Examples with NodeListener org.eol.globi.util.NodeListener used on opensource projects

Example 1 with NodeListener

use of org.eol.globi.util.NodeListener in project eol-globi-data by jhpoelen.

the class DatasetImporterForTSVTest method assertArgumentType.

private void assertArgumentType(String firstFewLines, final RelTypes argumentType) throws StudyImporterException {
    DatasetImpl dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLines);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    final AtomicBoolean foundStudy = new AtomicBoolean(false);
    NodeUtil.findStudies(getGraphDb(), new NodeListener() {

        @Override
        public void on(Node node) {
            assertTrue(node.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(argumentType)));
            foundStudy.set(true);
        }
    });
    assertThat(foundStudy.get(), is(true));
}

Example 2 with NodeListener

use of org.eol.globi.util.NodeListener in project eol-globi-data by jhpoelen.

the class NameResolver method resolveNames.

public void resolveNames(Long batchSize, GraphDatabaseService graphService) {
    StopWatch watchForEntireRun = new StopWatch();
    watchForEntireRun.start();
    StopWatch watchForBatch = new StopWatch();
    watchForBatch.start();
    final AtomicLong nameCount = new AtomicLong(0L);
    final TransactionPerBatch batchListener = new TransactionPerBatch(graphService);
    NodeListener listener = node -> nameCount.set(resolveNamesInStudy(batchSize, watchForBatch, nameCount.get(), node, batchListener));
    LOG.info("resolving names...");
    NodeUtil.processNodes(batchSize, graphService, listener, StudyConstant.TITLE, "*", "studies", batchListener);
    watchForEntireRun.stop();
    LOG.info("resolved [" + nameCount + "] names in " + getProgressMsg(nameCount.get(), watchForEntireRun.getTime()));
}

Example 3 with NodeListener

use of org.eol.globi.util.NodeListener in project eol-globi-data by jhpoelen.

the class DatasetImporterForWrastTest method createAndPopulateStudyFromLavacaBay.

