Issue #731 Metabolic pathways

server/catgenome/build.gradle

@@ -78,6 +78,9 @@ ext {
 // >>>>> repositories that should be used to find any external dependencies
 repositories {
     mavenCentral()
+    maven {
+        url "https://jitpack.io"
+    }
     flatDir {
         dirs 'lib'
     }
@@ -188,6 +191,9 @@ dependencies {
     // newick format
     compile group: "com.github.qurben", name: "libnewicktree", version: "1.0"
 
+    // sbgn format
+    compile group: "com.github.sbgn", name: "libsbgn", version: "b619268"
+
     // >>>>> dependencies used to compile tests; in fact no need to include them into artifact
     testCompile("org.springframework.boot:spring-boot-starter-test")
     testCompile group: "org.unitils", name: "unitils-core", version: project.ext.versionUnitils

server/catgenome/profiles/dev/catgenome.properties

@@ -136,3 +136,4 @@ homologene.index.directory=${HOMOLOGENE_INDEX_DIR:@rootDirPath@/contents/homolog
 
 #METABOLIC PATHWAY
 pathway.index.directory=${PATHWAY_INDEX_DIRECTORY:@rootDirPath@/contents/pathway}
+pathway.top.hits=${PATHWAY_TOP_HITS:100}

server/catgenome/src/main/java/com/epam/catgenome/constant/MessagesConstants.java

@@ -294,6 +294,8 @@ public final class MessagesConstants {
 
     //Pathway
     public static final String ERROR_PATHWAY_NOT_FOUND = "error.pathway.not.found";
+    public static final String ERROR_PATHWAY_NO_GLYPHS = "error.pathway.no.glyphs.found";
+    public static final String ERROR_PATHWAY_NO_ARCS = "error.pathway.no.arcs.found";
 
     //Attributes
     public static final String ERROR_ATTRIBUTE_INVALID_VALUE = "error.attribute.invalid.value";

server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java

@@ -28,16 +28,27 @@
 import com.epam.catgenome.controller.Result;
 import com.epam.catgenome.controller.vo.registration.PathwayRegistrationRequest;
 import com.epam.catgenome.entity.pathway.Pathway;
+import com.epam.catgenome.entity.pathway.SbgnElement;
+import com.epam.catgenome.util.db.Page;
 import com.epam.catgenome.manager.pathway.PathwaySecurityService;
+import com.epam.catgenome.util.db.QueryParameters;
 import com.wordnik.swagger.annotations.Api;
 import com.wordnik.swagger.annotations.ApiOperation;
 import com.wordnik.swagger.annotations.ApiResponse;
 import com.wordnik.swagger.annotations.ApiResponses;
 import lombok.RequiredArgsConstructor;
 import org.apache.lucene.queryparser.classic.ParseException;
 import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.*;
+import org.springframework.web.bind.annotation.DeleteMapping;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
 
+import javax.servlet.http.HttpServletResponse;
+import javax.xml.bind.JAXBException;
 import java.io.IOException;
 import java.util.List;
 
@@ -57,20 +68,49 @@ public class PathwayController extends AbstractRESTController {
             value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
             })
     public Result<Pathway> loadPathway(@PathVariable final Long pathwayId,
-                                             @RequestParam(required = false) final Long projectId) {
+                                       @RequestParam(required = false) final Long projectId) {
         return Result.success(pathwaySecurityService.loadPathway(pathwayId, projectId));
     }
 
