#4381 Variable taxonomies service added to support other taxonomies providers, in addition to the opal one

Author: ymarcon

mica-core/src/main/java/org/obiba/mica/core/upgrade/Mica510upgrade.java

@@ -2,11 +2,15 @@
 
 import javax.inject.Inject;
 
+import com.mongodb.client.MongoCollection;
+import org.bson.Document;
+import org.json.JSONException;
 import org.obiba.mica.micaConfig.service.CacheService;
 import org.obiba.runtime.Version;
 import org.obiba.runtime.upgrade.UpgradeStep;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.data.mongodb.core.MongoTemplate;
 import org.springframework.stereotype.Component;
 
 @Component
@@ -16,14 +20,17 @@ public class Mica510upgrade implements UpgradeStep {
 
   private CacheService cacheService;
 
+  private final MongoTemplate mongoTemplate;
+
   @Inject
-  public Mica510upgrade(CacheService cacheService) {
+  public Mica510upgrade(CacheService cacheService, MongoTemplate mongoTemplate) {
     this.cacheService = cacheService;
+    this.mongoTemplate = mongoTemplate;
   }
 
   @Override
   public String getDescription() {
-    return "Clear caches for 5.1.0";
+    return "Clear caches and updating config for 5.1.0";
   }
 
   @Override
@@ -34,7 +41,36 @@ public Version getAppliesTo() {
   @Override
   public void execute(Version currentVersion) {
     logger.info("Executing Mica upgrade to version 5.1.0");
+
+    try {
+      logger.info("Updating 'Mica Config'...");
+      updateMicaConfig();
+    } catch (JSONException e) {
+      logger.error("Error occurred while Updating 'Mica Config'");
+    }
+
+    logger.info("Clearing all caches...");
     cacheService.clearAllCaches();
+
+    // TODO get updated search plugin and rebuild search index
+  }
+
+  private void updateMicaConfig() throws JSONException {
+    Document micaConfig = getDBObjectSafely("micaConfig");
+    // delete field anonymousCanCreateCart to reset to default
+    if (null != micaConfig) {
+      micaConfig.remove("opal");
+      mongoTemplate.save(micaConfig, "micaConfig");
+    }
   }
-  
+
+  private Document getDBObjectSafely(String collectionName) {
+    if (mongoTemplate.collectionExists(collectionName)) {
+      MongoCollection<Document> existingCollection = mongoTemplate.getCollection(collectionName);
+      return existingCollection.find().first();
+    }
+
+    return null;
+  }
+
 }

mica-core/src/main/java/org/obiba/mica/micaConfig/domain/MicaConfig.java

@@ -41,10 +41,6 @@ public class MicaConfig extends AbstractAuditableDocument {
 
   public static final String DEFAULT_CHARSET = Charsets.UTF_8.toString();
 
-  public static final String DEFAULT_OPAL = "https://localhost:8443";
-
-  public static final String DEFAULT_PUBLIC_URL = "http://localhost:8082";
-
   public static final String[] LAYOUT_OPTIONS = {"layout1", "layout2"};
 
   public static final long DEFAULT_MAX_ITEMS_PER_SET = 20000;
@@ -64,8 +60,7 @@ public class MicaConfig extends AbstractAuditableDocument {
   @NotBlank
   private String defaultCharacterSet = DEFAULT_CHARSET;
 
-  @NotBlank
-  private String opal = DEFAULT_OPAL;
+  private String opal;
 
   private List<String> roles = Lists.newArrayList(Membership.CONTACT, Membership.INVESTIGATOR);
 
@@ -222,6 +217,10 @@ public void setDefaultCharacterSet(String defaultCharacterSet) {
     this.defaultCharacterSet = defaultCharacterSet;
   }
 
+  public boolean hasOpal() {
+    return !Strings.isNullOrEmpty(opal);
+  }
+
   public String getOpal() {
     return opal;
   }

mica-core/src/main/java/org/obiba/mica/micaConfig/service/CacheService.java

@@ -43,18 +43,18 @@ public class CacheService {
   private EventBus eventBus;
 
   @Inject
-  private TaxonomyService taxonomyService;
+  private TaxonomiesService taxonomiesService;
 
   @CacheEvict(value = "opal-taxonomies", allEntries = true, beforeInvocation = true)
   public void clearOpalTaxonomiesCache() {
     log.info("Clearing opal taxonomies cache");
-    taxonomyService.getOpalTaxonomies();
+    taxonomiesService.getVariableTaxonomies();
   }
 
   @CacheEvict(value = "micaConfig", allEntries = true)
   public void clearMicaConfigCache() {
     log.info("Clearing mica config cache");
-    taxonomyService.refresh();
+    taxonomiesService.refresh();
   }
 
   @CacheEvict(value = "aggregations-metadata", allEntries = true)

mica-core/src/main/java/org/obiba/mica/micaConfig/service/MicaConfigurationProvider.java

@@ -27,7 +27,7 @@ public class MicaConfigurationProvider implements ConfigurationProvider {
 
   @Inject
   @Lazy
-  private TaxonomyService taxonomyService;
+  private TaxonomiesService taxonomiesService;
 
   @Override
   public List<String> getLocales() {
@@ -46,26 +46,26 @@ public ObjectMapper getObjectMapper() {
 
   @Override
   public Taxonomy getNetworkTaxonomy() {
-    return taxonomyService.getNetworkTaxonomy();
+    return taxonomiesService.getNetworkTaxonomy();
   }
 
   @Override
   public Taxonomy getStudyTaxonomy() {
-    return taxonomyService.getStudyTaxonomy();
+    return taxonomiesService.getStudyTaxonomy();
   }
 
   @Override
   public Taxonomy getVariableTaxonomy() {
-    return taxonomyService.getVariableTaxonomy();
+    return taxonomiesService.getVariableTaxonomy();
   }
 
   @Override
   public Taxonomy getDatasetTaxonomy() {
-    return taxonomyService.getDatasetTaxonomy();
+    return taxonomiesService.getDatasetTaxonomy();
   }
 
   @Override
   public List<Taxonomy> getVariableTaxonomies() {
-    return taxonomyService.getVariableTaxonomies();
+    return taxonomiesService.getAllVariableTaxonomies();
   }
 }