Issue #731 Metabolic pathways

docs/md/cli/command-reference.md

@@ -900,6 +900,55 @@ Deletes a specified lineage tree from NGB server.
 $ ngb del_lineage 2
 ```
 
+## Metabolic pathway commands
+### Register pathway
+```
+ngb reg_pathway|rp [<PATH>] [options]
+//Options:
+//-n (--name)                   Pathway name
+//-pt (--pretty)                Pathway pretty name
+
+```
+*Description*
+
+Registers a Pathway. One argument has to be specified:
+* Pathway file path
+
+*Example*
+```bash
+# Create new pathway with path "pathway.sbml"
+$ ngb reg_pathway "pathway.sbml"
+```
+
+### List metabolic pathways
+```
+ngb list_pathway|lp
+```
+
+*Description*
+
+List all pathways registered on NGB server.
+
+*Example*
+```bash
+# List all pathways registered on NGB server
+$ ngb list_pathway
+```
+
+### Delete metabolic pathway
+```
+ngb del_pathway|dp [<ID>]
+```
+*Description*
+
+Deletes a specified pathway from NGB server.
+
+*Example*
+```bash
+# Delete pathway with id 2
+$ ngb del_pathway 2
+```
+
 ## Utility commands
 ### Sort feature file
 ```

server/catgenome/profiles/dev/catgenome.properties

@@ -134,3 +134,5 @@ export.page.size=${EXPORT_PAGE_SIZE:100}
 #HOMOLOGENE
 homologene.index.directory=${HOMOLOGENE_INDEX_DIR:@rootDirPath@/contents/homologene}
 
+#METABOLIC PATHWAY
+pathway.index.directory=${PATHWAY_INDEX_DIRECTORY:@rootDirPath@/contents/pathway}

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

@@ -292,6 +292,9 @@ public final class MessagesConstants {
     public static final String ERROR_LINEAGE_NOT_UNIQUE_NODE_NAME = "error.lineage.not.unique.node.name";
     public static final String ERROR_LINEAGE_INCORRECT_EDGE = "error.lineage.incorrect.edge";
 
+    //Pathway
+    public static final String ERROR_PATHWAY_NOT_FOUND = "error.pathway.not.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

@@ -0,0 +1,101 @@
+/*
+ * 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.controller.pathway;
+
+import com.epam.catgenome.controller.AbstractRESTController;
+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.manager.pathway.PathwaySecurityService;
+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 java.io.IOException;
+import java.util.List;
+
+@RestController
+@Api(value = "pathway", description = "Metabolic Pathways Management")
+@RequiredArgsConstructor
+public class PathwayController extends AbstractRESTController {
+
+    private final PathwaySecurityService pathwaySecurityService;
+
+    @GetMapping(value = "/pathway/{pathwayId}")
+    @ApiOperation(
+            value = "Returns a pathway by id",
+            notes = "Returns a pathway by id",
+            produces = MediaType.APPLICATION_JSON_VALUE)
+    @ApiResponses(
+            value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
+            })
+    public Result<Pathway> loadPathway(@PathVariable final Long pathwayId,
+                                             @RequestParam(required = false) final Long projectId) {
+        return Result.success(pathwaySecurityService.loadPathway(pathwayId, projectId));
+    }
+
+    @GetMapping(value = "/pathways")
+    @ApiOperation(
+            value = "Returns all pathways",
+            notes = "Returns all pathways",
+            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());
+    }
+
+    @PostMapping(value = "/pathway")
+    @ApiOperation(
+            value = "Registers new pathway",
+            notes = "Registers new pathway",
+            produces = MediaType.APPLICATION_JSON_VALUE)
+    @ApiResponses(
+            value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
+            })
+    public Result<Pathway> createPathway(@RequestBody final PathwayRegistrationRequest request)
+            throws IOException, ParseException {
+        return Result.success(pathwaySecurityService.createPathway(request));
+    }
+
+    @DeleteMapping(value = "/pathway/{pathwayId}")
+    @ApiOperation(
+            value = "Deletes a pathway, specified by id",
+            notes = "Deletes a pathway, specified by id",
+            produces = MediaType.APPLICATION_JSON_VALUE)
+    @ApiResponses(
+            value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
+            })
+    public Result<Boolean> deletePathway(@PathVariable final long pathwayId) throws IOException {
+        pathwaySecurityService.deletePathway(pathwayId);
+        return Result.success(null);
+    }
+}

server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/PathwayRegistrationRequest.java

@@ -0,0 +1,36 @@
+/*
+ * 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.controller.vo.registration;
+
+import lombok.Getter;
+import lombok.Setter;
+
+@Getter
+@Setter
+public class PathwayRegistrationRequest extends DefaultFileRegistrationRequest {
+    private String name;
+    private String prettyName;
+    private String path;
+    private String pathwayDesc;
+}

server/catgenome/src/main/java/com/epam/catgenome/dao/BiologicalDataItemDao.java

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2016-2021 EPAM Systems
+ * Copyright (c) 2016-2022 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
@@ -47,6 +47,7 @@
 import com.epam.catgenome.entity.heatmap.HeatmapDataType;
 import com.epam.catgenome.entity.lineage.LineageTree;
 import com.epam.catgenome.entity.maf.MafFile;
+import com.epam.catgenome.entity.pathway.Pathway;
 import com.epam.catgenome.entity.reference.Reference;
 import com.epam.catgenome.entity.seg.SegFile;
 import com.epam.catgenome.entity.vcf.VcfFile;
@@ -287,6 +288,9 @@ public enum BiologicalDataItemParameters {
         NODES_PATH,
         EDGES_PATH,
 
+        PATHWAY_ID,
+        PATHWAY_DESC,
+
         INDEX_ID,
         INDEX_NAME,
         INDEX_TYPE,
@@ -383,6 +387,9 @@ private static BiologicalDataItem mapSpecialFields(ResultSet rs, BiologicalDataI
                 case LINEAGE_TREE:
                     dataItem = mapLineageTree(rs);
                     break;
+                case PATHWAY:
+                    dataItem = mapPathway(rs);
+                    break;
                 default:
                     dataItem = mapBioDataItem(rs);
             }
@@ -413,6 +420,15 @@ private static BiologicalDataItem mapLineageTree(final ResultSet rs) throws SQLE
             return lineageTree;
         }
 
+        private static BiologicalDataItem mapPathway(final ResultSet rs) throws SQLException {
+            final Pathway pathway = Pathway.builder().build();
+            pathway.setId(rs.getLong(PATHWAY_ID.name()));
+            pathway.setPathwayId(rs.getLong(PATHWAY_ID.name()));
+            pathway.setPathwayDesc(rs.getString(PATHWAY_DESC.name()));
+            pathway.setBioDataItemId(rs.getLong(BIO_DATA_ITEM_ID.name()));
+            return pathway;
+        }
+
         private static BiologicalDataItem mapBioDataItem(ResultSet rs) throws SQLException {
             BiologicalDataItem dataItem = new BiologicalDataItem();
             dataItem.setId(rs.getLong(BIO_DATA_ITEM_ID.name()));