Examples with StudyNode org.eol.globi.domain.StudyNode used on opensource projects

Example 6 with StudyNode

use of org.eol.globi.domain.StudyNode in project eol-globi-data by jhpoelen.

the class LinkerDOITest method createStudyDOIlookup.

@Test
public void createStudyDOIlookup() throws NodeFactoryException {
    StudyNode study = getNodeFactory().getOrCreateStudy(new StudyImpl("title", "some source", null, "some citation"));
    new LinkerDOI(getGraphDb()).linkStudy(new DOIResolverThatExplodes(), study);
    assertThat(study.getSource(), is("some source"));
    assertThat(study.getCitation(), is("some citation"));
    assertThat(study.getTitle(), is("title"));
}

Example 7 with StudyNode

use of org.eol.globi.domain.StudyNode in project eol-globi-data by jhpoelen.

the class LinkerDOITest method assertLinkMany.

public void assertLinkMany(int numberOfStudies) throws NodeFactoryException {
    StudyNode study = getNodeFactory().getOrCreateStudy(new StudyImpl("title", "some source", null, DOIResolverImplIT.HOCKING));
    getNodeFactory().getOrCreateStudy(new StudyImpl("title1", "some source", null, DOIResolverImplIT.MEDAN));
    assertThat(study.getDOI(), is(nullValue()));
    for (int i = 0; i < numberOfStudies; i++) {
        getNodeFactory().getOrCreateStudy(new StudyImpl("id" + i, "some source", null, "foo bar this is not a citation" + i));
    }
    new LinkerDOI(getGraphDb()).link();
    StudyNode studyResolved = getNodeFactory().getOrCreateStudy(study);
    assertThat(studyResolved.getDOI(), is(DOIResolverImplIT.HOCKING_DOI));
}

Example 8 with StudyNode

use of org.eol.globi.domain.StudyNode in project eol-globi-data by jhpoelen.

the class ReportGenerator method generateReportForStudySources.

void generateReportForStudySources(SourceHandler sourceHandler) {
    final Set<String> groupByKeys = new HashSet<String>();
    NodeUtil.findStudies(getGraphDb(), new StudyNodeListener() {

        @Override
        public void onStudy(StudyNode study) {
            String groupByKey = sourceHandler.parse(study);
            if (StringUtils.isNotBlank(groupByKey)) {
                groupByKeys.add(groupByKey);
            }
        }
    });
    for (final String groupByKey : groupByKeys) {
        final Set<Long> distinctTaxonIds = new HashSet<>();
        final Set<Long> distinctTaxonIdsNoMatch = new HashSet<>();
        final Counter counter = new Counter();
        final Counter studyCounter = new Counter();
        final Set<String> distinctSources = new HashSet<String>();
        final Set<String> distinctDatasets = new HashSet<String>();
        NodeUtil.findStudies(getGraphDb(), new StudyNodeListener() {

            @Override
            public void onStudy(StudyNode study) {
                if (sourceHandler.matches(study, groupByKey)) {
                    Iterable<Relationship> specimens = NodeUtil.getSpecimens(study);
                    countInteractionsAndTaxa(specimens, distinctTaxonIds, counter, distinctTaxonIdsNoMatch);
                    studyCounter.count();
                    distinctSources.add(study.getSource());
                    distinctDatasets.add(study.getSourceId());
                }
            }
        });
        Transaction tx = getGraphDb().beginTx();
        try {
            final Node node = getGraphDb().createNode();
            node.setProperty(sourceHandler.getGroupByKeyName(), groupByKey);
            node.setProperty(PropertyAndValueDictionary.COLLECTION, GLOBI_COLLECTION_NAME);
            node.setProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS, counter.getCount() / 2);
            node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA, distinctTaxonIds.size());
            node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA_NO_MATCH, distinctTaxonIdsNoMatch.size());
            node.setProperty(PropertyAndValueDictionary.NUMBER_OF_STUDIES, studyCounter.getCount());
            node.setProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES, distinctSources.size());
            node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS, distinctDatasets.size());
            getGraphDb().index().forNodes("reports").add(node, sourceHandler.getGroupByKeyName(), groupByKey);
            tx.success();
        } finally {
            tx.finish();
        }
    }
}

