Copy over src folder from atlas-web-core (sha: 05c86f0e91f222bde8a29ce56050d9eaf2c1c4d9)

build.gradle

@@ -1,20 +1,9 @@
 plugins {
-    id 'java'
+    id 'atlas-web-bulk.java-conventions'
     id 'org.springframework.boot' version '3.4.1' apply false
     id 'io.spring.dependency-management' version '1.1.7'
 }
 
-group = 'uk.ac.ebi.atlas'
-version = '1.0-SNAPSHOT'
-
-java {
-    sourceCompatibility = '17'
-}
-
-repositories {
-    mavenCentral()
-}
-
 dependencyManagement {
     imports {
         mavenBom org.springframework.boot.gradle.plugin.SpringBootPlugin.BOM_COORDINATES
@@ -23,10 +12,49 @@ dependencyManagement {
 
 dependencies {
     implementation 'org.springframework.boot:spring-boot'
+    implementation 'org.springframework.boot:spring-boot-starter-web'
+    implementation 'org.springframework.boot:spring-boot-starter-jdbc'
+    implementation 'org.springframework.boot:spring-boot-starter-webflux'
+
+    implementation 'org.slf4j:slf4j-api'
+    implementation 'org.apache.commons:commons-lang3'
+    implementation 'org.apache.commons:commons-math:2.2'
+    implementation 'commons-io:commons-io:2.16.1'
+    implementation 'commons-beanutils:commons-beanutils:1.9.4'
+    implementation 'commons-jxpath:commons-jxpath:1.3'
+    implementation 'io.atlassian.util.concurrent:atlassian-util-concurrent:4.0.1'
+    implementation 'com.google.guava:guava'
+    implementation 'com.google.code.gson:gson'
+    implementation 'com.google.auto.value:auto-value-annotations:1.11.0'
+    annotationProcessor 'com.google.auto.value:auto-value:1.11.0'
+    implementation 'com.fasterxml.jackson.core:jackson-databind'
+
+    implementation 'org.eclipse.jdt:org.eclipse.jdt.annotation:2.3.0'
+    implementation 'org.eclipse.jetty:jetty-http:9.4.27.v20200227'
+    implementation 'org.eclipse.jetty:jetty-io:9.4.27.v20200227'
+    implementation 'org.eclipse.jetty:jetty-client:9.4.27.v20200227'
+    implementation 'org.eclipse.jetty:jetty-util:9.4.27.v20200227'
+
+    implementation 'joda-time:joda-time:2.10.10'
+
+    implementation 'au.com.bytecode:opencsv:2.4'
+
+    implementation ('org.apache.solr:solr-core:8.7.0') {
+        exclude group: 'org.apache.logging.log4j', module: 'log4j-slf4j-impl'
+    }
+
+    implementation 'uk.ac.ebi.fg:ae-efo-loader:1.0.5'
+
     compileOnly 'org.springframework.boot:spring-boot-devtools'
     testImplementation 'org.springframework.boot:spring-boot-starter-test'
+    testImplementation 'io.projectreactor:reactor-test'
     testImplementation platform('org.junit:junit-bom:5.10.0')
     testImplementation 'org.junit.jupiter:junit-jupiter'
+    testImplementation 'org.hamcrest:java-hamcrest:2.0.0.0'
+    testImplementation 'org.assertj:assertj-guava'
+    // For JUnit 4 tests
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine'
+    testImplementation 'junit:junit:4.12'
 }
 
 tasks.withType(JavaCompile).configureEach {
@@ -35,4 +63,4 @@ tasks.withType(JavaCompile).configureEach {
 
 test {
     useJUnitPlatform()
-}
+}

gradle.properties

@@ -0,0 +1,3 @@
+dataFilesLocation = /atlas-data
+experimentFilesLocation = /atlas-data/exp
+experimentDesignLocation = /atlas-data/expdesign

