Update endpoints and annotations for OpenAPI

pom.xml

@@ -12,10 +12,10 @@
     <maven.compiler.target>11</maven.compiler.target>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-    <quarkus-plugin.version>1.4.2.Final</quarkus-plugin.version>
+    <quarkus-plugin.version>1.9.2.Final</quarkus-plugin.version>
     <quarkus.platform.artifact-id>quarkus-universe-bom</quarkus.platform.artifact-id>
     <quarkus.platform.group-id>io.quarkus</quarkus.platform.group-id>
-    <quarkus.platform.version>1.4.2.Final</quarkus.platform.version>
+    <quarkus.platform.version>1.9.2.Final</quarkus.platform.version>
     <surefire-plugin.version>2.22.1</surefire-plugin.version>
   </properties>
   <dependencyManagement>

src/main/java/de/unigoettingen/ibeetlebase/AppServiceBean.java → src/main/java/de/unigoettingen/ibeetlebase/geneinfo/AppServiceBean.java

-package de.unigoettingen.ibeetlebase;
+package de.unigoettingen.ibeetlebase.geneinfo;
 
 import javax.enterprise.context.ApplicationScoped;
 import javax.enterprise.event.Observes;

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/GeneinfoApplication.java

+package de.unigoettingen.ibeetlebase.geneinfo;
+
+import javax.ws.rs.core.Application;
+
+import org.eclipse.microprofile.openapi.annotations.OpenAPIDefinition;
+import org.eclipse.microprofile.openapi.annotations.info.Info;
+
+@OpenAPIDefinition(
+        info = @Info(title = "Gene Info Service",
+                description = "Get general information for fly and tribolium genes.",
+                version = "1.0")
+)
+public class GeneinfoApplication extends Application {
+
+}

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/model/FlybaseGene.java

+package de.unigoettingen.ibeetlebase.geneinfo.model;
+
+import java.util.Set;
+
+import io.quarkus.runtime.annotations.RegisterForReflection;
+
+@RegisterForReflection
+public class FlybaseGene {
+    private String id;
+    private String taxanomyId;
+    private String type;
+    private String symbol;
+    private String fullname;
+    private String annotationId;
+    private String transcriptType;
+    private Set<String> transcriptIds;
+    
+    public FlybaseGene(String id, String taxanomyId, String type, String symbol,
+            String fullname, String annotationId, String transcriptType,
+            Set<String> transcriptIds) {
+        super();
+        this.id = id;
+        this.taxanomyId = taxanomyId;
+        this.type = type;
+        this.symbol = symbol;
+        this.fullname = fullname;
+        this.annotationId = annotationId;
+        this.transcriptType = transcriptType;
+        this.transcriptIds = transcriptIds;
+    }
+    
+    
+    public String getId() {
+        return id;
+    }
+    public void setId(String id) {
+        this.id = id;
+    }
+    public String getTaxanomyId() {
+        return taxanomyId;
+    }
+    public void setTaxanomyId(String taxanomyId) {
+        this.taxanomyId = taxanomyId;
+    }
+    public String getType() {
+        return type;
+    }
+    public void setType(String type) {
+        this.type = type;
+    }
+    public String getSymbol() {
+        return symbol;
+    }
+    public void setSymbol(String symbol) {
+        this.symbol = symbol;
+    }
+    public String getFullname() {
+        return fullname;
+    }
+    public void setFullname(String fullname) {
+        this.fullname = fullname;
+    }
+    public String getAnnotationId() {
+        return annotationId;
+    }
+    public void setAnnotationId(String annotationId) {
+        this.annotationId = annotationId;
+    }
+    public String getTranscriptType() {
+        return transcriptType;
+    }
+    public void setTranscriptType(String transcriptType) {
+        this.transcriptType = transcriptType;
+    }
+    public Set<String> getTranscriptIds() {
+        return transcriptIds;
+    }
+    public void setTranscriptId(Set<String> transcriptIds) {
+        this.transcriptIds = transcriptIds;
+    }
+}

src/main/java/de/unigoettingen/ibeetlebase/api/core/Gene.java → src/main/java/de/unigoettingen/ibeetlebase/geneinfo/model/Gene.java

-package de.unigoettingen.ibeetlebase.api.core;
+package de.unigoettingen.ibeetlebase.geneinfo.model;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.Map;
 
 public class Gene {
     private String format = "flybase";                  // Identifier for the source database which also implies a certain format of the contained information

