Add search by symbol, fullname and annotationId

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

@@ -5,7 +5,7 @@ import java.util.Set;
 import io.quarkus.runtime.annotations.RegisterForReflection;
 
 @RegisterForReflection
-public class FlybaseGene {
+public class DrosophilaGene {
     private String id;
     private String taxanomyId;
     private String type;
@@ -15,7 +15,7 @@ public class FlybaseGene {
     private String transcriptType;
     private Set<String> transcriptIds;
     
-    public FlybaseGene(String id, String taxanomyId, String type, String symbol,
+    public DrosophilaGene(String id, String taxanomyId, String type, String symbol,
             String fullname, String annotationId, String transcriptType,
             Set<String> transcriptIds) {
         super();

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/repository/DrosophilaGeneRepository.java

+package de.unigoettingen.ibeetlebase.geneinfo.repository;
+
+import java.util.Collection;
+
+import de.unigoettingen.ibeetlebase.geneinfo.model.DrosophilaGene;
+
+public interface DrosophilaGeneRepository extends Repository<DrosophilaGene> {
+    Collection<DrosophilaGene> getBySymbol(String symbol);
+    Collection<DrosophilaGene> getByFullname(String fullname);
+    Collection<DrosophilaGene> getByAnnotationId(String annotationId);
+}
\ No newline at end of file

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/repository/InMemoryDrosophilaGeneRepository.java

+package de.unigoettingen.ibeetlebase.geneinfo.repository;
+
+import static java.util.stream.Collectors.groupingBy;
+import static java.util.stream.Collectors.toCollection;
+import static java.util.stream.Collectors.toMap;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import javax.annotation.PostConstruct;
+import javax.enterprise.context.ApplicationScoped;
+import javax.inject.Inject;
+
+import de.unigoettingen.ibeetlebase.geneinfo.model.DrosophilaGene;
+import de.unigoettingen.ibeetlebase.geneinfo.model.Gene;
+import de.unigoettingen.ibeetlebase.geneinfo.service.FlyBase;
+import io.quarkus.runtime.Startup;
+
+@Startup
+@ApplicationScoped
+public class InMemoryDrosophilaGeneRepository implements DrosophilaGeneRepository {
+
+    @Inject
+    FlyBase service;
+    
+    private Map<String, DrosophilaGene> mapFromId;
+    private Map<String, Collection<DrosophilaGene>> mapFromSymbol;
+    private Map<String, Collection<DrosophilaGene>> mapFromFullname;
+    private Map<String, Collection<DrosophilaGene>> mapFromAnnotationId;
+    
+    @Override
+    public DrosophilaGene get(String id) {
+        return mapFromId.get(id);
+    }
+
+    @Override
+    public Collection<DrosophilaGene> get() {
+        return mapFromId.values();
+    }
+
+    @Override
+    public Collection<DrosophilaGene> getBySymbol(String symbol) {
+        return mapFromSymbol.getOrDefault(symbol, Collections.emptyList());
+    }
+
+    @Override
+    public Collection<DrosophilaGene> getByFullname(String fullname) {
+        return mapFromFullname.getOrDefault(fullname, Collections.emptyList());
+    }
+
+    @Override
+    public Collection<DrosophilaGene> getByAnnotationId(String annotationId) {
+        return mapFromAnnotationId.getOrDefault(annotationId, Collections.emptyList());
+    }
+
+    @PostConstruct
+    void init() {
+        loadData();
+    }
+
+    private void loadData() {
+        mapFromId = service.getDB().entrySet()
+                .stream()
+                .collect(toMap(Map.Entry::getKey, 
+                        entry -> convertToFlybaseGene(entry.getValue())));
+        
+        mapFromSymbol = mapFromId.values()
+                .stream()
+                .collect(groupingBy(DrosophilaGene::getSymbol, toCollection(LinkedList::new)));
+        
+        mapFromFullname = mapFromId.values()
+                .stream()
+                .collect(groupingBy(DrosophilaGene::getFullname, toCollection(LinkedList::new)));
+
+        mapFromAnnotationId = mapFromId.values()
+                .stream()
+                .collect(groupingBy(DrosophilaGene::getAnnotationId, toCollection(LinkedList::new)));
+    }
+    
+    private DrosophilaGene convertToFlybaseGene(Gene gene) {
+        Map<String, Collection<String>> info = gene.getInformation();
+        return new DrosophilaGene(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 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(", "));
+    }
+}

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/repository/InMemoryTriboliumGeneRepository.java

