Merge pull request #303 from ncats/syncTool

WIP: please do not merge. Sync tool
ncats · Apr 23, 2024 · ce9ff52 · ce9ff52
2 parents 1c919bf + d9ab1bf
commit ce9ff52
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Showing 17 changed files with 108 additions and 16 deletions.
diff --git a/...ension/src/main/java/fda/gsrs/substance/indexers/SubstanceApplicationIndexValueMaker.java b/...ension/src/main/java/fda/gsrs/substance/indexers/SubstanceApplicationIndexValueMaker.java
@@ -7,15 +7,17 @@
 import ix.core.search.text.IndexValueMaker;
 import ix.core.search.text.IndexableValue;
 import ix.ginas.models.v1.Substance;
-
+import ix.utils.Util;
 import gov.hhs.gsrs.applications.api.*;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
 
+import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
+import java.util.Set;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
 
@@ -31,6 +33,16 @@ public class SubstanceApplicationIndexValueMaker implements IndexValueMaker<Subs
 	public Class<Substance> getIndexedEntityClass() {
 		return Substance.class;
 	}
+
+	@Override
+	public Set<String> getTags(){
+		return Util.toSet("external","applications");		
+	} 
+
+	@Override	
+	public Set<String> getFieldNames(){
+		return Util.toSet("Application Status","Application Center","Application Type");
+	}
 
     @Override
     public void createIndexableValues(Substance substance, Consumer<IndexableValue> consumer) {

diff --git a/...rc/main/java/fda/gsrs/substance/indexers/SubstanceClinicalEuropeTrialIndexValueMaker.java b/...rc/main/java/fda/gsrs/substance/indexers/SubstanceClinicalEuropeTrialIndexValueMaker.java
@@ -7,11 +7,13 @@
 import ix.core.search.text.IndexValueMaker;
 import ix.core.search.text.IndexableValue;
 import ix.ginas.models.v1.Substance;
+import ix.utils.Util;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 
 import java.util.List;
+import java.util.Set;
 import java.util.function.Consumer;
 @Slf4j
 public class SubstanceClinicalEuropeTrialIndexValueMaker implements IndexValueMaker<Substance> {
@@ -26,6 +28,16 @@ public class SubstanceClinicalEuropeTrialIndexValueMaker implements IndexValueMa
 	public Class<Substance> getIndexedEntityClass() {
 		return Substance.class;
 	}
+
+	@Override
+	public Set<String> getTags(){
+		return Util.toSet("external","clinicalEuropeTrial");		
+	} 
+
+	@Override	
+	public Set<String> getFieldNames(){
+		return Util.toSet("Clinical Trial Europe Status","Clinical Trial Europe Count");
+	}
 
 	private static final long[] countBuckets = new long[]{1,2,3,4,5,10,15,20,25,30,40,50,75,100,250,500,1000,2000,3000,5000};
 

diff --git a/...on/src/main/java/fda/gsrs/substance/indexers/SubstanceClinicalUSTrialIndexValueMaker.java b/...on/src/main/java/fda/gsrs/substance/indexers/SubstanceClinicalUSTrialIndexValueMaker.java
@@ -7,11 +7,13 @@
 import ix.core.search.text.IndexValueMaker;
 import ix.core.search.text.IndexableValue;
 import ix.ginas.models.v1.Substance;
+import ix.utils.Util;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 
 import java.util.List;
+import java.util.Set;
 import java.util.function.Consumer;
 
 @Slf4j
@@ -27,6 +29,16 @@ public class SubstanceClinicalUSTrialIndexValueMaker implements IndexValueMaker<
 	public Class<Substance> getIndexedEntityClass() {
 		return Substance.class;
 	}
+
+	@Override
+	public Set<String> getTags(){
+		return Util.toSet("external","clinicalUSTrial");		
+	} 
+
+	@Override	
+	public Set<String> getFieldNames(){
+		return Util.toSet("Clinical Trial US Status","Clinical Trial US Count");
+	}
 
 	private static final long[] countBuckets = new long[]{1,2,3,4,5,10,15,20,25,30,40,50,75,100,250,500,1000,2000,3000,5000};
 

diff --git a/...-extension/src/main/java/fda/gsrs/substance/indexers/SubstanceProductIndexValueMaker.java b/...-extension/src/main/java/fda/gsrs/substance/indexers/SubstanceProductIndexValueMaker.java
@@ -9,12 +9,14 @@
 import ix.core.search.text.IndexValueMaker;
 import ix.core.search.text.IndexableValue;
 import ix.ginas.models.v1.Substance;
+import ix.utils.Util;
 import ix.ginas.models.v1.Code;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import org.springframework.beans.factory.annotation.Value;
 
+import java.util.Set;
 import java.util.List;
 import java.util.Optional;
 import java.util.function.Consumer;
@@ -28,10 +30,20 @@ public class SubstanceProductIndexValueMaker implements IndexValueMaker<Substanc
     @Autowired
     public ProductsApi productsApi;
 
