Merge pull request #42 from alliance-genome/load-syn-refactor

Refactored generators
alliance-genome · Sep 13, 2021 · c5c25bc · c5c25bc
2 parents ecd8150 + 79c9b3f
commit c5c25bc
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Showing 14 changed files with 61 additions and 75 deletions.
diff --git a/...ava/org/alliancegenome/curation_api/bulk/controllers/DiseaseAnnotationBulkController.java b/...ava/org/alliancegenome/curation_api/bulk/controllers/DiseaseAnnotationBulkController.java
@@ -3,7 +3,7 @@
 import lombok.extern.jbosslog.JBossLog;
 import org.alliancegenome.curation_api.interfaces.bulk.DiseaseAnnotationBulkRESTInterface;
 import org.alliancegenome.curation_api.model.ingest.json.dto.DiseaseAnnotationMetaDataDTO;
-import org.alliancegenome.curation_api.services.helpers.diseaseAnnotations.DiseaseAnnotationService;
+import org.alliancegenome.curation_api.services.DiseaseAnnotationService;
 
 import javax.enterprise.context.RequestScoped;
 import javax.inject.Inject;

diff --git a/...in/java/org/alliancegenome/curation_api/crud/controllers/DiseaseAnnotationController.java b/...in/java/org/alliancegenome/curation_api/crud/controllers/DiseaseAnnotationController.java
@@ -8,7 +8,7 @@
 import org.alliancegenome.curation_api.dao.DiseaseAnnotationDAO;
 import org.alliancegenome.curation_api.interfaces.rest.DiseaseAnnotationRESTInterface;
 import org.alliancegenome.curation_api.model.entities.DiseaseAnnotation;
-import org.alliancegenome.curation_api.services.helpers.diseaseAnnotations.DiseaseAnnotationService;
+import org.alliancegenome.curation_api.services.DiseaseAnnotationService;
 
 @RequestScoped
 public class DiseaseAnnotationController extends BaseController<DiseaseAnnotationService, DiseaseAnnotation, DiseaseAnnotationDAO> implements DiseaseAnnotationRESTInterface {

diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/json/dto/EvidenceDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/json/dto/EvidenceDTO.java
@@ -1,27 +1,15 @@
 package org.alliancegenome.curation_api.model.ingest.json.dto;
 
-import lombok.Data;
+import java.util.List;
+
 import org.alliancegenome.curation_api.base.BaseDTO;
-import org.alliancegenome.curation_api.services.CurieGenerator;
-import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang3.StringUtils;
 
-import java.util.Comparator;
-import java.util.List;
+import lombok.Data;
 
 @Data
 public class EvidenceDTO extends BaseDTO {
 
     private PublicationDTO publication;
     private List<String> evidenceCodes;
 
-    public String getCurie() {
-        CurieGenerator curie = new CurieGenerator();
-        curie.add(publication.getPublicationId());
-        if (CollectionUtils.isNotEmpty(evidenceCodes)) {
-            evidenceCodes.sort(Comparator.naturalOrder());
-            curie.add(StringUtils.join(evidenceCodes, "::"));
-        }
-        return curie.getCurie();
-    }
 }
diff --git a/.../java/org/alliancegenome/curation_api/model/ingest/json/dto/ExperimentalConditionDTO.java b/.../java/org/alliancegenome/curation_api/model/ingest/json/dto/ExperimentalConditionDTO.java
@@ -1,12 +1,8 @@
 package org.alliancegenome.curation_api.model.ingest.json.dto;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
 import org.alliancegenome.curation_api.base.BaseDTO;
 
-import com.fasterxml.jackson.annotation.JsonProperty;
-
 import lombok.Data;
-import org.alliancegenome.curation_api.services.CurieGenerator;
 
 @Data
 public class ExperimentalConditionDTO extends BaseDTO {
@@ -20,12 +16,4 @@ public class ExperimentalConditionDTO extends BaseDTO {
     private String ncbitaxonId;
     private String chemicalOntologyId;
 
