diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java index b9746f153b..ede7aa7b48 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java @@ -113,7 +113,7 @@ public class XmlIndexingJob { }); } - private static String toIndexRecord(Transformer tr, final String record) { + protected static String toIndexRecord(Transformer tr, final String record) { final StreamResult res = new StreamResult(new StringWriter()); try { tr.transform(new StreamSource(new StringReader(record)), res); @@ -135,7 +135,7 @@ public class XmlIndexingJob { * @throws IOException could happen * @throws TransformerException could happen */ - private static String getLayoutTransformer(String format, String fields, String xslt) + protected static String getLayoutTransformer(String format, String fields, String xslt) throws TransformerException { final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 2cff2124e1..ce1c71312e 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -9,10 +9,7 @@ import java.io.IOException; import java.io.Serializable; import java.io.StringReader; import java.io.StringWriter; -import java.util.ArrayList; -import java.util.List; -import java.util.Map; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; import javax.xml.transform.*; @@ -47,7 +44,7 @@ import eu.dnetlib.dhp.schema.oaf.Result; public class XmlRecordFactory implements Serializable { - public static final String REL_SUBTYPE_DEDUP = "dedup"; + private static final String REL_SUBTYPE_DEDUP = "dedup"; private final Map accumulators; private final Set specialDatasourceTypes; @@ -100,8 +97,8 @@ public class XmlRecordFactory implements Serializable { final List relations = je .getLinks() .stream() - .filter(t -> !REL_SUBTYPE_DEDUP.equalsIgnoreCase(t.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, contexts)) + .filter(link -> !isDuplicate(link)) + .map(link -> mapRelation(contexts, templateFactory, type, link)) .collect(Collectors.toCollection(ArrayList::new)); final String mainType = ModelSupport.getMainType(type); @@ -936,7 +933,7 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType)); } - private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set contexts) { + private List mapFields(Tuple2 link, Set contexts) { final Relation rel = link.getRelation(); final RelatedEntity re = link.getRelatedEntity(); final String targetType = link.getRelatedEntity().getType(); @@ -1040,38 +1037,47 @@ public class XmlRecordFactory implements Serializable { default: throw new IllegalArgumentException("invalid target type: " + targetType); } - final DataInfo info = rel.getDataInfo(); - final String scheme = ModelSupport.getScheme(re.getType(), targetType); - - if (StringUtils.isBlank(scheme)) { - throw new IllegalArgumentException( - String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); - } final String accumulatorName = getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); if (accumulators.containsKey(accumulatorName)) { accumulators.get(accumulatorName).add(1); } + return metadata; + } + + private String mapRelation(Set contexts, TemplateFactory templateFactory, EntityType type, Tuple2 link) { + final Relation rel = link.getRelation(); + final String targetType = link.getRelatedEntity().getType(); + final String scheme = ModelSupport.getScheme(type.toString(), targetType); + + if (StringUtils.isBlank(scheme)) { + throw new IllegalArgumentException( + String.format("missing scheme for: <%s - %s>", type.toString(), targetType)); + } + final HashSet fields = Sets.newHashSet(mapFields(link, contexts)); return templateFactory .getRel( - targetType, rel.getTarget(), Sets.newHashSet(metadata), rel.getRelClass(), scheme, info); + targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo()); } private List listChildren( final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) { - final List children = Lists.newArrayList(); EntityType entityType = EntityType.valueOf(je.getEntity().getType()); - children - .addAll( - je - .getLinks() - .stream() - .filter(link -> REL_SUBTYPE_DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, null)) - .collect(Collectors.toCollection(ArrayList::new))); + List children = je + .getLinks() + .stream() + .filter(link -> isDuplicate(link)) + .map(link -> { + final String targetType = link.getRelatedEntity().getType(); + final String name = ModelSupport.getMainType(EntityType.valueOf(targetType)); + final HashSet fields = Sets.newHashSet(mapFields(link, null)); + return templateFactory + .getChild(name, link.getRelatedEntity().getId(), Lists.newArrayList(fields)); + }) + .collect(Collectors.toCollection(ArrayList::new)); if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { final List instances = ((Result) entity).getInstance(); @@ -1178,6 +1184,10 @@ public class XmlRecordFactory implements Serializable { return children; } + private boolean isDuplicate(Tuple2 link) { + return REL_SUBTYPE_DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType()); + } + private