[BI-1613] - Add Term Type to Ontology Term Import

src/main/java/org/breedinginsight/brapps/importer/model/imports/TermTypeTranslator.java

@@ -0,0 +1,17 @@
+package org.breedinginsight.brapps.importer.model.imports;
+
+import org.breedinginsight.dao.db.enums.TermType;
+import java.util.Map;
+import java.util.Optional;
+
+public class TermTypeTranslator {
+
+    private static final Map<String, TermType> userDisplayToTermTypeMap = Map.of(
+            "Phenotype", TermType.PHENOTYPE,
+            "Germplasm Attribute", TermType.GERM_ATTRIBUTE,
+            "Germplasm Passport", TermType.GERM_PASSPORT);
+
+    public static Optional<TermType> getTermTypeFromUserDisplayName(String userDisplayName) {
+        return Optional.ofNullable(userDisplayToTermTypeMap.get(userDisplayName));
+    }
+}

src/main/java/org/breedinginsight/model/Trait.java

@@ -91,6 +91,7 @@ public Trait(TraitEntity traitEntity) {
         this.setUpdatedAt(traitEntity.getUpdatedAt());
         this.setUpdatedBy(traitEntity.getUpdatedBy());
         this.setActive(traitEntity.getActive());
+        this.setTermType(traitEntity.getTermType());
     }
 
     public static Trait parseSqlRecord(Record record) {
@@ -106,6 +107,7 @@ public static Trait parseSqlRecord(Record record) {
             .updatedAt(record.getValue(TRAIT.UPDATED_AT))
             .updatedBy(record.getValue(TRAIT.UPDATED_BY))
             .active(record.getValue(TRAIT.ACTIVE))
+            .termType(record.getValue(TRAIT.TERM_TYPE))
             .build();
     }
 

src/main/java/org/breedinginsight/services/TraitService.java

@@ -217,6 +217,7 @@ public List<Trait> createTraits(UUID programId, List<Trait> traits, Authenticate
                             .createdBy(actingUser.getId())
                             .updatedBy(actingUser.getId())
                             .active(true)
+                            .termType(trait.getTermType())
                             .build();
                     traitDAO.insert(jooqTrait);
                     trait.setId(jooqTrait.getId());
@@ -416,6 +417,7 @@ public List<Trait> updateTraits(UUID programId, List<Trait> traits, Authenticate
                     existingTraitEntity.setObservationVariableName(updatedTrait.getObservationVariableName());
                     existingTraitEntity.setProgramObservationLevelId(updatedTrait.getProgramObservationLevel().getId());
                     existingTraitEntity.setUpdatedBy(user.getId());
+                    existingTraitEntity.setTermType(updatedTrait.getTermType());
                     traitDAO.update(existingTraitEntity);
 
                     // Update in brapi

src/main/java/org/breedinginsight/services/parsers/ParsingExceptionType.java

@@ -32,7 +32,8 @@ public enum ParsingExceptionType {
     INVALID_SCALE_DECIMAL_PLACES("Invalid scale decimal places value"),
     INVALID_SCALE_LOWER_LIMIT("Invalid scale lower limit value. Value must be numeric and be a whole number."),
     INVALID_SCALE_UPPER_LIMIT("Invalid scale upper limit value. Value must be numeric and be a whole number."),
-    INVALID_SCALE_CATEGORIES("Invalid scale categories format");
+    INVALID_SCALE_CATEGORIES("Invalid scale categories format"),
+    INVALID_TERM_TYPE("Invalid term type");
 
     private String value;
 

src/main/java/org/breedinginsight/services/parsers/trait/TraitFileColumns.java

@@ -38,7 +38,9 @@ public enum TraitFileColumns {
     SCALE_UPPER_LIMIT("Scale upper limit"),
     SCALE_CATEGORIES("Scale categories"),
     TAGS("Tags"),
-    FULL_NAME("Full name");
+    FULL_NAME("Full name"),
+    TERM_TYPE("Term Type");
+
 
     private String value;
 

src/main/java/org/breedinginsight/services/parsers/trait/TraitFileParser.java

@@ -16,18 +16,20 @@
  */
 package org.breedinginsight.services.parsers.trait;
 
