From 17e6f1934edb0eab39a74173a443c58184272776 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 12 Feb 2021 11:48:11 +0100 Subject: [PATCH] fixed NPE on cleaner --- .../datacite/AbstractRestClient.scala | 14 +- .../dhp/transformation/xslt/Cleaner.java | 6 +- .../transformation/TransformationJobTest.java | 12 +- .../eu/dnetlib/dhp/transform/ext_simple.xsl | 1 + .../eu/dnetlib/dhp/transform/input.xml | 2 +- .../eu/dnetlib/dhp/transform/input_zenodo.xml | 99 ++++ .../eu/dnetlib/dhp/transform/zenodo_tr.xslt | 444 ++++++++++++++++++ 7 files changed, 571 insertions(+), 7 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_zenodo.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/zenodo_tr.xslt diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala index 852147ccd..3c7770075 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala @@ -53,11 +53,21 @@ abstract class AbstractRestClient extends Iterator[String]{ } + + private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={ val client = HttpClients.createDefault try { - val response = client.execute(r) - IOUtils.toString(response.getEntity.getContent) + var tries = 4 + while (tries > 0) { + val response = client.execute(r) + if (response.getStatusLine.getStatusCode > 400) { + tries -= 1 + } + else + return IOUtils.toString(response.getEntity.getContent) + } + "" } catch { case e: Throwable => throw new RuntimeException("Error on executing request ", e) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java index 7b0fdd484..8b7024cbe 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java @@ -27,13 +27,17 @@ public class Cleaner implements ExtensionFunction, Serializable { @Override public SequenceType[] getArgumentTypes() { return new SequenceType[] { - SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE), + SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ZERO_OR_MORE), SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE) }; } @Override public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException { + XdmValue r = xdmValues[0]; + if (r.size() == 0){ + return new XdmAtomicValue(""); + } final String currentValue = xdmValues[0].itemAt(0).getStringValue(); final String vocabularyName = xdmValues[1].itemAt(0).getStringValue(); Qualifier cleanedValue = vocabularies.getSynonymAsQualifier(vocabularyName, currentValue); diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index 997727e33..69b31b30f 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -61,13 +61,19 @@ public class TransformationJobTest extends AbstractVocabularyTest { // We Set the input Record getting the XML from the classpath final MetadataRecord mr = new MetadataRecord(); - mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input.xml"))); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_zenodo.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/ext_simple.xsl"); + XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + + + MetadataRecord result = tr.call(mr); + + + // Print the record - System.out.println(tr.call(mr).getBody()); + System.out.println(result.getBody()); // TODO Create significant Assert } diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl index becd3a05e..c114217c2 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl @@ -6,6 +6,7 @@ version="2.0" exclude-result-prefixes="xsl vocabulary"> + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml index ebe8e919b..3d136d56d 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml @@ -6,7 +6,7 @@ PSNCRepository:PSNCExternalRepository:Departments PSNCRepository:PSNCExternalRepository:Departments:NetworkServices PSNCRepository:PSNCExternalRepository - PSNCRepository:PSNCExternalRepository:publications + aRTIcle - Letter to the editor PSNCRepository diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_zenodo.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_zenodo.xml new file mode 100644 index 000000000..043eae343 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_zenodo.xml @@ -0,0 +1,99 @@ + + + + r37b0ad08687::000374d100a9db469bd42b69dbb40b36 + 10.5281/zenodo.3234526 + 2020-03-23T03:03:50.72Z + r37b0ad08687 + oai:zenodo.org:3234526 + 2020-03-19T10:58:08Z + openaire_data + user-epfl + + + + true + 3.1 + CERN.ZENODO + + + 10.5281/zenodo.3234526 + + + Nouchi, Vincent + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Lavanchy, Sébastien + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Baracchini, Theo + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Wüest, Alfred + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Bouffard, Damien + Eawag, Swiss Federal Institute of Aquatic Science and Technology, Surface Waters – Research and Management, Kastanienbaum, 6047, Switzerland + + + + Temperature and ADCP data collected on Lake Geneva between 2015 and 2017 + + Zenodo + 2019 + + Lake Geneva + temperature + ADCP + + + 2019-05-29 + + + + 10.5281/zenodo.3234525 + https://zenodo.org/communities/epfl + + 1.0.0 + + Creative Commons Attribution 4.0 International + Open Access + + +

Data collected between 2015 and 2017 on Lake Geneva by Acoustic Doppler Current Profiler (ADCP) and CTDs. One file includes all the temperature profiles, the two others are the ADCP data (up- and down-looking) at the SHL2 station (centre of the main basin). Coordinates of the SHL2 station are 534700 and 144950 in the Swiss CH1903 coordinate system. The file with the CTD data contains the coordinates of the sample location (lat, lon), times (in MATLAB time), depths (in meters) and temperatures (in &deg;C).

+ +

All files are in MATLAB .mat format.

 + + + + + + + + + https%3A%2F%2Fzenodo.org%2Foai2d + oai:zenodo.org:3234526 + 2020-03-19T10:58:08Z + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/zenodo_tr.xslt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/zenodo_tr.xslt new file mode 100644 index 000000000..e67ed9dda --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/zenodo_tr.xslt @@ -0,0 +1,444 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + OPEN + + + + + CLOSED + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file