@Test
public void createAndPopulateStudyFromLavacaBay() throws StudyImporterException {
    String csvString = "\"Month\",\"Day\",\"Year\",\"Region\",\"Season\",\"Habitat\",\"Site\",\"Family\",\"Predator Species\",\"TL (mm)\",\"Prey Item Species\",\"Prey item\",\"Number\",\"Condition Index\",\"Volume\",\"Percent Content\",\"Prey Item Trophic Level\",\"Notes\",\"Call #\"\n";
    csvString += "7,24,2001,\"Lower\",\"Fall\",\"Marsh\",1,\"Sciaenidae\",\"Sciaenops ocellatus\",420,\"Acrididae spp. \",\"Acrididae \",1,\"III\",0.4,3.2520325203,2.5,,1\n";
    csvString += "7,25,2001,\"Lower\",\"Spring\",\"Non-Veg \",1,\"Ariidae\",\"Arius felis\",176,\"Aegathoa oculata \",\"Aegathoa oculata\",4,\"I\",0.01,3.3333333333,2.1,,2\n";
    csvString += "7,26,2001,\"Upper\",\"Spring\",\"Reef\",2,\"Depth\",\"Missing depth\",176,\"Aegathoa oculata \",\"Aegathoa oculata\",4,\"I\",0.01,3.3333333333,2.1,,2\n";
    Map<String, String> contentMap = new TreeMap<>();
    String locationString = "\"Location\",\"Latitude\",\"Longitude\",,\"Region\",\"Habitat\",\"Site\"\n" + "\"LM1\",28.595267,-96.477033,,\"Lower\",\"Marsh edge\",1\n" + "\"LSG1\",28.596233,-96.476483,,\"Lower\",\"Marsh edge\",1\n" + "\"LM2\",28.593150,-96.474633,,\"Lower\",\"Marsh edge\",2\n" + "\"LSG2\",28.594833,-96.473967,,\"Lower\",\"Marsh edge\",2\n" + "\"LNV1A\",28.608417,-96.475517,,\"Lower\",\"Non-Veg \",1\n" + "\"LNV1B\",28.607217,-96.474500,,\"Lower\",\"Non-Veg \",1\n" + "\"LNV2A\",28.592400,-96.483033,,\"Lower\",\"Non-Veg \",2\n" + "\"LNV2B\",28.590883,-96.484133,,\"Lower\",\"Non-Veg \",2\n" + "\"UR2B\",28.656483,-96.597217,,\"Upper\",\"Reef\",2";
    String envString = "\"Date\",\"Season\",\"Upper/Lower\",\"Habitat\",\"Site\",\"Air Temp (ºC)\",\"Wind Chill (ºC)\",\"Relative Humidity (%)\",\"Heat Index (ºC)\",\"Dew Point (ºC)\",\"Max Wind intensity (mph)\",\"Ave Wind intensity (mph)\",\"Wind Direction\",\"Cloud Cover (%)\",\"Rain?\",\"Depth (m)\",\"Temp (ºC) Surface\",\"Temp (ºC) Bottom\",\"Mean Temp Surface/Bottom\",\"pH Surface\",\"pH Bottom\",\"Mean pH Surface/Bottom\",\"DO (mg/L) Surface\",\"DO (mg/L) Bottom\",\"Mean DO Surface/Bottom\",\"Sal (o/oo) Surface\",\"Sal (o/oo) Bottom\",\"Mean Sal Surface/Bottom\",\"Secchi (m)\"\n" + "7/24/2006,\"Summer\",\"L\",\"R\",1,\"81.3 (F)\",\"81.5 (F)\",71.8,\"86.2 (F)\",\"70.6 (F)\",8.5,8.1,\"SE\",75,\"Yes\",1.9,30.79,30.34,30.565,8.11,8.13,8.12,5.16,4.8,4.98,22.8,23.07,22.935,0.4\n" + "7/24/2006,\"Summer\",\"L\",\"R\",2,\"81.3 (F)\",\"81.5 (F)\",71.8,\"86.2 (F)\",\"70.6 (F)\",8.5,8.1,\"SE\",75,\"Yes\",2.1,31.07,30.14,30.605,8.11,8.1,8.105,5.14,4.64,4.89,23.37,23.84,23.605,0.48\n" + "10/26/2006,\"Fall\",\"L\",\"M\",1,26.8,26.5,78,30,22.4,17.9,15,\"S \",95,\"No\",0.8,25.57,,25.57,8.29,,8.29,8.32,,8.32,21.26,,21.26,\"Bottom\"\n" + "10/26/2006,\"Fall\",\"L\",\"M\",2,26.8,26.5,78,30,22.4,17.9,15,\"S \",95,\"No\",0.4,25.84,,25.84,8.32,,8.32,8.21,,8.21,21.47,,21.47,\"Bottom\"\n" + "10/26/2006,\"Fall\",\"L\",\"SG\",1,26.8,26.5,78,30,22.4,17.9,15,\"S \",95,\"No\",0.8,25.57,,25.57,8.29,,8.29,8.32,,8.32,21.26,,21.26,\"Bottom\"\n" + "4/27/2007,\"Spring\",\"L\",\"R\",1,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",1.6,23.43,23.39,23.41,,,,7.31,7.09,7.2,14.64,14.64,14.64,0.32\n" + "4/27/2007,\"Spring\",\"L\",\"R\",2,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",2,23.77,23.77,23.77,,,,7.01,6.82,6.915,15.04,15.04,15.04,0.38\n" + "4/27/2007,\"Spring\",\"L\",\"NV\",1,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",2,23.85,23.85,23.85,,,,6.96,6.81,6.885,14.65,14.65,14.65,0.48\n" + "4/27/2007,\"Spring\",\"L\",\"NV\",2,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",1.8,23.78,23.78,23.78,,,,6.87,6.65,6.76,15.11,15.18,15.145,0.45";
    contentMap.put(DatasetImporterForWrast.LAVACA_BAY_LOCATIONS.toString(), locationString);
    contentMap.put(DatasetImporterForWrast.LAVACA_BAY_DATA_SOURCE.toString(), csvString);
    contentMap.put(DatasetImporterForWrast.LAVACA_BAY_ENVIRONMENTAL.toString(), envString);
    DatasetImporterForWrast importer = new DatasetImporterForWrast(new TestParserFactory(contentMap), nodeFactory);
    importStudy(importer);
    assertThat(getSpecimenCount(getStudySingleton(getGraphDb())), is(5));
    assertNotNull(taxonIndex.findTaxonByName("Sciaenops ocellatus"));
    assertNotNull(taxonIndex.findTaxonByName("Arius felis"));
    assertNotNull(taxonIndex.findTaxonByName("Aegathoa oculata"));
    assertNotNull(nodeFactory.findSeason("spring"));
    assertNotNull(nodeFactory.findSeason("fall"));
    AtomicReference<StudyNode> foundStudyRef = new AtomicReference<>();
    NodeUtil.findStudies(getGraphDb(), new NodeListener() {