-import io.micronaut.core.util.StringUtils;
 import io.micronaut.http.HttpStatus;
 import lombok.NonNull;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVRecord;
+import org.apache.commons.text.WordUtils;
 import org.apache.poi.EncryptedDocumentException;
 import org.apache.poi.ss.usermodel.*;
 import org.brapi.v2.model.pheno.BrAPIScaleValidValuesCategories;
 import org.breedinginsight.api.model.v1.response.ValidationError;
 import org.breedinginsight.api.model.v1.response.ValidationErrors;
+import org.breedinginsight.brapps.importer.model.imports.TermTypeTranslator;
 import org.breedinginsight.dao.db.enums.DataType;
+import org.breedinginsight.dao.db.enums.TermType;
 import org.breedinginsight.model.*;
 import org.breedinginsight.services.exceptions.UnprocessableEntityException;
 import org.breedinginsight.services.exceptions.ValidatorException;
@@ -250,6 +252,21 @@ private List<Trait> excelRecordsToTraits(List<ExcelRecord> records) throws Valid
             String tagsString = parseExcelValueAsString(record, TraitFileColumns.TAGS);
             List<String> traitTags = parseListValue(tagsString);
 
+            //Set to backend value for user input term type, if none, set to default
+            TermType termType = TermType.PHENOTYPE;
+
+            String termTypeVal = parseExcelValueAsString(record, TraitFileColumns.TERM_TYPE);
+            if ((!Objects.isNull(termTypeVal)) && (!termTypeVal.isBlank())) {
+                Optional<TermType> termTypeOpt = TermTypeTranslator.getTermTypeFromUserDisplayName(WordUtils.capitalizeFully(termTypeVal));
+                if (termTypeOpt.isPresent()) {
+                    termType = termTypeOpt.get();
+                } else {
+                    ValidationError error = new ValidationError(TraitFileColumns.TERM_TYPE.toString(),
+                            ParsingExceptionType.INVALID_TERM_TYPE.toString(), HttpStatus.UNPROCESSABLE_ENTITY);
+                    validationErrors.addError(traitValidatorError.getRowNumber(i), error);
+                }
+            }
+
             Trait trait = Trait.builder()
                     .observationVariableName(parseExcelValueAsString(record, TraitFileColumns.NAME))
                     .traitDescription(parseExcelValueAsString(record, TraitFileColumns.DESCRIPTION))
@@ -263,6 +280,7 @@ private List<Trait> excelRecordsToTraits(List<ExcelRecord> records) throws Valid
                     .method(method)
                     .scale(scale)
                     .tags(traitTags)
+                    .termType(termType)
                     .build();
 
             traits.add(trait);

src/main/java/org/breedinginsight/utilities/response/mappers/TraitQueryMapper.java

@@ -73,7 +73,8 @@ public TraitQueryMapper() {
                 Map.entry("updatedByUserId",
                         trait -> trait.getUpdatedByUser() != null ? trait.getUpdatedByUser().getId() : null),
                 Map.entry("updatedByUserName",
-                        trait -> trait.getUpdatedByUser() != null ? trait.getUpdatedByUser().getName() : null)
+                        trait -> trait.getUpdatedByUser() != null ? trait.getUpdatedByUser().getName() : null),
+                Map.entry("termType", Trait::getTermType)
         );
     }
 

src/main/resources/db/migration/V1.0.10__add_onto_term_type.sql

@@ -0,0 +1,25 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+CREATE TYPE "term_type" AS ENUM (
+  'PHENOTYPE',
+  'GERM_ATTRIBUTE',
+  'GERM_PASSPORT'
+);
+
+ALTER TABLE trait ADD COLUMN term_type term_type NOT NULL DEFAULT 'PHENOTYPE';
+UPDATE trait SET term_type='PHENOTYPE';

src/test/java/org/breedinginsight/api/v1/controller/TraitUploadControllerIntegrationTest.java