-    public String getCurie() {
-        CurieGenerator generator = new CurieGenerator();
-        generator.add(conditionClassId);
-        generator.add(conditionStatement);
-        generator.add(conditionId);
-        generator.add(conditionQuantity);
-        return generator.getCurie();
-    }
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/json/dto/PublicationDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/json/dto/PublicationDTO.java
@@ -1,22 +1,13 @@
 package org.alliancegenome.curation_api.model.ingest.json.dto;
 
-import lombok.Data;
 import org.alliancegenome.curation_api.base.BaseDTO;
-import org.alliancegenome.curation_api.services.CurieGenerator;
+
+import lombok.Data;
 
 @Data
 public class PublicationDTO extends BaseDTO {
 
     private String publicationId;
     private CrossReferenceDTO crossReference;
 
-    public String getCurie() {
-        CurieGenerator curie = new CurieGenerator();
-        curie.add(publicationId);
-        if (crossReference != null) {
-            curie.add(crossReference.getId());
-        }
-        return curie.getCurie();
-    }
-
 }
diff --git a/...Annotations/DiseaseAnnotationService.java → ...pi/services/DiseaseAnnotationService.java b/...Annotations/DiseaseAnnotationService.java → ...pi/services/DiseaseAnnotationService.java
@@ -1,30 +1,23 @@
-package org.alliancegenome.curation_api.services.helpers.diseaseAnnotations;
+package org.alliancegenome.curation_api.services;
 
-import lombok.extern.jbosslog.JBossLog;
-import org.alliancegenome.curation_api.base.BaseService;
-import org.alliancegenome.curation_api.dao.BiologicalEntityDAO;
-import org.alliancegenome.curation_api.dao.DiseaseAnnotationDAO;
-import org.alliancegenome.curation_api.dao.DoTermDAO;
-import org.alliancegenome.curation_api.dao.ReferenceDAO;
-import org.alliancegenome.curation_api.model.entities.BiologicalEntity;
-import org.alliancegenome.curation_api.model.entities.DiseaseAnnotation;
-import org.alliancegenome.curation_api.model.entities.Reference;
-import org.alliancegenome.curation_api.model.entities.ontology.DOTerm;
-import org.alliancegenome.curation_api.model.ingest.json.dto.DiseaseAnnotationMetaDataDTO;
-import org.alliancegenome.curation_api.model.ingest.json.dto.DiseaseModelAnnotationDTO;
-import org.alliancegenome.curation_api.model.ingest.json.dto.ExperimentalConditionDTO;
-import org.alliancegenome.curation_api.services.CurieGenerator;
-import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
-import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.collections4.ListUtils;
+import java.util.*;
+import java.util.stream.Collectors;
 
 import javax.annotation.PostConstruct;
 import javax.enterprise.context.RequestScoped;
 import javax.inject.Inject;
 import javax.transaction.Transactional;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.stream.Collectors;
+
+import org.alliancegenome.curation_api.base.BaseService;
+import org.alliancegenome.curation_api.dao.*;
+import org.alliancegenome.curation_api.model.entities.*;
+import org.alliancegenome.curation_api.model.entities.ontology.DOTerm;
+import org.alliancegenome.curation_api.model.ingest.json.dto.*;
+import org.alliancegenome.curation_api.services.helpers.diseaseAnnotations.DiseaseAnnotationCurieManager;
+import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
+import org.apache.commons.collections4.ListUtils;
+
+import lombok.extern.jbosslog.JBossLog;
 
 @JBossLog
 @RequestScoped
@@ -64,7 +57,6 @@ private DiseaseAnnotation upsertAnnotation(DiseaseModelAnnotationDTO annotationD
         return annotation;
     }
 
-
     @Transactional
     public DiseaseAnnotation upsert(DiseaseModelAnnotationDTO annotationDTO) {
         String entityId = annotationDTO.getObjectId();

diff --git a/...liancegenome/curation_api/services/helpers/diseaseAnnotations/DiseaseAnnotationCurie.java b/...liancegenome/curation_api/services/helpers/diseaseAnnotations/DiseaseAnnotationCurie.java
@@ -1,16 +1,43 @@
 package org.alliancegenome.curation_api.services.helpers.diseaseAnnotations;
 
