push origin feature/BI-2017-2

src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java

@@ -78,7 +78,7 @@ public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm,
         for (BrAPIGermplasm germplasmEntry: germplasm) {
             HashMap<String, Object> row = new HashMap<>();
             row.put("GID", Integer.valueOf(germplasmEntry.getAccessionNumber()));
-            row.put("Name", germplasmEntry.getGermplasmName());
+            row.put("Germplasm Name", germplasmEntry.getGermplasmName());
             row.put("Breeding Method", germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD).getAsString());
             String source = germplasmEntry.getSeedSource();
             row.put("Source", source);

src/main/java/org/breedinginsight/services/parsers/germplasm/GermplasmFileColumns.java

@@ -25,7 +25,7 @@
 public enum GermplasmFileColumns {
 
     GID("GID", Column.ColumnDataType.INTEGER),
-    NAME("Name", Column.ColumnDataType.STRING),
+    NAME("Germplasm Name", Column.ColumnDataType.STRING),
     BREEDING_METHOD("Breeding Method", Column.ColumnDataType.STRING),
     SOURCE("Source", Column.ColumnDataType.STRING),
     FEMALE_PARENT_GID("Female Parent GID", Column.ColumnDataType.INTEGER),

src/main/resources/db/migration/V1.20.0__germplasm_change_name_field.sql

@@ -0,0 +1,21 @@
+/*
+ * 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.
+ */
+
+update importer_mapping
+set mapping = '[{"id": "f8d43c7e-a618-4c16-8829-3085f7202a67", "mapping": [{"id": "f384837e-ad8d-4dbe-b54e-87b57070bed1", "value": {"fileFieldName": "Germplasm Name"}, "objectId": "germplasmName"}, {"id": "39628d14-458b-429b-8e66-bb48e0445a83", "value": {"fileFieldName": "Breeding Method"}, "objectId": "breedingMethod"}, {"id": "f1ba63e1-f5e4-433f-a53e-1c2f3e2fa71f", "value": {"fileFieldName": "Source"}, "objectId": "germplasmSource"}, {"id": "f5892565-f888-4596-be82-ab8eeabf37ce", "value": {"fileFieldName": "External UID"}, "objectId": "externalUID"}, {"id": "65507e5d-2d66-4595-8763-e772fe25c870", "value": {"fileFieldName": "Entry No"}, "objectId": "entryNo"}, {"id": "3eae24c1-ca4a-48a2-96d0-3cf4630acd3a", "value": {"fileFieldName": "Female Parent GID"}, "objectId": "femaleParentDBID"}, {"id": "2dbd7262-93a1-44b0-86b7-f5fca290b965", "value": {"fileFieldName": "Male Parent GID"}, "objectId": "maleParentDBID"}, {"id": "6f7f1539-6e8f-4ede-b7d3-3423cc63abec", "value": {"fileFieldName": "Female Parent Entry No"}, "objectId": "femaleParentEntryNo"}, {"id": "25fe9954-bca7-42f1-818a-5f71e242fa1f", "value": {"fileFieldName": "Male Parent Entry No"}, "objectId": "maleParentEntryNo"}, {"id": "b910adfe-a474-47a0-8410-514578898436", "value": {"fileFieldName": "Synonyms"}, "objectId": "synonyms"}, {"id": "15836d5f-8194-40a8-a771-114eaae31eb4", "objectId": "germplasmPUI"}, {"id": "675b6af8-5a17-4146-a503-2e4e1a65d5fa", "objectId": "acquisitionDate"}, {"id": "69a3bd3c-cebc-435c-acdd-0be62dda25ed", "objectId": "countryOfOrigin"}, {"id": "8ab25267-20f2-450e-89ca-21634ff8fadb", "objectId": "collection"}, {"id": "ce1701e2-2f61-4250-8595-9536e3f5ddcf", "objectId": "AdditionalInfo"}, {"id": "3470e9df-a028-45b7-943f-198bc62b6dbe", "objectId": "ExternalReference"}], "objectId": "Germplasm"}]',
