From 1aa61ea46ae35ca547cbd7fd801b991914967d52 Mon Sep 17 00:00:00 2001 From: xflv Date: Thu, 11 Aug 2022 11:23:02 +0800 Subject: [PATCH 01/25] In order to resolve #8838 in Add CSTR to Harvard Dataverse Related Publication ID Type list, we refer to the arXiv logo and Please review the code and make the changes. --- .../source/_static/api/ddi_dataset.xml | 12 +++++++++ ...dataset-create-new-all-default-fields.json | 26 +++++++++++++++++++ scripts/api/data/metadatablocks/citation.tsv | 3 ++- scripts/issues/2102/ready-state.sql | 2 ++ .../export/openaire/OpenAireExportUtil.java | 1 + .../java/propertyFiles/citation.properties | 1 + .../export/OpenAireExportUtilTest.java | 3 +++ .../export/SchemaDotOrgExporterTest.java | 3 ++- .../dataverse/export/dataset-all-defaults.txt | 26 +++++++++++++++++++ .../dataset-create-new-all-ddi-fields.json | 26 +++++++++++++++++++ .../iq/dataverse/export/ddi/exportfull.xml | 12 +++++++++ 11 files changed, 113 insertions(+), 2 deletions(-) diff --git a/doc/sphinx-guides/source/_static/api/ddi_dataset.xml b/doc/sphinx-guides/source/_static/api/ddi_dataset.xml index 79e0581131e..8b5dddacb64 100644 --- a/doc/sphinx-guides/source/_static/api/ddi_dataset.xml +++ b/doc/sphinx-guides/source/_static/api/ddi_dataset.xml @@ -163,8 +163,10 @@ RelatedMaterial1 RelatedMaterial2 + RelatedMaterial3 RelatedDatasets1 RelatedDatasets2 + RelatedDatasets3 @@ -183,8 +185,18 @@ + + + + RelatedPublicationIDNumber3 + + RelatedPublicationCitation3 + + + OtherReferences1 OtherReferences2 + OtherReferences3 StudyLevelErrorNotes diff --git a/scripts/api/data/dataset-create-new-all-default-fields.json b/scripts/api/data/dataset-create-new-all-default-fields.json index d7ae8cefbf7..e51f4d9e1b5 100644 --- a/scripts/api/data/dataset-create-new-all-default-fields.json +++ b/scripts/api/data/dataset-create-new-all-default-fields.json @@ -369,6 +369,32 @@ "typeClass": "primitive", "value": "http://RelatedPublicationURL2.org" } + }, + { + "publicationCitation": { + "typeName": "publicationCitation", + "multiple": false, + "typeClass": "primitive", + "value": "RelatedPublicationCitation3" + }, + "publicationIDType": { + "typeName": "publicationIDType", + "multiple": false, + "typeClass": "controlledVocabulary", + "value": "CSTR" + }, + "publicationIDNumber": { + "typeName": "publicationIDNumber", + "multiple": false, + "typeClass": "primitive", + "value": "RelatedPublicationIDNumber3" + }, + "publicationURL": { + "typeName": "publicationURL", + "multiple": false, + "typeClass": "primitive", + "value": "http://RelatedPublicationURL3.org" + } } ] }, diff --git a/scripts/api/data/metadatablocks/citation.tsv b/scripts/api/data/metadatablocks/citation.tsv index 94aa509334f..e17db407ae7 100644 --- a/scripts/api/data/metadatablocks/citation.tsv +++ b/scripts/api/data/metadatablocks/citation.tsv @@ -110,7 +110,8 @@ publicationIDType purl 13 publicationIDType upc 14 publicationIDType url 15 - publicationIDType urn 16 + publicationIDType urn 16 + publicationIDType CSTR 17 contributorType Data Collector 0 contributorType Data Curator 1 contributorType Data Manager 2 diff --git a/scripts/issues/2102/ready-state.sql b/scripts/issues/2102/ready-state.sql index 96ccf58d865..03ab805531e 100644 --- a/scripts/issues/2102/ready-state.sql +++ b/scripts/issues/2102/ready-state.sql @@ -3284,6 +3284,7 @@ COPY controlledvocabalternate (id, strvalue, controlledvocabularyvalue_id, datas 22 United States of America 472 79 23 U.S.A. 472 79 24 YEMEN 483 79 +25 CSTR 825 30 \. @@ -4116,6 +4117,7 @@ COPY controlledvocabularyvalue (id, displayorder, identifier, strvalue, datasetf 822 29 review article 154 823 30 translation 154 824 31 other 154 +825 17 CSTR 30 \. diff --git a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java index 49fe203b96d..ffce432ce3b 100644 --- a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java +++ b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java @@ -964,6 +964,7 @@ public static void writeRelatedIdentifierElement(XMLStreamWriter xmlw, DatasetVe relatedIdentifierTypeMap.put("URL".toLowerCase(), "URL"); relatedIdentifierTypeMap.put("URN".toLowerCase(), "URN"); relatedIdentifierTypeMap.put("WOS".toLowerCase(), "WOS"); + relatedIdentifierTypeMap.put("CSTR".toLowerCase(), "CSTR"); } for (Map.Entry entry : datasetVersionDTO.getMetadataBlocks().entrySet()) { diff --git a/src/main/java/propertyFiles/citation.properties b/src/main/java/propertyFiles/citation.properties index bdcc48b5bf1..47356b404b8 100644 --- a/src/main/java/propertyFiles/citation.properties +++ b/src/main/java/propertyFiles/citation.properties @@ -250,6 +250,7 @@ controlledvocabulary.subject.social_sciences=Social Sciences controlledvocabulary.subject.other=Other