Merge branch '35276_add_metagenomic_workflow_resource' of github.com:…

…AAFC-BICoE/seqdb-api into 35276_add_metagenomic_workflow_resource
AAFC-BICoE · Dec 3, 2024 · eb2ac0a · eb2ac0a
2 parents b43c16a + 745c62b
commit eb2ac0a
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Showing 4 changed files with 67 additions and 19 deletions.
diff --git a/src/main/java/ca/gc/aafc/seqdb/api/dto/MetagenomicsBatchItemDto.java b/src/main/java/ca/gc/aafc/seqdb/api/dto/MetagenomicsBatchItemDto.java
@@ -9,6 +9,9 @@
 import io.crnk.core.resource.annotations.JsonApiResource;
 import java.time.OffsetDateTime;
 import java.util.UUID;
+
+import org.javers.core.metamodel.annotation.ShallowReference;
+
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
@@ -37,6 +40,10 @@ public class MetagenomicsBatchItemDto {
   @JsonApiRelation
   private PcrBatchItemDto pcrBatchItem;
 
+  @ShallowReference
+  @JsonApiRelation
+  private MolecularAnalysisRunItemDto molecularAnalysisRunItem;
+
   @JsonApiRelation
   private NgsIndexDto indexI5;
 

diff --git a/src/main/java/ca/gc/aafc/seqdb/api/entities/MetagenomicsBatchItem.java b/src/main/java/ca/gc/aafc/seqdb/api/entities/MetagenomicsBatchItem.java
@@ -61,6 +61,10 @@ public class MetagenomicsBatchItem implements DinaEntity {
   @JoinColumn(name = "pcr_batch_item_id")
   private PcrBatchItem pcrBatchItem;
 
+  @ManyToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "molecular_analysis_run_item_id")
+  private MolecularAnalysisRunItem molecularAnalysisRunItem;
+
   @ManyToOne(fetch = FetchType.LAZY)
   @JoinColumn(name = "indexi5_id")
   private NgsIndex indexI5;

diff --git a/src/main/resources/db/changelog/migrations/54-Add_metagenomics_tables.xml b/src/main/resources/db/changelog/migrations/54-Add_metagenomics_tables.xml
@@ -1,9 +1,9 @@
 <?xml version="1.1" encoding="UTF-8" standalone="no"?>
 <databaseChangeLog
-        xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
-        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-        xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog https://local.xsd/dbchangelog-4.4.xsd"
-        objectQuotingStrategy="QUOTE_ONLY_RESERVED_WORDS">
+    xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog https://local.xsd/dbchangelog-4.4.xsd"
+    objectQuotingStrategy="QUOTE_ONLY_RESERVED_WORDS">
 
     <changeSet id="54-Add_metagenomics_tables" context="schema-change" author="cgendreau">
         <createTable tableName="metagenomics_batch">
@@ -14,19 +14,20 @@
                 <constraints nullable="false" unique="true" />
             </column>
             <column name="created_by" type="VARCHAR(250)">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
             <column name="_group" type="VARCHAR(50)">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
-            <column name="created_on" type="timestamptz" defaultValueComputed="current_timestamp"/>
+            <column name="created_on" type="timestamptz" defaultValueComputed="current_timestamp" />
             <column name="name" type="VARCHAR(100)">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
-            <column name="protocol" type="uuid"/>
+            <column name="protocol" type="uuid" />
 
             <column name="index_set_id" type="integer">
-                <constraints foreignKeyName="fk_metagenomics_index_set_id_to_indexset" references="indexsets(id)"/>
+                <constraints foreignKeyName="fk_metagenomics_index_set_id_to_indexset"
+                    references="indexsets(id)" />
             </column>
 
         </createTable>
@@ -39,24 +40,31 @@
                 <constraints nullable="false" unique="true" />
             </column>
             <column name="created_by" type="VARCHAR(250)">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
-            <column name="created_on" type="timestamptz" defaultValueComputed="current_timestamp"/>
+            <column name="created_on" type="timestamptz" defaultValueComputed="current_timestamp" />
 
             <column name="metagenomics_batch_id" type="integer">
-                <constraints foreignKeyName="fk_metagenomics_batch_item_to_batch_id" references="metagenomics_batch(id)"/>
+                <constraints foreignKeyName="fk_metagenomics_batch_item_to_batch_id"
+                    references="metagenomics_batch(id)" />
             </column>
 
