From 33e587643ef9b2b0d2b903191ed35c6faa5b0699 Mon Sep 17 00:00:00 2001 From: LeonardoGonzales Date: Fri, 29 Sep 2023 16:11:54 +0100 Subject: [PATCH 1/4] TRM-29901: new xref pumba --- controlled-vocabulary/pom.xml | 2 +- .../src/main/resources/META-INF/drlineconfiguration.json | 6 ++++++ .../java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java | 2 +- core-common/pom.xml | 2 +- core-domain-utils/pom.xml | 2 +- core-domain/pom.xml | 2 +- core-parser/pom.xml | 2 +- ff-parser/pom.xml | 2 +- jacoco-aggregate-report/pom.xml | 2 +- json-parser/pom.xml | 2 +- pom.xml | 2 +- tools-entry-scorer/pom.xml | 2 +- xml-parser/pom.xml | 2 +- 13 files changed, 18 insertions(+), 12 deletions(-) diff --git a/controlled-vocabulary/pom.xml b/controlled-vocabulary/pom.xml index a6e2462e2..bc83fe82e 100644 --- a/controlled-vocabulary/pom.xml +++ b/controlled-vocabulary/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.26 + 1.0.26.2 ../ diff --git a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json index ee781f644..125a8db9a 100644 --- a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json +++ b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json @@ -634,6 +634,12 @@ "uriLink": "https://www.proteomicsdb.org/proteomicsdb/#protein/proteinDetails/%id", "idMappingName": "PROTEOMICSDB_ID" }, + { + "name": "Pumba", + "displayName": "Pumba", + "category": "PROTEOMIC", + "uriLink": "https://pumba.dcsr.unil.ch/lanes/%id" + }, { "name": "TopDownProteomics", "displayName": "TopDownProteomics", diff --git a/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java b/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java index 87c0b2034..21084dd3b 100644 --- a/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java +++ b/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java @@ -304,7 +304,7 @@ void testDatabaseFieldSize() { UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENERIC_VARIATION_DATABASES), 5); verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(D2_GEL_DATABASES), 7); verifyGroupSize( - UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMIC_DATABASES), 11); + UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMIC_DATABASES), 12); verifyGroupSize( UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory( PROTOCOLS_AND_MATERIALS_DATABASES), diff --git a/core-common/pom.xml b/core-common/pom.xml index f8c359e19..91fd67063 100644 --- a/core-common/pom.xml +++ b/core-common/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26 + 1.0.26.2 ../ diff --git a/core-domain-utils/pom.xml b/core-domain-utils/pom.xml index 839587558..0deda28a2 100644 --- a/core-domain-utils/pom.xml +++ b/core-domain-utils/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.26 + 1.0.26.2 4.0.0 diff --git a/core-domain/pom.xml b/core-domain/pom.xml index 65ac09977..749564682 100644 --- a/core-domain/pom.xml +++ b/core-domain/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26 + 1.0.26.2 ../ diff --git a/core-parser/pom.xml b/core-parser/pom.xml index 2c4932404..f81dad8ee 100644 --- a/core-parser/pom.xml +++ b/core-parser/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26 + 1.0.26.2 ../ diff --git a/ff-parser/pom.xml b/ff-parser/pom.xml index d340d8c3d..de598a6f8 100644 --- a/ff-parser/pom.xml +++ b/ff-parser/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.26 + 1.0.26.2 ../ diff --git a/jacoco-aggregate-report/pom.xml b/jacoco-aggregate-report/pom.xml index 68969823e..856cfc768 100644 --- a/jacoco-aggregate-report/pom.xml +++ b/jacoco-aggregate-report/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.26 + 1.0.26.2 4.0.0 diff --git a/json-parser/pom.xml b/json-parser/pom.xml index 83d4d0a08..1bc4e7046 100644 --- a/json-parser/pom.xml +++ b/json-parser/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26 + 1.0.26.2 ../ 4.0.0 diff --git a/pom.xml b/pom.xml index 974f5d307..dac49f82f 100644 --- a/pom.xml +++ b/pom.xml @@ -7,7 +7,7 @@ org.uniprot core-parent pom - 1.0.26 + 1.0.26.2 UniProt Core Aggregator diff --git a/tools-entry-scorer/pom.xml b/tools-entry-scorer/pom.xml index f199a5eb8..c7939f5c6 100644 --- a/tools-entry-scorer/pom.xml +++ b/tools-entry-scorer/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.26 + 1.0.26.2 ../ 4.0.0 diff --git a/xml-parser/pom.xml b/xml-parser/pom.xml index 2d3388d9d..a03848ff3 100644 --- a/xml-parser/pom.xml +++ b/xml-parser/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.26 + 1.0.26.2 ../ From e2a7f2fd931a490be2a0564e79bb1cec6c1c7c09 Mon Sep 17 00:00:00 