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/model/TriboliumGene.java

+package de.unigoettingen.ibeetlebase.geneinfo.model;
+
+import io.quarkus.runtime.annotations.RegisterForReflection;
+
+@RegisterForReflection
+public class TriboliumGene {
+
+    private String id;
+    private String taxonomyId;
+    private String seqname;
+    private String source;
+    private String feature;
+    private String start;
+    private String end;
+    private String score;
+    private String strand;
+    private String frame;
+    private String locusTag;
+    
+    public TriboliumGene(String id, String taxonomyId, String seqname, String source,
+            String feature, String start, String end, String score,
+            String strand, String frame, String locusTag) {
+        super();
+        this.id = id;
+        this.taxonomyId = taxonomyId;
+        this.seqname = seqname;
+        this.source = source;
+        this.feature = feature;
+        this.start = start;
+        this.end = end;
+        this.score = score;
+        this.strand = strand;
+        this.frame = frame;
+        this.locusTag = locusTag;
+    }
+    
+    public String getId() {
+        return id;
+    }
+    public void setId(String id) {
+        this.id = id;
+    }
+    public String getSeqname() {
+        return seqname;
+    }
+    public void setSeqname(String seqname) {
+        this.seqname = seqname;
+    }
+    public String getSource() {
+        return source;
+    }
+    public void setSource(String source) {
+        this.source = source;
+    }
+    public String getFeature() {
+        return feature;
+    }
+    public void setFeature(String feature) {
+        this.feature = feature;
+    }
+    public String getStart() {
+        return start;
+    }
+    public void setStart(String start) {
+        this.start = start;
+    }
+    public String getEnd() {
+        return end;
+    }
+    public void setEnd(String end) {
+        this.end = end;
+    }
+    public String getScore() {
+        return score;
+    }
+    public void setScore(String score) {
+        this.score = score;
+    }
+    public String getStrand() {
+        return strand;
+    }
+    public void setStrand(String strand) {
+        this.strand = strand;
+    }
+    public String getFrame() {
+        return frame;
+    }
+    public void setFrame(String frame) {
+        this.frame = frame;
+    }
+    public String getLocusTag() {
+        return locusTag;
+    }
+    public void setLocusTag(String locusTag) {
+        this.locusTag = locusTag;
+    }
+
+    public String getTaxonomyId() {
+        return taxonomyId;
+    }
+
+    public void setTaxonomyId(String taxonomyId) {
+        this.taxonomyId = taxonomyId;
+    }
+}

src/main/java/de/unigoettingen/ibeetlebase/api/GeneinfoResource.java → src/main/java/de/unigoettingen/ibeetlebase/geneinfo/resource/GeneResource.java

-package de.unigoettingen.ibeetlebase.api;
+package de.unigoettingen.ibeetlebase.geneinfo.resource;
 
-import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
-
-import io.quarkus.runtime.Quarkus;
-import io.quarkus.runtime.QuarkusApplication;
-import io.quarkus.runtime.annotations.QuarkusMain;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 import javax.inject.Inject;
 import javax.ws.rs.GET;
@@ -15,18 +14,26 @@ import javax.ws.rs.PathParam;
 import javax.ws.rs.Produces;
 import javax.ws.rs.QueryParam;
 import javax.ws.rs.core.MediaType;
-import org.eclipse.microprofile.metrics.annotation.Metered;
-import de.unigoettingen.ibeetlebase.api.core.FlyBase;
-import de.unigoettingen.ibeetlebase.api.core.Gene;
-import de.unigoettingen.ibeetlebase.api.core.OrthoAPI;
-import de.unigoettingen.ibeetlebase.api.core.Tribolium;
 
-@Path("/geneinfo")
+import org.eclipse.microprofile.metrics.annotation.Metered;
+import org.eclipse.microprofile.openapi.annotations.Operation;
+import org.eclipse.microprofile.openapi.annotations.enums.ParameterIn;
+import org.eclipse.microprofile.openapi.annotations.media.ExampleObject;
+import org.eclipse.microprofile.openapi.annotations.parameters.Parameter;
+
+import de.unigoettingen.ibeetlebase.geneinfo.model.FlybaseGene;
+import de.unigoettingen.ibeetlebase.geneinfo.model.Gene;
+import de.unigoettingen.ibeetlebase.geneinfo.model.TriboliumGene;
+import de.unigoettingen.ibeetlebase.geneinfo.service.FlyBase;
+import de.unigoettingen.ibeetlebase.geneinfo.service.OrthoAPI;
+import de.unigoettingen.ibeetlebase.geneinfo.service.Tribolium;
+
+@Path("/")
 @Produces(MediaType.APPLICATION_JSON)
-@QuarkusMain
-public class GeneinfoResource implements QuarkusApplication {
+//@QuarkusMain
+public class GeneResource { //implements QuarkusApplication {
 
-    private static final String VERSION_STRING = "/{dataversion : [0-9]{6}|current}/v1";
+    // private static final String VERSION_STRING = "/{dataversion : [0-9]{6}|current}/v1";
 