controlledvocabulary.publicationIDType.ark=ark controlledvocabulary.publicationIDType.arxiv=arXiv +controlledvocabulary.publicationIDType.CSTR=CSTR controlledvocabulary.publicationIDType.bibcode=bibcode controlledvocabulary.publicationIDType.doi=doi controlledvocabulary.publicationIDType.ean13=ean13 diff --git a/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java b/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java index 7f7cc203506..8064b8e20f5 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java +++ b/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java @@ -609,6 +609,9 @@ public void testWriteRelatedIdentifierElement() throws XMLStreamException, IOExc + "RelatedPublicationIDNumber1" + "" + "RelatedPublicationIDNumber2" + + "" + + "" + + "RelatedPublicationIDNumber3" + "", stringWriter.toString()); } diff --git a/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java b/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java index b5453e75fe5..5f0d4dfd106 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java +++ b/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java @@ -408,7 +408,8 @@ private static void mockDatasetFieldSvc() { new ControlledVocabularyValue(3l, "bibcode", publicationIdTypes), new ControlledVocabularyValue(4l, "doi", publicationIdTypes), new ControlledVocabularyValue(5l, "ean13", publicationIdTypes), - new ControlledVocabularyValue(6l, "handle", publicationIdTypes) + new ControlledVocabularyValue(6l, "handle", publicationIdTypes), + new ControlledVocabularyValue(17l, "CSTR", publicationIdTypes) // Etc. There are more. )); publicationChildTypes.add(datasetFieldTypeSvc.add(publicationIdTypes)); diff --git a/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt b/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt index a3f0dffc767..a2a6d9c0778 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt +++ b/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt @@ -362,6 +362,32 @@ "typeClass": "primitive", "value": "http://RelatedPublicationURL2.org" } + }, + { + "publicationCitation": { + "typeName": "publicationCitation", + "multiple": false, + "typeClass": "primitive", + "value": "RelatedPublicationCitation3" + }, + "publicationIDType": { + "typeName": "publicationIDType", + "multiple": false, + "typeClass": "controlledVocabulary", + "value": "CSTR" + }, + "publicationIDNumber": { + "typeName": "publicationIDNumber", + "multiple": false, + "typeClass": "primitive", + "value": "RelatedPublicationIDNumber3" + }, + "publicationURL": { + "typeName": "publicationURL", + "multiple": false, + "typeClass": "primitive", + "value": "http://RelatedPublicationURL3.org" + } } ] }, diff --git a/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json b/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json index 1b327c15496..362a4ae4d90 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json +++ b/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json @@ -321,6 +321,32 @@ "typeClass": "primitive", "value": "http://RelatedPublicationURL2.org" } + }, + { + "publicationCitation": { + "typeName": "publicationCitation", + "multiple": false, + "typeClass": "primitive", + "value": "RelatedPublicationCitation3" + }, + "publicationIDType": { + "typeName": "publicationIDType", + "multiple": false, + "typeClass": "controlledVocabulary", + "value": "CSTR" + }, + "publicationIDNumber": { + "typeName": "publicationIDNumber", + "multiple": false, + "typeClass": "primitive", + "value": "RelatedPublicationIDNumber3" + }, + "publicationURL": { + "typeName": "publicationURL", + "multiple": false, + "typeClass": "primitive", + "value": "http://RelatedPublicationURL3.org" + } } ] }, diff --git a/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml b/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml index 0570c832e4f..4314775c7a2 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml +++ b/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml @@ -166,8 +166,10 @@ RelatedMaterial1 RelatedMaterial2 + RelatedMaterial3 RelatedDatasets1 RelatedDatasets2 + RelatedDatasets3 @@ -185,9 +187,19 @@ RelatedPublicationCitation2 + + + + + RelatedPublicationIDNumber3 + + RelatedPublicationCitation3 + + OtherReferences1 OtherReferences2 + OtherReferences3 StudyLevelErrorNotes From 8948faa4c7215acfd5bf805c8f4b23477b3cf0d8 Mon Sep 17 00:00:00 2001 From: xflv Date: Mon, 22 Aug 2022 15:21:57 +0800 Subject: [PATCH 02/25] Hi reviewer, We have fixed the lowercase and sequential issues. Please review the code and make the changes. --- scripts/api/data/metadatablocks/citation.tsv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/api/data/metadatablocks/citation.tsv