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Refactored generators #42

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Sep 13, 2021
Merged

Refactored generators #42

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2 changes: 1 addition & 1 deletion ...ava/org/alliancegenome/curation_api/bulk/controllers/DiseaseAnnotationBulkController.java
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Expand Up @@ -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;
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2 changes: 1 addition & 1 deletion ...in/java/org/alliancegenome/curation_api/crud/controllers/DiseaseAnnotationController.java
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Expand Up @@ -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 {
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18 changes: 3 additions & 15 deletions src/main/java/org/alliancegenome/curation_api/model/ingest/json/dto/EvidenceDTO.java
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@@ -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();
}
}
12 changes: 0 additions & 12 deletions .../java/org/alliancegenome/curation_api/model/ingest/json/dto/ExperimentalConditionDTO.java
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@@ -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 {
Expand All @@ -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();
}
}
13 changes: 2 additions & 11 deletions src/main/java/org/alliancegenome/curation_api/model/ingest/json/dto/PublicationDTO.java
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@@ -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();
}

}
36 changes: 14 additions & 22 deletions ...Annotations/DiseaseAnnotationService.java → ...pi/services/DiseaseAnnotationService.java
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@@ -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
Expand Down Expand Up @@ -64,7 +57,6 @@ private DiseaseAnnotation upsertAnnotation(DiseaseModelAnnotationDTO annotationD
return annotation;
}


@Transactional
public DiseaseAnnotation upsert(DiseaseModelAnnotationDTO annotationDTO) {
String entityId = annotationDTO.getObjectId();
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37 changes: 32 additions & 5 deletions ...liancegenome/curation_api/services/helpers/diseaseAnnotations/DiseaseAnnotationCurie.java
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@@ -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();
}
}
2 changes: 1 addition & 1 deletion ...enome/curation_api/services/helpers/diseaseAnnotations/DiseaseAnnotationCurieManager.java
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Expand Up @@ -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());
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2 changes: 1 addition & 1 deletion ...ncegenome/curation_api/services/helpers/diseaseAnnotations/FlyDiseaseAnnotationCurie.java
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Expand Up @@ -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();
}
}
2 changes: 1 addition & 1 deletion ...ncegenome/curation_api/services/helpers/diseaseAnnotations/MGIDiseaseAnnotationCurie.java
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Expand Up @@ -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();
}
}
2 changes: 1 addition & 1 deletion ...ncegenome/curation_api/services/helpers/diseaseAnnotations/RGDDiseaseAnnotationCurie.java
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Expand Up @@ -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();
}
}
2 changes: 1 addition & 1 deletion ...ncegenome/curation_api/services/helpers/diseaseAnnotations/SGDDiseaseAnnotationCurie.java
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Expand Up @@ -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();
}
}
2 changes: 1 addition & 1 deletion ...cegenome/curation_api/services/helpers/diseaseAnnotations/WormDiseaseAnnotationCurie.java
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Expand Up @@ -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();
}
}
4 changes: 2 additions & 2 deletions ...cegenome/curation_api/services/helpers/diseaseAnnotations/ZFINDiseaseAnnotationCurie.java
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Expand Up @@ -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))
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