     @Inject
     FlyBase fb;
@@ -35,57 +42,67 @@ public class GeneinfoResource implements QuarkusApplication {
     @Inject
     OrthoAPI oa;
 
-    /**
-     * REST Endpoint for the Flybase data
-     * @param dataversion Version ID of the requested data - Required so older versions can be requested in the future
-     * @param fbgn The flybase identifier that information is requested for
-     * @return Gene information for all matching flybase gene identifiers (FBgn)
-     */
+
     @GET
     @Metered
-    @Path(VERSION_STRING + "/flybase/{fbgn: FBgn[0-9]{7}}")
-    public Gene getFlybaseInfo(@PathParam("dataversion") final String dataversion, @PathParam("fbgn") final String fbgn) {
-        if (!checkFBgnID(fbgn)) {
-            return null;
-        }
-        return fb.retrieve(fbgn);
+    @Path("/flybase/genes/{id: FBgn[0-9]{7}}")
+    @Operation(summary = "Get information for a fly gene.")
+    public FlybaseGene getFlybaseGene(
+            @Parameter(
+                    description = "Flybase gene identifier in format FBgn[0-9]{7}.",
+                    example = "FBgn0000015")
+            @PathParam("id") String id) {
+        return Optional.ofNullable(fb.retrieve(id)).map(this::convertToFlybaseGene).orElse(null);
+    }
+    
+    @GET
+    @Metered
+    @Path("/flybase/genes")
+    @Operation(summary = "Get information for a list of fly genes")
+    public List<FlybaseGene> getFlybaseGenes(
+            @Parameter(
+                    in = ParameterIn.QUERY,
+                    description = "Flybase gene identifiers in format FBgn[0-9]{7}",
+                    examples = @ExampleObject(name = "FBgn0000015", value = "FBgn0000015"))
+            @QueryParam("ids") Set<String> ids) {
+        return ids.stream()
+                .filter(id -> checkFBgnID(id))
+                .map(id -> fb.retrieve(id))
+                .filter(gene -> gene != null)
+                .map(this::convertToFlybaseGene)
+                .collect(Collectors.toList());
     }
 
-    /**
-     * REST Endpoint for the Tribolium data (from the iBB gff file)
-     * @param dataversion Version ID of the requested data - Required so older versions can be requested in the future
-     * @param tc The TC identifier that information is requested for
-     * @return Gene information for all matching tribolium gene identifiers (TC)
-     */
+
     @GET
     @Metered
-    @Path(VERSION_STRING + "/tribolium/{tc: TC[0-9]{6}}")
-    public Gene getTriboliumInfo(@PathParam("dataversion") final String dataversion, @PathParam("tc") final String tc) {
-        if (!checkTCID(tc)) {
-            return null;
-        }
-        return tb.retrieve(tc);
+    @Path("/tribolium/genes/{id: TC[0-9]{6}}")
+    @Operation(summary = "Get information for a tribolium gene.")
+    public TriboliumGene getTriboliumGene(
+            @Parameter(
+                    description = "Tribolium gene identifier in format TC[0-9]{6}}.",
+                    example = "TC001906")
+            @PathParam("id") String tc) {
+        return Optional.ofNullable(tb.retrieve(tc)).map(this::convertToTriboliumGene).orElse(null);
     }
 
-    /**
-     * Accepts multiple comma-separated gene IDs and returns the resulting gene information.
-     * @param ids The list of IDs
-     * @return Gene information for each queried ID
-     */
+
     @GET
     @Metered
-    @Path(VERSION_STRING + "/gene")
-    public List<Gene> getInfo(@QueryParam("ids") final String ids) {
-        List<Gene> result_list = new ArrayList<Gene>();
-        for (String id : ids.split(",")) {
-            if (checkTCID(id)) {
-                result_list.add(tb.retrieve(id));
-            }
-            else if (checkFBgnID(id)) {
-                result_list.add(fb.retrieve(id));
-            }
-        }
-        return result_list;
+    @Path("/tribolium/genes")
+    @Operation(summary = "Get information for a list of fly genes")
+    public List<TriboliumGene> getTriboliumGenes(
+            @Parameter(
+                    in = ParameterIn.QUERY,
+                    description = "Tribolium gene identifiers in format TC[0-9]{6}",
+                    examples = @ExampleObject(name = "TC001906", value = "TC001906"))
+            @QueryParam("ids") Set<String> ids) {
+        return ids.stream()
+                .filter(id -> checkTCID(id))
+                .map(id -> tb.retrieve(id))
+                .filter(gene -> gene != null)
+                .map(this::convertToTriboliumGene)
+                .collect(Collectors.toList());
     }
 
