From 1517bf7c926f82afc6d52c63bfa62a7546b85a8f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 13 May 2021 16:11:22 +0200 Subject: [PATCH] IndexRecordTransformerTest for producing a record that can be manually submitted to solr --- .../provision/IndexRecordTransformerTest.java | 81 +- .../oa/provision/XmlRecordFactoryTest.java | 4 +- .../eu/dnetlib/dhp/oa/provision/fields.xml | 9 +- .../eu/dnetlib/dhp/oa/provision/record.xml | 852 ++---------------- 4 files changed, 155 insertions(+), 791 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index b1e39c696..be5f75f05 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -1,39 +1,100 @@ package eu.dnetlib.dhp.oa.provision; +import static org.junit.jupiter.api.Assertions.assertNotNull; + import java.io.IOException; -import java.io.StringReader; -import java.io.StringWriter; -import java.nio.file.Files; -import java.nio.file.Path; +import java.util.List; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerException; -import javax.xml.transform.stream.StreamResult; -import javax.xml.transform.stream.StreamSource; import org.apache.commons.io.IOUtils; +import org.apache.solr.client.solrj.util.ClientUtils; +import org.apache.solr.common.SolrInputDocument; +import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Lists; + +import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; +import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; +import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; +import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; +import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory; +import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; public class IndexRecordTransformerTest { + public static final String VERSION = "2021-04-15T10:05:53Z"; + public static final String DSID = "b9ee796a-c49f-4473-a708-e7d67b84c16d_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"; + + private ContextMapper contextMapper; + + @BeforeEach + public void setUp() { + contextMapper = new ContextMapper(); + } + @Test - public void testTrasformRecord() throws IOException, TransformerException { - String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml")); + public void testPreBuiltRecordTransformation() throws IOException, TransformerException { String record = IOUtils.toString(getClass().getResourceAsStream("record.xml")); + + testRecordTransformation(record); + } + + @Test + public void testPublicationRecordTransformation() throws IOException, TransformerException { + + XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, + XmlRecordFactoryTest.otherDsTypeId); + + Publication p = load("publication.json", Publication.class); + Project pj = load("project.json", Project.class); + Relation rel = load("relToValidatedProject.json", Relation.class); + + JoinedEntity je = new JoinedEntity<>(p); + je + .setLinks( + Lists + .newArrayList( + new RelatedEntityWrapper(rel, + CreateRelatedEntitiesJob_phase1.asRelatedEntity(pj, Project.class)))); + + String record = xmlRecordFactory.build(je); + + assertNotNull(record); + + testRecordTransformation(record); + } + + private void testRecordTransformation(String record) throws IOException, TransformerException { + String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml")); String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl")); String transformer = XmlIndexingJob.getLayoutTransformer("DMF", fields, xslt); Transformer tr = SaxonTransformerFactory.newInstance(transformer); - String a = XmlIndexingJob.toIndexRecord(tr, record); + String indexRecordXML = XmlIndexingJob.toIndexRecord(tr, record); - System.out.println(a); + SolrInputDocument solrDoc = new StreamingInputDocumentFactory(VERSION, DSID).parseDocument(indexRecordXML); + final String xmlDoc = ClientUtils.toXML(solrDoc); + + Assertions.assertNotNull(xmlDoc); + System.out.println(xmlDoc); + } + + private T load(String fileName, Class clazz) throws IOException { + return XmlRecordFactoryTest.OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream(fileName)), clazz); } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 27860ca32..75805f66c 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -29,9 +29,9 @@ import eu.dnetlib.dhp.schema.oaf.Relation; public class XmlRecordFactoryTest { - private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource"; + public static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource"; - private static ObjectMapper OBJECT_MAPPER = new ObjectMapper() + public static ObjectMapper OBJECT_MAPPER = new ObjectMapper() .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml index 58b37ad0e..c47975c9d 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml @@ -61,7 +61,7 @@ - + @@ -72,7 +72,6 @@ - @@ -131,9 +130,9 @@ - - - + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml index 2d6049416..31376875c 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml @@ -1,774 +1,78 @@ - -