+    file = '[{"Germplasm Name": "BITest Pinot Noir", "Source": "Unknown", "Entry No": "1", "External UID": "", "Breeding Method": "UMM", "Male Parent GID": "", "Female Parent GID": "", "Male Parent Entry No": "", "Female Parent Entry No": "", "Synonyms": "test1;test2"}, {"Name": "BITest Pixie", "Source": "Winters Nursery", "Entry No": "2", "External UID": "", "Breeding Method": "CFV", "Male Parent GID": "", "Female Parent GID": "", "Male Parent Entry No": "", "Female Parent Entry No": "1", "Synonyms": "test1;test2"}, {"Name": "BITest BI002", "Source": "Ithaca Nursery", "Entry No": "7", "External UID": "12231321", "Breeding Method": "Biparental cross", "Male Parent GID": "", "Female Parent GID": "", "Male Parent Entry No": "", "Female Parent Entry No": "2", "Synonyms": "test1;test2"}, {"Name": "BITest BI003", "Source": "Ithaca Nursery", "Entry No": "8", "External UID": "", "Breeding Method": "BPC", "Male Parent GID": "", "Female Parent GID": "", "Male Parent Entry No": "7", "Female Parent Entry No": "2", "Synonyms": "test1;test2"}, {"Name": "BITest Pinot Noir", "Source": "Unknown", "Entry No": "3", "External UID": "", "Breeding Method": "UMM", "Male Parent GID": "", "Female Parent GID": "5fb01ea5-c212-4cfa-84e4-6d190379341f", "Male Parent Entry No": "", "Female Parent Entry No": "", "Synonyms": "test1;test2"}, {"Name": "BITest Pixie", "Source": "Winters Nursery", "Entry No": "4", "External UID": "", "Breeding Method": "CFV", "Male Parent GID": "640e8b58-1b1c-44a6-91a6-85b2b773376b", "Female Parent GID": "5fb01ea5-c212-4cfa-84e4-6d190379341f", "Male Parent Entry No": "", "Female Parent Entry No": "", "Synonyms": "test1;test2"}, {"Name": "BITest BI002", "Source": "Ithaca Nursery", "Entry No": "5", "External UID": "12231321", "Breeding Method": "Biparental cross", "Male Parent GID": "", "Female Parent GID": "5fb01ea5-c212-4cfa-84e4-6d190379341f", "Male Parent Entry No": "", "Female Parent Entry No": "2", "Synonyms": "test1;test2"}]'
+where name = 'GermplasmTemplateMap';

src/test/java/org/breedinginsight/brapps/importer/GermplasmFileImportTest.java

@@ -167,7 +167,7 @@ public void fullImportPreviewSuccess() {
 
             // Check preview specific items
             // Germplasm name (display name)
-            assertEquals(fileData.getString(i, "Name"), germplasm.get("germplasmName").getAsString());
+            assertEquals(fileData.getString(i, "Germplasm Name"), germplasm.get("germplasmName").getAsString());
             JsonObject additionalInfo = germplasm.getAsJsonObject("additionalInfo");
             // Created Date (not present)
             assertFalse(additionalInfo.has(BrAPIAdditionalInfoFields.CREATED_DATE), "createdDate is present, but should not be");
@@ -229,7 +229,7 @@ public void fullImportCommitSuccess() {
 