@@ -38,6 +38,7 @@
 import org.breedinginsight.api.model.v1.request.query.SearchRequest;
 import org.breedinginsight.api.v1.controller.metadata.SortOrder;
 import org.breedinginsight.dao.db.enums.DataType;
+import org.breedinginsight.dao.db.enums.TermType;
 import org.breedinginsight.dao.db.tables.daos.ProgramDao;
 import org.breedinginsight.dao.db.tables.pojos.BiUserEntity;
 import org.breedinginsight.dao.db.tables.pojos.ProgramEntity;
@@ -570,6 +571,8 @@ private void checkValidTraitUpload(JsonObject traitUpload) {
         assertEquals("Leaf", observationLevel.get("name").getAsString(), "wrong level name");
 
         assertEquals(true, trait.get("active").getAsBoolean(), "wrong status");
+        assertEquals(TermType.GERM_PASSPORT.toString(), trait.get("termType").getAsString());
+
         // TODO: trait lists
 
         JsonObject method = trait.get("method").getAsJsonObject();

src/test/java/org/breedinginsight/services/parsers/TraitFileParserUnitTest.java

@@ -22,6 +22,7 @@
 import org.breedinginsight.api.model.v1.response.ValidationError;
 import org.breedinginsight.api.model.v1.response.ValidationErrors;
 import org.breedinginsight.dao.db.enums.DataType;
+import org.breedinginsight.dao.db.enums.TermType;
 import org.breedinginsight.model.Method;
 import org.breedinginsight.model.Scale;
 import org.breedinginsight.model.Trait;
@@ -182,6 +183,7 @@ void parseCsvConvertToTraitsError() {
         expectedErrors3.put(TraitFileColumns.SCALE_DECIMAL_PLACES.toString(), ParsingExceptionType.INVALID_SCALE_DECIMAL_PLACES);
         expectedErrors3.put(TraitFileColumns.SCALE_LOWER_LIMIT.toString(), ParsingExceptionType.INVALID_SCALE_LOWER_LIMIT);
         expectedErrors3.put(TraitFileColumns.SCALE_UPPER_LIMIT.toString(), ParsingExceptionType.INVALID_SCALE_UPPER_LIMIT);
+        expectedErrors3.put(TraitFileColumns.TERM_TYPE.toString(), ParsingExceptionType.INVALID_TERM_TYPE);
 
         checkParsingExceptionErrors(rowErrors.getRowErrors().get(0), expectedErrors1);
         checkParsingExceptionErrors(rowErrors.getRowErrors().get(1), expectedErrors2);
@@ -286,6 +288,7 @@ private void assertTestTraitEquals(Trait trait) {
         assertEquals("leaf", trait.getEntity(), "wrong entity");
         assertEquals("powdery mildew severity", trait.getAttribute(), "wrong attribute");
         assertEquals(true, trait.getActive(), "wrong status");
+        assertEquals(TermType.GERM_PASSPORT, trait.getTermType(), "wrong term type");
         // TODO: trait lists
         Method method = trait.getMethod();
         assertEquals("Powdery Mildew severity, leaf", method.getDescription(), "wrong method description");

src/test/resources/files/columns_no_data.csv

@@ -1 +1 @@
-Name,Synonyms,Description,Trait entity,Trait attribute,Status,Tags,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Full Name
+Name,Synonyms,Description,Trait entity,Trait attribute,Status,Tags,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Full Name,Term Type

src/test/resources/files/data_duplicate_headers.csv

@@ -1,2 +1,2 @@
-Name,ONTOLOgY TErM NaME,Trait Abbreviations,trAit synoNyms,trait Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,ScALe Upper limit,Scale CAtegories,Full Name
-PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",Plant,active,mildew,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation",Observed severity of Powdery Mildew on leaves,Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,2,9999,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,
+Name,ONTOLOgY TErM NaME,Trait Abbreviations,trAit synoNyms,trait Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,ScALe Upper limit,Scale CAtegories,Full Name,Term Type
+PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",Plant,active,mildew,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation",Observed severity of Powdery Mildew on leaves,Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,2,9999,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,,