-import lombok.extern.jbosslog.JBossLog;
-import org.alliancegenome.curation_api.model.ingest.json.dto.DiseaseModelAnnotationDTO;
+import java.util.Comparator;
 
-import java.util.HashMap;
-import java.util.Map;
+import org.alliancegenome.curation_api.model.ingest.json.dto.*;
+import org.alliancegenome.curation_api.services.CurieGenerator;
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.lang3.StringUtils;
 
-@JBossLog
 public abstract class DiseaseAnnotationCurie {
 
     public static final String DELIMITER = "|";
 
     public abstract String getCurieID(DiseaseModelAnnotationDTO annotationDTO);
 
+    public String getExperimentalConditionCurie(ExperimentalConditionDTO dto) {
+        CurieGenerator curie = new CurieGenerator();
+        curie.add(dto.getConditionClassId());
+        curie.add(dto.getConditionStatement());
+        curie.add(dto.getConditionId());
+        curie.add(dto.getConditionQuantity());
+        return curie.getCurie();
+    }
+
+    public String getEvidenceCurie(EvidenceDTO dto) {
+        CurieGenerator curie = new CurieGenerator();
+        curie.add(dto.getPublication().getPublicationId());
+        if (CollectionUtils.isNotEmpty(dto.getEvidenceCodes())) {
+            dto.getEvidenceCodes().sort(Comparator.naturalOrder());
+            curie.add(StringUtils.join(dto.getEvidenceCodes(), "::"));
+        }
+        return curie.getCurie();
+    }
+
+    public String getPublicationCurie(PublicationDTO dto) {
+        CurieGenerator curie = new CurieGenerator();
+        curie.add(dto.getPublicationId());
+        if (dto.getCrossReference() != null) {
+            curie.add(dto.getCrossReference().getId());
+        }
+        return curie.getCurie();
+    }
 }
diff --git a/...enome/curation_api/services/helpers/diseaseAnnotations/DiseaseAnnotationCurieManager.java b/...enome/curation_api/services/helpers/diseaseAnnotations/DiseaseAnnotationCurieManager.java
@@ -12,7 +12,7 @@ public abstract class DiseaseAnnotationCurieManager {
 
     static {
         curieTaxonMap.put("NCBITaxon:7955", new ZFINDiseaseAnnotationCurie());
-        //curieTaxonMap.put("NCBITaxon:9606", new ZFINDiseaseAnnotationCurie());
+        //curieTaxonMap.put("NCBITaxon:9606", new HUMANDiseaseAnnotationCurie());
         curieTaxonMap.put("NCBITaxon:10116", new RGDDiseaseAnnotationCurie());
         curieTaxonMap.put("NCBITaxon:10090", new MGIDiseaseAnnotationCurie());
         curieTaxonMap.put("NCBITaxon:6239", new WormDiseaseAnnotationCurie());

