Examples with ExecutionEngine org.neo4j.cypher.javacompat.ExecutionEngine used on opensource projects

Example 1 with ExecutionEngine

use of org.neo4j.cypher.javacompat.ExecutionEngine in project eol-globi-data by jhpoelen.

the class ExporterTaxaDistinct method exportAllDistinctTaxa.

private void exportAllDistinctTaxa(Writer writer, GraphDatabaseService graphDatabase) throws IOException {
    ExecutionEngine engine = new ExecutionEngine(graphDatabase);
    ExecutionResult results = engine.execute("START taxon = node:taxons('*:*') " + "MATCH taxon<-[:CLASSIFIED_AS]-specimen " + "WHERE has(taxon.externalId) AND taxon.externalId <> '" + PropertyAndValueDictionary.NO_MATCH + "' " + "AND has(taxon.name) AND taxon.name <> '" + PropertyAndValueDictionary.NO_MATCH + "' " + "RETURN distinct(taxon)" + ", taxon.name as scientificName" + ", taxon.path? as path" + ", taxon.pathNames? as pathNames" + ", taxon.rank? as rank" + ", taxon.externalId as taxonId");
    Map<String, String> row = new HashMap<String, String>();
    for (Map<String, Object> result : results) {
        resultsToRow(row, result);
        writeProperties(writer, row);
        row.clear();
    }
}

Example 2 with ExecutionEngine

use of org.neo4j.cypher.javacompat.ExecutionEngine in project eol-globi-data by jhpoelen.

the class StudyImporterForBioInfoTest method importAbout600Records.

@Test
public void importAbout600Records() throws StudyImporterException {
    StudyImporter importer = new StudyImporterTestFactory(nodeFactory).instantiateImporter((Class) StudyImporterForBioInfo.class);
    final List<String> msgs = new ArrayList<String>();
    importer.setLogger(new ImportLogger() {

        @Override
        public void warn(LogContext study, String message) {
            msgs.add(message);
        }

        @Override
        public void info(LogContext study, String message) {
            msgs.add(message);
        }

        @Override
        public void severe(LogContext study, String message) {
            msgs.add(message);
        }
    });
    // limit the number of line to be imported to make test runs reasonably fast
    importer.setFilter(recordNumber -> recordNumber < 1000 || recordNumber == 4585 || (recordNumber > 47310 && recordNumber < 47320) || (recordNumber > 24220 && recordNumber < 24340));
    importStudy(importer);
    Study vectorStudy = nodeFactory.findStudy(TaxonomyProvider.BIO_INFO + "ref:153303");
    assertThat(vectorStudy, is(notNullValue()));
    Study study = nodeFactory.findStudy(TaxonomyProvider.BIO_INFO + "ref:60527");
    for (Relationship collectedRel : NodeUtil.getSpecimens(study)) {
        SpecimenNode specimen = new SpecimenNode(collectedRel.getEndNode());
        String externalId = specimen.getExternalId();
        assertThat(externalId, is(notNullValue()));
        assertThat(externalId, containsString(TaxonomyProvider.BIO_INFO + "rel:"));
    }
    ExecutionEngine engine = new ExecutionEngine(getGraphDb());
    ExecutionResult result = engine.execute("START taxon = node:taxons('*:*') MATCH taxon<-[:CLASSIFIED_AS]-specimen-[r]->targetSpecimen-[:CLASSIFIED_AS]->targetTaxon RETURN taxon.externalId + ' ' + lower(type(r)) + ' ' + targetTaxon.externalId as interaction");
    ResourceIterator<Map<String, Object>> iterator = result.iterator();
    List<String> interactions = new ArrayList<String>();
    while (iterator.hasNext()) {
        Map<String, Object> next = iterator.next();
        interactions.add((String) next.get("interaction"));
    }
    assertThat(interactions, hasItem("NBN:NHMSYS0000455771 interacts_with NBN:NBNSYS0000024890"));
    assertThat(interactions, hasItem("NBN:NBNSYS0000030148 endoparasitoid_of NBN:NHMSYS0000502366"));
    assertThat(interactions, hasItem("NBN:NHMSYS0000500943 has_endoparasitoid NBN:NBNSYS0000030148"));
    assertThat(interactions, hasItem("bioinfo:taxon:160260 has_vector bioinfo:taxon:162065"));
    assertThat(study.getTitle(), is("bioinfo:ref:60527"));
    assertThat(study.getSource(), is("Food Webs and Species Interactions in the Biodiversity of UK and Ireland (Online). 2015. Data provided by Malcolm Storey. Also available from http://bioinfo.org.uk."));
    assertThat("found unexpected log messages: [" + StringUtils.join(msgs, "\n") + "]", msgs.size(), is(1));
    assertThat(msgs.get(0), is("empty/no taxon name for bioinfo taxon id [149359] on line [4171]"));
}

Example 3 with ExecutionEngine

use of org.neo4j.cypher.javacompat.ExecutionEngine in project eol-globi-data by jhpoelen.

the class ImageLinker method link.