             // Check commit specific items
             // Germplasm name (display name)
-            String expectedGermplasmName = String.format("%s [%s-%s]", fileData.getString(i, "Name"), validProgram.getKey(), germplasm.get("accessionNumber").getAsString());
+            String expectedGermplasmName = String.format("%s [%s-%s]", fileData.getString(i, "Germplasm Name"), validProgram.getKey(), germplasm.get("accessionNumber").getAsString());
             assertEquals(expectedGermplasmName, germplasm.get("germplasmName").getAsString());
             // Created Date
             JsonObject additionalInfo = germplasm.getAsJsonObject("additionalInfo");
@@ -531,8 +531,8 @@ public void emptyRequiredFieldsError() {
         assertEquals(1, errors.size(), "Not enough errors were returned");
         JsonObject error = errors.get(0).getAsJsonObject();
         assertEquals(422, error.get("httpStatusCode").getAsInt(), "Incorrect http status code");
-        assertEquals("Name", error.get("field").getAsString(), "Incorrect field name");
-        assertEquals(importService.getBlankRequiredFieldMsg("Name"), error.get("errorMessage").getAsString(), "Incorrect error message");
+        assertEquals("Germplasm Name", error.get("field").getAsString(), "Incorrect field name");
+        assertEquals(importService.getBlankRequiredFieldMsg("Germplasm Name"), error.get("errorMessage").getAsString(), "Incorrect error message");
 
         JsonObject rowError2 = rowErrors.get(1).getAsJsonObject();
         JsonArray errors2 = rowError2.getAsJsonArray("errors");
@@ -648,7 +648,7 @@ public void selfReferenceParentError() {
     public void checkBasicResponse(JsonObject germplasm, Table fileData, Integer i) {
 
         // Germplasm display name
-        assertEquals(fileData.getString(i, "Name"), germplasm.get("defaultDisplayName").getAsString(), "Wrong display name");
+        assertEquals(fileData.getString(i, "Germplasm Name"), germplasm.get("defaultDisplayName").getAsString(), "Wrong display name");
         // Entry Number
         gson.fromJson(germplasm.getAsJsonObject("additionalInfo").getAsJsonObject("listEntryNumbers"), Map.class).forEach((listId, entryNumber) -> assertEquals(fileData.getString(i, "Entry No"), entryNumber, "Wrong entry number"));
         JsonObject additionalInfo = germplasm.getAsJsonObject("additionalInfo");

src/test/resources/files/fileutil/file_all_null_rows.csv

@@ -1,4 +1,4 @@
-Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID
+Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID
 Buzz-1,BPC,Middle Earth,1,16,,,,
 Buzz-2,CFV,Middle Earth,10,,,,,
 ,,,,,,,,

src/test/resources/files/fileutil/file_some_null_rows.csv

@@ -1,4 +1,4 @@
-Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID
+Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID
 Buzz-1,BPC,Middle Earth,1,16,,,,
 Buzz-2,CFV,Middle Earth,10,,,,,
 yeah,,,,,,,,

src/test/resources/files/germplasm_import/bad_breeding_methods.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,ANE,Wild,,,,,,,
 ,Germplasm 2,BAD,Wild,,,,,,,
 ,Germplasm 3,BAD1,Wild,,,,,,,

src/test/resources/files/germplasm_import/circular_parent_dependencies.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,,1,2,3,1234,
 ,Germplasm 2,BCR,Wild,,,2,1,2,5678,
 ,Germplasm 3,BCR,Wild,,,3,2,3,9123,

src/test/resources/files/germplasm_import/duplicate_db_names.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Full Germplasm 1,ANE,Wild,,,,,,,
 ,Full Germplasm 2,ANE,Wild,,,,,,,
 ,Full Germplasm 3,ANE,Wild,,,,,,,

src/test/resources/files/germplasm_import/duplicate_entry_numbers.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,,1,,,,
 ,Germplasm 2,BCR,Wild,,,1,,,,
 ,Germplasm 3,BCR,Wild,,,3,,,,

src/test/resources/files/germplasm_import/empty_required_fields.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,ANE,Wild,,,,,,,
 ,,ANE,Wild,,,,,,,
 ,Germplasm 3,ANE,,,,,,,,

src/test/resources/files/germplasm_import/empty_values_required_fields.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,,Wild,,,,,,,
 ,,,Wild,,,,,,,
 ,Germplasm 3,,,,,,,,,

