From 408be3c632ad607afa1e79ce4a7b9a0b2de7b642 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 27 Mar 2020 11:44:50 +0100 Subject: [PATCH 1/2] test and fixed a problem with datacite namespaces --- .../dhp/migration/step2/AbstractMdRecordToOafMapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java index 7c3000fba..18a62124b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java @@ -69,7 +69,7 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); - final Document doc = DocumentHelper.parseText(xml); + final Document doc = DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3")); final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name")); From f6e86b44a6df4a46c03930628662768dbe1acdd0 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 27 Mar 2020 11:46:37 +0100 Subject: [PATCH 2/2] tests --- .../dhp/migration/step2/MappersTest.java | 109 +++++++++++++++++ .../dhp/migration/step2/oaf_record.xml | 80 +++++++++++++ .../dhp/migration/step2/odf_dataset.xml | 113 ++++++++++++++++++ .../dhp/migration/step2/odf_software.xml | 82 +++++++++++++ 4 files changed, 384 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step2/MappersTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/oaf_record.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_dataset.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_software.xml diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step2/MappersTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step2/MappersTest.java new file mode 100644 index 000000000..894355bcb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step2/MappersTest.java @@ -0,0 +1,109 @@ +package eu.dnetlib.dhp.migration.step2; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.when; + +import java.io.IOException; +import java.util.List; +import java.util.Map; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Software; + +@ExtendWith(MockitoExtension.class) +public class MappersTest { + + @Mock + private Map code2name; + + @BeforeEach + void setUp() throws Exception { + when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); + } + + @Test + void testPublication() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); + + final List list = new OafToOafMapper(code2name).processMdRecord(xml); + + assertEquals(3, list.size()); + assertTrue(list.get(0) instanceof Publication); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); + + final Publication p = (Publication) list.get(0); + final Relation r1 = (Relation) list.get(1); + final Relation r2 = (Relation) list.get(2); + + assertValidId(p.getId()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertTrue(p.getAuthor().size() > 0); + assertTrue(p.getSubject().size() > 0); + assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); + assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); + + assertValidId(r1.getSource()); + assertValidId(r2.getSource()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + assertTrue(StringUtils.isNotBlank(r1.getRelClass())); + assertTrue(StringUtils.isNotBlank(r2.getRelClass())); + assertTrue(StringUtils.isNotBlank(r1.getRelType())); + assertTrue(StringUtils.isNotBlank(r2.getRelType())); + } + + @Test + void testDataset() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); + + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Dataset); + + final Dataset d = (Dataset) list.get(0); + + assertValidId(d.getId()); + assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); + assertTrue(d.getAuthor().size() > 0); + assertTrue(d.getSubject().size() > 0); + } + + @Test + void testSoftware() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); + + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Software); + + final Software s = (Software) list.get(0); + + assertValidId(s.getId()); + assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); + assertTrue(s.getAuthor().size() > 0); + assertTrue(s.getSubject().size() > 0); + } + + private void assertValidId(final String id) { + assertEquals(49, id.length()); + assertEquals('|', id.charAt(2)); + assertEquals(':', id.charAt(15)); + assertEquals(':', id.charAt(16)); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/oaf_record.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/oaf_record.xml new file mode 100644 index 000000000..e898d4434 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/oaf_record.xml @@ -0,0 +1,80 @@ + + +
+ pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2 + 10.3897/oneeco.2.e13718 + + + + + + 2020-03-23T00:20:51.392Z + 2020-03-23T00:26:59.078Z + pensoft_____ +
+ + Ecosystem Service capacity is higher in areas of multiple designation types + Nikolaidou,Charitini + Votsi,Nefta + Sgardelis,Steanos + Halley,John + Pantis,John + Tsiafouli,Maria + 2017 + The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management. + text/html + https://doi.org/10.3897/oneeco.2.e13718 + https://oneecosystem.pensoft.net/article/13718/ + eng + Pensoft Publishers + info:eu-repo/semantics/altIdentifier/eissn/2367-8194 + info:eu-repo/grantAgreement/EC/FP7/226852 + One Ecosystem 2: e13718 + Ecosystem Services hotspots + Natura 2000 + Quiet Protected Areas + Biodiversity + Agriculture + Elevation + Slope + Ecosystem Service trade-offs and synergies + cultural services + provisioning services + regulating services + supporting services + Research Article + 0001 + 2017-01-01 + corda_______::226852 + OPEN + + + 10.3897/oneeco.2.e13718 + https://oneecosystem.pensoft.net/article/13718/ + One Ecosystem + + + + + http%3A%2F%2Fzookeys.pensoft.net%2Foai.php + 10.3897/oneeco.2.e13718 + 2017-09-08 + http://www.openarchives.org/OAI/2.0/oai_dc/ + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_dataset.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_dataset.xml new file mode 100644 index 000000000..0c36e8686 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_dataset.xml @@ -0,0 +1,113 @@ + + + + r37b0ad08687::000374d100a9db469bd42b69dbb40b36 + 10.5281/zenodo.3234526 + 2020-03-21T00:05:35.927Z + r37b0ad08687 + oai:zenodo.org:3234526 + 2020-03-19T10:58:08Z + openaire_data + user-epfl + + + + 10.5281/zenodo.3234526 + + + Nouchi, Vincent + Vincent + Nouchi + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Lavanchy, Sébastien + Sébastien + Lavanchy + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Baracchini, Theo + Theo + Baracchini + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Wüest, Alfred + Alfred + Wüest + Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + + + Bouffard, Damien + Damien + Bouffard + 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 C).

+ +

All files are in MATLAB .mat format.

 + + + 0021 + 2019-01-01 + OPEN + und + + + + + + + + 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/migration/step2/odf_software.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_software.xml new file mode 100644 index 000000000..fd3fdd473 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_software.xml @@ -0,0 +1,82 @@ + + + + __bioTools__::001321907fcc9f8d020f05230f9d3ddf + chainy + 2020-02-05T10:49:49.694Z + __bioTools__ + 2020-02-05T10:56:28.875Z + + + + Web application + bio.tools + + http://maplab.imppc.org/chainy/ + 10.1093/bioinformatics/btw839 + + + https://bio.tools/ + + https://bio.tools/ + + Chainy + + + + Mallona, Izaskun + Izaskun + Mallona + + + + + Universal tool for standardized relative quantification in real-time PCR. + Linux + Windows + Mac + + + PCR experiment + Gene expression + Protein binding sites + + + 0029 + + + 2018-06-06 + + + + + https%3A%2F%2Fbio.tools%2Fapi%2Ftool + + + + + + + false + false + 0.9 + + + + + \ No newline at end of file