             <column name="pcr_batch_item_id" type="integer">
-                <constraints foreignKeyName="fk_metagenomics_batch_item_to_pcr_batch_item" references="pcr_batch_item(id)"/>
+                <constraints foreignKeyName="fk_metagenomics_batch_item_to_pcr_batch_item"
+                    references="pcr_batch_item(id)" />
+            </column>
+            <column name="molecular_analysis_run_item_id" type="integer">
+                <constraints foreignKeyName="fk_metagenomics_batch_item_to_molecular_analysis_run_item_id"
+                    references="molecular_analysis_run_item(id)" />
             </column>
-
             <column name="indexi5_id" type="integer">
-                <constraints foreignKeyName="fk_metagenomics_batch_item_indexi5_to_ngsindex" references="ngsindexes(id)"/>
+                <constraints foreignKeyName="fk_metagenomics_batch_item_indexi5_to_ngsindex"
+                    references="ngsindexes(id)" />
             </column>
             <column name="indexi7_id" type="integer">
-                <constraints foreignKeyName="fk_metagenomics_batch_item_indexi7_to_ngsindex" references="ngsindexes(id)"/>
+                <constraints foreignKeyName="fk_metagenomics_batch_item_indexi7_to_ngsindex"
+                    references="ngsindexes(id)" />
             </column>
         </createTable>
     </changeSet>
-</databaseChangeLog>
+</databaseChangeLog>
diff --git a/src/test/java/ca/gc/aafc/seqdb/api/repository/MetagenomicsBatchIT.java b/src/test/java/ca/gc/aafc/seqdb/api/repository/MetagenomicsBatchIT.java
@@ -4,10 +4,16 @@
 
 import ca.gc.aafc.seqdb.api.dto.MetagenomicsBatchDto;
 import ca.gc.aafc.seqdb.api.dto.MetagenomicsBatchItemDto;
+import ca.gc.aafc.seqdb.api.dto.MolecularAnalysisResultDto;
+import ca.gc.aafc.seqdb.api.dto.MolecularAnalysisRunDto;
+import ca.gc.aafc.seqdb.api.dto.MolecularAnalysisRunItemDto;
 import ca.gc.aafc.seqdb.api.dto.pcr.PcrBatchDto;
 import ca.gc.aafc.seqdb.api.dto.pcr.PcrBatchItemDto;
 import ca.gc.aafc.seqdb.api.testsupport.fixtures.MetagenomicsBatchItemTestFixture;
 import ca.gc.aafc.seqdb.api.testsupport.fixtures.MetagenomicsBatchTestFixture;
+import ca.gc.aafc.seqdb.api.testsupport.fixtures.MolecularAnalysisResultFixture;
+import ca.gc.aafc.seqdb.api.testsupport.fixtures.MolecularAnalysisRunItemTestFixture;
+import ca.gc.aafc.seqdb.api.testsupport.fixtures.MolecularAnalysisRunTestFixture;
 import ca.gc.aafc.seqdb.api.testsupport.fixtures.PcrBatchItemTestFixture;
 import ca.gc.aafc.seqdb.api.testsupport.fixtures.PcrBatchTestFixture;
 
@@ -27,20 +33,43 @@ public class MetagenomicsBatchIT extends BaseRepositoryTestV2 {
   @Inject
   private PcrBatchItemRepository pcrBatchItemRepository;
 
+  @Inject
+  private MolecularAnalysisRunRepository molecularAnalysisRunRepository;
+
+  @Inject
+  private MolecularAnalysisRunItemRepository molecularAnalysisRunItemRepository;
+
+  @Inject
+  private MolecularAnalysisResultRepository molecularAnalysisResultRepository;
+
   @Test
   public void onValidDto_dtoSavedWithoutExceptions() {
 
     MetagenomicsBatchDto metagenomicsBatchDto = metagenomicsBatchRepository
-      .create(MetagenomicsBatchTestFixture.newMetagenomicsBatch());
+        .create(MetagenomicsBatchTestFixture.newMetagenomicsBatch());
 
     PcrBatchDto pcrBatchDto = PcrBatchTestFixture.newPcrBatch();
     pcrBatchDto = pcrBatchRepository.create(pcrBatchDto);
 
     PcrBatchItemDto pcrBatchItemDto = PcrBatchItemTestFixture.newPcrBatchItem(pcrBatchDto);
     pcrBatchItemDto = pcrBatchItemRepository.create(pcrBatchItemDto);
 
+    MolecularAnalysisRunDto runDto = molecularAnalysisRunRepository
+        .create(MolecularAnalysisRunTestFixture.newMolecularAnalysisRun());
+
+    MolecularAnalysisResultDto resultDto = molecularAnalysisResultRepository
+        .create(MolecularAnalysisResultFixture.newMolecularAnalysisResult());
+
+    MolecularAnalysisRunItemDto runItemDto = MolecularAnalysisRunItemTestFixture
+        .newMolecularAnalysisRunItem();
+    runItemDto.setRun(runDto);
+    runItemDto.setResult(resultDto);
+
+    runItemDto = molecularAnalysisRunItemRepository.create(runItemDto);
+
     MetagenomicsBatchItemDto itemDto = MetagenomicsBatchItemTestFixture.newMetagenomicsBatchItem(metagenomicsBatchDto);
     itemDto.setPcrBatchItem(pcrBatchItemDto);
+    itemDto.setMolecularAnalysisRunItem(runItemDto);
 
     metagenomicsBatchItemRepository.create(itemDto);
   }