src/test/resources/files/germplasm_import/female_dbid_not_exist.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,1000,,,,,,
 ,Germplasm 2,BCR,Cultivated,1001,,,,,,
 ,Germplasm 3,BCR,Kinda Wild,1002,,,,,,

src/test/resources/files/germplasm_import/female_entry_number_not_exist.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,,,1,,,
 ,Germplasm 2,BCR,Cultivated,,,,2,,,
 ,Germplasm 3,BCR,Kinda Wild,,,,3,,,

src/test/resources/files/germplasm_import/full_import.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Full Germplasm 1,ANE,Wild,1,2,2,,,1234,test1;test2
 ,Full Germplasm 2,ANE,Wild,2,,3,,,5678,test3;test2
 ,Full Germplasm 3,ANE,Wild,,,4,2,3,9123,test3;test4

src/test/resources/files/germplasm_import/germplasm_column_casing.csv

@@ -1,2 +1,2 @@
-GID,Name,BREEDING METHOD,SOURCE,fEmAlE pArEnT gId,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,BREEDING METHOD,SOURCE,fEmAlE pArEnT gId,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germ A,ANE,the shire,,,1,,,ABC-123,

src/test/resources/files/germplasm_import/male_dbid_no_female_success.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,,Wild,,100,,,,,
 ,Germplasm 2,,Cultivated,,101,,,,,
 ,Germplasm 3,,Kinda Wild,,102,,,,,

src/test/resources/files/germplasm_import/male_dbid_not_exist.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,100,,,,,
 ,Germplasm 2,BCR,Cultivated,,101,,,,,
 ,Germplasm 3,BCR,Kinda Wild,,102,,,,,

src/test/resources/files/germplasm_import/male_entry_number_not_exist.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,,,,1,,
 ,Germplasm 2,BCR,Cultivated,,,,,2,,
 ,Germplasm 3,BCR,Kinda Wild,,,,,3,,

src/test/resources/files/germplasm_import/minimal_germplasm_import.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,,,,,,
 ,Germplasm 2,BCR,Cultivated,,,,,,,
 ,Germplasm 3,BCR,Kinda Wild,,,,,,,

src/test/resources/files/germplasm_import/missing_optional_header.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,ANE,Wild,,,,,,
 ,Germplasm 2,ANE,Wild,,,,,,
 ,Germplasm 3,ANE,Wild,,,,,,

src/test/resources/files/germplasm_import/missing_required_header.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,,,,,,,,
 ,Germplasm 2,,,,,,,,
 ,Germplasm 3,,,,,,,,

src/test/resources/files/germplasm_import/no_female_parent_blank_pedigree.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,0,2,,,,1234,
 ,Germplasm 2,BCR,Wild,0,3,,,,5678,
 ,Germplasm 3,BCR,Wild,0,3,,,,9123,

src/test/resources/files/germplasm_import/nonnumerical_entry_numbers.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,,Wild,,,a,,,,
 ,Germplasm 2,,Wild,,,b,,,,
 ,Germplasm 3,,Wild,,,3,,,,

src/test/resources/files/germplasm_import/self_ref_parent_dependencies.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,,1,1,1,1234,
 ,Germplasm 2,BCR,Wild,,,2,2,2,5678,
 ,Germplasm 3,BCR,Wild,,,3,3,3,9123,

src/test/resources/files/germplasm_import/some_entry_numbers.csv

@@ -1,4 +1,4 @@
-GID,Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
+GID,Germplasm Name,Breeding Method,Source,Female Parent GID,Male Parent GID,Entry No,Female Parent Entry No,Male Parent Entry No,External UID,Synonyms
 ,Germplasm 1,BCR,Wild,,,1,,,,
 ,Germplasm 2,BCR,Wild,,,,,,,
 ,Germplasm 3,BCR,Wild,,,3,,,,