b/scripts/api/data/metadatablocks/citation.tsv index e17db407ae7..7cc14043b2a 100644 --- a/scripts/api/data/metadatablocks/citation.tsv +++ b/scripts/api/data/metadatablocks/citation.tsv @@ -96,7 +96,8 @@ subject Other D12 13 publicationIDType ark 0 publicationIDType arXiv 1 - publicationIDType bibcode 2 + publicationIDType bibcode 2 + publicationIDType cstr 17 publicationIDType doi 3 publicationIDType ean13 4 publicationIDType eissn 5 @@ -110,8 +111,7 @@ publicationIDType purl 13 publicationIDType upc 14 publicationIDType url 15 - publicationIDType urn 16 - publicationIDType CSTR 17 + publicationIDType urn 16 contributorType Data Collector 0 contributorType Data Curator 1 contributorType Data Manager 2 From 2f664d0886031feee1ea006d0a77b269303ccc1c Mon Sep 17 00:00:00 2001 From: xflv Date: Mon, 29 Aug 2022 14:01:45 +0800 Subject: [PATCH 03/25] We have modified the AdminIT.java file as per example #8775 provided by qqmyers, please check if the conflict has been resolved. As we do not have access to the conflict details, if the modification does not resolve the conflict, please follow up with the file name and line number of the conflict and we will follow up with the modification. --- src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java b/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java index c34ee2dd4bf..df505224817 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java @@ -761,7 +761,7 @@ public void testLoadMetadataBlock_NoErrorPath() { Map>> data = JsonPath.from(body).getMap("data"); assertEquals(1, data.size()); List> addedElements = data.get("added"); - assertEquals(321, addedElements.size()); + assertEquals(322, addedElements.size()); Map statistics = new HashMap<>(); for (Map unit : addedElements) { @@ -777,7 +777,7 @@ public void testLoadMetadataBlock_NoErrorPath() { assertEquals(3, statistics.size()); assertEquals(1, (int) statistics.get("MetadataBlock")); assertEquals(78, (int) statistics.get("DatasetField")); - assertEquals(242, (int) statistics.get("Controlled Vocabulary")); + assertEquals(243, (int) statistics.get("Controlled Vocabulary")); } @Test From 0bd68429d35e75f2c34e8090fa42dbda082423e4 Mon Sep 17 00:00:00 2001 From: cstr Date: Wed, 14 Sep 2022 08:46:04 +0800 Subject: [PATCH 04/25] Update OpenAireExportUtilTest.java --- .../edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java b/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java index 8064b8e20f5..40664527cfc 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java +++ b/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java @@ -609,7 +609,6 @@ public void testWriteRelatedIdentifierElement() throws XMLStreamException, IOExc + "RelatedPublicationIDNumber1" + "" + "RelatedPublicationIDNumber2" - + "" + "" + "RelatedPublicationIDNumber3" + "", From 561d8b7fecf9a1c64266bf17e6b1f0923f783e11 Mon Sep 17 00:00:00 2001 From: cstr Date: Wed, 14 Sep 2022 09:02:17 +0800 Subject: [PATCH 05/25] Update SchemaDotOrgExporterTest.java --- .../harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java b/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java index 5f0d4dfd106..d21d24a5432 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java +++ b/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java @@ -409,7 +409,7 @@ private static void mockDatasetFieldSvc() { new ControlledVocabularyValue(4l, "doi", publicationIdTypes), new ControlledVocabularyValue(5l, "ean13", publicationIdTypes), new ControlledVocabularyValue(6l, "handle", publicationIdTypes), - new ControlledVocabularyValue(17l, "CSTR", publicationIdTypes) + new ControlledVocabularyValue(17l, "cstr", publicationIdTypes) // Etc. There are more. )); publicationChildTypes.add(datasetFieldTypeSvc.add(publicationIdTypes)); From 39fdcaba2db17e393d388ba97c83682d38ef0f96 Mon Sep 17 00:00:00 2001 From: cstr Date: Wed, 14 Sep 2022 09:12:34 +0800 Subject: [PATCH 06/25] Update ready-state.sql Override --- scripts/issues/2102/ready-state.sql | 2 -- 1 file changed, 2 deletions(-) diff --git a/scripts/issues/2102/ready-state.sql b/scripts/issues/2102/ready-state.sql index 03ab805531e..96ccf58d865 100644 --- a/scripts/issues/2102/ready-state.sql +++ b/scripts/issues/2102/ready-state.sql @@ -3284,7 +3284,6 @@ COPY controlledvocabalternate (id, strvalue, controlledvocabularyvalue_id, datas 22 United States of America 472 79 23 U.S.A. 472 79 24 YEMEN 483 79 -25 CSTR 825 30 \. @@ -4117,7 +4116,6 @@ COPY controlledvocabularyvalue (id, displayorder, identifier, strvalue, datasetf 822 29 review article 154 823 30 translation 154 824 31 other 154 -825 17 CSTR 30 \. From ffde80e9b09dec1bd0bfcf793a0ed53320edc332 Mon Sep 17 00:00:00 2001 From: cstr Date: Wed, 14 Sep 2022 09:22:23 +0800 Subject: [PATCH 07/25] Update citation.tsv Adjusted sequence number --- scripts/api/data/metadatablocks/citation.tsv | 32 ++++++++++---------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/scripts/api/data/metadatablocks/citation.tsv b/scripts/api/data/metadatablocks/citation.tsv index a6d54a9a1ad..1b1ff0ae819 100644 --- a/scripts/api/data/metadatablocks/citation.tsv +++ b/scripts/api/data/metadatablocks/citation.tsv @@ -97,22 +97,22 @@ publicationIDType ark 0 publicationIDType arXiv 1 publicationIDType bibcode 2 - publicationIDType cstr 17 - publicationIDType doi 3 - publicationIDType ean13 4 - publicationIDType eissn 5 - publicationIDType handle 6 - publicationIDType isbn 7 - publicationIDType issn 8 - publicationIDType istc 9 - publicationIDType lissn 10 - publicationIDType lsid 11 - publicationIDType pmid 12 - publicationIDType purl 13 - publicationIDType upc 14 - publicationIDType url 15 - publicationIDType urn 16 - publicationIDType DASH-NRS 17 + publicationIDType cstr 3 + publicationIDType doi 4 + publicationIDType ean13 5 + publicationIDType eissn 6 + publicationIDType handle 7 + publicationIDType isbn 8 + publicationIDType issn 9 + publicationIDType istc 10 + publicationIDType lissn 11 + publicationIDType lsid 12 + publicationIDType pmid 13 + publicationIDType purl 14 + publicationIDType upc 15 + publicationIDType url 16 + publicationIDType urn 17 + publicationIDType DASH-NRS 18 contributorType Data Collector 0 contributorType Data Curator 1 contributorType Data Manager 2 From 7afa2935d72410df2e7f3ad847ceea4037d9244f Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 17:40:25 +0800 Subject: [PATCH 08/25] Update dataset-create-new-all-ddi-fields.json override --- .../dataset-create-new-all-ddi-fields.json | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json b/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json index 362a4ae4d90..1b327c15496 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json +++ b/src/test/java/edu/harvard/iq/dataverse/export/ddi/dataset-create-new-all-ddi-fields.json @@ -321,32 +321,6 @@ "typeClass": "primitive", "value": "http://RelatedPublicationURL2.org" } - }, - { - "publicationCitation": { - "typeName": "publicationCitation", - "multiple": false, - "typeClass": "primitive", - "value": "RelatedPublicationCitation3" - }, - "publicationIDType": { - "typeName": "publicationIDType", - "multiple": false, - "typeClass": "controlledVocabulary", - "value": "CSTR" - }, - "publicationIDNumber": { - "typeName": "publicationIDNumber", - "multiple": false, - "typeClass": "primitive", - "value": "RelatedPublicationIDNumber3" - }, - "publicationURL": { - "typeName": "publicationURL", - "multiple": false, - "typeClass": "primitive", - "value": "http://RelatedPublicationURL3.org" - } } ] }, From 627adf7ad565928ef812ef425f32db0eaa07bb34 Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 17:41:01 +0800 Subject: [PATCH 09/25] Update exportfull.xml override --- .../harvard/iq/dataverse/export/ddi/exportfull.xml | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml b/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml index 4314775c7a2..0570c832e4f 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml +++ b/src/test/java/edu/harvard/iq/dataverse/export/ddi/exportfull.xml @@ -166,10 +166,8 @@ RelatedMaterial1 RelatedMaterial2 - RelatedMaterial3 RelatedDatasets1 RelatedDatasets2 - RelatedDatasets3 @@ -187,19 +185,9 @@ RelatedPublicationCitation2 - - - - - RelatedPublicationIDNumber3 - - RelatedPublicationCitation3 - - OtherReferences1 OtherReferences2 - OtherReferences3 StudyLevelErrorNotes From 09c30a902ff776e721959a72d4d253e597b0730f Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 17:46:15 +0800 Subject: [PATCH 10/25] Update dataset-all-defaults.txt override --- .../dataverse/export/dataset-all-defaults.txt | 28 +------------------ 1 file changed, 1 insertion(+), 27 deletions(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt b/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt index a2a6d9c0778..7348d54b7dd 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt +++ b/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt @@ -16,7 +16,7 @@ "createTime": "2015-09-24T16:47:50Z", "license": { "name": "CC0 1.0", - "uri": "http://creativecommons.org/publicdomain/zero/1.0/" + "uri": "https://creativecommons.org/publicdomain/zero/1.0/" }, "metadataBlocks": { "citation": { @@ -362,32 +362,6 @@ "typeClass": "primitive", "value": "http://RelatedPublicationURL2.org" } - }, - { - "publicationCitation": { - "typeName": "publicationCitation", - "multiple": false, - "typeClass": "primitive", - "value": "RelatedPublicationCitation3" - }, - "publicationIDType": { - "typeName": "publicationIDType", - "multiple": false, - "typeClass": "controlledVocabulary", - "value": "CSTR" - }, - "publicationIDNumber": { - "typeName": "publicationIDNumber", - "multiple": false, - "typeClass": "primitive", - "value": "RelatedPublicationIDNumber3" - }, - "publicationURL": { - "typeName": "publicationURL", - "multiple": false, - "typeClass": "primitive", - "value": "http://RelatedPublicationURL3.org" - } } ] }, From af57e5dad41a303ec969b9ff9270a2a55ed83d4c Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 18:12:31 +0800 Subject: [PATCH 11/25] Update ddi_dataset.xml override --- .../source/_static/api/ddi_dataset.xml | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/doc/sphinx-guides/source/_static/api/ddi_dataset.xml b/doc/sphinx-guides/source/_static/api/ddi_dataset.xml index 0c5d5857b54..1e86f911a46 100644 --- a/doc/sphinx-guides/source/_static/api/ddi_dataset.xml +++ b/doc/sphinx-guides/source/_static/api/ddi_dataset.xml @@ -164,10 +164,8 @@ RelatedMaterial1 RelatedMaterial2 - RelatedMaterial3 RelatedDatasets1 RelatedDatasets2 - RelatedDatasets3 @@ -185,19 +183,9 @@ RelatedPublicationCitation2 - - - - - RelatedPublicationIDNumber3 - - RelatedPublicationCitation3 - - - + OtherReferences1 OtherReferences2 - OtherReferences3 StudyLevelErrorNotes From 6b6ab875203964c113e2cec2bebf9bd1c61917bd Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 18:17:03 +0800 Subject: [PATCH 12/25] Update dataset-create-new-all-default-fields.json override --- ...dataset-create-new-all-default-fields.json | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/scripts/api/data/dataset-create-new-all-default-fields.json b/scripts/api/data/dataset-create-new-all-default-fields.json index e51f4d9e1b5..d7ae8cefbf7 100644 --- a/scripts/api/data/dataset-create-new-all-default-fields.json +++ b/scripts/api/data/dataset-create-new-all-default-fields.json @@ -369,32 +369,6 @@ "typeClass": "primitive", "value": "http://RelatedPublicationURL2.org" } - }, - { - "publicationCitation": { - "typeName": "publicationCitation", - "multiple": false, - "typeClass": "primitive", - "value": "RelatedPublicationCitation3" - }, - "publicationIDType": { - "typeName": "publicationIDType", - "multiple": false, - "typeClass": "controlledVocabulary", - "value": "CSTR" - }, - "publicationIDNumber": { - "typeName": "publicationIDNumber", - "multiple": false, - "typeClass": "primitive", - "value": "RelatedPublicationIDNumber3" - }, - "publicationURL": { - "typeName": "publicationURL", - "multiple": false, - "typeClass": "primitive", - "value": "http://RelatedPublicationURL3.org" - } } ] }, From f62474691479f4d1c246c72f53ceb7c2c650350f Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 18:17:54 +0800 Subject: [PATCH 13/25] Update ddi_dataset.xml remove space --- doc/sphinx-guides/source/_static/api/ddi_dataset.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/_static/api/ddi_dataset.xml b/doc/sphinx-guides/source/_static/api/ddi_dataset.xml index 1e86f911a46..05eaadc3458 100644 --- a/doc/sphinx-guides/source/_static/api/ddi_dataset.xml +++ b/doc/sphinx-guides/source/_static/api/ddi_dataset.xml @@ -183,7 +183,7 @@ RelatedPublicationCitation2 - + OtherReferences1 OtherReferences2 From f1b1e3680cf0a4767d1535bff8aaf508a791ae02 Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 18:21:34 +0800 Subject: [PATCH 14/25] Create maven-publish.yml --- .github/workflows/maven-publish.yml | 54 +++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 .github/workflows/maven-publish.yml diff --git a/.github/workflows/maven-publish.yml b/.github/workflows/maven-publish.yml new file mode 100644 index 00000000000..05c017789db --- /dev/null +++ b/.github/workflows/maven-publish.yml @@ -0,0 +1,54 @@ +name: Maven Unit Tests + +on: + push: + paths: + - "**.java" + - "pom.xml" + - "modules/**/pom.xml" + pull_request: + paths: + - "**.java" + - "pom.xml" + - "modules/**/pom.xml" + +jobs: + unittest: + name: (${{ matrix.status}} / JDK ${{ matrix.jdk }}) Unit Tests + strategy: + fail-fast: false + matrix: + jdk: [ '11' ] + experimental: [false] + status: ["Stable"] + # + # JDK 17 builds disabled due to non-essential fails marking CI jobs as completely failed within + # Github Projects, PR lists etc. This was consensus on Slack #dv-tech. See issue #8094 + # (This is a limitation of how Github is currently handling these things.) + # + #include: + # - jdk: '17' + # experimental: true + # status: "Experimental" + continue-on-error: ${{ matrix.experimental }} + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up JDK ${{ matrix.jdk }} + uses: actions/setup-java@v2 + with: + java-version: ${{ matrix.jdk }} + distribution: 'adopt' + - name: Cache Maven packages + uses: actions/cache@v2 + with: + path: ~/.m2 + key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }} + restore-keys: ${{ runner.os }}-m2 + - name: Build with Maven + run: mvn -DcompilerArgument=-Xlint:unchecked -Dtarget.java.version=${{ matrix.jdk }} -P all-unit-tests clean test + - name: Maven Code Coverage + env: + CI_NAME: github + COVERALLS_SECRET: ${{ secrets.GITHUB_TOKEN }} + run: mvn -V -B jacoco:report coveralls:report -DrepoToken=${COVERALLS_SECRET} -DpullRequest=${{ github.event.number }} From 8e7509d906cce8e61d3bb8d15f20b35e98d4f8f8 Mon Sep 17 00:00:00 2001 From: cstr Date: Thu, 15 Sep 2022 18:32:24 +0800 Subject: [PATCH 15/25] Delete maven-publish.yml --- .github/workflows/maven-publish.yml | 54 ----------------------------- 1 file changed, 54 deletions(-) delete mode 100644 .github/workflows/maven-publish.yml diff --git a/.github/workflows/maven-publish.yml b/.github/workflows/maven-publish.yml deleted file mode 100644 index 05c017789db..00000000000 --- a/.github/workflows/maven-publish.yml +++ /dev/null @@ -1,54 +0,0 @@ -name: Maven Unit Tests - -on: - push: - paths: - - "**.java" - - "pom.xml" - - "modules/**/pom.xml" - pull_request: - paths: - - "**.java" - - "pom.xml" - - "modules/**/pom.xml" - -jobs: - unittest: - name: (${{ matrix.status}} / JDK ${{ matrix.jdk }}) Unit Tests - strategy: - fail-fast: false - matrix: - jdk: [ '11' ] - experimental: [false] - status: ["Stable"] - # - # JDK 17 builds disabled due to non-essential fails marking CI jobs as completely failed within - # Github Projects, PR lists etc. This was consensus on Slack #dv-tech. See issue #8094 - # (This is a limitation of how Github is currently handling these things.) - # - #include: - # - jdk: '17' - # experimental: true - # status: "Experimental" - continue-on-error: ${{ matrix.experimental }} - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - name: Set up JDK ${{ matrix.jdk }} - uses: actions/setup-java@v2 - with: - java-version: ${{ matrix.jdk }} - distribution: 'adopt' - - name: Cache Maven packages - uses: actions/cache@v2 - with: - path: ~/.m2 - key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }} - restore-keys: ${{ runner.os }}-m2 - - name: Build with Maven - run: mvn -DcompilerArgument=-Xlint:unchecked -Dtarget.java.version=${{ matrix.jdk }} -P all-unit-tests clean test - - name: Maven Code Coverage - env: - CI_NAME: github - COVERALLS_SECRET: ${{ secrets.GITHUB_TOKEN }} - run: mvn -V -B jacoco:report coveralls:report -DrepoToken=${COVERALLS_SECRET} -DpullRequest=${{ github.event.number }} From c231fb05e933e8a04b8ca9abdee19e723abc4336 Mon Sep 17 00:00:00 2001 From: cstr Date: Mon, 19 Sep 2022 08:45:02 +0800 Subject: [PATCH 16/25] Update OpenAireExportUtilTest.java override --- .../edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java b/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java index 40664527cfc..7f7cc203506 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java +++ b/src/test/java/edu/harvard/iq/dataverse/export/OpenAireExportUtilTest.java @@ -609,8 +609,6 @@ public void testWriteRelatedIdentifierElement() throws XMLStreamException, IOExc + "RelatedPublicationIDNumber1" + "" + "RelatedPublicationIDNumber2" - + "" - + "RelatedPublicationIDNumber3" + "", stringWriter.toString()); } From 1d47db41e4c7e2c92fe17eb61dff140808042b25 Mon Sep 17 00:00:00 2001 From: cstr Date: Mon, 19 Sep 2022 08:46:33 +0800 Subject: [PATCH 17/25] Update citation.properties --- src/main/java/propertyFiles/citation.properties | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/main/java/propertyFiles/citation.properties b/src/main/java/propertyFiles/citation.properties index edb418b0416..b382f8a5a1e 100644 --- a/src/main/java/propertyFiles/citation.properties +++ b/src/main/java/propertyFiles/citation.properties @@ -251,7 +251,7 @@ controlledvocabulary.subject.social_sciences=Social Sciences controlledvocabulary.subject.other=Other controlledvocabulary.publicationIDType.ark=ark controlledvocabulary.publicationIDType.arxiv=arXiv -controlledvocabulary.publicationIDType.CSTR=CSTR +controlledvocabulary.publicationIDType.cstr=CSTR controlledvocabulary.publicationIDType.bibcode=bibcode controlledvocabulary.publicationIDType.doi=doi controlledvocabulary.publicationIDType.ean13=ean13 @@ -346,7 +346,7 @@ controlledvocabulary.language.galician=Galician controlledvocabulary.language.georgian=Georgian controlledvocabulary.language.german=German controlledvocabulary.language.greek_(modern)=Greek (modern) -controlledvocabulary.language.guarani=Guaraní +controlledvocabulary.language.guarani=Guaraní controlledvocabulary.language.gujarati=Gujarati controlledvocabulary.language.haitian,_haitian_creole=Haitian, Haitian Creole