-    @Override
-    public Class<Substance> getIndexedEntityClass() {
-        return Substance.class;
-    }
+	@Override
+	public Class<Substance> getIndexedEntityClass() {
+		return Substance.class;
+	}
+
+	@Override
+	public Set<String> getTags(){
+		return Util.toSet("external","product");		
+	} 
+
+	@Override	
+	public Set<String> getFieldNames(){
+		return Util.toSet("Product Type","Product Ingredient Type","Product Dosage Form");
+	}
 
     @Override
     public void createIndexableValues(Substance substance, Consumer<IndexableValue> consumer) {

diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceEntityService.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceEntityService.java
@@ -6,6 +6,7 @@
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 
+import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
 
@@ -25,6 +26,9 @@ public interface SubstanceEntityService extends GsrsEntityService<Substance, UUI
 
     @Override
     long count();
+
+    @Override
+    List<UUID> getIDs();
 
     Optional<Substance> get(UUID id);
 

diff --git a/...odule-substances-core/src/main/java/gsrs/module/substance/SubstanceEntityServiceImpl.java b/...odule-substances-core/src/main/java/gsrs/module/substance/SubstanceEntityServiceImpl.java
@@ -20,6 +20,7 @@
 import ix.core.models.ForceUpdatableModel;
 import ix.core.models.Role;
 import ix.core.util.EntityUtils;
+import ix.core.util.EntityUtils.Key;
 import ix.core.util.LogUtil;
 import ix.core.validator.*;
 import ix.ginas.models.v1.Substance;
@@ -473,4 +474,10 @@ public UpdateResult<Substance> updateEntityWithoutValidation(JsonNode updatedEnt
         });
     }
 
+	@Override
+	public List<UUID> getIDs() {
+		List<UUID> IDs = repository.getAllIds();		
+		return IDs;
+	}
+
 }
diff --git a/...ances-core/src/main/java/gsrs/module/substance/indexers/UserSavedListIndexValueMaker.java b/...ances-core/src/main/java/gsrs/module/substance/indexers/UserSavedListIndexValueMaker.java
@@ -17,6 +17,7 @@
 import ix.core.search.text.IndexableValue;
 import ix.core.util.EntityUtils.EntityWrapper;
 import ix.ginas.models.v1.Substance;
+import ix.utils.Util;
 import lombok.extern.slf4j.Slf4j;
 
 @Slf4j
@@ -36,9 +37,13 @@ public Class<Substance> getIndexedEntityClass() {
 
 	@Override
 	public Set<String> getFieldNames(){
-		return Stream.of("User List").collect(Collectors.toSet());
+		return Util.toSet("User List");
+	}
+
+	@Override
+	public Set<String> getTags(){
+		return Util.toSet("user_list");
 	}
-
 
 	@Override
     public void createIndexableValues(Substance substance, Consumer<IndexableValue> consumer) {

diff --git a/...module-substances-core/src/main/java/gsrs/module/substance/repository/CodeRepository.java b/...module-substances-core/src/main/java/gsrs/module/substance/repository/CodeRepository.java
@@ -30,4 +30,8 @@ public interface CodeRepository extends GsrsVersionedRepository<Code, UUID> {
     List<Code> findByUuidStartingWith(String partialUUID);
 
     List<Code> findByCodeIgnoreCase(String code);
+
+    @Query("select c.uuid from Code c")
+    List<UUID> getAllIDs();
+
 }
diff --git a/...module-substances-core/src/main/java/gsrs/module/substance/repository/NameRepository.java b/...module-substances-core/src/main/java/gsrs/module/substance/repository/NameRepository.java
@@ -28,5 +28,8 @@ public interface NameRepository extends GsrsVersionedRepository<Name, UUID> {
 
     @Query("select n.uuid from Name n")
     List<String> getAllUuids();
+
+    @Query("select n.uuid from Name n")
+    List<UUID> getAllIDs();
 
 }
diff --git a/...bstances-core/src/main/java/gsrs/module/substance/repository/ProcessingJobRepository.java b/...bstances-core/src/main/java/gsrs/module/substance/repository/ProcessingJobRepository.java
@@ -3,6 +3,7 @@
 import ix.core.models.Keyword;
 import ix.core.models.ProcessingJob;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.stereotype.Repository;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -14,4 +15,7 @@
 public interface ProcessingJobRepository extends JpaRepository<ProcessingJob, Long> {
 
