add diamon priority for 2.7.7 for fix vocabulary switching(https://gi… (#1552)

* add diamon priority for 2.7.7 for fix vocabulary switching(OHDSI/Atlas#2223)

* add diamon priority for 2.7.7 add JDoc for for SourcePriorityService class

* add migration for priority

Author: molodkov yaroslav

src/main/java/org/ohdsi/webapi/service/SourcePriorityService.java

@@ -0,0 +1,88 @@
+package org.ohdsi.webapi.service;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import org.apache.commons.collections4.map.PassiveExpiringMap;
+import org.ohdsi.sql.SqlTranslate;
+import org.ohdsi.webapi.shiro.management.datasource.SourceAccessor;
+import org.ohdsi.webapi.source.Source;
+import org.ohdsi.webapi.source.SourceDaimon;
+import org.ohdsi.webapi.source.SourceRepository;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.jdbc.CannotGetJdbcConnectionException;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.stereotype.Service;
+
+/**
+ * This code was extracted from the master branch to fix https://github.com/OHDSI/Atlas/issues/2223 issue.
+ * There is no need to merge it into the master as the same functionality implemented there in another place.
+ */
+@Service
+public class SourcePriorityService extends AbstractDaoService {
+
+    @Autowired
+    private SourceRepository sourceRepository;
+    @Autowired
+    private SourceAccessor sourceAccessor;
+
+    private Map<Source, Boolean> connectionAvailability = Collections.synchronizedMap(new PassiveExpiringMap<>(5000));
+
+    public Source getPrioritySourceForDaimon(SourceDaimon.DaimonType daimonType) {
+
+        List<Source> sourcesByDaimonPriority = sourceRepository.findAllSortedByDiamonPrioirty(daimonType);
+
+        for (Source source : sourcesByDaimonPriority) {
+            if (!(sourceAccessor.hasAccess(source) && connectionAvailability.computeIfAbsent(source, this::checkConnectionSafe))) {
+                continue;
+            }
+            return source;
+        }
+
+        return null;
+    }
+
+    public Map<SourceDaimon.DaimonType, Source> getPriorityDaimons() {
+
+        class SourceValidator {
+            private Map<Integer, Boolean> checkedSources = new HashMap<>();
+
+            private boolean isSourceAvaialble(Source source) {
+
+                return checkedSources.computeIfAbsent(source.getSourceId(),
+                        v -> sourceAccessor.hasAccess(source) && connectionAvailability.computeIfAbsent(source, SourcePriorityService.this::checkConnectionSafe));
+            }
+        }
+
+        SourceValidator sourceValidator = new SourceValidator();
+        Map<SourceDaimon.DaimonType, Source> priorityDaimons = new HashMap<>();
+        Arrays.asList(SourceDaimon.DaimonType.values()).forEach(d -> {
+
+            List<Source> sources = sourceRepository.findAllSortedByDiamonPrioirty(d);
+            Optional<Source> source = sources.stream().filter(sourceValidator::isSourceAvaialble)
+                    .findFirst();
+            source.ifPresent(s -> priorityDaimons.put(d, s));
+        });
+        return priorityDaimons;
+    }
+
+    private boolean checkConnectionSafe(Source source) {
+
+        try {
+            checkConnection(source);
+            return true;
+        } catch (CannotGetJdbcConnectionException ex) {
+            return false;
+        }
+    }
+
+    public void checkConnection(Source source) {
+
+        final JdbcTemplate jdbcTemplate = getSourceJdbcTemplate(source);
+        jdbcTemplate.execute(SqlTranslate.translateSql("select 1;", source.getSourceDialect()).replaceAll(";$", ""));
+    }
+
+}

src/main/java/org/ohdsi/webapi/service/SourceService.java

@@ -11,7 +11,6 @@
 import org.glassfish.jersey.media.multipart.FormDataParam;
 import org.jasypt.encryption.pbe.PBEStringEncryptor;
 import org.jasypt.properties.PropertyValueEncryptionUtils;
-import org.ohdsi.sql.SqlTranslate;
 import org.ohdsi.webapi.common.SourceMapKey;
 import org.ohdsi.webapi.shiro.management.Security;
 import org.ohdsi.webapi.shiro.management.datasource.SourceAccessor;
@@ -56,13 +55,16 @@ public class SourceService extends AbstractDaoService {
   private ApplicationEventPublisher publisher;
   @Autowired
   private VocabularyService vocabularyService;
+  @Autowired
+  private SourcePriorityService sourcePriorityService;
 
   @Autowired
   private SourceAccessor sourceAccessor;
 
   @Value("${datasource.ohdsi.schema}")
   private String schema;
 
+
   private boolean encryptorPasswordSet = false;
 