2001 From: LeonardoGonzales Date: Mon, 23 Oct 2023 00:07:01 +0100 Subject: [PATCH 2/4] Add TAIR evidence Xref --- .../core/uniprotkb/evidence/EvidenceDatabaseTypes.java | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java index 5e4040d56..d55764b5d 100644 --- a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java +++ b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java @@ -160,6 +160,13 @@ private void init() { "SMART", "A", "http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%value")); + typeMap.put( + "TAIR", + evd( + "TAIR", + "TAIR", + "I", + "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=%value")); typeMap.put( "UniRule", evd("UniRule", "UniRule", "A", "https://www.uniprot.org/unirule/%value")); From 66854ca5f635ce8c3056b359ca517c6e5642f7bb Mon Sep 17 00:00:00 2001 From: LeonardoGonzales Date: Mon, 23 Oct 2023 00:18:57 +0100 Subject: [PATCH 3/4] Update pom to 1.0.27-SNAPSHOT --- controlled-vocabulary/pom.xml | 2 +- core-common/pom.xml | 2 +- core-domain-utils/pom.xml | 2 +- core-domain/pom.xml | 2 +- core-parser/pom.xml | 2 +- ff-parser/pom.xml | 2 +- jacoco-aggregate-report/pom.xml | 2 +- json-parser/pom.xml | 2 +- pom.xml | 2 +- tools-entry-scorer/pom.xml | 2 +- xml-parser/pom.xml | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/controlled-vocabulary/pom.xml b/controlled-vocabulary/pom.xml index bc83fe82e..95345a55e 100644 --- a/controlled-vocabulary/pom.xml +++ b/controlled-vocabulary/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.26.2 + 1.0.27-SNAPSHOT ../ diff --git a/core-common/pom.xml b/core-common/pom.xml index 91fd67063..75139f5d0 100644 --- a/core-common/pom.xml +++ b/core-common/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26.2 + 1.0.27-SNAPSHOT ../ diff --git a/core-domain-utils/pom.xml b/core-domain-utils/pom.xml index 0deda28a2..81904e295 100644 --- a/core-domain-utils/pom.xml +++ b/core-domain-utils/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.26.2 + 1.0.27-SNAPSHOT 4.0.0 diff --git a/core-domain/pom.xml b/core-domain/pom.xml index 749564682..dfc98a974 100644 --- a/core-domain/pom.xml +++ b/core-domain/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26.2 + 1.0.27-SNAPSHOT ../ diff --git a/core-parser/pom.xml b/core-parser/pom.xml index f81dad8ee..d8794a22c 100644 --- a/core-parser/pom.xml +++ b/core-parser/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26.2 + 1.0.27-SNAPSHOT ../ diff --git a/ff-parser/pom.xml b/ff-parser/pom.xml index de598a6f8..6f324defc 100644 --- a/ff-parser/pom.xml +++ b/ff-parser/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.26.2 + 1.0.27-SNAPSHOT ../ diff --git a/jacoco-aggregate-report/pom.xml b/jacoco-aggregate-report/pom.xml index 856cfc768..ad63e8df0 100644 --- a/jacoco-aggregate-report/pom.xml +++ b/jacoco-aggregate-report/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.26.2 + 1.0.27-SNAPSHOT 4.0.0 diff --git a/json-parser/pom.xml b/json-parser/pom.xml index 1bc4e7046..9d5bb4f6b 100644 --- a/json-parser/pom.xml +++ b/json-parser/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.26.2 + 1.0.27-SNAPSHOT ../ 4.0.0 diff --git a/pom.xml b/pom.xml index dac49f82f..4614b716e 100644 --- a/pom.xml +++ b/pom.xml @@ -7,7 +7,7 @@ org.uniprot core-parent pom - 1.0.26.2 + 1.0.27-SNAPSHOT UniProt Core Aggregator diff --git a/tools-entry-scorer/pom.xml b/tools-entry-scorer/pom.xml index c7939f5c6..02ab9b52f 100644 --- a/tools-entry-scorer/pom.xml +++ b/tools-entry-scorer/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.26.2 + 1.0.27-SNAPSHOT ../ 4.0.0 diff --git a/xml-parser/pom.xml b/xml-parser/pom.xml index a03848ff3..72e748e59 100644 --- a/xml-parser/pom.xml +++ b/xml-parser/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.26.2 + 1.0.27-SNAPSHOT ../ From 6f3632e5d348de756eb64f81c1a7033e439339e3 Mon Sep 17 00:00:00 2001 From: LeonardoGonzales Date: Mon, 23 Oct 2023 10:43:56 +0100 Subject: [PATCH 4/4] fix test for evidence types --- .../core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java b/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java index c4676ea32..1b21a6eb0 100644 --- a/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java +++ b/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java @@ -24,7 +24,7 @@ void testGetAllEvidenceDatabases() { List evidenceDatabases = EvidenceDatabaseTypes.INSTANCE.getAllEvidenceDatabases(); assertNotNull(evidenceDatabases); - assertEquals(51, evidenceDatabases.size()); + assertEquals(52, evidenceDatabases.size()); } @Test