Merge pull request #292 from Breeding-Insight/feature/BI-1847

BI-1847 - Experiment import template formatting improvements

src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java

@@ -400,7 +400,7 @@ private void addReference(List<BrAPIExternalReference> refs, UUID uuid, String r
     public static final class Columns {
         public static final String GERMPLASM_NAME = "Germplasm Name";
         public static final String GERMPLASM_GID = "Germplasm GID";
-        public static final String TEST_CHECK = "Test (T) or Check (C )";
+        public static final String TEST_CHECK = "Test (T) or Check (C)";
         public static final String EXP_TITLE = "Exp Title";
         public static final String EXP_DESCRIPTION = "Exp Description";
         public static final String EXP_UNIT = "Exp Unit";

src/main/resources/db/migration/V1.15.0__update_test_or_check_name.sql

@@ -0,0 +1,26 @@
+/*
+ * 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.
+ */
+
+DO $$
+
+BEGIN
+update importer_mapping
+set
+    mapping = '[{"id": "726a9f10-4892-4204-9e52-bd2b1d735f65", "value": {"fileFieldName": "Germplasm Name"}, "objectId": "germplasmName"}, {"id": "98774e20-6f89-4d6a-a7c9-f88887228ed6", "value": {"fileFieldName": "Germplasm GID"}, "objectId": "gid"}, {"id": "880ef0c9-4e3e-42d4-9edc-667684a91889", "value": {"fileFieldName": "Test (T) or Check (C)"}, "objectId": "test_or_check"}, {"id": "b693eca7-efcd-4518-a9d3-db0b037a76ee", "value": {"fileFieldName": "Exp Title"}, "objectId": "exp_title"}, {"id": "df340215-db6e-4219-a3b7-119f297b81c3", "value": {"fileFieldName": "Exp Description"}, "objectId": "expDescription"}, {"id": "9ca7cc81-562c-43a7-989a-41da309f603d", "value": {"fileFieldName": "Exp Unit"}, "objectId": "expUnit"}, {"id": "27215777-c8f9-4fe7-a7ac-918d6168b0dd", "value": {"fileFieldName": "Exp Type"}, "objectId": "expType"}, {"id": "19d220e2-dff0-4a3a-ad6e-32f4d8602b5c", "value": {"fileFieldName": "Env"}, "objectId": "env"}, {"id": "861518b9-5c9e-4fe5-b31e-baf16e27155d", "value": {"fileFieldName": "Env Location"}, "objectId": "envLocation"}, {"id": "667355c3-dae1-4a64-94c8-ac2d543bd474", "value": {"fileFieldName": "Env Year"}, "objectId": "envYear"}, {"id": "ad11f2df-c5b4-4a05-8e52-c57625140061", "value": {"fileFieldName": "Exp Unit ID"}, "objectId": "expUnitId"}, {"id": "639b40ec-20f8-4659-8464-6a4be997ac7a", "value": {"fileFieldName": "Exp Replicate #"}, "objectId": "expReplicateNo"}, {"id": "2a62a80f-d8ba-42c4-9997-3b4ac8a965aa", "value": {"fileFieldName": "Exp Block #"}, "objectId": "expBlockNo"}, {"id": "f3e7de69-21ad-4cda-b1cc-a5e1987fb931", "value": {"fileFieldName": "Row"}, "objectId": "row"}, {"id": "251c5bbd-fc4d-4371-a4ce-4e2686f6837e", "value": {"fileFieldName": "Column"}, "objectId": "column"}, {"id": "ce5f61f2-f1de-45a4-8baf-e2471a5d863d", "value": {"fileFieldName": "Treatment Factors"}, "objectId": "treatmentFactors"}, {"id": "c5b8276f-e777-4385-a80f-5199abe63aac", "value": {"fileFieldName": "ObsUnitID"}, "objectId": "ObsUnitID"}]',
+    file    = '[{"Env": "New Study", "Row": 4, "Column": 5, "Env Year": 2012, "Exp Type": "phenotyping", "Exp Unit": "plot", "Exp Title": "New Trial", "ObsUnitID": "", "Exp Block #": 2, "Exp Unit ID": 3, "Env Location": "New Location", "Germplasm GID": 1, "Germplasm Name": "Test", "Exp Description": "A new trial", "Exp Replicate #": 0, "Treatment Factors": "Jam application", "Test (T) or Check (C)": true}]'
+where import_type_id = 'ExperimentImport';
+END $$;