controlledvocabulary.language.hausa=Hausa @@ -406,7 +406,7 @@ controlledvocabulary.language.navajo,_navaho=Navajo, Navaho controlledvocabulary.language.northern_ndebele=Northern Ndebele controlledvocabulary.language.nepali=Nepali controlledvocabulary.language.ndonga=Ndonga -controlledvocabulary.language.norwegian_bokmal=Norwegian Bokmål +controlledvocabulary.language.norwegian_bokmal=Norwegian BokmÃ¥l controlledvocabulary.language.norwegian_nynorsk=Norwegian Nynorsk controlledvocabulary.language.norwegian=Norwegian controlledvocabulary.language.nuosu=Nuosu @@ -468,7 +468,7 @@ controlledvocabulary.language.urdu=Urdu controlledvocabulary.language.uzbek=Uzbek controlledvocabulary.language.venda=Venda controlledvocabulary.language.vietnamese=Vietnamese -controlledvocabulary.language.volapuk=Volapük +controlledvocabulary.language.volapuk=Volapük controlledvocabulary.language.walloon=Walloon controlledvocabulary.language.welsh=Welsh controlledvocabulary.language.wolof=Wolof @@ -478,4 +478,4 @@ controlledvocabulary.language.yiddish=Yiddish controlledvocabulary.language.yoruba=Yoruba controlledvocabulary.language.zhuang,_chuang=Zhuang, Chuang controlledvocabulary.language.zulu=Zulu -controlledvocabulary.language.not_applicable=Not applicable \ No newline at end of file +controlledvocabulary.language.not_applicable=Not applicable From 8093406b5a700582a11cf7d2b016c564757ec479 Mon Sep 17 00:00:00 2001 From: cstr Date: Mon, 19 Sep 2022 08:48:22 +0800 Subject: [PATCH 18/25] Update dataset-all-defaults.txt --- .../edu/harvard/iq/dataverse/export/dataset-all-defaults.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt b/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt index 7348d54b7dd..a3f0dffc767 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt +++ b/src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt @@ -16,7 +16,7 @@ "createTime": "2015-09-24T16:47:50Z", "license": { "name": "CC0 1.0", - "uri": "https://creativecommons.org/publicdomain/zero/1.0/" + "uri": "http://creativecommons.org/publicdomain/zero/1.0/" }, "metadataBlocks": { "citation": { From 744030bd1c07d7ee62ff1d9aecd60f7b256dd57b Mon Sep 17 00:00:00 2001 From: cstr Date: Mon, 19 Sep 2022 09:49:22 +0800 Subject: [PATCH 19/25] Update SchemaDotOrgExporterTest.java --- .../iq/dataverse/export/SchemaDotOrgExporterTest.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java b/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java index d21d24a5432..644848d2776 100644 --- a/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java +++ b/src/test/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporterTest.java @@ -406,10 +406,10 @@ private static void mockDatasetFieldSvc() { new ControlledVocabularyValue(1l, "ark", publicationIdTypes), new ControlledVocabularyValue(2l, "arXiv", publicationIdTypes), new ControlledVocabularyValue(3l, "bibcode", publicationIdTypes), - new ControlledVocabularyValue(4l, "doi", publicationIdTypes), - new ControlledVocabularyValue(5l, "ean13", publicationIdTypes), - new ControlledVocabularyValue(6l, "handle", publicationIdTypes), - new ControlledVocabularyValue(17l, "cstr", publicationIdTypes) + new ControlledVocabularyValue(4l, "cstr", publicationIdTypes), + new ControlledVocabularyValue(5l, "doi", publicationIdTypes), + new ControlledVocabularyValue(6l, "ean13", publicationIdTypes), + new ControlledVocabularyValue(7l, "handle", publicationIdTypes) // Etc. There are more. )); publicationChildTypes.add(datasetFieldTypeSvc.add(publicationIdTypes)); From 43c0681e568856f330f183b4585c2d4535cc2a99 Mon Sep 17 00:00:00 2001 From: cstr Date: Wed, 21 Sep 2022 17:55:37 +0800 Subject: [PATCH 20/25] Update OpenAireExportUtil.java --- .../iq/dataverse/export/openaire/OpenAireExportUtil.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java index ffce432ce3b..87604cdc988 100644 --- a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java +++ b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java @@ -964,7 +964,7 @@ public static void writeRelatedIdentifierElement(XMLStreamWriter xmlw, DatasetVe relatedIdentifierTypeMap.put("URL".toLowerCase(), "URL"); relatedIdentifierTypeMap.put("URN".toLowerCase(), "URN"); relatedIdentifierTypeMap.put("WOS".toLowerCase(), "WOS"); - relatedIdentifierTypeMap.put("CSTR".toLowerCase(), "CSTR"); + relatedIdentifierTypeMap.put("CSTR".toLowerCase(), "cstr"); } for (Map.Entry entry : datasetVersionDTO.getMetadataBlocks().entrySet()) { From c715bb88e979f2fa21dd1b27fa9cf7b3108ee60f Mon Sep 17 00:00:00 2001 From: cstr Date: Wed, 21 Sep 2022 18:06:38 +0800 Subject: [PATCH 21/25] Update OpenAireExportUtil.java --- .../harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java index 