src/test/resources/files/data_duplicate_method_name.csv

@@ -1,2 +1,2 @@
-Name,Synonyms,Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Full Name
-PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew severity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ",blah,"Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,2,9999,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",
+Name,Synonyms,Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Full Name,Term Type
+PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew severity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ",blah,"Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,2,9999,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,

src/test/resources/files/data_min_max_swap.csv

@@ -1,2 +1,2 @@
-Name,Synonyms,Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Tags,Full Name
-PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew severity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation","Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,9999,2.11,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,
+Name,Synonyms,Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Tags,Full Name,Term Type
+PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew severity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation","Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,9999,2.11,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,,

src/test/resources/files/data_mismatched_cases.csv

@@ -1,2 +1,2 @@
-name,synoNyms,deScription,Trait entity,Trait attribute,StaTus,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,ScALe Upper limit,Scale CAtegories,Tags,Full Name
-PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew severity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation","Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,2,9999,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,
+name,synoNyms,deScription,Trait entity,Trait attribute,StaTus,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,ScALe Upper limit,Scale CAtegories,Tags,Full Name,Term Type
+PM_Leaf,Powdery Mildew; Powdery Mildew Severity,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew severity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation","Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,2,2,9999,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,,Germplasm PASSPORT

src/test/resources/files/data_multiple_rows.csv

@@ -1,4 +1,4 @@
-Name,Synonyms,Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Tags,Full Name
-PM_leaf,Powdery Mildew Leaf; Powdery Mildew Severity Leaf,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew deverity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ","Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,,,,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,Powdery Mildew Severity Leaf
-PM_bud,Powdery Mildew Bud; Powdery Mildew Severity Bud,"Powdery mildew (PM) due to Erysiphe necator severity in field, bud only ",bud,powdery mildew deverity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ","Powdery Mildew severity, bud",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,,,,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,Powdery Mildew Severity Bud
-PM_stem,Powdery Mildew Stem; Powdery Mildew Severity Stem,"Powdery mildew (PM) due to Erysiphe necator severity in field, stem only ",stem,powdery mildew deverity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ","Powdery Mildew severity, stem",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,,,,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,Powdery Mildew Severity Stem
+Name,Synonyms,Description,Trait entity,Trait attribute,Status,Trait lists,Method name,Method description,Method class,Method formula,Units,Scale class,Scale decimal places,Scale lower limit,Scale upper limit,Scale categories,Tags,Full Name,Term Type
+PM_leaf,Powdery Mildew Leaf; Powdery Mildew Severity Leaf,"Powdery mildew (PM) due to Erysiphe necator severity in field, leaves only ",leaf,powdery mildew deverity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ","Powdery Mildew severity, leaf",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,,,,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,Powdery Mildew Severity Leaf,Germplasm Attribute
+PM_bud,Powdery Mildew Bud; Powdery Mildew Severity Bud,"Powdery mildew (PM) due to Erysiphe necator severity in field, bud only ",bud,powdery mildew deverity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ","Powdery Mildew severity, bud",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,,,,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,Powdery Mildew Severity Bud,
+PM_stem,Powdery Mildew Stem; Powdery Mildew Severity Stem,"Powdery mildew (PM) due to Erysiphe necator severity in field, stem only ",stem,powdery mildew deverity,active,Nursery evaluation; Greenhouse evaluation; Trial evaluation,"Powdery Mildew severity, leaves - Estimation ","Powdery Mildew severity, stem",Estimation,a^2 + b^2 = c^2,1-4 Parlier field response score,Ordinal,,,,"1=No visible infection; 2=Very few, small colonies; 3=< 50% coverage; 4=>50% coverage",,Powdery Mildew Severity Stem,phenotype