54,4 +54,5 @@ MI\:1097(uniprot)=protein MI\:0485(uniparc)=protein MI\:0486(uniprotkb)=protein MI\:1098(swiss-prot)=protein -MI\:1099(trembl)=protein \ No newline at end of file +MI\:1099(trembl)=protein +MI\:1357(rnacentral)=nucleic_acid \ No newline at end of file diff --git a/jami-core/src/main/resources/interactorType.properties b/jami-core/src/main/resources/interactorType.properties index 477a71a9a0..20d6ea61cd 100644 --- a/jami-core/src/main/resources/interactorType.properties +++ b/jami-core/src/main/resources/interactorType.properties @@ -35,4 +35,5 @@ MI\:0250(gene)=gene MI\:1304(molecule\ set)=interactor_set MI\:1305(candidate\ set)=interactor_set MI\:1307(defined\ set)=interactor_set -MI\:1306(open\ set)=interactor_set \ No newline at end of file +MI\:1306(open\ set)=interactor_set +MI\:2204(mirna)=nucleic_acid \ No newline at end of file diff --git a/jami-crosslink-csv/pom.xml b/jami-crosslink-csv/pom.xml index 2b39c47154..faec5d654f 100644 --- a/jami-crosslink-csv/pom.xml +++ b/jami-crosslink-csv/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-crosslink-csv diff --git a/jami-enricher/pom.xml b/jami-enricher/pom.xml index 07a431c29b..8e100decb7 100644 --- a/jami-enricher/pom.xml +++ b/jami-enricher/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-enricher diff --git a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/CompositeInteractorEnricher.java b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/CompositeInteractorEnricher.java index c087d64b04..0c6c205c6e 100644 --- a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/CompositeInteractorEnricher.java +++ b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/CompositeInteractorEnricher.java @@ -176,6 +176,8 @@ public void enrich(Interactor object) throws EnricherException { if (object instanceof Polymer) { if (object instanceof Protein && this.proteinEnricher != null) { this.proteinEnricher.enrich((Protein) object); + } else if (object instanceof NucleicAcid && this.nucleicAcidEnricher != null) { + this.nucleicAcidEnricher.enrich((NucleicAcid) object); } else if (this.polymerBaseEnricher != null) { this.polymerBaseEnricher.enrich((Polymer) object); } else { @@ -183,8 +185,6 @@ public void enrich(Interactor object) throws EnricherException { } } else if (object instanceof Gene && this.geneEnricher != null) { this.geneEnricher.enrich((Gene) object); - } else if (object instanceof NucleicAcid && this.nucleicAcidEnricher != null) { - this.nucleicAcidEnricher.enrich((NucleicAcid) object); } else if (object instanceof BioactiveEntity && this.bioactiveEntityEnricher != null) { this.bioactiveEntityEnricher.enrich((BioactiveEntity) object); } else if (object instanceof Complex && this.complexEnricher != null) { @@ -222,6 +222,8 @@ public void enrich(Interactor object, Interactor objectSource) throws EnricherEx if (object instanceof Polymer && objectSource instanceof Polymer) { if (object instanceof Protein && objectSource instanceof Protein && this.proteinEnricher != null) { this.proteinEnricher.enrich((Protein) object, (Protein) objectSource); + } else if (object instanceof NucleicAcid && objectSource instanceof NucleicAcid && this.nucleicAcidEnricher != null) { + this.nucleicAcidEnricher.enrich((NucleicAcid) object, (NucleicAcid) objectSource); } else if (this.polymerBaseEnricher != null) { this.polymerBaseEnricher.enrich((Polymer) object, (Polymer) objectSource); } else { @@ -306,6 +308,9 @@ public void setCvTermEnricher(CvTermEnricher enricher) { if (getInteractorPoolEnricher() != null) { getInteractorPoolEnricher().setCvTermEnricher(enricher); } + if (getNucleicAcidEnricher() != null) { + getNucleicAcidEnricher().setCvTermEnricher(enricher); + } } /** @@ -331,5 +336,8 @@ public void setOrganismEnricher(OrganismEnricher enricher) { if (getInteractorPoolEnricher() != null) { getInteractorPoolEnricher().setOrganismEnricher(enricher); } + if (getNucleicAcidEnricher() != null) { + getNucleicAcidEnricher().setOrganismEnricher(enricher); + } } } diff --git a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidEnricher.java b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidEnricher.java index 7ef5f20353..97910e2884 100644 --- a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidEnricher.java +++ b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidEnricher.java @@ -2,12 +2,9 @@ import psidev.psi.mi.jami.bridges.fetcher.GeneFetcher; import psidev.psi.mi.jami.bridges.fetcher.NucleicAcidFetcher; -import psidev.psi.mi.jami.enricher.impl.minimal.MinimalGeneEnricher; import psidev.psi.mi.jami.enricher.impl.minimal.MinimalNucleicAcidEnricher; import psidev.psi.mi.jami.enricher.listener.NucleicAcidEnricherListener; -import psidev.psi.mi.jami.enricher.listener.ProteinEnricherListener; import psidev.psi.mi.jami.model.NucleicAcid; -import psidev.psi.mi.jami.model.Protein; /** * A full enricher for genes. diff --git a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidUpdater.java b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidUpdater.java index 60441c2c4c..6328a99232 100644 --- a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidUpdater.java +++ b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/full/FullNucleicAcidUpdater.java @@ -2,12 +2,9 @@ import psidev.psi.mi.jami.bridges.fetcher.GeneFetcher; import psidev.psi.mi.jami.bridges.fetcher.NucleicAcidFetcher; -import psidev.psi.mi.jami.enricher.impl.minimal.MinimalGeneUpdater; import psidev.psi.mi.jami.enricher.impl.minimal.MinimalNucleicAcidUpdater; import psidev.psi.mi.jami.enricher.listener.NucleicAcidEnricherListener; -import psidev.psi.mi.jami.enricher.listener.ProteinEnricherListener; import psidev.psi.mi.jami.model.NucleicAcid; -import psidev.psi.mi.jami.model.Protein; /** * A full updater for genes. diff --git a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/minimal/MinimalNucleicAcidEnricher.java b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/minimal/MinimalNucleicAcidEnricher.java index 55307b0642..e1fa85f702 100644 --- a/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/minimal/MinimalNucleicAcidEnricher.java +++ b/jami-enricher/src/main/java/psidev/psi/mi/jami/enricher/impl/minimal/MinimalNucleicAcidEnricher.java @@ -124,6 +124,8 @@ protected boolean canEnrichInteractor(NucleicAcid entityToEnrich, NucleicAcid fe // if the interactor type is not a valid bioactive entity interactor type, we cannot enrich if (entityToEnrich.getInteractorType() != null && !CvTermUtils.isCvTerm(entityToEnrich.getInteractorType(), NucleicAcid.NULCEIC_ACID_MI, NucleicAcid.NULCEIC_ACID) + && !CvTermUtils.isCvTerm(entityToEnrich.getInteractorType(), NucleicAcid.MRNA_MI, NucleicAcid.MRNA) + && !CvTermUtils.isCvTerm(entityToEnrich.getInteractorType(), NucleicAcid.MIRNA_MI, NucleicAcid.MIRNA) && !CvTermUtils.isCvTerm(entityToEnrich.getInteractorType(), Interactor.UNKNOWN_INTERACTOR_MI, Interactor.UNKNOWN_INTERACTOR)) { return false; } diff --git a/jami-examples/pom.xml b/jami-examples/pom.xml index 9b2e5b3f15..578a3a7425 100644 --- a/jami-examples/pom.xml +++ b/jami-examples/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-examples diff --git a/jami-html/pom.xml b/jami-html/pom.xml index f3e8b50204..1e722e9cf3 100644 --- a/jami-html/pom.xml +++ b/jami-html/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-html diff --git a/jami-imex-updater/pom.xml b/jami-imex-updater/pom.xml index a1bfa9e451..e307fae554 100644 --- a/jami-imex-updater/pom.xml +++ b/jami-imex-updater/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-imex-updater diff --git a/jami-interactionviewer-json/pom.xml b/jami-interactionviewer-json/pom.xml index 88e8857130..80993e488b 100644 --- a/jami-interactionviewer-json/pom.xml +++ b/jami-interactionviewer-json/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-interactionviewer-json diff --git a/jami-mitab/pom.xml b/jami-mitab/pom.xml index 4c2d825503..3e5780f86b 100644 --- a/jami-mitab/pom.xml +++ b/jami-mitab/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-mitab diff --git a/jami-xml/pom.xml b/jami-xml/pom.xml index 2944308f87..cd105562af 100644 --- a/jami-xml/pom.xml +++ b/jami-xml/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT jami-xml diff --git a/pom.xml b/pom.xml index aef8aa372d..23009117a3 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ psidev.psi.mi.jami psi-jami - 3.5.0 + 3.5.1-SNAPSHOT pom PSI :: JAMI - Java framework for molecular interactions