   @PostConstruct
@@ -171,22 +173,7 @@ public Collection<SourceInfo> refreshSources() {
   @GET
   @Produces(MediaType.APPLICATION_JSON)
   public SourceInfo getPriorityVocabularySourceInfo() {
-    int priority = 0;
-    SourceInfo priorityVocabularySourceInfo = null;
-
-    for (Source source : sourceRepository.findAll()) {
-      for (SourceDaimon daimon : source.getDaimons()) {
-        if (daimon.getDaimonType() == SourceDaimon.DaimonType.Vocabulary && sourceAccessor.hasAccess(source)) {
-          int daimonPriority = daimon.getPriority();
-          if (daimonPriority >= priority) {
-            priority = daimonPriority;
-            priorityVocabularySourceInfo = new SourceInfo(source);
-          }
-        }
-      }
-    }
-
-    return priorityVocabularySourceInfo;
+    return new SourceInfo(sourcePriorityService.getPrioritySourceForDaimon(SourceDaimon.DaimonType.Vocabulary));
   }
 
   @Path("{key}")
@@ -341,12 +328,24 @@ public Response delete(@PathParam("sourceId") Integer sourceId) throws Exception
   public SourceInfo checkConnection(@PathParam("key") final String sourceKey) {
 
     final Source source = sourceRepository.findBySourceKey(sourceKey);
-    final JdbcTemplate jdbcTemplate = getSourceJdbcTemplate(source);
-    jdbcTemplate.execute(SqlTranslate.translateSql("select 1;", source.getSourceDialect()).replaceAll(";$", ""));
+    sourcePriorityService.checkConnection(source);
     return source.getSourceInfo();
   }
 
 
+  @Path("daimon/priority")
+  @GET
+  @Produces(MediaType.APPLICATION_JSON)
+  public Map<SourceDaimon.DaimonType, SourceInfo> getPriorityDaimons() {
+
+    return sourcePriorityService.getPriorityDaimons()
+            .entrySet().stream()
+            .collect(Collectors.toMap(
+                    Map.Entry::getKey,
+                    e -> new SourceInfo(e.getValue())
+            ));
+  }
+
   @Path("{sourceKey}/daimons/{daimonType}/set-priority")
   @POST
   @Produces(MediaType.APPLICATION_JSON)

src/main/java/org/ohdsi/webapi/source/SourceRepository.java

@@ -15,6 +15,8 @@
  */
 package org.ohdsi.webapi.source;
 
+import java.util.List;
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 
 /**
@@ -24,4 +26,7 @@
 public interface SourceRepository extends CrudRepository<Source, Integer> {
   Source findBySourceKey(String sourceKey);
   Source findBySourceId(int sourceId);
+  @Query("SELECT s FROM Source s JOIN s.daimons sd WHERE sd.daimonType = ?1 ORDER BY sd.priority DESC")
+  List<Source> findAllSortedByDiamonPrioirty(SourceDaimon.DaimonType daimonType);
+
 }

src/main/resources/db/migration/oracle/V2.8.0.20190809215200__daimon-priority.sql

@@ -0,0 +1,9 @@
+INSERT INTO ${ohdsiSchema}.sec_permission(id, value, description) VALUES
+  (${ohdsiSchema}.sec_permission_id_seq.nextval, 'source:daimon:priority:get', 'Get priority of Source Daimons');
+
+INSERT INTO ${ohdsiSchema}.sec_role_permission(id, role_id, permission_id)
+  SELECT ${ohdsiSchema}.sec_role_permission_sequence.nextval, sr.id, sp.id
+  FROM ${ohdsiSchema}.sec_permission SP, ${ohdsiSchema}.sec_role sr
+  WHERE sp.value IN (
+    'source:daimon:priority:get'
+  ) AND sr.name IN ('Atlas users');

src/main/resources/db/migration/postgresql/V2.8.0.20190809215200__daimon-priority.sql

@@ -0,0 +1,9 @@
+INSERT INTO ${ohdsiSchema}.sec_permission(id, value, description) VALUES
+  (nextval('${ohdsiSchema}.sec_permission_id_seq'), 'source:daimon:priority:get', 'Get priority of Source Daimons');
+
+INSERT INTO ${ohdsiSchema}.sec_role_permission(id, role_id, permission_id)
+  SELECT nextval('${ohdsiSchema}.sec_role_permission_sequence'), sr.id, sp.id
+  FROM ${ohdsiSchema}.sec_permission SP, ${ohdsiSchema}.sec_role sr
+  WHERE sp.value IN (
+    'source:daimon:priority:get'
+  ) AND sr.name IN ('Atlas users');

src/main/resources/db/migration/sqlserver/V2.8.0.20190809215200__daimon-priority.sql

@@ -0,0 +1,9 @@
+INSERT INTO ${ohdsiSchema}.sec_permission(id, value, description) VALUES
+  (NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'source:daimon:priority:get', 'Get priority of Source Daimons');
+
+INSERT INTO ${ohdsiSchema}.sec_role_permission(id, role_id, permission_id)
+  SELECT NEXT VALUE FOR ${ohdsiSchema}.sec_role_permission_sequence, sr.id, sp.id
+  FROM ${ohdsiSchema}.sec_permission SP, ${ohdsiSchema}.sec_role sr
+  WHERE sp.value IN (
+    'source:daimon:priority:get'
+  ) AND sr.name IN ('Atlas users');