src/main/java/uk/ac/ebi/atlas/bioentity/geneset/GeneSetPropertyService.java

@@ -0,0 +1,71 @@
+package uk.ac.ebi.atlas.bioentity.geneset;
+
+import com.google.common.collect.ImmutableList;
+import com.google.common.collect.ImmutableMap;
+import com.google.common.collect.ImmutableSet;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Component;
+import uk.ac.ebi.atlas.bioentity.go.GoPoTrader;
+import uk.ac.ebi.atlas.bioentity.interpro.InterProTrader;
+import uk.ac.ebi.atlas.model.OntologyTerm;
+import uk.ac.ebi.atlas.solr.bioentities.BioentityPropertyName;
+import uk.ac.ebi.atlas.utils.ReactomeClient;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import static uk.ac.ebi.atlas.solr.bioentities.BioentityPropertyName.DESCRIPTION;
+import static uk.ac.ebi.atlas.solr.bioentities.BioentityPropertyName.GO;
+import static uk.ac.ebi.atlas.solr.bioentities.BioentityPropertyName.INTERPRO;
+import static uk.ac.ebi.atlas.solr.bioentities.BioentityPropertyName.PATHWAYID;
+import static uk.ac.ebi.atlas.solr.bioentities.BioentityPropertyName.PO;
+
+@Profile("!cli")
+@Component
+public class GeneSetPropertyService {
+    private final GoPoTrader goPoTermTrader;
+    private final InterProTrader interProTermTrader;
+    private final ReactomeClient reactomeClient;
+
+    public GeneSetPropertyService(GoPoTrader goPoTermTrader,
+                                  InterProTrader interProTermTrader,
+                                  ReactomeClient reactomeClient) {
+        this.goPoTermTrader = goPoTermTrader;
+        this.interProTermTrader = interProTermTrader;
+        this.reactomeClient = reactomeClient;
+    }
+
+    public static final List<BioentityPropertyName> ALL =
+            ImmutableList.of(PATHWAYID, GO, PO, INTERPRO);
+
+    public Map<BioentityPropertyName, Set<String>> propertyValuesByType(String identifier, boolean isPlant) {
+        identifier = identifier.toUpperCase();
+
+        if (GeneSetUtil.matchesReactomeID(identifier)) {
+            if (isPlant) {
+                return propertyValuesByType(
+                        PATHWAYID, identifier, reactomeClient.getPlantPathwayName(identifier).orElse(""));
+            } else {
+                return propertyValuesByType(
+                        PATHWAYID, identifier, reactomeClient.getPathwayName(identifier).orElse(""));
+            }
+        } else if (GeneSetUtil.matchesGeneOntologyAccession(identifier)) {
+            return propertyValuesByType(
+                    GO, identifier, goPoTermTrader.get(identifier).map(OntologyTerm::name).orElse(""));
+        } else if (GeneSetUtil.matchesPlantOntologyAccession(identifier)) {
+            return propertyValuesByType(
+                    PO, identifier, goPoTermTrader.get(identifier).map(OntologyTerm::name).orElse(""));
+        } else if (GeneSetUtil.matchesInterProAccession(identifier)) {
+            return propertyValuesByType(
+                    INTERPRO, identifier, interProTermTrader.get(identifier).map(OntologyTerm::name).orElse(""));
+        } else {
+            return ImmutableMap.of();
+        }
+    }
+
+    private Map<BioentityPropertyName, Set<String>> propertyValuesByType(BioentityPropertyName which,
+                                                                         String identifier, String value) {
+        return ImmutableMap.of(which, ImmutableSet.of(identifier), DESCRIPTION, ImmutableSet.of(value));
+    }
+}