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

@@ -1,4 +1,4 @@
-Germplasm Name,Germplasm GID,Test (T) or Check (C ),Exp Title,Exp Description,Exp Unit,Exp Type,Env,Env Location,Env Year,Exp Unit ID,Exp Replicate #,Exp Block #,Row,Column,Treatment Factors,ObsUnitID,Color,INCAUDPS,INCW10SUM,INCW6SUM,,,
+Germplasm Name,Germplasm GID,Test (T) or Check (C),Exp Title,Exp Description,Exp Unit,Exp Type,Env,Env Location,Env Year,Exp Unit ID,Exp Replicate #,Exp Block #,Row,Column,Treatment Factors,ObsUnitID,Color,INCAUDPS,INCW10SUM,INCW6SUM,,,
 BRG,453,C,KRSP22-3,INSV phenotyping trial BRG x Eruption RIL population and parents,Plot,Disease resistance screening,"Salinas, CA 2022","Salinas, CA",2022,89,1,1,,,,,Green,120,6,0,,,
 Eruption,454,C,KRSP22-3,INSV phenotyping trial BRG x Eruption RIL population and parents,Plot,Disease resistance screening,"Salinas, CA 2022","Salinas, CA",2022,90,1,1,,,,,Medium red,110,4,0,,,
 BxE16-001,455,,KRSP22-3,INSV phenotyping trial BRG x Eruption RIL population and parents,Plot,Disease resistance screening,"Salinas, CA 2022","Salinas, CA",2022,91,1,1,,,,,Dark red,110,6,0,,,

src/test/resources/sql/ImportControllerIntegrationTest.sql

@@ -32,8 +32,8 @@ INSERT INTO public.importer_mapping (name,import_type_id,mapping,file,draft,crea
 
