Datasets tree visualizing - optimized

Author: sidoruka

client/client/app/shared/projectContext/index.js

@@ -614,15 +614,41 @@ export default class projectContext {
         this._datasetsAreLoading = true;
         this._datasetsArePrepared = false;
         this.dispatcher.emitSimpleEvent('datasets:loading:started', null);
-        this._datasets = (await this.projectDataService.getProjects() || []);
+        this._datasets = (await this.projectDataService.getProjects(this._datasetsFilter) || []);
         this._datasetsLoaded = true;
         this._datasetsAreLoading = false;
         this.dispatcher.emitSimpleEvent('datasets:loading:finished', null);
     }
 
+    refreshReferencesPromise;
+    _referencesAreLoading = false;
+
     async refreshReferences(forceRefresh = false) {
         if (forceRefresh || !this._references) {
-            this._references = await this.genomeDataService.loadAllReference();
+            if (this._referencesAreLoading) {
+                return this.refreshReferencesPromise;
+            }
+            this._referencesAreLoading = true;
+            this.refreshReferencesPromise = new Promise((resolve) => {
+                this.genomeDataService.loadAllReference(this._datasetsFilter).then(data => {
+                    this._references = data;
+                    this._references.forEach(r => {
+                        if (!r.annotationFiles) {
+                            r.annotationFiles = [];
+                        }
+                        if (r.geneFile && r.annotationFiles.filter(a =>
+                                a.name.toLowerCase() === r.geneFile.name.toLowerCase() && a.format.toLowerCase() === r.geneFile.format.toLowerCase()
+                            ).length === 0) {
+                            r.geneFile.selected = true;
+                            r.geneFile.isGeneFile = true;
+                            r.annotationFiles.push(r.geneFile);
+                        }
+                    });
+                    this._referencesAreLoading = false;
+                    resolve();
+                });
+            });
+            return this.refreshReferencesPromise;
         }
     }
 

client/client/dataServices/genome/genome-data-service.js

@@ -16,8 +16,9 @@ export class GenomeDataService extends DataService {
      * Returns all reference genomes that are available in the system at the moment.
      * @returns {promise}
      */
-    loadAllReference() {
-        return this.get('reference/loadAll');
+    loadAllReference(referenceName) {
+        const url = referenceName ? `reference/loadAll?referenceName=${referenceName}` : 'reference/loadAll';
+        return this.get(url);
     }
 
     loadReferenceTrack(reference) {

client/client/dataServices/project/project-data-service.js

@@ -6,9 +6,10 @@ import {DataService} from '../data-service';
  */
 export class ProjectDataService extends DataService {
 
-    getProjects() {
+    getProjects(referenceName) {
         return new Promise((resolve) => {
-            this.get('project/tree').catch(() => resolve([])).then(data => {
+            const url = referenceName ? `project/tree?referenceName=${referenceName}` : 'project/tree';
+            this.get(url).catch(() => resolve([])).then(data => {
                 if (data !== null && data !== undefined) {
                     resolve(data);
                 }

server/catgenome/profiles/jar/catgenome.properties

@@ -24,3 +24,4 @@ database.driver.class=org.h2.Driver
 database.jdbc.url=jdbc:h2:file:./H2/catgenome
 #vcf.filter.whitelist=AA,DP,HM2,HM3
 vcf.extended.info.patterns='|'
+use.embedded.tomcat=true

server/catgenome/src/main/java/com/epam/catgenome/app/AppMVCConfiguration.java

@@ -3,6 +3,7 @@
 import java.util.List;
 
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.autoconfigure.condition.ConditionalOnClass;
 import org.springframework.boot.context.embedded.EmbeddedServletContainerCustomizer;
 import org.springframework.boot.context.embedded.EmbeddedServletContainerFactory;
@@ -36,17 +37,35 @@
 @ComponentScan(basePackages = {"com.epam.catgenome.config", "com.epam.catgenome.controller"})
 public class AppMVCConfiguration extends WebMvcConfigurerAdapter {
 
+    private static final int CACHE_PERIOD = 60 * 60 * 24;
+    private static final int CACHE_SIZE = 1024 * 1024 * 100;
+    private static final int TOMCAT_CACHE_PERIOD = CACHE_PERIOD * 1000;
+
     @Autowired
     private ApplicationContext applicationContext;
 
-    //to skip tld scan completely
+    @Value("#{catgenome['use.embedded.tomcat']}")
+    private String useEmbedded;
+
+    @Bean
+    public TomcatConfigurer tomcatConfigurerImpl() {
+        if (useEmbeddedContainer()) {
+            return new TomcatConfigurerImpl();
+        } else {
+            return null;
+        }
+    }
+
     @Bean
     @ConditionalOnClass({EmbeddedServletContainerFactory.class })
     public EmbeddedServletContainerCustomizer tomcatContainerCustomizer() {
         return container -> {
             TomcatEmbeddedServletContainerFactory tomcat = (TomcatEmbeddedServletContainerFactory) container;
             tomcat.setTldSkip("*.jar");
-
+            if (useEmbeddedContainer()) {
+                TomcatConfigurer configurer = applicationContext.getBean(TomcatConfigurer.class);
+                configurer.configure(tomcat, CACHE_SIZE, TOMCAT_CACHE_PERIOD);
+            }
         };
     }
 