+    @GetMapping(value = "/pathway/content/{pathwayId}")
+    @ApiOperation(
+            value = "Returns a pathway file content by pathway id",
+            notes = "Returns a pathway file content by pathway id",
+            produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
+    @ApiResponses(
+            value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
+            })
+    public void loadPathwayContent(@PathVariable final Long pathwayId,
+                                   @RequestParam(required = false) final Long projectId,
+                                   final HttpServletResponse response) throws IOException {
+        byte[] bytes = pathwaySecurityService.loadPathwayContent(pathwayId, projectId);
+        response.getOutputStream().write(bytes);
+        response.flushBuffer();
+    }
+
+    @PostMapping(value = "/pathway/search")
+    @ApiOperation(
+            value = "Searches sbgn file elements",
+            notes = "Searches sbgn file elements",
+            produces = MediaType.APPLICATION_JSON_VALUE)
+    @ApiResponses(
+            value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
+            })
+    public Result<List<SbgnElement>> searchElements(@RequestBody SbgnElement sbgnElement)
+            throws IOException, ParseException {
+        return Result.success(pathwaySecurityService.searchElements(sbgnElement));
+    }
+
     @GetMapping(value = "/pathways")
     @ApiOperation(
-            value = "Returns all pathways",
-            notes = "Returns all pathways",
+            value = "Returns pathways page",
+            notes = "Returns pathways page",
             produces = MediaType.APPLICATION_JSON_VALUE)
     @ApiResponses(
             value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
             })
-    public Result<List<Pathway>> loadPathways() {
-        return Result.success(pathwaySecurityService.loadPathways());
+    public Result<Page<Pathway>> loadPathways(final QueryParameters queryParameters) {
+        return Result.success(pathwaySecurityService.loadPathways(queryParameters));
     }
 
     @PostMapping(value = "/pathway")
@@ -82,7 +122,7 @@ public Result<List<Pathway>> loadPathways() {
             value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
             })
     public Result<Pathway> createPathway(@RequestBody final PathwayRegistrationRequest request)
-            throws IOException, ParseException {
+            throws IOException, ParseException, JAXBException {
         return Result.success(pathwaySecurityService.createPathway(request));
     }
 

server/catgenome/src/main/java/com/epam/catgenome/dao/pathway/PathwayDao.java

@@ -27,6 +27,7 @@
 import com.epam.catgenome.entity.BiologicalDataItemFormat;
 import com.epam.catgenome.entity.BiologicalDataItemResourceType;
 import com.epam.catgenome.entity.pathway.Pathway;
+import com.epam.catgenome.util.db.QueryParameters;
 import lombok.AllArgsConstructor;
 import lombok.NoArgsConstructor;
 import lombok.Setter;
@@ -42,6 +43,8 @@
 import java.sql.SQLException;
 import java.util.List;
 
+import static com.epam.catgenome.util.Utils.addParametersToQuery;
+
 @Setter
 @NoArgsConstructor
 @AllArgsConstructor
@@ -54,6 +57,7 @@ public class PathwayDao extends NamedParameterJdbcDaoSupport {
     private String deletePathwayQuery;
     private String loadPathwayQuery;
     private String loadPathwaysQuery;
+    private String getTotalCountQuery;
 
     /**
      * Persists new Pathway record.
@@ -89,8 +93,13 @@ public Pathway loadPathway(final long pathwayId) {
      * Loads {@code Pathways} from a database.
      * @return a {@code List<Pathway>} from the database
      */
-    public List<Pathway> loadAllPathways() {
-        return getJdbcTemplate().query(loadPathwaysQuery, PathwayParameters.getRowMapper());
+    public List<Pathway> loadAllPathways(final QueryParameters queryParameters) {
+        final String query = addParametersToQuery(loadPathwaysQuery, queryParameters);
+        return getJdbcTemplate().query(query, PathwayParameters.getRowMapper());
+    }
+
+    public long getTotalCount() {
+        return getJdbcTemplate().queryForObject(getTotalCountQuery, Long.class);
     }
 
     enum PathwayParameters {

server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/PathwayEntry.java → server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/SbgnElement.java

@@ -30,7 +30,10 @@
 @Getter
 @Setter
 @Builder
-public class PathwayEntry {
+public class SbgnElement {
     private Long pathwayId;
-    //TODO
+    private SbgnElementType type;
+    private String clazz;
+    private String entryId;
+    private String label;
 }

server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/SbgnElementType.java

@@ -0,0 +1,48 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2022 EPAM Systems
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+package com.epam.catgenome.entity.pathway;
+
+public enum SbgnElementType {
+    GLYPH("glyph"),
+    ARC("arc");
+
+    public String getName() {
+        return name;
+    }
+
+    private final String name;
+
+    SbgnElementType(String name) {
+        this.name = name;
+    }
+
+    public static SbgnElementType getByName(final String name) {
+        for (SbgnElementType type : SbgnElementType.values()) {
+            if (name.equals(type.getName())) {
+                return type;
+            }
+        }
+        return null;
+    }
+}