- dedup_wf_001::113ca964590682d906a3588d3d6b4838 - 2020-03-15T05:46:43.509Z - 2020-03-15T21:17:13.902Z -
- - - - - - - - - - oai:pubmedcentral.nih.gov:5657733 - oai:doaj.org/article:f26495a4c1d149099049e1a604fa1256 - 10.1177/0963689717714320 - 28933215 - PMC5657733 - 10.1177/0963689717714320 - Extract Protects Model Neurons - from Traumatic Injury - - Jain, Subhash C. - Citron, Bruce A. - Vijayalakshmi Ravindranath - Saykally, Jessica N. - Keeley, Kristen L. - Haris Hatic - Baglioni, Miriam - De Bonis, Michele - 2017-06-01 - Withania somnifera has been used in traditional medicine for a variety - of neural disorders. Recently, chronic neurodegenerative conditions have been - shown to benefit from treatment with this extract. To evaluate the action of - this extract on traumatically injured neurons, the efficacy of W. somnifera root - extract as a neuroprotective agent was examined in cultured model neurons - exposed to an in vitro injury system designed to mimic mild traumatic brain - injury (TBI). Neuronal health was evaluated by staining with annexin V (an - early, apoptotic feature) and monitoring released lactate dehydrogenase activity - (a terminal cell loss parameter). Potential mechanisms underlying the observed - neuroprotection were examined. Additionally, morphological changes were - monitored following injury and treatment. Although no differences were found in - the expression of the antioxidant transcription factor nuclear factor erythroid - 2-like 2 (Nrf2) or other Nrf2-related downstream components, significant changes - were seen in apoptotic signaling. Treatment with the extract resulted in an - increased length of neurites projecting from the neuronal cell body after - injury. W. somnifera extract treatment also resulted in reduced cell death in - the model neuron TBI system. The cell death factor Bax was involved (its - expression was reduced 2-fold by the treatment) and injury-induced reduction in - neurite lengths and numbers was reversed by the treatment. This all indicates - that W. somnifera root extract was neuroprotective and could have therapeutic - potential to target factors involved in secondary injury and long-term sequelae - of mild TBI. - - Withania - somnifera - R - Cell Biology - neuroprotection - SH-SY5Y - Biomedical Engineering - Transplantation - traumatic - brain injury - neurites - Ayurveda - Medicine - - 2018-11-13 - 2017-6-30 - 2017-7-1 - SAGE Publishing - Cell Transplantation, Vol 26 (2017) - Cell Transplantation - - - Cell Transplantation - - - - - true - false - 0.9 - dedup-similarity-result-levenstein - - - - - wt__________::4de25ac59f6cb729d5716260164bb67c - Indian Institute Of Science - - - nih_________::ba7da8316fd53d04a985bc935e438555 - INDIAN INSTITUTE OF SCIENCE - - - dedup_wf_001::0047940c0207b6a83e79cd803ecf17d1 - - MRC - MRC Laboratory of Molecular Biology - LMB - - - rcuk________::2558c4f3132f6907f7b23c69009f0d87 - INDIAN INSTUTUTE OF SCIENCE - - - dedup_wf_001::d2fdc8e80f8b4365091bcea83f918ccf - - University of Delhi - University of Delhi - - - doiboost____::d5177e3ad00bd9288201b60206a0b5d0 - 2017-6-30 - - - - 10.1177/0963689717714320 - - - od_______267::fb470352a4b33af7c83391c02117c4fc - - SAGE Publications - PMC5657733 - 28933215 - 2017-06-01 - 10.1177/0963689717714320 - - - nih_________::24e81ae35bbcb50c778df1039f912617 - - - nih_________::NIH::VETERANS_AFFAIRS - - Preventing TBI-Induced Chronic Functional Loss with a Neuroprotective - Antioxidant - 1I01RX001520-01A1 - - - wt__________::52e59d4aa1c57bda1ec144f409de83fc - Indian Institute of Science - - - dedup_wf_001::0499ff413ba8e7fa686531725ba12338 - IISc - - Indian Institute of Science - - - wt__________::ba1db3669859a46e72f222052a9a26d8 - University of Delhi - - - dedup_wf_001::17c785347dfb060aa115af824b0c6789 - IISc - - Indian Institute of Science Bangalore - - - scholexplore::16181ec1a2484116e8ed6b3348858fe7 - - 28933215 - - - doajarticles::cac994ec6c322070c41474486eb5c595 - 2017-07-01 - - SAGE Publishing - 10.1177/0963689717714320 - - - r37980778c78::39a72c53d5801325784f728b543a49a1 - - 10.1371/journal.pone.0006628 - 2016-01-01 - Figshare - - - rcuk________::23feba2a5ca7f6b6016bf3a45180da50 - University of Delhi - - - true - corda_______::30c6b5ab90f30666de1d112fb93d8c77 - 227878 - - - ec__________::EC::FP7 - ec__________::EC::FP7::SP2 - ec__________::EC::FP7::SP2::ERC - - Complex structure and dynamics of collective motion - COLLMOT - - - - irb_hr______::2330a1d0dac71ffbe15fbcbc807288d4 - 108-1083570-3635 - - - - Pentadecapeptide BPC 157 - further investigations - - - - - - - - - - https://www.ncbi.nlm.nih.gov/pubmed/28933215 - - - - - - - 2017-06-01 - - - http://europepmc.org/articles/PMC5657733 - - - - - - - - - http://journals.sagepub.com/doi/full-xml/10.1177/0963689717714320 - - - http://journals.sagepub.com/doi/pdf/10.1177/0963689717714320 - - - https://academic.microsoft.com/#/detail/2588640354 - - - - - - - 2017-07-01 - - - https://doi.org/10.1177/0963689717714320 - - - https://doaj.org/toc/0963-6897 - - - https://doaj.org/toc/1555-3892 - - - - - - - - - http://dx.doi.org/10.1177/0963689717714320 - - - - - - - - - https://journals.sagepub.com/doi/pdf/10.1177/0963689717714320 - - - - - - - - 1 Bryan-Hancock C Harrison J The global burden of traumatic brain - injury: preliminary results from the Global Burden of Disease Project. - Inj Prev. 2010;16(Suppl 1):A17. - - - 2 Gardner RC Yaffe K Epidemiology of mild traumatic brain injury - and neurodegenerative disease. Mol Cell Neurosci. 2015;66(Pt - B):75–80.25748121 - - - - - 3 Stern RA Riley DO Daneshvar DH Nowinski CJ Cantu RC McKee AC - Long-term consequences of repetitive brain trauma: chronic traumatic - encephalopathy. PM R. 2011;3(10 Suppl 2):S460–S467.22035690 - - - - - 4 Mac Donald CL Johnson AM Cooper D Nelson EC Werner NJ Shimony JS - Snyder AZ Raichle ME Witherow JR Fang R Detection of blast-related - traumatic brain injury in U.S. military personnel. N Engl J Med. - 2011;364(22):2091–2100.21631321 - - - - - 5 Hatic H Kane MJ Saykally JN Citron BA Modulation of transcription - factor Nrf2 in an in vitro model of traumatic brain injury. J - Neurotrauma. 2012;29(6):1188–1196.22201269 - - - - - 6 Saykally JN Rachmany L Hatic H Shaer A Rubovitch V Pick CG Citron - BA The nuclear factor erythroid 2-like 2 activator, - tert-butylhydroquinone, improves cognitive performance in mice after - mild traumatic brain injury. Neuroscience. - 2012;223:305–314.22890082 - - - - - 7 Hall ED Vaishnav RA Mustafa AG Antioxidant therapies for - traumatic brain injury. Neurotherapeutics. - 2010;7(1):51–61.20129497 - - - - - 8 Scartezzini P Speroni E Review on some plants of Indian - traditional medicine with antioxidant activity. J Ethnopharmacol. - 2000;71(1–2):23–43.10904144 - - - - - 9 Mishra LC Singh BB Dagenais S Scientific basis for the - therapeutic use of Withania somnifera (ashwagandha): a review. Altern - Med Rev. 2000;5(4):334–346.10956379 - - - - - 10 Singh RH Exploring larger evidence-base for contemporary - Ayurveda. Int J Ayurveda Res. 2010;1(2):65–66.20814517 - - - - - 11 Alam N Hossain M Mottalib MA Sulaiman SA Gan SH Khalil MI - Methanolic extracts of Withania somnifera leaves, fruits and roots - possess antioxidant properties and antibacterial activities. 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Pharmacognosy Res. - 2014;6(1):12–18.24497737 - - - - - 26 Prabhakaran Y Dinakaran SK Macharala SP Ghosh S Karanam SR - Kanthasamy N Avasarala H Molecular docking studies of withanolides - against Cox-2 enzyme. Pak J Pharm Sci. - 2012;25(3):595–598.22713947 - - - - - 27 Mohan R Hammers HJ Bargagna-Mohan P Zhan XH Herbstritt CJ Ruiz A - Zhang L Hanson AD Conner BP Rougas J Withaferin A is a potent inhibitor - of angiogenesis. Angiogenesis. 2004;7(2):115–122.15516832 - - - - - 28 Friedemann T Otto B Klatschke K Schumacher U Tao Y Leung AK - Efferth T Schroder S Coptis chinensis Franch. exhibits neuroprotective - properties against oxidative stress in human neuroblastoma cells. J - Ethnopharmacol. 2014;155(1):607–615.24929105 - - - - - 29 Hu S Han R Mak S Han Y Protection against - 1-methyl-4-phenylpyridinium ion (MPP+)-induced apoptosis by water - extract of ginseng (Panax ginseng C.A. Meyer) in SH-SY5Y cells. 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Br J Pharmacol. - 2005;144(7):961–971.15711595 - - - - - 42 Kuboyama T Tohda C Komatsu K Withanoside IV and its active - metabolite, sominone, attenuate Abeta(25-35)-induced neurodegeneration - Eur J Neurosci. 2006;23(6):1417–1426.16553605 - - - - - 43 Jarrard LE On the role of the hippocampus in learning and memory - in the rat. Behav Neural Biol. 1993;60(1):9–26.8216164 - - - - - 44 Vareed SK Bauer AK Nair KM Liu Y Jayaprakasam B Nair MG - Blood-brain barrier permeability of bioactive withanamides present in - Withania somnifera fruit extract. Phytother Res. - 2014;28(8):1260–1264.24458838 - - - - - - - - + + + +
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