87604cdc988..49fe203b96d 100644 --- a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java +++ b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java @@ -964,7 +964,6 @@ public static void writeRelatedIdentifierElement(XMLStreamWriter xmlw, DatasetVe relatedIdentifierTypeMap.put("URL".toLowerCase(), "URL"); relatedIdentifierTypeMap.put("URN".toLowerCase(), "URN"); relatedIdentifierTypeMap.put("WOS".toLowerCase(), "WOS"); - relatedIdentifierTypeMap.put("CSTR".toLowerCase(), "cstr"); } for (Map.Entry entry : datasetVersionDTO.getMetadataBlocks().entrySet()) { From 5c79de8fb1ea1c50455595819864262f8f891e74 Mon Sep 17 00:00:00 2001 From: cstr Date: Fri, 23 Sep 2022 11:29:23 +0800 Subject: [PATCH 22/25] Update AdminIT.java resolve AdminIT junit.framework.AssertionFailedError: expected:<322> but was:<323> --- src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java b/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java index cf06fd9937b..91f78ca6238 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java @@ -762,7 +762,7 @@ public void testLoadMetadataBlock_NoErrorPath() { assertEquals(1, data.size()); List> addedElements = data.get("added"); //Note -test depends on the number of elements in the production citation block, so any changes to the # of elements there can break this test - assertEquals(322, addedElements.size()); + assertEquals(323, addedElements.size()); Map statistics = new HashMap<>(); for (Map unit : addedElements) { From 4bfca4a243ae2795329a8df8ffd3a2f3f1aa36d6 Mon Sep 17 00:00:00 2001 From: cstr Date: Mon, 26 Sep 2022 09:16:25 +0800 Subject: [PATCH 23/25] Update AdminIT.java I should find the reason for the failure, please rebuild --- src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java b/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java index 91f78ca6238..bcee8d18e17 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java @@ -778,7 +778,7 @@ public void testLoadMetadataBlock_NoErrorPath() { assertEquals(3, statistics.size()); assertEquals(1, (int) statistics.get("MetadataBlock")); assertEquals(78, (int) statistics.get("DatasetField")); - assertEquals(243, (int) statistics.get("Controlled Vocabulary")); + assertEquals(244, (int) statistics.get("Controlled Vocabulary")); } @Test From 614c33df0ac120de33dcd448dbd0b4d72dcd8434 Mon Sep 17 00:00:00 2001 From: cstr Date: Fri, 14 Oct 2022 11:13:59 +0800 Subject: [PATCH 24/25] encoding change. From de6be210c10c491eeba8fb5dce9d74a3cff06926 Mon Sep 17 00:00:00 2001 From: xflv Date: Fri, 14 Oct 2022 11:27:52 +0800 Subject: [PATCH 25/25] update encoding change. --- src/main/java/propertyFiles/citation.properties | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/propertyFiles/citation.properties b/src/main/java/propertyFiles/citation.properties index b382f8a5a1e..ef8b44d7114 100644 --- a/src/main/java/propertyFiles/citation.properties +++ b/src/main/java/propertyFiles/citation.properties @@ -346,7 +346,7 @@ controlledvocabulary.language.galician=Galician controlledvocabulary.language.georgian=Georgian controlledvocabulary.language.german=German controlledvocabulary.language.greek_(modern)=Greek (modern) -controlledvocabulary.language.guarani=Guaraní +controlledvocabulary.language.guarani=Guaraní controlledvocabulary.language.gujarati=Gujarati controlledvocabulary.language.haitian,_haitian_creole=Haitian, Haitian Creole controlledvocabulary.language.hausa=Hausa @@ -406,7 +406,7 @@ controlledvocabulary.language.navajo,_navaho=Navajo, Navaho controlledvocabulary.language.northern_ndebele=Northern Ndebele controlledvocabulary.language.nepali=Nepali controlledvocabulary.language.ndonga=Ndonga -controlledvocabulary.language.norwegian_bokmal=Norwegian BokmÃ¥l +controlledvocabulary.language.norwegian_bokmal=Norwegian Bokmål controlledvocabulary.language.norwegian_nynorsk=Norwegian Nynorsk controlledvocabulary.language.norwegian=Norwegian controlledvocabulary.language.nuosu=Nuosu @@ -468,7 +468,7 @@ controlledvocabulary.language.urdu=Urdu controlledvocabulary.language.uzbek=Uzbek controlledvocabulary.language.venda=Venda controlledvocabulary.language.vietnamese=Vietnamese -controlledvocabulary.language.volapuk=Volapük +controlledvocabulary.language.volapuk=Volapük controlledvocabulary.language.walloon=Walloon controlledvocabulary.language.welsh=Welsh controlledvocabulary.language.wolof=Wolof @@ -478,4 +478,4 @@ controlledvocabulary.language.yiddish=Yiddish controlledvocabulary.language.yoruba=Yoruba controlledvocabulary.language.zhuang,_chuang=Zhuang, Chuang controlledvocabulary.language.zulu=Zulu -controlledvocabulary.language.not_applicable=Not applicable +controlledvocabulary.language.not_applicable=Not applicable \ No newline at end of file