Examples with InteractionListener org.eol.globi.process.InteractionListener used on opensource projects

Example 41 with InteractionListener

use of org.eol.globi.process.InteractionListener in project eol-globi-data by jhpoelen.

the class DatasetImporterForGlobalWebDb method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    InteractionListener interactionListener = getInteractionListener();
    importDietMatrices(URI.create("https://www.globalwebdb.com/Service/DownloadArchive"), dietMatrixString -> {
        try {
            parseDietMatrix(interactionListener, dietMatrixString, getSourceCitation());
        } catch (IOException e) {
            throw new StudyImporterException(e);
        }
    });
}

Example 42 with InteractionListener

use of org.eol.globi.process.InteractionListener in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method assertImportsSomethingOfType.

private void assertImportsSomethingOfType(URI archiveRoot, AtomicInteger recordCounter, String defaultResourceType, String... expectedProperties) throws StudyImporterException {
    final Set<String> resourceTypes = new TreeSet<>();
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", archiveRoot, inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            for (String expectedProperty : expectedProperties) {
                assertThat("no [" + expectedProperty + "] found in " + interaction, interaction.containsKey(expectedProperty), is(true));
                assertThat("no value of [" + expectedProperty + "] found in " + interaction, interaction.get(expectedProperty), is(notNullValue()));
            }
            assertThat(interaction.get(RESOURCE_TYPES), is(notNullValue()));
            String[] types = splitByPipes(interaction.get(RESOURCE_TYPES));
            resourceTypes.addAll(Arrays.asList(types));
            recordCounter.incrementAndGet();
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(recordCounter.get(), greaterThan(0));
    String[] items = splitByPipes(defaultResourceType);
    assertThat(resourceTypes, containsInAnyOrder(items));
    assertThat(recordCounter.get(), greaterThan(0));
}

Example 43 with InteractionListener

use of org.eol.globi.process.InteractionListener in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method hasResourceRelationshipsOccurrenceToOccurrenceMissingTargetReference.

@Test
public void hasResourceRelationshipsOccurrenceToOccurrenceMissingTargetReference() throws IOException, URISyntaxException {
    URI sampleArchive = getClass().getResource("fmnh-rr-unresolved-targetid-test.zip").toURI();
    Archive archive = DwCAUtil.archiveFor(sampleArchive, "target/tmp");
    AtomicInteger numberOfFoundLinks = new AtomicInteger(0);
    importResourceRelationshipExtension(archive, new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            numberOfFoundLinks.incrementAndGet();
            assertThat(interaction.get(relatedResourceID.qualifiedName()), is("http://n2t.net/ark:/65665/37d63a454-d948-4b1d-89db-89809887ef41"));
            assertThat(interaction.get(SOURCE_TAXON_NAME), is("Trichobius parasparsus Wenzel, 1976"));
            assertThat(interaction.get(SOURCE_OCCURRENCE_ID), is("8afec7db-7b19-44f7-8ac8-8d98614e71d2"));
            assertThat(interaction.get(INTERACTION_TYPE_NAME), is("Ectoparasite of"));
            assertThat(interaction.get(INTERACTION_TYPE_ID), is(nullValue()));
            assertThat(interaction.get(DatasetImporterForTSV.BASIS_OF_RECORD_NAME), is("PreservedSpecimen"));
            assertThat(interaction.get(TaxonUtil.TARGET_TAXON_NAME), is(nullValue()));
            assertThat(interaction.get(DatasetImporterForTSV.TARGET_OCCURRENCE_ID), is("http://n2t.net/ark:/65665/37d63a454-d948-4b1d-89db-89809887ef41"));
            assertThat(interaction.get(DatasetImporterForTSV.TARGET_CATALOG_NUMBER), is(nullValue()));
            assertThat(interaction.get(DatasetImporterForTSV.TARGET_COLLECTION_CODE), is(nullValue()));
            assertThat(interaction.get(DatasetImporterForTSV.TARGET_INSTITUTION_CODE), is(nullValue()));
            assertThat(interaction.get(DatasetImporterForTSV.REFERENCE_CITATION), is("A. L. Tuttle | M. D. Tuttle"));
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
        }
    });
    assertThat(numberOfFoundLinks.get(), is(1));
}

Example 44 with InteractionListener

use of org.eol.globi.process.InteractionListener in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method nonInteractionRecordMessage.

@Test
public void nonInteractionRecordMessage() throws StudyImporterException, URISyntaxException {
    List<String> msgs = new ArrayList<>();
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/mcz-adjusted/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    AtomicInteger recordCounter = new AtomicInteger(0);
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setLogger(new NullImportLogger() {

        @Override
        public void info(LogContext ctx, String message) {
            msgs.add(message);
        }
    });
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", archiveRoot, inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
            recordCounter.incrementAndGet();
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(recordCounter.get(), is(0));
    String joinedMsgs = StringUtils.join(msgs, "\n");
    assertThat(joinedMsgs, containsString("]: indexing interaction records"));
    assertThat(joinedMsgs, containsString("]: scanned [1] record(s)"));
}

Example 45 with InteractionListener

use of org.eol.globi.process.InteractionListener in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method importTaxonDescriptionsFromDirNoInteractionType.

@Test
public void importTaxonDescriptionsFromDirNoInteractionType() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/coetzer-no-interaction-type/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    List<Map<String, String>> links = new ArrayList<>();
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", archiveRoot, inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
            links.add(interaction);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(links.size(), is(0));
}