List listExtraInfo(OafEntity entity) { final List extraInfo = entity.getExtraInfo(); return extraInfo != null diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st index 89f81e16bf..1d3cffea09 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st @@ -1,3 +1,3 @@ -> - $metadata:{ it | $it$ }$ - \ No newline at end of file +<$name$$if(hasId)$ objidentifier="$id$"$else$$endif$> + $metadata:{$it$}$ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java deleted file mode 100644 index 1336a1cf7c..0000000000 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.oa.provision; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.junit.jupiter.api.BeforeEach; - -public class GraphJoinerTest { - - private final ClassLoader cl = getClass().getClassLoader(); - private Path workingDir; - private Path inputDir; - private Path outputDir; - - @BeforeEach - public void before() throws IOException { - workingDir = Files.createTempDirectory("promote_action_set"); - inputDir = workingDir.resolve("input"); - outputDir = workingDir.resolve("output"); - } - - private static void copyFiles(Path source, Path target) throws IOException { - Files - .list(source) - .forEach( - f -> { - try { - if (Files.isDirectory(f)) { - Path subTarget = Files.createDirectories(target.resolve(f.getFileName())); - copyFiles(f, subTarget); - } else { - Files.copy(f, target.resolve(f.getFileName())); - } - } catch (IOException e) { - e.printStackTrace(); - throw new RuntimeException(e); - } - }); - } -} 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 new file mode 100644 index 0000000000..b1e39c6963 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -0,0 +1,39 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.IOException; +import java.io.StringReader; +import java.io.StringWriter; +import java.nio.file.Files; +import java.nio.file.Path; + +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.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; + +public class IndexRecordTransformerTest { + + @Test + public void testTrasformRecord() throws IOException, TransformerException { + String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml")); + String record = IOUtils.toString(getClass().getResourceAsStream("record.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); + + System.out.println(a); + + } + +} 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 new file mode 100644 index 0000000000..f74da5d071 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml @@ -0,0 +1,166 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/layoutToRecordTransformer.xsl b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/layoutToRecordTransformer.xsl new file mode 100644 index 0000000000..d814baa8e7 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/layoutToRecordTransformer.xsl @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + . + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file 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 new file mode 100644 index 0000000000..b617dbea25 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml @@ -0,0 +1,750 @@ + +
+ 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 + 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 + + + + + + + + + + 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. BMC + Complement Altern Med. 2012;12:175.23039061 + + + + + 12 Gupta GL Rana AC Withania somnifera (ashwagandha): a review. + Pharmacognosy Rev. 2007;1(1):129–136. + + + 13 Durg S Dhadde SB Vandal R Shivakumar BS Charan CS Withania + somnifera (ashwagandha) in neurobehavioural disorders induced by brain + oxidative stress in rodents: a systematic review and meta-analysis. J + Pharm Pharmacol. 2015;67(7):879–899.25828061 + + + + + 14 Kuboyama T Tohda C Komatsu K Effects of ashwagandha (roots of + Withania somnifera) on neurodegenerative diseases. Biol Pharm Bull. + 2014;37(6):892–897.24882401 + + + + + 15 Mirjalili MH Moyano E Bonfill M Cusido RM Palazon J Steroidal + lactones from Withania somnifera, an ancient plant for novel medicine. + Molecules. 2009;14(7):2373–2393.19633611 + + + + + 16 Ven Murthy MR Ranjekar PK Ramassamy C Deshpande M Scientific + basis for the use of Indian ayurvedic medicinal plants in the treatment + of neurodegenerative disorders: ashwagandha. Cent Nerv Syst Agents Med + Chem. 2010;10(3):238–246.20528765 + + + + + 17 Singh RH Narsimhamurthy K Singh G Neuronutrient impact of + Ayurvedic Rasayana therapy in brain aging. Biogerontology. + 2008;9(6):369–374.18931935 + + + + + 18 Kulkarni SK Dhir A Withania somnifera: an Indian ginseng. Prog + Neuropsychopharmacol Biol Psychiatry. + 2008;32(5):1093–1105.17959291 + + + + + 19 Cooley K Szczurko O Perri D Mills EJ Bernhardt B Zhou Q Seely D + Naturopathic care for anxiety: a randomized controlled trial + ISRCTN78958974. PLoS One. 2009;4(8):e6628.19718255 + + + + + 20 Chopra A Lavin P Patwardhan B Chitre D A 32-week randomized, + placebo-controlled