src/main/java/uk/ac/ebi/atlas/bioentity/geneset/GeneSetUtil.java

@@ -0,0 +1,65 @@
+package uk.ac.ebi.atlas.bioentity.geneset;
+
+import uk.ac.ebi.atlas.search.SemanticQuery;
+import uk.ac.ebi.atlas.search.SemanticQueryTerm;
+
+import java.util.regex.Pattern;
+
+public class GeneSetUtil {
+    private static final Pattern GO_REGEX = Pattern.compile("GO:\\d+", Pattern.CASE_INSENSITIVE);
+    private static final Pattern PO_REGEX = Pattern.compile("PO:\\d+", Pattern.CASE_INSENSITIVE);
+    private static final Pattern REACTOME_REGEX = Pattern.compile("R-[A-Z]{3}-\\d+", Pattern.CASE_INSENSITIVE);
+    private static final Pattern INTER_PRO_REGEX = Pattern.compile("IPR" + "(\\d)+", Pattern.CASE_INSENSITIVE);
+    private static final Pattern PLANT_REACTOME_REGEX = Pattern.compile("[\\d]+", Pattern.CASE_INSENSITIVE);
+
+    private static final String GO_CATEGORY = "go";
+    private static final String PO_CATEGORY = "po";
+    private static final String REACTOME_CATEGORY = "pathwayid";
+    private static final String INTERPRO_CATEGORY = "interpro";
+
+    protected GeneSetUtil() {
+        throw new UnsupportedOperationException();
+    }
+
+    public static boolean matchesInterProAccession(String identifier) {
+        return INTER_PRO_REGEX.matcher(identifier).matches();
+    }
+
+    public static boolean matchesGeneOntologyAccession(String identifier) {
+        return GO_REGEX.matcher(identifier).matches();
+    }
+
+    public static boolean matchesPlantOntologyAccession(String identifier) {
+        return PO_REGEX.matcher(identifier).matches();
+    }
+
+    public static boolean matchesReactomeID(String identifier) {
+        return REACTOME_REGEX.matcher(identifier).matches();
+    }
+
+    public static boolean matchesPlantReactomeID(String identifier) {
+        return PLANT_REACTOME_REGEX.matcher(identifier).matches();
+    }
+
+    public static boolean matchesGeneSetAccession(String identifier) {
+        return matchesReactomeID(identifier) || matchesInterProAccession(identifier) ||
+                matchesGeneOntologyAccession(identifier) || matchesPlantOntologyAccession(identifier) ||
+                matchesPlantReactomeID(identifier);
+    }
+
+    private static boolean hasGeneSetCategory(String category) {
+        return category.equalsIgnoreCase(GO_CATEGORY) || category.equalsIgnoreCase(PO_CATEGORY) ||
+                category.equalsIgnoreCase(REACTOME_CATEGORY) || category.equalsIgnoreCase(INTERPRO_CATEGORY);
+    }
+
+    public static boolean matchesGeneSetCategoryOrGeneSetValue(SemanticQuery geneQuery) {
+        if (geneQuery.isEmpty() || geneQuery.size() > 1) {
+            return false;
+        }
+
+        SemanticQueryTerm term = geneQuery.iterator().next();
+        return term.category().isPresent() ?
+                hasGeneSetCategory(term.category().get()) :
+                matchesGeneSetAccession(term.value());
+    }
+}

src/main/java/uk/ac/ebi/atlas/bioentity/go/GoPoTrader.java

@@ -0,0 +1,38 @@
+package uk.ac.ebi.atlas.bioentity.go;
+
+import au.com.bytecode.opencsv.CSVReader;
+import com.google.common.collect.ImmutableMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Component;
+import uk.ac.ebi.atlas.model.OntologyTerm;
+import uk.ac.ebi.atlas.utils.CsvReaderFactory;
+
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.file.Path;
+import java.util.Optional;
+
+@Profile("!cli")
+@Component
+public class GoPoTrader {
+    private static final Logger LOGGER = LoggerFactory.getLogger(GoPoTrader.class);
+    private final ImmutableMap<String, OntologyTerm> accessionToTerm;
+
+    public GoPoTrader(Path goPoFilePath) {
+        try (CSVReader tsvReader = CsvReaderFactory.createForTsv(goPoFilePath.toString())) {
+            accessionToTerm = new GoPoTsvParser(tsvReader).parse();
+        } catch (IOException e) {
+            throw new UncheckedIOException(e);
+        }
+    }
+
+    public Optional<OntologyTerm> get(String accession) {
+        if (accessionToTerm.get(accession) == null) {
+            LOGGER.warn("Unable to find GO/PO accession {}", accession);
+        }
+
+        return Optional.ofNullable(accessionToTerm.get(accession));
+    }
+}