+package de.unigoettingen.ibeetlebase.geneinfo.repository;
+
+import static java.util.stream.Collectors.toMap;
+
+import java.util.Collection;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import javax.annotation.PostConstruct;
+import javax.enterprise.context.ApplicationScoped;
+import javax.inject.Inject;
+
+import de.unigoettingen.ibeetlebase.geneinfo.model.Gene;
+import de.unigoettingen.ibeetlebase.geneinfo.model.TriboliumGene;
+import de.unigoettingen.ibeetlebase.geneinfo.service.Tribolium;
+import io.quarkus.runtime.Startup;
+
+@Startup
+@ApplicationScoped
+public class InMemoryTriboliumGeneRepository implements TriboliumGeneRepository {
+
+    @Inject
+    Tribolium service;
+    
+    private Map<String, TriboliumGene> mapFromId;
+    
+    @Override
+    public TriboliumGene get(String id) {
+        return mapFromId.get(id);
+    }
+
+    @Override
+    public Collection<TriboliumGene> get() {
+        return mapFromId.values();
+    }
+
+    @PostConstruct
+    void init() {
+        loadData();
+    }
+
+    private void loadData() {
+        mapFromId = service.getDB().entrySet()
+                .stream()
+                .collect(toMap(Map.Entry::getKey,
+                        entry -> convertToTriboliumGene(entry.getValue())));
+    }
+    
+    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 String collectionToString(Collection<String> items) {
+        return items.stream().collect(Collectors.joining(", "));
+    }
+}

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/repository/Repository.java

+package de.unigoettingen.ibeetlebase.geneinfo.repository;
+
+import java.util.Collection;
+
+public interface Repository<T> {
+    T get(String id);
+    Collection<T> get();
+}

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/repository/TriboliumGeneRepository.java

+package de.unigoettingen.ibeetlebase.geneinfo.repository;
+
+import de.unigoettingen.ibeetlebase.geneinfo.model.TriboliumGene;
+
+public interface TriboliumGeneRepository extends Repository<TriboliumGene>{
+
+}

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/resource/GeneResource.java

 package de.unigoettingen.ibeetlebase.geneinfo.resource;
 
+import static java.util.stream.Collectors.toList;
+
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
-import java.util.Map;
-import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import javax.inject.Inject;
 import javax.ws.rs.GET;
@@ -14,63 +16,97 @@ import javax.ws.rs.PathParam;
 import javax.ws.rs.Produces;
 import javax.ws.rs.QueryParam;
 import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.Response.Status;
 
 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.enums.SchemaType;
+import org.eclipse.microprofile.openapi.annotations.media.Content;
 import org.eclipse.microprofile.openapi.annotations.media.ExampleObject;
+import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import org.eclipse.microprofile.openapi.annotations.parameters.Parameter;
+import org.eclipse.microprofile.openapi.annotations.responses.APIResponse;
 
-import de.unigoettingen.ibeetlebase.geneinfo.model.FlybaseGene;
-import de.unigoettingen.ibeetlebase.geneinfo.model.Gene;
+import de.unigoettingen.ibeetlebase.geneinfo.model.DrosophilaGene;
 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;
+import de.unigoettingen.ibeetlebase.geneinfo.repository.DrosophilaGeneRepository;
+import de.unigoettingen.ibeetlebase.geneinfo.repository.TriboliumGeneRepository;
 
 @Path("/")
 @Produces(MediaType.APPLICATION_JSON)
 //@QuarkusMain
-public class GeneResource { //implements QuarkusApplication {
-
-    // private static final String VERSION_STRING = "/{dataversion : [0-9]{6}|current}/v1";
+public class GeneResource {
 
     @Inject
-    FlyBase fb;
-    @Inject
-    Tribolium tb;
+    DrosophilaGeneRepository dGeneRepo;
+    
     @Inject
-    OrthoAPI oa;
-
+    TriboliumGeneRepository tGeneRepo;
 
     @GET
     @Metered
     @Path("/flybase/genes/{id: FBgn[0-9]{7}}")
     @Operation(summary = "Get information for a fly gene.")
-    public FlybaseGene getFlybaseGene(
+    public DrosophilaGene 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);
+        return dGeneRepo.get(id);
     }
     
