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Avoids errors due to non parseable integer elements OT percentile ranks #112

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Avoids errors due to non parseable integer elements OT percentile ranks #112

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25 changes: 17 additions & 8 deletions app/src/main/java/uk/ac/ebi/atlas/experimentpage/json/opentargets/EvidenceService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,11 @@
import com.google.gson.JsonPrimitive;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import uk.ac.ebi.atlas.commons.readers.TsvStreamer;
import uk.ac.ebi.atlas.commons.streams.ObjectInputStream;
import uk.ac.ebi.atlas.home.AtlasInformationDao;
import uk.ac.ebi.atlas.model.experiment.sample.AssayGroup;
import uk.ac.ebi.atlas.model.GeneProfilesList;
import uk.ac.ebi.atlas.model.OntologyTerm;
Expand All @@ -29,23 +32,22 @@

import java.text.MessageFormat;
import java.text.SimpleDateFormat;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import java.util.*;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;

import static java.util.stream.Collectors.joining;

public class EvidenceService<X extends DifferentialExpression,
E extends DifferentialExperiment,
O extends DifferentialProfileStreamOptions,
P extends Profile<Contrast, X, P>> {
private static final double MIN_P_VALUE = 1e-234;
private static final String ACTIVITY_URL_TEMPLATE = "http://identifiers.org/cttv.activity/{0}";
private static final Logger LOGGER = LoggerFactory.getLogger(EvidenceService.class);


private final ProfileStreamFactory<Contrast, X, E, O, P> differentialProfileStreamFactory;
private final DataFileHub dataFileHub;
Expand Down Expand Up @@ -477,7 +479,7 @@ public static DiseaseAssociation create(SampleCharacteristic biosampleInfo,
private static String factorBasedSummaryLabel(final ExperimentDesign experimentDesign, AssayGroup assayGroup) {
return experimentDesign.getFactorValues(assayGroup.getFirstAssayId()).values().stream()
.filter(StringUtils::isNotEmpty)
.collect(Collectors.joining("; "));
.collect(joining("; "));
}

/*
Expand Down Expand Up @@ -555,17 +557,24 @@ private Map<String, Map<Contrast, Integer>> readPercentileRanks(E experiment, Ob
var whichContrastInWhichLine = percentileRanksColumnsFromHeader(lines.readNext(), experiment);
var geneToRankedContrast = new HashMap<String, Map<Contrast, Integer>>();

var unparseableNumbers = new HashSet<String>();
for (var line : new IterableObjectInputStream<>(lines)) {
var resultForThisGene = new HashMap<Contrast, Integer>();

for (var entry : whichContrastInWhichLine.entrySet()) {
String value = line[entry.getKey()];
if (!"NA".equals(value)) {
try {
resultForThisGene.put(entry.getValue(), Integer.parseInt(value));
} catch (NumberFormatException e) {
unparseableNumbers.add(value);
}
}
geneToRankedContrast.put(line[0], resultForThisGene);
}
if (unparseableNumbers.size() > 0) {
var examples = unparseableNumbers.stream().map(item -> "'"+item+"'").collect(joining(", "));
LOGGER.warn("%s percentile ranks file has the following unparseable text entries: %s", experiment.getAccession(), examples);
}

return geneToRankedContrast;
}
Expand Down