src/main/java/uk/ac/ebi/atlas/bioentity/go/GoPoTsvParser.java

@@ -0,0 +1,76 @@
+package uk.ac.ebi.atlas.bioentity.go;
+
+import au.com.bytecode.opencsv.CSVReader;
+import com.google.common.base.Joiner;
+import com.google.common.collect.ImmutableMap;
+import com.google.common.collect.ImmutableMultimap;
+import uk.ac.ebi.atlas.model.OntologyTerm;
+
+import java.io.IOException;
+import java.util.Collection;
+
+public class GoPoTsvParser {
+
+    private static final String[] VALID_PREFIXES = {"GO:", "PO:"};
+
+    private static final int TERM_ACCESSION_COLUMN_INDEX = 0;
+    private static final int TERM_NAME_COLUMN_INDEX = 1;
+    private static final int TERM_DEPTH_COLUMN_INDEX = 2;
+    public static final int DEFAULT_DEPTH = 1;
+
+    private final CSVReader csvReader;
+
+    public GoPoTsvParser(CSVReader csvReader) {
+        this.csvReader = csvReader;
+    }
+
+    ImmutableMap<String, OntologyTerm> parse() throws IOException {
+
+        String startsWithGoPoRegex = "^(" + Joiner.on("|").join(VALID_PREFIXES) + ").+";
+
+        ImmutableMultimap.Builder<String, OntologyTerm> multimapBuilder = ImmutableMultimap.builder();
+        String[] line;
+        while ((line = csvReader.readNext()) != null) {
+            if (line.length > TERM_ACCESSION_COLUMN_INDEX) {
+                String accession = line[TERM_ACCESSION_COLUMN_INDEX];
+                if (accession.matches(startsWithGoPoRegex)) {
+                    String name = line.length > TERM_NAME_COLUMN_INDEX ? line[TERM_NAME_COLUMN_INDEX] : "";
+                    int depth = parseDepth(line);
+                    multimapBuilder.put(accession, OntologyTerm.create(accession, name, "", depth));
+                }
+            }
+        }
+        ImmutableMultimap<String, OntologyTerm> accessionToGoPoTerms = multimapBuilder.build();
+
+
+        ImmutableMap.Builder<String, OntologyTerm> mapBuilder = ImmutableMap.builder();
+        for (String accession : accessionToGoPoTerms.keySet()) {
+
+            int minDepth = minDepthOfTerms(accessionToGoPoTerms.get(accession));
+            String name = accessionToGoPoTerms.get(accession).iterator().next().name();
+
+            mapBuilder.put(accession, OntologyTerm.create(accession, name, "", minDepth));
+        }
+
+        return mapBuilder.build();
+    }
+
+    private int minDepthOfTerms(Collection<OntologyTerm> terms) {
+        int minDepth = Integer.MAX_VALUE;
+        for (OntologyTerm term : terms) {
+            minDepth = term.depth() < minDepth ? term.depth() : minDepth;
+        }
+        return minDepth;
+    }
+
+    private int parseDepth(String[] line) {
+        try {
+            return line.length > TERM_DEPTH_COLUMN_INDEX ?
+                    Integer.parseInt(line[TERM_DEPTH_COLUMN_INDEX]) :
+                    DEFAULT_DEPTH;
+        } catch (NumberFormatException e) {
+            return DEFAULT_DEPTH;
+        }
+    }
+
+}

src/main/java/uk/ac/ebi/atlas/bioentity/interpro/InterProTrader.java

@@ -0,0 +1,40 @@
+package uk.ac.ebi.atlas.bioentity.interpro;
+
+import com.google.common.collect.ImmutableMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Component;
+import uk.ac.ebi.atlas.commons.readers.TsvStreamer;
+import uk.ac.ebi.atlas.model.OntologyTerm;
+
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Optional;
+
+@Profile("!cli")
+@Component
+public class InterProTrader {
+    private static final Logger LOGGER = LoggerFactory.getLogger(InterProTrader.class);
+    private final ImmutableMap<String, OntologyTerm> accessionToTerm;
+
+    public InterProTrader(Path interProFilePath) {
+        try (TsvStreamer tsvStreamer =
+                     new TsvStreamer(Files.newBufferedReader(interProFilePath, StandardCharsets.UTF_8))) {
+            accessionToTerm = InterProTsvParser.parse(tsvStreamer);
+        } catch (IOException e) {
+            throw new UncheckedIOException(e);
+        }
+    }
+
+    public Optional<OntologyTerm> get(String accession) {
+        if (accessionToTerm.get(accession) == null) {
+            LOGGER.warn("Unable to find InterPro accession {}", accession);
+        }
+
+        return Optional.ofNullable(accessionToTerm.get(accession));
+    }
+}