From 65ac01a4a655176351b0a74a8daf5b701a418d35 Mon Sep 17 00:00:00 2001 From: "Gantner, Florian Klaus" Date: Thu, 7 Mar 2024 15:31:03 +0100 Subject: [PATCH 1/3] use datacite api response for recordscount and paginated calls. update test file for response as expected from the api. --- ...taCiteImportMetadataSourceServiceImpl.java | 39 ++++++++++++++++++- .../org/dspace/app/rest/dataCite-test.json | 2 +- 2 files changed, 38 insertions(+), 3 deletions(-) diff --git a/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java b/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java index 2f723c24df..10cbab3f95 100644 --- a/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java @@ -73,8 +73,32 @@ public class DataCiteImportMetadataSourceServiceImpl @Override public int getRecordsCount(String query) throws MetadataSourceException { - Collection records = getRecords(query, 0, -1); - return records == null ? 0 : records.size(); + String id = getID(query); + Map> params = new HashMap<>(); + Map uriParameters = new HashMap<>(); + params.put("uriParameters", uriParameters); + if (StringUtils.isBlank(id)) { + id = query; + } + uriParameters.put("query", id); + uriParameters.put("page[size]", "1"); + int timeoutMs = configurationService.getIntProperty("datacite.timeout", 180000); + String url = configurationService.getProperty("datacite.url", "https://api.datacite.org/dois/"); + String responseString = liveImportClient.executeHttpGetRequest(timeoutMs, url, params); + JsonNode jsonNode = convertStringJsonToJsonNode(responseString); + if (jsonNode == null) { + log.warn("DataCite returned invalid JSON"); + throw new MetadataSourceException("Could not read datacite source"); + } + JsonNode dataNode = jsonNode.at("/meta/total"); + if (dataNode != null) { + try { + return Integer.valueOf(dataNode.toString()); + } catch (Exception e) { + log.debug("Could not read integer value" + dataNode.toString()); + } + } + return 0; } @Override @@ -95,6 +119,17 @@ public class DataCiteImportMetadataSourceServiceImpl id = query; } uriParameters.put("query", id); + // start = current dspace page / datacite page number starting with 1 + // dspace rounds up/down to the next configured pagination settings. + if (start > 0 && count > 0) { + uriParameters.put("page[number]", Integer.toString((start / count) + 1)); + } + + // count = dspace page size / default datacite page size is currently 25 https://support.datacite.org/docs/pagination + if (count > 0) { + uriParameters.put("page[size]", Integer.toString(count)); + } + int timeoutMs = configurationService.getIntProperty("datacite.timeout", 180000); String url = configurationService.getProperty("datacite.url", "https://api.datacite.org/dois/"); String responseString = liveImportClient.executeHttpGetRequest(timeoutMs, url, params); diff --git a/dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-test.json b/dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-test.json index 8ede6f29a0..1b7f63cd89 100644 --- a/dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-test.json +++ b/dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-test.json @@ -1 +1 @@ -{"data":{"id":"10.48550/arxiv.2207.04779","type":"dois","attributes":{"doi":"10.48550/arxiv.2207.04779","prefix":"10.48550","suffix":"arxiv.2207.04779","identifiers":[{"identifier":"2207.04779","identifierType":"arXiv"}],"alternateIdentifiers":[{"alternateIdentifierType":"arXiv","alternateIdentifier":"2207.04779"}],"creators":[{"name":"Bayer, Jonas","nameType":"Personal","givenName":"Jonas","familyName":"Bayer","affiliation":[],"nameIdentifiers":[]},{"name":"Benzmüller, Christoph","nameType":"Personal","givenName":"Christoph","familyName":"Benzmüller","affiliation":[],"nameIdentifiers":[]},{"name":"Buzzard, Kevin","nameType":"Personal","givenName":"Kevin","familyName":"Buzzard","affiliation":[],"nameIdentifiers":[]},{"name":"David, Marco","nameType":"Personal","givenName":"Marco","familyName":"David","affiliation":[],"nameIdentifiers":[]},{"name":"Lamport, Leslie","nameType":"Personal","givenName":"Leslie","familyName":"Lamport","affiliation":[],"nameIdentifiers":[]},{"name":"Matiyasevich, Yuri","nameType":"Personal","givenName":"Yuri","familyName":"Matiyasevich","affiliation":[],"nameIdentifiers":[]},{"name":"Paulson, Lawrence","nameType":"Personal","givenName":"Lawrence","familyName":"Paulson","affiliation":[],"nameIdentifiers":[]},{"name":"Schleicher, Dierk","nameType":"Personal","givenName":"Dierk","familyName":"Schleicher","affiliation":[],"nameIdentifiers":[]},{"name":"Stock, Benedikt","nameType":"Personal","givenName":"Benedikt","familyName":"Stock","affiliation":[],"nameIdentifiers":[]},{"name":"Zelmanov, Efim","nameType":"Personal","givenName":"Efim","familyName":"Zelmanov","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Mathematical