diff --git a/...ncegenome/curation_api/services/helpers/diseaseAnnotations/FlyDiseaseAnnotationCurie.java b/...ncegenome/curation_api/services/helpers/diseaseAnnotations/FlyDiseaseAnnotationCurie.java
@@ -16,7 +16,7 @@ public String getCurieID(DiseaseModelAnnotationDTO annotationDTO) {
         CurieGenerator curie = new CurieGenerator();
         curie.add(annotationDTO.getObjectId());
         curie.add(annotationDTO.getDoId());
-        curie.add(annotationDTO.getEvidence().getCurie());
+        curie.add(getEvidenceCurie(annotationDTO.getEvidence()));
         return curie.getCurie();
     }
 }
diff --git a/...ncegenome/curation_api/services/helpers/diseaseAnnotations/MGIDiseaseAnnotationCurie.java b/...ncegenome/curation_api/services/helpers/diseaseAnnotations/MGIDiseaseAnnotationCurie.java
@@ -16,7 +16,7 @@ public String getCurieID(DiseaseModelAnnotationDTO annotationDTO) {
         CurieGenerator curie = new CurieGenerator();
         curie.add(annotationDTO.getObjectId());
         curie.add(annotationDTO.getDoId());
-        curie.add(annotationDTO.getEvidence().getPublication().getCurie());
+        curie.add(getPublicationCurie(annotationDTO.getEvidence().getPublication()));
         return curie.getCurie();
     }
 }
diff --git a/...ncegenome/curation_api/services/helpers/diseaseAnnotations/RGDDiseaseAnnotationCurie.java b/...ncegenome/curation_api/services/helpers/diseaseAnnotations/RGDDiseaseAnnotationCurie.java
@@ -16,7 +16,7 @@ public String getCurieID(DiseaseModelAnnotationDTO annotationDTO) {
         CurieGenerator curie = new CurieGenerator();
         curie.add(annotationDTO.getObjectId());
         curie.add(annotationDTO.getDoId());
-        curie.add(annotationDTO.getEvidence().getCurie());
+        curie.add(getEvidenceCurie(annotationDTO.getEvidence()));
         return curie.getCurie();
     }
 }
diff --git a/...ncegenome/curation_api/services/helpers/diseaseAnnotations/SGDDiseaseAnnotationCurie.java b/...ncegenome/curation_api/services/helpers/diseaseAnnotations/SGDDiseaseAnnotationCurie.java
@@ -16,7 +16,7 @@ public String getCurieID(DiseaseModelAnnotationDTO annotationDTO) {
         CurieGenerator curie = new CurieGenerator();
         curie.add(annotationDTO.getObjectId());
         curie.add(annotationDTO.getDoId());
-        curie.add(annotationDTO.getEvidence().getCurie());
+        curie.add(getEvidenceCurie(annotationDTO.getEvidence()));
         return curie.getCurie();
     }
 }
diff --git a/...cegenome/curation_api/services/helpers/diseaseAnnotations/WormDiseaseAnnotationCurie.java b/...cegenome/curation_api/services/helpers/diseaseAnnotations/WormDiseaseAnnotationCurie.java
@@ -16,7 +16,7 @@ public String getCurieID(DiseaseModelAnnotationDTO annotationDTO) {
         CurieGenerator curie = new CurieGenerator();
         curie.add(annotationDTO.getObjectId());
         curie.add(annotationDTO.getDoId());
-        curie.add(annotationDTO.getEvidence().getPublication().getCurie());
+        curie.add(getPublicationCurie(annotationDTO.getEvidence().getPublication()));
         return curie.getCurie();
     }
 }
diff --git a/...cegenome/curation_api/services/helpers/diseaseAnnotations/ZFINDiseaseAnnotationCurie.java b/...cegenome/curation_api/services/helpers/diseaseAnnotations/ZFINDiseaseAnnotationCurie.java
@@ -20,14 +20,14 @@ public String getCurieID(DiseaseModelAnnotationDTO annotationDTO) {
         CurieGenerator curie = new CurieGenerator();
         curie.add(annotationDTO.getObjectId());
         curie.add(annotationDTO.getDoId());
-        curie.add(annotationDTO.getEvidence().getCurie());
+        curie.add(getEvidenceCurie(annotationDTO.getEvidence()));
         if (CollectionUtils.isNotEmpty(annotationDTO.getConditionRelations())) {
             curie.add(annotationDTO.getConditionRelations().stream()
                     .map(conditionDTO -> {
                         CurieGenerator gen = new CurieGenerator();
                         gen.add(conditionDTO.getConditionRelationType());
                         gen.add(conditionDTO.getConditions().stream()
-                                .map(ExperimentalConditionDTO::getCurie).collect(Collectors.joining(DELIMITER))
+                                .map(e -> getExperimentalConditionCurie(e)).collect(Collectors.joining(DELIMITER))
                         );
                         return gen.getCurie();
                     }).collect(Collectors.joining(DELIMITER))