- CHG: Version bump for bugfix release.

- FIX: Fixed issues with trait data import duplicate plot detection.
germinateplatform · Jun 5, 2024 · 8e9f711 · 8e9f711
1 parent 0f67f8f
commit 8e9f711
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Showing 7 changed files with 68 additions and 45 deletions.
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
diff --git a/build.gradle b/build.gradle
@@ -3,7 +3,7 @@ plugins {
 }
 
 group 'uk.ac.hutton.germinate-importer'
-version '4.7.2'
+version '4.7.3'
 
 compileJava.options.encoding = 'UTF-8'
 sourceCompatibility = 11

diff --git a/lib/germinate-codegen-4.7.2.jar → lib/germinate-codegen-4.7.3.jar b/lib/germinate-codegen-4.7.2.jar → lib/germinate-codegen-4.7.3.jar
diff --git a/lib/germinate-core-4.7.2.jar → lib/germinate-core-4.7.3.jar b/lib/germinate-core-4.7.2.jar → lib/germinate-core-4.7.3.jar
diff --git a/src/main/java/jhi/germinate/server/util/importer/DatasheetImporter.java b/src/main/java/jhi/germinate/server/util/importer/DatasheetImporter.java
@@ -172,8 +172,8 @@ private void checkCollaboratorsSheet(Sheet s)
 					 addImportResult(ImportStatus.GENERIC_MISSING_REQUIRED_VALUE, r.getRowNum(), "First Name");
 				 if (StringUtils.isEmpty(lastName))
 					 addImportResult(ImportStatus.GENERIC_MISSING_REQUIRED_VALUE, r.getRowNum(), "Last Name");
-				 if (!StringUtils.isEmpty(country) && !countryCode2ToId.containsKey(country))
-					 addImportResult(ImportStatus.GENERIC_INVALID_COUNTRY_CODE, r.getRowNum(), country);
+//				 if (!StringUtils.isEmpty(country) && !countryCode2ToId.containsKey(country))
+//					 addImportResult(ImportStatus.GENERIC_INVALID_COUNTRY_CODE, r.getRowNum(), country);
 			 });
 		}
 		catch (IOException e)
@@ -543,22 +543,27 @@ private void getOrCreateCollaborators(DSLContext context, ReadableWorkbook wb)
 					   String address = getCellValue(r, collaboratorLabelToColIndex.get("Address"));
 					   String countryCode = getCellValue(r, collaboratorLabelToColIndex.get("Country"));
 
-					   Integer countryId = countryCode2ToId.get(countryCode);
-
-					   InstitutionsRecord institution = context.selectFrom(INSTITUTIONS)
-															   .where(INSTITUTIONS.NAME.isNotDistinctFrom(institutionName))
-															   .and(INSTITUTIONS.ADDRESS.isNotDistinctFrom(address))
-															   .and(INSTITUTIONS.COUNTRY_ID.isNotDistinctFrom(countryId))
-															   .fetchAny();
+					   InstitutionsRecord institution = null;
 
-					   if (!StringUtils.isEmpty(institutionName) && institution == null)
+					   if (!StringUtils.isEmpty(institutionName))
 					   {
-						   institution = context.newRecord(INSTITUTIONS);
-						   institution.setName(institutionName);
-						   institution.setAddress(address);
-						   institution.setCountryId(countryId);
-						   institution.setCreatedOn(new Timestamp(System.currentTimeMillis()));
-						   institution.store();
+						   Integer countryId = countryCode2ToId.get(countryCode);
+
+						   institution = context.selectFrom(INSTITUTIONS)
+																   .where(INSTITUTIONS.NAME.isNotDistinctFrom(institutionName))
+																   .and(INSTITUTIONS.ADDRESS.isNotDistinctFrom(address))
+																   .and(INSTITUTIONS.COUNTRY_ID.isNotDistinctFrom(countryId))
+																   .fetchAny();
+
+						   if (institution == null)
+						   {
+							   institution = context.newRecord(INSTITUTIONS);
+							   institution.setName(institutionName);
+							   institution.setAddress(address);
+							   institution.setCountryId(countryId);
+							   institution.setCreatedOn(new Timestamp(System.currentTimeMillis()));
+							   institution.store();
+						   }
 					   }
 
 					   CollaboratorsRecord collaborator = context.selectFrom(COLLABORATORS)

diff --git a/src/main/java/jhi/germinate/server/util/importer/ImageImporter.java b/src/main/java/jhi/germinate/server/util/importer/ImageImporter.java
@@ -273,7 +273,7 @@ protected void checkFile()
 			for (Map.Entry<String, ViewTableImages> entry : filenameToImage.entrySet())
 			{
 				if (!filenames.contains(entry.getKey()))
-					addImportResult(ImportStatus.IMAGE_IMAGE_MISSING, -1, "Image not found for template definition: '" + entry.getValue().getImageForeignId() + "-" + entry.getValue().getReferenceName());
+					addImportResult(ImportStatus.IMAGE_IMAGE_MISSING, -1, "Image not found for template definition: '" + entry.getKey() + "(foreign id: + " + entry.getValue().getImageForeignId() + ", reference name: " + entry.getValue().getReferenceName() + ")");
 			}
 		}
 		catch (IOException e)

diff --git a/src/main/java/jhi/germinate/server/util/importer/TraitDataImporter.java b/src/main/java/jhi/germinate/server/util/importer/TraitDataImporter.java
@@ -283,6 +283,7 @@ private void checkRowColumn(Row r)
 		String germplasm = getCellValue(r, dataColumnNameToIndex, "Line/Phenotype");
 		String row = getCellValue(r, dataColumnNameToIndex, "Row");
 		String column = getCellValue(r, dataColumnNameToIndex, "Column");
+		String location = getCellValue(r, dataColumnNameToIndex, "Location");
 
 		if (row != null)
 		{
@@ -310,11 +311,11 @@ private void checkRowColumn(Row r)
 
 		if (!StringUtils.isEmpty(row) || !StringUtils.isEmpty(column))
 		{
-			String key = row + "|" + column;
+			String key = row + "|" + column + "|" + location;
 			String value = rowColToGermplasm.get(key);
 
 			if (!StringUtils.isEmpty(value) && !Objects.equals(germplasm, value))
-				addImportResult(ImportStatus.TRIALS_ROW_COL_MISMATCH, r.getRowNum(), "Row: " + row + ", Column: " + column);
+				addImportResult(ImportStatus.TRIALS_ROW_COL_MISMATCH, r.getRowNum(), "Row: " + row + ", Column: " + column + ", Location: " + location);
 			else
 				rowColToGermplasm.put(key, germplasm);
 		}