@Override
public void link() {
    ExecutionEngine engine = new ExecutionEngine(graphDb);
    ExecutionResult executionResult = engine.execute("START taxon = node:taxons('*:*')\n" + "WHERE not(has(taxon.thumbnailUrl)) AND has(taxon.externalId) AND taxon.externalId <> 'no:match'\n" + "RETURN id(taxon) as `id`, taxon.externalId as `externalId`");
    for (Map<String, Object> externalIdMap : executionResult) {
        final String externalId = (String) externalIdMap.get("externalId");
        final Long nodeId = (Long) externalIdMap.get("id");
        TaxonImage taxonImage = null;
        try {
            taxonImage = new EOLTaxonImageService().lookupImageForExternalId(externalId);
        } catch (IOException e) {
            LOG.warn("failed to lookup externalId [" + externalId + "]", e);
        }
        if (taxonImage == null) {
            if (out != null) {
                out.println(StringUtils.join(Arrays.asList("EOL:12345", "", "", ""), "\t"));
            }
        } else {
            final String infoURL = taxonImage.getInfoURL() == null ? "" : taxonImage.getInfoURL();
            final String thumbnailURL = taxonImage.getThumbnailURL() == null ? "" : taxonImage.getThumbnailURL();
            final String imageURL = taxonImage.getImageURL() == null ? "" : taxonImage.getImageURL();
            ExecutionResult execute = engine.execute("START taxon = node({nodeId})\n" + "SET taxon.externalUrl={infoUrl}, taxon.imageUrl={imageUrl}, taxon.thumbnailUrl={thumbnailUrl}\n" + "RETURN taxon.externalId, taxon.externalUrl, taxon.thumbnailUrl, taxon.imageUrl", new HashMap<String, Object>() {

                {
                    put("nodeId", nodeId);
                    put("infoUrl", infoURL);
                    put("imageUrl", imageURL);
                    put("thumbnailUrl", thumbnailURL);
                }
            });
            if (out != null) {
                for (Map<String, Object> stringObjectMap : execute) {
                    out.println(StringUtils.join(CSVTSVUtil.escapeValues(stringObjectMap.values()), "\t"));
                }
            }
            if (execute != null && execute.iterator() != null) {
                execute.iterator().close();
            }
        }
    }
}

Example 4 with ExecutionEngine

use of org.neo4j.cypher.javacompat.ExecutionEngine in project eol-globi-data by jhpoelen.

the class IndexInteractions method link.

@Override
public void link() {
    LinkProgress progress = new LinkProgress(LOG::info, 10);
    progress.start();
    boolean done;
    ExecutionEngine engine = new ExecutionEngine(graphDb);
    do {
        ExecutionResult result = engine.execute("START dataset = node:datasets('*:*')\n" + "MATCH dataset<-[:IN_DATASET]-study-[:COLLECTED]->specimen\n" + "WHERE not(specimen<-[:HAS_PARTICIPANT]-())\n" + "WITH specimen, study, dataset LIMIT {batchSize}\n" + "MATCH specimen-[i:" + InteractUtil.allInteractionsCypherClause() + "]->otherSpecimen\n" + "WHERE not(has(i.inverted))\n" + "CREATE specimen<-[:HAS_PARTICIPANT]-interaction-[:DERIVED_FROM]->study" + ", interaction-[:HAS_PARTICIPANT]->otherSpecimen " + ", interaction-[:ACCESSED_AT]->dataset\n" + "RETURN id(interaction)", MapUtil.map("batchSize", this.batchSize));
        done = !result.iterator().hasNext();
        result.iterator().close();
        progress.progress();
    } while (!done);
}

Example 5 with ExecutionEngine

use of org.neo4j.cypher.javacompat.ExecutionEngine in project eol-globi-data by jhpoelen.

the class StudyImporterForByrnesTest method importAll.

@Test
public void importAll() throws StudyImporterException {
    StudyImporterForByrnes studyImporterForByrnes = new StudyImporterForByrnes(new ParserFactoryLocal(), nodeFactory);
    studyImporterForByrnes.importStudy();
    resolveNames();
    List<String> citationList = new ArrayList<String>();
    Set<String> citations = new HashSet<String>();
    List<Study> studies = NodeUtil.findAllStudies(getGraphDb());
    assertTrue(studies.size() > 0);
    for (Study study : studies) {
        assertThat(study.getTitle(), is(notNullValue()));
        assertThat(study.getSource(), is(notNullValue()));
        assertThat(study.getCitation(), is(notNullValue()));
        citations.add(study.getCitation());
        citationList.add(study.getCitation());
    }
    assertThat("found duplicates in citation list", citationList.size(), is(citations.size()));
    assertNotNull(taxonIndex.findTaxonByName("Anisotremus davidsonii"));
    assertThat(citations, hasItem("Pennings, S. C. 1990. Size-related shifts in herbivory: specialization in the sea hare Aplysia californica Cooper. Journal of Experimental Marine Biology and Ecology 142:43-61."));
    assertThat(citations, hasItem("Barry, J. and M. Ehret. 1993. Diet, food preference, and algal availability for fishes and crabs on intertidal reef communities in southern California. Environmental Biology of Fishes 37:75-95."));
    assertThat(citations, hasItem("Byrnes, J.E. et al., 2011. Climate-driven increases in storm frequency simplify kelp forest food webs. Global Change Biology, 17(8), pp.2513–2524. Available at: http://dx.doi.org/10.1111/j.1365-2486.2011.02409.x."));
    assertThat(citations, not(hasItem("17(8)")));
    ExecutionEngine executionEngine = new ExecutionEngine(getGraphDb());
    ExecutionResult result = executionEngine.execute("START taxon = node:taxons(name=\"Strongylocentrotus purpuratus\")" + " MATCH taxon<-[:CLASSIFIED_AS]-specimen-[:ATE]->prey-[:CLASSIFIED_AS]->preyTaxon " + " RETURN collect(distinct(preyTaxon.name))");
    assertThat(result.dumpToString(), containsString("Bossiella orbigiana"));
}