Proof Between Generations"}],"publisher":"arXiv","container":{},"publicationYear":2022,"subjects":[{"lang":"en","subject":"History and Overview (math.HO)","subjectScheme":"arXiv"},{"lang":"en","subject":"Logic in Computer Science (cs.LO)","subjectScheme":"arXiv"},{"subject":"FOS: Mathematics","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Mathematics","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"}],"contributors":[],"dates":[{"date":"2022-07-08T14:42:33Z","dateType":"Submitted","dateInformation":"v1"},{"date":"2022-07-13T00:14:24Z","dateType":"Updated","dateInformation":"v1"},{"date":"2022-07","dateType":"Available","dateInformation":"v1"},{"date":"2022","dateType":"Issued"}],"language":null,"types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"CreativeWork","resourceType":"Article","resourceTypeGeneral":"Preprint"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":"1","rightsList":[{"rights":"arXiv.org perpetual, non-exclusive license","rightsUri":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/"}],"descriptions":[{"description":"A proof is one of the most important concepts of mathematics. 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However, there is a striking difference between how a proof is defined in theory and how it is used in practice. This puts the unique status of mathematics as exact science into peril. Now may be the time to reconcile theory and practice, i.e. precision and intuition, through the advent of computer proof assistants. For the most time this has been a topic for experts in specialized communities. However, mathematical proofs have become increasingly sophisticated, stretching the boundaries of what is humanly comprehensible, so that leading mathematicians have asked for formal verification of their proofs. At the same time, major theorems in mathematics have recently been computer-verified by people from outside of these communities, even by beginning students. This article investigates the gap between the different definitions of a proof and possibilities to build bridges. It is written as a polemic or a collage by different members of the communities in mathematics and computer science at different stages of their careers, challenging well-known preconceptions and exploring new perspectives.","descriptionType":"Abstract"},{"description":"17 pages, 1 figure","descriptionType":"Other"}],"geoLocations":[],"fundingReferences":[],"url":"https://arxiv.org/abs/2207.04779","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":1,"created":"2022-07-12T01:41:56Z","registered":"2022-07-12T01:41:57Z","published":null,"updated":"2024-03-05T11:33:47Z"},"relationships":{"client":{"data":{"id":"arxiv.content","type":"clients"}}}}],"meta":{"total":1,"totalPages":1,"page":1,"states":[{"id":"findable","title":"Findable","count":1}],"resourceTypes":[{"id":"text","title":"Text","count":1}],"created":[{"id":"2022","title":"2022","count":1}],"published":[{"id":"2022","title":"2022","count":1}],"registered":[{"id":"2022","title":"2022","count":1}],"providers":[{"id":"arxiv","title":"arXiv","count":1}],"clients":[{"id":"arxiv.content","title":"arXiv","count":1}],"affiliations":[],"prefixes":[{"id":"10.48550","title":"10.48550","count":1}],"certificates":[],"licenses":[],"schemaVersions":[{"id":"4","title":"Schema 4","count":1}],"linkChecksStatus":[],"subjects":[{"id":"FOS: Computer and information sciences","title":"Fos: Computer And Information Sciences","count":1},{"id":"FOS: Mathematics","title":"Fos: Mathematics","count":1},{"id":"History and Overview (math.HO)","title":"History And Overview (Math.Ho)","count":1},{"id":"Logic in Computer Science (cs.LO)","title":"Logic In Computer Science (Cs.Lo)","count":1}],"fieldsOfScience":[{"id":"computer_and_information_sciences","title":"Computer and information sciences","count":1},{"id":"mathematics","title":"Mathematics","count":1}],"citations":[],"views":[],"downloads":[]},"links":{"self":"https://api.datacite.org/dois?query=10.48550/arxiv.2207.04779"}} From 9cd1a1093d08d74da6773112645dfd79b69dfdd0 Mon Sep 17 00:00:00 2001 From: "Gantner, Florian Klaus" Date: Tue, 16 Apr 2024 12:02:48 +0200 Subject: [PATCH 2/3] datacite api test for no results count --- ...DataCiteImportMetadataSourceServiceIT.java | 19 +++++++++++++++++++ .../dspace/app/rest/dataCite-noResults.json | 1 + 2 files changed, 20 insertions(+) create mode 100644 dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-noResults.json diff --git a/dspace-server-webapp/src/test/java/org/dspace/app/rest/DataCiteImportMetadataSourceServiceIT.java b/dspace-server-webapp/src/test/java/org/dspace/app/rest/DataCiteImportMetadataSourceServiceIT.java index 569e1ea94e..35b4810d92 100644 --- a/dspace-server-webapp/src/test/java/org/dspace/app/rest/DataCiteImportMetadataSourceServiceIT.java +++ b/dspace-server-webapp/src/test/java/org/dspace/app/rest/DataCiteImportMetadataSourceServiceIT.java @@ -146,4 +146,23 @@ public class DataCiteImportMetadataSourceServiceIT extends AbstractLiveImportInt return records; } + @Test + public void dataCiteImportMetadataNoResultsTest() throws Exception { + context.turnOffAuthorisationSystem(); + CloseableHttpClient originalHttpClient = liveImportClientImpl.getHttpClient(); + CloseableHttpClient httpClient = Mockito.mock(CloseableHttpClient.class); + try (InputStream dataciteResp = getClass().getResourceAsStream("dataCite-noResults.json")) { + String dataciteTextResp = IOUtils.toString(dataciteResp, Charset.defaultCharset()); + liveImportClientImpl.setHttpClient(httpClient); + CloseableHttpResponse response = mockResponse(dataciteTextResp, 200, "OK"); + when(httpClient.execute(ArgumentMatchers.any())).thenReturn(response); + context.restoreAuthSystemState(); + int tot = dataCiteServiceImpl.getRecordsCount("nocontent"); + assertEquals(0, tot); + Collection importRecords = dataCiteServiceImpl.getRecords("nocontent", 0 , -1); + assertEquals(0, importRecords.size()); + } finally { + liveImportClientImpl.setHttpClient(originalHttpClient); + } + } } diff --git a/dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-noResults.json b/dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-noResults.json new file mode 100644 index 0000000000..c54fbe3636 --- /dev/null +++ b/dspace-server-webapp/src/test/resources/org/dspace/app/rest/dataCite-noResults.json @@ -0,0 +1 @@ +{"data":[],"meta":{"total":0,"totalPages":0,"page":1},"links":{"self":"https://api.datacite.org/dois?query=nocontent"}} From 9667a3374d0aab18c91f53f59f8d6dc05e2df429 Mon Sep 17 00:00:00 2001 From: "Gantner, Florian Klaus" Date: Fri, 10 May 2024 18:08:19 +0200 Subject: [PATCH 3/3] avoid empty data to create phantom records for datacite import --- .../DataCiteImportMetadataSourceServiceImpl.java | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java b/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java index 10cbab3f95..ad6e260bd0 100644 --- a/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteImportMetadataSourceServiceImpl.java @@ -143,12 +143,16 @@ public class DataCiteImportMetadataSourceServiceImpl Iterator iterator = dataNode.iterator(); while (iterator.hasNext()) { JsonNode singleDoiNode = iterator.next(); - String json = singleDoiNode.at("/attributes").toString(); - records.add(transformSourceRecords(json)); + JsonNode singleDoiNodeAttribute = singleDoiNode.at("/attributes"); + if (!singleDoiNodeAttribute.isMissingNode()) { + records.add(transformSourceRecords(singleDoiNodeAttribute.toString())); + } } } else { - String json = dataNode.at("/attributes").toString(); - records.add(transformSourceRecords(json)); + JsonNode singleDoiNodeAttribute = dataNode.at("/attributes"); + if (!singleDoiNodeAttribute.isMissingNode()) { + records.add(transformSourceRecords(singleDoiNodeAttribute.toString())); + } } return records;