clinical evaluation of RA-11, an Ayurvedic drug, on + osteoarthritis of the knees. J Clin Rheumatol. + 2004;10(5):236–245.17043520 + + + + + 21 Chaudhary G Sharma U Jagannathan NR Gupta YK Evaluation of + Withania somnifera in a middle cerebral artery occlusion model of stroke + in rats. Clin Exp Pharmacol Physiol. + 2003;30(5–6):399–404.12859433 + + + + 22 Adams JD Jr Yang J Mishra LC Singh BB Effects of ashwagandha in + a rat model of stroke. Altern Ther Health Med. + 2002;8(5):18–19. + + + 23 Baitharu I Jain V Deep SN Hota KB Hota SK Prasad D Ilavazhagan G + Withania somnifera root extract ameliorates hypobaric hypoxia induced + memory impairment in rats. J Ethnopharmacol. + 2013;145(2):431–441.23211660 + + + + + 24 RajaSankar S Manivasagam T Sankar V Prakash S Muthusamy R + Krishnamurti A Surendran S Withania somnifera root extract improves + catecholamines and physiological abnormalities seen in a Parkinson’s + disease model mouse. J Ethnopharmacol. + 2009;125(3):369–373.19666100 + + + + + 25 Pingali U Pilli R Fatima N Effect of standardized aqueous + extract of Withania somnifera on tests of cognitive and psychomotor + performanc e in healthy human participants. 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. J + Ethnopharmacol. 2011;135(1):34–42.21349320 + + + + + 30 Kane MJ Hatic H Delic V Dennis JS Butler CL Saykally JN Citron + BA Modeling the pathobiology of repetitive traumatic brain injury in + immortalized neuronal cell lines. Brain Res. + 2011;1425:123–131.22018688 + + + + 31 Sehgal N Gupta A Valli RK Joshi SD Mills JT Hamel E Khanna P + Jain SC Thakur SS Ravindranath V Withania somnifera reverses Alzheimer’s + disease pathology by enhancing low-density lipoprotein receptor-related + protein in liver. Proc Natl Acad Sci U S A. + 2012;109(9):3510–3515.22308347 + + + + + 32 Arundine M Aarts M Lau A Tymianski M Vulnerability of central + neurons to secondary insults after in vitro mechanical stretch. J + Neurosci. 2004;24(37):8106–8123.15371512 + + + + + 33 Lau A Arundine M Sun HS Jones M Tymianski M Inhibition of + caspase-mediated apoptosis by peroxynitrite in traumatic brain injury. J + Neurosci. 2006;26(45):11540–11553.17093075 + + + + 34 Weber JT Rzigalinski BA Ellis EF Traumatic injury of cortical + neurons causes changes in intracellular calcium stores and capacitative + calcium influx. J Biol Chem. 2001;276(3):1800–1807.11050103 + + + + 35 Ellis EF McKinney JS Willoughby KA Liang S Povlishock JT A new + model for rapid stretch-induced injury of cells in culture: + characterization of the model using astrocytes. J Neurotrauma. + 1995;12(3):325–339.7473807 + + + + 36 Zhang Y Ba Y Liu C Sun G Ding L Gao S Hao J Yu Z Zhang J Zen K + PGC-1alpha induces apoptosis in human epithelial ovarian cancer cells + through a PPARgamma-dependent pathway. Cell Res. + 2007;17(4):363–373.17372612 + + + + 37 Brooks AR Lelkes PI Rubanyi GM Gene expression profiling of + human aortic endothelial cells exposed to disturbed flow and steady + laminar flow. Physiol Genomics. 2002;9(1):27–41.11948288 + + + + 38 Du Y Villeneuve NF Wang XJ Sun Z Chen W Li J Lou H Wong PK Zhang + DD Oridonin confers protection against arsenic-induced toxicity through + activation of the Nrf2-mediated defensive response. Environ Health + Perspect. 2008;116(9):1154–1161.18795156 + + + + + 39 Pool M Thiemann J Bar-Or A Fournier AE NeuriteTracer: a novel + ImageJ plugin for automated quantification of neurite outgrowth. J + Neurosci Methods. 2008;168(1):134–139.17936365 + + + + + 40 Chen J Wu X Shao B Zhao W Shi W Zhang S Ni L Shen A Increased + expression of TNF receptor-associated factor 6 after rat traumatic brain + injury. Cell Mol Neurobiol. 2011;31(2):269–275.21072581 + + + + 41 Kuboyama T Tohda C Komatsu K Neuritic regeneration and synaptic + reconstruction induced by withanolide A. 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 + + + + + + + + diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml index e2953693ff..ba7002cffc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml @@ -15,12 +15,12 @@ oozie.action.sharelib.for.spark spark2 - - hive_metastore_uris + + hiveMetastoreUris thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - hive_jdbc_url + hiveJdbcUrl jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index 19f3316d8a..6f63893621 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -14,11 +14,11 @@ the external stats that should be added since they are not included in the graph database - hive_metastore_uris + hiveMetastoreUris hive server metastore URIs - hive_jdbc_url + hiveJdbcUrl hive server jdbc url @@ -29,7 +29,7 @@ hive.metastore.uris - ${hive_metastore_uris} + ${hiveMetastoreUris} @@ -42,7 +42,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -53,7 +53,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -64,7 +64,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -75,7 +75,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -86,7 +86,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -97,7 +97,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -108,7 +108,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -119,7 +119,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -130,7 +130,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -141,7 +141,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -152,7 +152,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -163,7 +163,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -174,7 +174,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -185,7 +185,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -196,7 +196,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -207,7 +207,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -218,7 +218,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -229,7 +229,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -240,7 +240,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -251,7 +251,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -262,7 +262,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -273,7 +273,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -284,7 +284,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -295,7 +295,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -306,7 +306,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -317,7 +317,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -328,7 +328,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -339,7 +339,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -350,7 +350,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -361,7 +361,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -372,7 +372,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -383,7 +383,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -394,7 +394,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -405,7 +405,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -416,7 +416,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -427,7 +427,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -438,7 +438,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -449,7 +449,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -460,7 +460,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -471,7 +471,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -482,7 +482,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -493,7 +493,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -504,7 +504,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -515,7 +515,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -526,7 +526,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -537,7 +537,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -548,7 +548,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -559,7 +559,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -570,7 +570,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -581,7 +581,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -592,7 +592,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -603,7 +603,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -614,7 +614,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -625,7 +625,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -636,7 +636,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -647,7 +647,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -658,7 +658,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -669,7 +669,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -680,7 +680,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -691,7 +691,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -702,7 +702,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -713,7 +713,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -724,7 +724,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -735,7 +735,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -746,7 +746,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -757,7 +757,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -768,7 +768,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -779,7 +779,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -790,7 +790,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -801,7 +801,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -813,7 +813,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -824,7 +824,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -835,7 +835,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -846,7 +846,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -857,7 +857,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -868,7 +868,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -879,7 +879,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -890,7 +890,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -901,7 +901,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -912,7 +912,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name}