     /**
@@ -111,24 +128,28 @@ public class GeneinfoResource implements QuarkusApplication {
      * @param dataversion Version ID of the requested data - Required so older versions can be requested in the future
      * @return All flybase gene identifiers and their according gene names
      */
+    /*
     @GET
     @Metered
-    @Path(VERSION_STRING + "/flybase/identifiers")
-    public Map<String, String> getAllFlybaseIDs(@PathParam("dataversion") final String dataversion) {
+    @Path("/flybase/identifiers")
+    public Map<String, String> getAllFlybaseIDs() {
         return fb.getAllIDs();
     }
+    */
 
     /**
      * REST Endpoint that returns all tribolium gene identifiers and their according gene names
      * @param dataversion Version ID of the requested data - Required so older versions can be requested in the future
      * @return All TC gene identifiers and their according gene names
      */
+    /*
     @GET
     @Metered
-    @Path(VERSION_STRING + "/tribolium/identifiers")
-    public Map<String, String> getAllTriboliumIDs(@PathParam("dataversion") final String dataversion) {
+    @Path("/tribolium/identifiers")
+    public Map<String, String> getAllTriboliumIDs() {
         return tb.getAllIDs();
     }
+    */
 
     /**
      * This function (requiring Quarkus 1.4.2) is called when the application is started
@@ -136,6 +157,7 @@ public class GeneinfoResource implements QuarkusApplication {
      * @param args The command line arguments
      * @return The exit status (0)
      */
+    /*
     @Override
 	public int run(String... args) throws Exception {
 
@@ -147,5 +169,54 @@ public class GeneinfoResource implements QuarkusApplication {
         Quarkus.waitForExit();
 		return 0;
     }
-
+    */
+
+    private FlybaseGene convertToFlybaseGene(Gene gene) {
+        Map<String, Collection<String>> info = gene.getInformation();
+        return new FlybaseGene(gene.getGeneID(),
+                collectionToString(organismToTaxonomyId(info.get("organism"))),
+                collectionToString(info.get("gene_type")),
+                collectionToString(info.get("gene_symbol")),
+                collectionToString(info.get("gene_fullname")),
+                collectionToString(info.get("annotation_ID")),
+                collectionToString(info.get("transcript_Type")),
+                info.get("transcript_ID").stream().collect(Collectors.toSet()));
+    }
+    
+    private TriboliumGene convertToTriboliumGene(Gene gene) {
+        Map<String, Collection<String>> info = gene.getInformation();
+        return new TriboliumGene(gene.getGeneID(),
+                "7070", 
+                collectionToString(info.get("seqname")),
+                collectionToString(info.get("source")), 
+                collectionToString(info.get("feature")),
+                collectionToString(info.get("start")),
+                collectionToString(info.get("end")),
+                collectionToString(info.get("score")),
+                collectionToString(info.get("strand")),
+                collectionToString(info.get("frame")),
+                collectionToString(info.get("locus_tag")));
+    }
+    
+    private Collection<String> organismToTaxonomyId(Collection<String> organisms) {
+        return organisms.stream().map(o -> {
+            switch (o) {
+            case "Dana":
+                return "7217";
+            case "Dmel":
+                return "7227";
+            case "Dvir":
+                return "7244";
+            case "Dpse":
+                return "7237";
+            case "Dsim":
+                return "7240";
+            }
+            return null;
+        }).collect(Collectors.toList());
+    }
+    
+    private String collectionToString(Collection<String> items) {
+        return items.stream().collect(Collectors.joining(", "));
+    }
 }
\ No newline at end of file

src/main/java/de/unigoettingen/ibeetlebase/api/core/FlyBase.java → src/main/java/de/unigoettingen/ibeetlebase/geneinfo/service/FlyBase.java

-package de.unigoettingen.ibeetlebase.api.core;
+package de.unigoettingen.ibeetlebase.geneinfo.service;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
@@ -9,7 +9,9 @@ import java.util.Map;
 import java.util.LinkedList;
 import javax.enterprise.context.ApplicationScoped;
 import javax.inject.Inject;
-import de.unigoettingen.ibeetlebase.AppServiceBean;
+
+import de.unigoettingen.ibeetlebase.geneinfo.AppServiceBean;
+import de.unigoettingen.ibeetlebase.geneinfo.model.Gene;
 
 @ApplicationScoped
 public class FlyBase implements GeneSource {

src/main/java/de/unigoettingen/ibeetlebase/api/core/GeneSource.java → src/main/java/de/unigoettingen/ibeetlebase/geneinfo/service/GeneSource.java

-package de.unigoettingen.ibeetlebase.api.core;
+package de.unigoettingen.ibeetlebase.geneinfo.service;
+
+import de.unigoettingen.ibeetlebase.geneinfo.model.Gene;
 
 public interface GeneSource {