        @Override
        public void on(Node node) {
            foundStudyRef.set(new StudyNode(node));
        }
    });
    StudyNode foundStudy = foundStudyRef.get();
    assertNotNull(foundStudy);
    assertThat(foundStudy.getTitle(), is("Wrast 2008"));
    RelationshipListener handler = relationship -> {
        Date unixEpochProperty = null;
        try {
            unixEpochProperty = nodeFactory.getUnixEpochProperty(new SpecimenNode(relationship.getEndNode()));
        } catch (NodeFactoryException e) {
            fail(e.getMessage());
        }
        SimpleDateFormat simpleDateFormat = DatasetImporterForWrast.getSimpleDateFormat();
        Date endDate = null;
        try {
            endDate = simpleDateFormat.parse("7/27/2001");
        } catch (ParseException e) {
            fail(e.getMessage());
        }
        Date startDate = null;
        try {
            startDate = simpleDateFormat.parse("7/23/2001");
        } catch (ParseException e) {
            fail(e.getMessage());
        }
        assertThat(unixEpochProperty.before(endDate), is(true));
        assertThat(unixEpochProperty.after(startDate), is(true));
        Specimen specimen = new SpecimenNode(relationship.getEndNode());
        for (Relationship ignored : NodeUtil.getStomachContents(specimen)) {
            TaxonNode taxon = new TaxonNode(relationship.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING).getEndNode());
            String scientificName = taxon.getName();
            if ("Sciaenops ocellatus".equals(scientificName)) {
                Location location = specimen.getSampleLocation();
                assertThat(location, is(not(nullValue())));
                assertThat(location.getLatitude(), is((28.595267 + 28.596233) / 2.0));
                assertThat(location.getLongitude(), is((-96.477033 - 96.476483) / 2.0));
                assertThat(location.getAltitude(), is(-0.8));
                Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(specimen);
                int count = 0;
                for (Relationship containsRel : stomachContents) {
                    Node endNode = containsRel.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING).getEndNode();
                    Object name = endNode.getProperty("name");
                    String name1 = (String) name;
                    assertThat(name1.replaceAll("\\W", ""), is("Acrididae"));
                    count++;
                }
                assertEquals(1, count);
                Season season = specimen.getSeason();
                assertEquals("fall", season.getTitle());
                assertEquals(420.0d, specimen.getLengthInMm(), 0.01);
            } else if ("Arius felis".equals(scientificName)) {
                Location location = specimen.getSampleLocation();
                assertThat(location, is(not(nullValue())));
                assertThat(location.getLatitude(), is((28.608417 + 28.607217) / 2.0));
                assertThat(location.getLongitude(), is((-96.475517 - 96.474500) / 2.0));
                assertThat(location.getAltitude(), is(-2.0d));
                Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(specimen);
                int count = 0;
                for (Relationship containsRel : stomachContents) {
                    Object name = containsRel.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING).getEndNode().getProperty("name");
                    assertEquals("Aegathoa oculata", name);
                    count++;
                }
                assertEquals(2, count);
                Season season = specimen.getSeason();
                assertEquals("spring", season.getTitle());
                assertEquals(176.0d, specimen.getLengthInMm(), 0.01);
            } else if ("Missing depth".equals(scientificName)) {
                Location location = specimen.getSampleLocation();
                assertThat(location, is(not(nullValue())));
                assertThat(location.getAltitude(), is(nullValue()));
            } else {
                fail("unexpected scientificName of predator [" + scientificName + "]");
            }
        }
    };
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(getStudySingleton(getGraphDb()).getUnderlyingNode()), handler);
}

Example 4 with NodeListener

use of org.eol.globi.util.NodeListener in project eol-globi-data by jhpoelen.

the class GraphExporterImpl method exportNames.

private void exportNames(GraphDatabaseService graphService, File baseDir, StudyExporter exporter, String filename) throws StudyImporterException {
    try {
        File filePath = new File(baseDir, filename);
        OutputStreamWriter writer = openStream(filePath);
        NodeUtil.findStudies(graphService, new NodeListener() {

            final AtomicBoolean isFirst = new AtomicBoolean(true);

            @Override
            public void on(Node node) {
                boolean includeHeader = isFirst.getAndSet(false);
                try {
                    exporter.exportStudy(new StudyNode(node), ExportUtil.AppenderWriter.of(writer), includeHeader);
                } catch (IOException e) {
                    throw new IllegalStateException("failed to export names to [" + filePath + "]");
                }
            }
        });
        closeStream(filePath, writer);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export unmatched source taxa", e);
    }
}

Example 5 with NodeListener

use of org.eol.globi.util.NodeListener in project eol-globi-data by jhpoelen.

the class GraphExporterImpl method export.

private void export(GraphDatabaseService graphService, File exportPath, String filename, DarwinCoreExporter studyExporter, FileWriter darwinCoreMeta) throws IOException {
    File exportFile = new File(exportPath, filename);
    OutputStreamWriter writer = openStream(exportFile);
    NodeUtil.findStudies(graphService, new NodeListener() {

        final AtomicBoolean isFirst = new AtomicBoolean(true);

        @Override
        public void on(Node node) {
            try {
                studyExporter.exportStudy(new StudyNode(node), ExportUtil.AppenderWriter.of(writer), isFirst.getAndSet(false));
            } catch (IOException e) {
                throw new IllegalStateException("failed to export to [" + exportFile.getAbsolutePath() + "]", e);
            }
        }
    });
    closeStream(exportFile, writer);
    LOG.info("darwin core meta file writing... ");
    studyExporter.exportDarwinCoreMetaTable(darwinCoreMeta, filename);
    LOG.info("darwin core meta file written. ");
}