    List<ProcessingJob> findByKeysIn(Collection<Keyword> keyword);
+
+   @Query("select pj.id from ProcessingJob pj")
+   List<Long> getAllIDs();
 }
diff --git a/...e-substances-core/src/main/java/gsrs/module/substance/repository/ReferenceRepository.java b/...e-substances-core/src/main/java/gsrs/module/substance/repository/ReferenceRepository.java
@@ -18,4 +18,7 @@ public interface ReferenceRepository extends GsrsVersionedRepository<Reference,
     //hibernate query will not convert uuid into a string so we have to concatenate it with empty string for this to work.
     @Query("select s from Reference s where CONCAT(s.uuid, '') like ?1%")
     List<Reference> findByUuidStartingWith(String partialUUID);
+
+    @Query("select r.id from Reference r")
+    List<UUID> getAllIDs();
 }
diff --git a/...odule-substances-core/src/main/java/gsrs/module/substance/services/CodeEntityService.java b/...odule-substances-core/src/main/java/gsrs/module/substance/services/CodeEntityService.java
@@ -294,5 +294,9 @@ public Code createNewSystemCode(Substance substance, String codeSystem, Function
         return c;
     }
 
+	@Override
+	public List<UUID> getIDs() {
+		return repository.getAllIDs();
+	}
 
 }
diff --git a/...odule-substances-core/src/main/java/gsrs/module/substance/services/NameEntityService.java b/...odule-substances-core/src/main/java/gsrs/module/substance/services/NameEntityService.java
@@ -241,7 +241,10 @@ protected Optional<UUID> flexLookupIdOnly(String someKindOfId) {
         return Optional.empty();
     }
 
-
-
+    @Override
+	public List<UUID> getIDs() {
+		List<UUID> IDs = repository.getAllIDs();
+		return IDs;
+	}
 
 }
diff --git a/...stances-core/src/main/java/gsrs/module/substance/services/ProcessingJobEntityService.java b/...stances-core/src/main/java/gsrs/module/substance/services/ProcessingJobEntityService.java
@@ -123,4 +123,9 @@ public Class<ProcessingJob> getEntityClass() {
     public Page page(Pageable pageable) {
         return processingJobRepository.findAll(pageable);
     }
+
+	@Override
+	public List<Long> getIDs() {		
+		return processingJobRepository.getAllIDs();
+	}
 }
diff --git a/...-substances-core/src/main/java/gsrs/module/substance/services/ReferenceEntityService.java b/...-substances-core/src/main/java/gsrs/module/substance/services/ReferenceEntityService.java
@@ -38,11 +38,11 @@
 @Scope(proxyMode = ScopedProxyMode.INTERFACES)
 @Service
 public class ReferenceEntityService extends AbstractGsrsEntityService<Reference, UUID> {
-    public static final String  CONTEXT = "names";
+    public static final String  CONTEXT = "references";
 
 
     public ReferenceEntityService() {
-        super(CONTEXT,  IdHelpers.UUID, "gsrs_exchange", "name.created", "name.updated");
+        super(CONTEXT,  IdHelpers.UUID, "gsrs_exchange", "reference.created", "reference.updated");
     }
 
     @Autowired
@@ -233,7 +233,9 @@ protected Optional<UUID> flexLookupIdOnly(String someKindOfId) {
         return Optional.empty();
     }
 
-
-
-
+	@Override
+	public List<UUID> getIDs() {
+		// TODO Auto-generated method stub
+		return new ArrayList<UUID>();
+	}
 }
diff --git a/...dule-substances-core/src/main/java/gsrs/module/substance/services/ReindexFromBackups.java b/...dule-substances-core/src/main/java/gsrs/module/substance/services/ReindexFromBackups.java
@@ -187,7 +187,7 @@ public void execute(Object id, SchedulerPlugin.TaskListener l) throws IOExceptio
                                                     // however, you could argue there SHOULD be a controller for them
                                                     if (seen.add(keyString)) {
                                                         //is this a good idea ?
-                                                        ReindexEntityEvent event = new ReindexEntityEvent(reindexId, key,Optional.of(wrapped));
+                                                        ReindexEntityEvent event = new ReindexEntityEvent(reindexId, key,Optional.of(wrapped), false);
                                                         eventConsumer.accept(event);
                                                     }
                                                 } catch (Throwable t) {

diff --git a/...nces-data-exchange/src/main/java/gsrs/dataexchange/SubstanceStagingAreaEntityService.java b/...nces-data-exchange/src/main/java/gsrs/dataexchange/SubstanceStagingAreaEntityService.java
@@ -215,7 +215,7 @@ public void IndexEntity(TextIndexer indexer, Object object) {
         EntityUtils.EntityWrapper<Substance> wrapper = EntityUtils.EntityWrapper.of(substance);
         log.trace("create wrapper with kind {} - id field {}", wrapper.getKind(), wrapper.getEntityInfo().getIDFieldInfo().get());
         UUID reindexUuid = UUID.randomUUID();
-        ReindexEntityEvent event = new ReindexEntityEvent(reindexUuid, wrapper.getKey(), Optional.of(wrapper),true);
+        ReindexEntityEvent event = new ReindexEntityEvent(reindexUuid, wrapper.getKey(), Optional.of(wrapper));
         applicationEventPublisher.publishEvent(event);
         log.info("submitted object for indexing");
     }