@@ -55,6 +74,9 @@ public void addResourceHandlers(ResourceHandlerRegistry registry) {
         registry.addResourceHandler("/swagger-ui/**")
                 .addResourceLocations("/swagger-ui/", "classpath:/static/swagger-ui/",
                         "classpath:/META-INF/resources/webjars/swagger-ui/2.0.24/");
+        registry.addResourceHandler("/**")
+                .addResourceLocations("classpath:/static/")
+                .setCachePeriod(CACHE_PERIOD);
     }
 
     @Override
@@ -138,4 +160,8 @@ public FilterRegistrationBean disableDefaultOAuth(OAuth2AuthenticationProcessing
         registration.setEnabled(false);
         return registration;
     }
+
+    private boolean useEmbeddedContainer() {
+        return useEmbedded != null && "true".equals(useEmbedded);
+    }
 }

server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurer.java

@@ -0,0 +1,11 @@
+package com.epam.catgenome.app;
+
+import org.springframework.boot.context.embedded.tomcat.TomcatEmbeddedServletContainerFactory;
+
+/**
+ * Enables configuration of Tomcat container, should be used only with embedded container
+ */
+public interface TomcatConfigurer {
+    void configure(TomcatEmbeddedServletContainerFactory tomcat, int cacheSize,
+            int tomcatCacheSize);
+}

server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurerImpl.java

@@ -0,0 +1,23 @@
+package com.epam.catgenome.app;
+
+import org.apache.catalina.webresources.StandardRoot;
+import org.springframework.boot.context.embedded.tomcat.TomcatEmbeddedServletContainerFactory;
+
+public class TomcatConfigurerImpl implements TomcatConfigurer {
+
+    public TomcatConfigurerImpl() {
+        // no op
+    }
+
+    @Override
+    public void configure(TomcatEmbeddedServletContainerFactory tomcat, int cacheSize,
+            int tomcatCacheSize) {
+        tomcat.addContextCustomizers((context) -> {
+            StandardRoot standardRoot = new StandardRoot(context);
+            standardRoot.setCachingAllowed(true);
+            standardRoot.setCacheMaxSize(cacheSize);
+            standardRoot.setCacheTtl(tomcatCacheSize);
+            context.setResources(standardRoot);
+        });
+    }
+}

server/catgenome/src/main/java/com/epam/catgenome/controller/project/ProjectController.java

@@ -103,8 +103,9 @@ public Result<List<ProjectVO>> loadProjectsForCurrentUser() {
     @ApiResponses(
         value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
         })
-    public Result<List<ProjectVO>> loadProjectsTreeForCurrentUser(@RequestParam(required = false) Long parentId) {
-        return Result.success(ProjectConverter.convertTo(projectManager.loadProjectTree(parentId)));
+    public Result<List<ProjectVO>> loadProjectsTreeForCurrentUser(@RequestParam(required = false) Long parentId,
+            @RequestParam(required = false) String referenceName) {
+        return Result.success(ProjectConverter.convertTo(projectManager.loadProjectTree(parentId, referenceName)));
     }
 
     @RequestMapping(value = "/project/{projectId}/load", method = RequestMethod.GET)

server/catgenome/src/main/java/com/epam/catgenome/controller/reference/ReferenceController.java

@@ -91,8 +91,9 @@ public class ReferenceController extends AbstractRESTController {
     @ApiResponses(
             value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
             })
-    public final Result<List<Reference>> loadAllReferences() throws IOException {
-        return Result.success(referenceGenomeManager.loadAllReferenceGenomes());
+    public final Result<List<Reference>> loadAllReferences(
+            @RequestParam(required = false) String referenceName) throws IOException {
+        return Result.success(referenceGenomeManager.loadAllReferenceGenomes(referenceName));
     }
 
     @ResponseBody

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

@@ -79,6 +79,7 @@ public class BiologicalDataItemDao extends NamedParameterJdbcDaoSupport {
     private String loadBiologicalDataItemsByNameStrictQuery;
     private String loadBiologicalDataItemsByNamesStrictQuery;
     private String loadBiologicalDataItemsByNameQuery;
+    private String loadBiologicalDataItemsByNameCaseInsensitiveQuery;
 
     @Autowired
     private DaoHelper daoHelper;
@@ -186,6 +187,15 @@ public List<BiologicalDataItem> loadFilesByNamesStrict(final List<String> names)
         return items;
     }
 
+    @Transactional(propagation = Propagation.MANDATORY)
+    public List<BiologicalDataItem> loadFilesByNameCaseInsensitive(final String name) {
+        final MapSqlParameterSource params = new MapSqlParameterSource();
+        params.addValue(BiologicalDataItemParameters.NAME.name(), name.toLowerCase());
+        return getNamedParameterJdbcTemplate().query(loadBiologicalDataItemsByNameCaseInsensitiveQuery,
+                params, getRowMapper());
+    }
+
+
     /**
      * Finds files with names matching a specified file name, performs substring, case insensitive search
      * @param name search query
@@ -559,4 +569,10 @@ public void setLoadBiologicalDataItemsByNameQuery(String loadBiologicalDataItems
     public void setLoadBiologicalDataItemsByNamesStrictQuery(String loadBiologicalDataItemsByNamesStrictQuery) {
         this.loadBiologicalDataItemsByNamesStrictQuery = loadBiologicalDataItemsByNamesStrictQuery;
     }
+
+
+    public void setLoadBiologicalDataItemsByNameCaseInsensitiveQuery(
+            String loadBiologicalDataItemsByNameCaseInsensitiveQuery) {
+        this.loadBiologicalDataItemsByNameCaseInsensitiveQuery = loadBiologicalDataItemsByNameCaseInsensitiveQuery;
+    }
 }