Example 9 with StudyNode

use of org.eol.globi.domain.StudyNode in project eol-globi-data by jhpoelen.

the class ReportGenerator method generateReportForCollection.

void generateReportForCollection() {
    final Set<Long> distinctTaxonIds = new HashSet<Long>();
    final Set<Long> distinctTaxonIdsNoMatch = new HashSet<Long>();
    final Counter counter = new Counter();
    final Counter studyCounter = new Counter();
    final Set<String> distinctSources = new HashSet<String>();
    final Set<String> distinctDatasets = new HashSet<String>();
    NodeUtil.findStudies(getGraphDb(), new StudyNodeListener() {

        @Override
        public void onStudy(StudyNode study) {
            Iterable<Relationship> specimens = NodeUtil.getSpecimens(study);
            countInteractionsAndTaxa(specimens, distinctTaxonIds, counter, distinctTaxonIdsNoMatch);
            studyCounter.count();
            distinctSources.add(study.getSource());
            distinctDatasets.add(study.getSourceId());
        }
    });
    Transaction tx = getGraphDb().beginTx();
    try {
        final Node node = getGraphDb().createNode();
        node.setProperty(PropertyAndValueDictionary.COLLECTION, GLOBI_COLLECTION_NAME);
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS, counter.getCount() / 2);
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA, distinctTaxonIds.size());
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA_NO_MATCH, distinctTaxonIdsNoMatch.size());
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_STUDIES, studyCounter.getCount());
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES, distinctSources.size());
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS, distinctDatasets.size());
        getGraphDb().index().forNodes("reports").add(node, PropertyAndValueDictionary.COLLECTION, GLOBI_COLLECTION_NAME);
        tx.success();
    } finally {
        tx.finish();
    }
}

Example 10 with StudyNode

use of org.eol.globi.domain.StudyNode in project eol-globi-data by jhpoelen.

the class ReportGenerator method generateReportForStudy.

protected void generateReportForStudy(StudyNode study, Set<Long> ids, Counter interactionCounter, HashSet<Long> idsNoMatch) {
    Iterable<Relationship> specimens = NodeUtil.getSpecimens(study);
    countInteractionsAndTaxa(specimens, ids, interactionCounter, idsNoMatch);
    Transaction tx = getGraphDb().beginTx();
    try {
        Node node = getGraphDb().createNode();
        if (StringUtils.isNotBlank(study.getSource())) {
            node.setProperty(StudyConstant.SOURCE, study.getSource());
        }
        if (StringUtils.isNotBlank(study.getSourceId())) {
            node.setProperty(StudyConstant.SOURCE_ID, study.getSourceId());
        }
        if (StringUtils.isNotBlank(study.getCitation())) {
            node.setProperty(StudyConstant.CITATION, study.getCitation());
        }
        if (StringUtils.isNotBlank(study.getDOI())) {
            node.setProperty(StudyConstant.DOI, study.getDOI());
        }
        if (StringUtils.isNotBlank(study.getExternalId())) {
            node.setProperty(PropertyAndValueDictionary.EXTERNAL_ID, study.getExternalId());
        }
        node.setProperty(StudyConstant.TITLE, study.getTitle());
        node.setProperty(PropertyAndValueDictionary.COLLECTION, GLOBI_COLLECTION_NAME);
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS, interactionCounter.getCount() / 2);
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA, ids.size());
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA_NO_MATCH, idsNoMatch.size());
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_STUDIES, 1);
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES, 1);
        node.setProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS, 1);
        getGraphDb().index().forNodes("reports").add(node, StudyConstant.TITLE, study.getTitle());
        getGraphDb().index().forNodes("reports").add(node, StudyConstant.SOURCE, study.getTitle());
        tx.success();
    } finally {
        tx.finish();
    }
}