 INSERT INTO public.importer_mapping (name,import_type_id,mapping,file,draft,created_by,updated_by) values
     ('ExperimentsTemplateMap','ExperimentImport',
-     '[{"id": "726a9f10-4892-4204-9e52-bd2b1d735f65", "value": {"fileFieldName": "Germplasm Name"}, "objectId": "germplasmName"}, {"id": "98774e20-6f89-4d6a-a7c9-f88887228ed6", "value": {"fileFieldName": "Germplasm GID"}, "objectId": "gid"}, {"id": "880ef0c9-4e3e-42d4-9edc-667684a91889", "value": {"fileFieldName": "Test (T) or Check (C )"}, "objectId": "test_or_check"}, {"id": "b693eca7-efcd-4518-a9d3-db0b037a76ee", "value": {"fileFieldName": "Exp Title"}, "objectId": "exp_title"}, {"id": "df340215-db6e-4219-a3b7-119f297b81c3", "value": {"fileFieldName": "Exp Description"}, "objectId": "expDescription"}, {"id": "9ca7cc81-562c-43a7-989a-41da309f603d", "value": {"fileFieldName": "Exp Unit"}, "objectId": "expUnit"}, {"id": "27215777-c8f9-4fe7-a7ac-918d6168b0dd", "value": {"fileFieldName": "Exp Type"}, "objectId": "expType"}, {"id": "19d220e2-dff0-4a3a-ad6e-32f4d8602b5c", "value": {"fileFieldName": "Env"}, "objectId": "env"}, {"id": "861518b9-5c9e-4fe5-b31e-baf16e27155d", "value": {"fileFieldName": "Env Location"}, "objectId": "envLocation"}, {"id": "667355c3-dae1-4a64-94c8-ac2d543bd474", "value": {"fileFieldName": "Env Year"}, "objectId": "envYear"}, {"id": "ad11f2df-c5b4-4a05-8e52-c57625140061", "value": {"fileFieldName": "Exp Unit ID"}, "objectId": "expUnitId"}, {"id": "639b40ec-20f8-4659-8464-6a4be997ac7a", "value": {"fileFieldName": "Exp Replicate #"}, "objectId": "expReplicateNo"}, {"id": "2a62a80f-d8ba-42c4-9997-3b4ac8a965aa", "value": {"fileFieldName": "Exp Block #"}, "objectId": "expBlockNo"}, {"id": "f3e7de69-21ad-4cda-b1cc-a5e1987fb931", "value": {"fileFieldName": "Row"}, "objectId": "row"}, {"id": "251c5bbd-fc4d-4371-a4ce-4e2686f6837e", "value": {"fileFieldName": "Column"}, "objectId": "column"}, {"id": "ce5f61f2-f1de-45a4-8baf-e2471a5d863d", "value": {"fileFieldName": "Treatment Factors"}, "objectId": "treatmentFactors"}, {"id": "c5b8276f-e777-4385-a80f-5199abe63aac", "value": {"fileFieldName": "ObsUnitID"}, "objectId": "ObsUnitID"}]',
-     '[{"Env": "New Study", "Row": 4, "Column": 5, "Env Year": 2012, "Exp Type": "phenotyping", "Exp Unit": "plot", "Exp Title": "New Trial", "ObsUnitID": "", "Exp Block #": 2, "Exp Unit ID": 3, "Env Location": "New Location", "Germplasm GID": 1, "Germplasm Name": "Test", "Exp Description": "A new trial", "Exp Replicate #": 0, "Treatment Factors": "Jam application", "Test (T) or Check (C )": true}]',
+     '[{"id": "726a9f10-4892-4204-9e52-bd2b1d735f65", "value": {"fileFieldName": "Germplasm Name"}, "objectId": "germplasmName"}, {"id": "98774e20-6f89-4d6a-a7c9-f88887228ed6", "value": {"fileFieldName": "Germplasm GID"}, "objectId": "gid"}, {"id": "880ef0c9-4e3e-42d4-9edc-667684a91889", "value": {"fileFieldName": "Test (T) or Check (C)"}, "objectId": "test_or_check"}, {"id": "b693eca7-efcd-4518-a9d3-db0b037a76ee", "value": {"fileFieldName": "Exp Title"}, "objectId": "exp_title"}, {"id": "df340215-db6e-4219-a3b7-119f297b81c3", "value": {"fileFieldName": "Exp Description"}, "objectId": "expDescription"}, {"id": "9ca7cc81-562c-43a7-989a-41da309f603d", "value": {"fileFieldName": "Exp Unit"}, "objectId": "expUnit"}, {"id": "27215777-c8f9-4fe7-a7ac-918d6168b0dd", "value": {"fileFieldName": "Exp Type"}, "objectId": "expType"}, {"id": "19d220e2-dff0-4a3a-ad6e-32f4d8602b5c", "value": {"fileFieldName": "Env"}, "objectId": "env"}, {"id": "861518b9-5c9e-4fe5-b31e-baf16e27155d", "value": {"fileFieldName": "Env Location"}, "objectId": "envLocation"}, {"id": "667355c3-dae1-4a64-94c8-ac2d543bd474", "value": {"fileFieldName": "Env Year"}, "objectId": "envYear"}, {"id": "ad11f2df-c5b4-4a05-8e52-c57625140061", "value": {"fileFieldName": "Exp Unit ID"}, "objectId": "expUnitId"}, {"id": "639b40ec-20f8-4659-8464-6a4be997ac7a", "value": {"fileFieldName": "Exp Replicate #"}, "objectId": "expReplicateNo"}, {"id": "2a62a80f-d8ba-42c4-9997-3b4ac8a965aa", "value": {"fileFieldName": "Exp Block #"}, "objectId": "expBlockNo"}, {"id": "f3e7de69-21ad-4cda-b1cc-a5e1987fb931", "value": {"fileFieldName": "Row"}, "objectId": "row"}, {"id": "251c5bbd-fc4d-4371-a4ce-4e2686f6837e", "value": {"fileFieldName": "Column"}, "objectId": "column"}, {"id": "ce5f61f2-f1de-45a4-8baf-e2471a5d863d", "value": {"fileFieldName": "Treatment Factors"}, "objectId": "treatmentFactors"}, {"id": "c5b8276f-e777-4385-a80f-5199abe63aac", "value": {"fileFieldName": "ObsUnitID"}, "objectId": "ObsUnitID"}]',
+     '[{"Env": "New Study", "Row": 4, "Column": 5, "Env Year": 2012, "Exp Type": "phenotyping", "Exp Unit": "plot", "Exp Title": "New Trial", "ObsUnitID": "", "Exp Block #": 2, "Exp Unit ID": 3, "Env Location": "New Location", "Germplasm GID": 1, "Germplasm Name": "Test", "Exp Description": "A new trial", "Exp Replicate #": 0, "Treatment Factors": "Jam application", "Test (T) or Check (C)": true}]',
      false,user_id,user_id);
 
 END $$;