Issue #731 Metabolic pathways search changes

epam · Jan 31, 2022 · d5c565c · d5c565c
1 parent e924dde
commit d5c565c
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Showing 8 changed files with 144 additions and 199 deletions.
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/constant/MessagesConstants.java b/server/catgenome/src/main/java/com/epam/catgenome/constant/MessagesConstants.java
@@ -76,6 +76,7 @@ public final class MessagesConstants {
     public static final String ERROR_SPECIES_NOT_SPECIFIED = "error.no.species";
     public static final String ERROR_INDEX_NOT_SPECIFIED = "error.no.index.cache";
     public static final String ERROR_INDEX_URL_NOT_SPECIFIED = "error.no.index.url.cache";
+    public static final String ERROR_INDEX_DIRECTORY_IS_EMPTY = "error.empty.index.directory";
     public static final String ERROR_CHROMOSOME_NOT_SPECIFIED = "error.no.chromosome";
     public static final String ERROR_STARTPOSITION_NOT_SPECIFIED = "error.no.startposition";
     public static final String ERROR_FINISHPOSITION_NOT_SPECIFIED = "error.no.finishposition";
@@ -294,8 +295,6 @@ 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";

diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java
@@ -28,10 +28,9 @@
 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.entity.pathway.PathwayQueryParams;
 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;
@@ -50,7 +49,6 @@
 import javax.servlet.http.HttpServletResponse;
 import javax.xml.bind.JAXBException;
 import java.io.IOException;
-import java.util.List;
 
 @RestController
 @Api(value = "pathway", description = "Metabolic Pathways Management")
@@ -88,19 +86,6 @@ public void loadPathwayContent(@PathVariable final Long pathwayId,
         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));
-    }
-
     @PostMapping(value = "/pathways")
     @ApiOperation(
             value = "Returns pathways page",
@@ -109,8 +94,9 @@ public Result<List<SbgnElement>> searchElements(@RequestBody SbgnElement sbgnEle
     @ApiResponses(
             value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
             })
-    public Result<Page<Pathway>> loadPathways(@RequestBody final QueryParameters queryParameters) {
-        return Result.success(pathwaySecurityService.loadPathways(queryParameters));
+    public Result<Page<Pathway>> loadPathways(@RequestBody final PathwayQueryParams params)
+            throws IOException, ParseException {
+        return Result.success(pathwaySecurityService.loadPathways(params));
     }
 
     @PostMapping(value = "/pathway")
@@ -122,7 +108,7 @@ public Result<Page<Pathway>> loadPathways(@RequestBody final QueryParameters que
             value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
             })
     public Result<Pathway> createPathway(@RequestBody final PathwayRegistrationRequest request)
-            throws IOException, ParseException, JAXBException {
+            throws IOException, JAXBException {
         return Result.success(pathwaySecurityService.createPathway(request));
     }
 

diff --git a/...catgenome/entity/pathway/SbgnElement.java → ...me/entity/pathway/PathwayQueryParams.java b/...catgenome/entity/pathway/SbgnElement.java → ...me/entity/pathway/PathwayQueryParams.java
@@ -23,17 +23,15 @@
  */
 package com.epam.catgenome.entity.pathway;
 
-import lombok.Builder;
+import com.epam.catgenome.util.db.PagingInfo;
+import com.epam.catgenome.util.db.SortInfo;
 import lombok.Getter;
 import lombok.Setter;
 
-@Getter
 @Setter
-@Builder
-public class SbgnElement {
-    private Long pathwayId;
-    private SbgnElementType type;
-    private String clazz;
-    private String entryId;
-    private String label;
+@Getter
+public class PathwayQueryParams {
+    private PagingInfo pagingInfo;
+    private String term;
+    private SortInfo sortInfo;
 }
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/SbgnElementType.java b/server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/SbgnElementType.java