     @GET
     @Metered
     @Path("/flybase/genes")
     @Operation(summary = "Get information for a list of fly genes")
-    public List<FlybaseGene> getFlybaseGenes(
+    @APIResponse(
+            responseCode = "200",
+            description = "A list of found genes.",
+            content = @Content(
+                    mediaType = "application/json",
+                    schema = @Schema(type = SchemaType.ARRAY, implementation = DrosophilaGene.class)))
+    @APIResponse(
+            responseCode = "400",
+            description = "Zero or more than one query params are provided.")
+    public Response 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());
+                    description = "Flybase gene identifiers in format FBgn[0-9]{7}")
+            @QueryParam("ids") Set<String> ids,
+            
+            @QueryParam("symbol") String symbol,
+            
+            @Parameter(
+                    in = ParameterIn.QUERY,
+                    example = "knirps")
+            @QueryParam("fullname") String fullname,
+            @QueryParam("annotationId") String annotationId) {
+        
+        long paramCnt = Stream.of(symbol, fullname, annotationId).filter(p -> p != null).count();
+        if (paramCnt > 0 && ids.size() > 0 || ids.size() == 0 && paramCnt != 1) {
+            return Response.status(Status.BAD_REQUEST).build();
+        }
+        
+        Collection<DrosophilaGene> dGenes;
+        
+        if (!ids.isEmpty()) {
+            dGenes = ids.stream()
+                    .filter(id -> checkFBgnID(id))
+                    .map(id -> dGeneRepo.get(id))
+                    .filter(gene -> gene != null)
+                    .collect(Collectors.toList());
+        } else if (symbol != null) {
+            dGenes = dGeneRepo.getBySymbol(symbol);
+        } else if (fullname != null) {
+            dGenes = dGeneRepo.getByFullname(fullname);
+        } else if (annotationId != null) {
+            dGenes = dGeneRepo.getByAnnotationId(annotationId);
+        } else {
+            dGenes = Collections.emptyList();
+        }
+        return Response.ok(dGenes.stream().collect(toList())).build();
     }
 
 
@@ -82,8 +118,8 @@ public class GeneResource { //implements QuarkusApplication {
             @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);
+            @PathParam("id") String id) {
+        return tGeneRepo.get(id);
     }
 
 
@@ -99,9 +135,8 @@ public class GeneResource { //implements QuarkusApplication {
             @QueryParam("ids") Set<String> ids) {
         return ids.stream()
                 .filter(id -> checkTCID(id))
-                .map(id -> tb.retrieve(id))
+                .map(id -> tGeneRepo.get(id))
                 .filter(gene -> gene != null)
-                .map(this::convertToTriboliumGene)
                 .collect(Collectors.toList());
     }
 
@@ -122,101 +157,4 @@ public class GeneResource { //implements QuarkusApplication {
     private boolean checkTCID(final String tc) {
         return tc.matches("TC[0-9]{6}");
     }
-
-    /**
-     * REST Endpoint that returns all flybase 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 flybase gene identifiers and their according gene names
-     */
-    /*
-    @GET
-    @Metered
-    @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("/tribolium/identifiers")
-    public Map<String, String> getAllTriboliumIDs() {
-        return tb.getAllIDs();
-    }
-    */
-
-    /**
-     * This function (requiring Quarkus 1.4.2) is called when the application is started
-     * If "orthoapi" is given as a command line argument in dev mode, the OrthoDB API calls are executed 
-     * @param args The command line arguments
-     * @return The exit status (0)
-     */
-    /*
-    @Override
-	public int run(String... args) throws Exception {
-
-        // Calls the relevant OrthoDB API methods for all genes
-        if (args.length > 0 && args[0].equals("list_file")) {
-            //Should write all identifiers to a file.
-        }
-        
-        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/geneinfo/service/FlyBase.java

 package de.unigoettingen.ibeetlebase.geneinfo.service;
 
 import java.io.BufferedReader;
-import java.io.FileReader;
 import java.io.File;
+import java.io.FileReader;
 import java.io.IOException;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.LinkedList;
+import java.util.Map;
+
 import javax.enterprise.context.ApplicationScoped;
 import javax.inject.Inject;
 
@@ -26,7 +27,7 @@ public class FlyBase implements GeneSource {
      * Fills the database with information from the gene file by calling the according method (only if the database is empty)
      * @return The database containing all information from the FlyBase gene file
      */
-    private Map<String, Gene> getDB() {
+    public Map<String, Gene> getDB() {
         if (this.database == null) {
             int[] column_ind = new int[]{0,1,2,3,4,5,6,7};
             String[] column_des = new String[]{"organism", "gene_type", "gene_ID", "gene_symbol", "gene_fullname",

src/main/java/de/unigoettingen/ibeetlebase/geneinfo/service/Tribolium.java

 package de.unigoettingen.ibeetlebase.geneinfo.service;
 
 import java.io.BufferedReader;
-import java.io.FileReader;
 import java.io.File;
+import java.io.FileReader;
 import java.io.IOException;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.LinkedList;
+import java.util.Map;
+
 import javax.enterprise.context.ApplicationScoped;
 import javax.inject.Inject;
 
@@ -27,7 +28,7 @@ public class Tribolium implements GeneSource {
      * Fills the database with information from the gene file by calling the according method (only if the database is empty)
      * @return The database containing all information from the tribolium gene file
      */
-    private Map<String, Gene> getDB() {
+    public Map<String, Gene> getDB() {
         if (this.database == null) {
             String[] column_des = new String[]{"seqname", "source", "feature", "start", "end", "score", "strand", "frame"};
             this.database = readGeneFile(column_des);