From 5c1b90a8fb8f51f5af31ef976e3afd8827b78609 Mon Sep 17 00:00:00 2001 From: Nick <53413353+nickpalladino@users.noreply.github.com> Date: Tue, 8 Apr 2025 15:49:31 -0400 Subject: [PATCH 1/2] Switched to using gids to track germplasm --- .../v2/services/BrAPIGermplasmService.java | 11 ++++--- .../breedinginsight/utilities/Utilities.java | 32 +++++++++++++++++++ 2 files changed, 39 insertions(+), 4 deletions(-) diff --git a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java index 7272e2b90..e0602e046 100644 --- a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java +++ b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java @@ -187,13 +187,13 @@ public List getGermplasmByList(UUID programId, String listDbId) // get list BrAPI germplasm variables List germplasmNames = listResponse.getResult().getData(); List germplasm = germplasmDAO.getGermplasmByRawName(germplasmNames, programId); - Map germplasmByName = new HashMap<>(); + Map germplasmByGid = new HashMap<>(); for (BrAPIGermplasm g : germplasm) { // set the list ID in the germplasm additional info g.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ID, listId); // Add to map. - germplasmByName.put(g.getGermplasmName(), g); + germplasmByGid.put(g.getAccessionNumber(), g); } // Get the program key. @@ -201,12 +201,15 @@ public List getGermplasmByList(UUID programId, String listDbId) .orElseThrow(ApiException::new) .getKey(); + // Extract gids from list names + List gids = germplasmNames.stream().map(Utilities::extractGid).collect(Collectors.toList()); + // Build list from BrAPI list that preserves ordering and duplicates and assigns sequential entry numbers. List germplasmList = new ArrayList<>(); int entryNumber = 0; - for (String germplasmName : germplasmNames) { + for (String gid : gids) { ++entryNumber; - BrAPIGermplasm listEntry = cloneBrAPIGermplasm(germplasmByName.get(Utilities.removeProgramKeyAndUnknownAdditionalData(germplasmName, programKey))); + BrAPIGermplasm listEntry = cloneBrAPIGermplasm(germplasmByGid.get(gid)); // Set entry number. listEntry.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER, entryNumber); germplasmList.add(listEntry); diff --git a/src/main/java/org/breedinginsight/utilities/Utilities.java b/src/main/java/org/breedinginsight/utilities/Utilities.java index 20f3254d6..31990928c 100644 --- a/src/main/java/org/breedinginsight/utilities/Utilities.java +++ b/src/main/java/org/breedinginsight/utilities/Utilities.java @@ -29,6 +29,7 @@ import java.sql.Statement; import java.util.*; import java.util.function.Function; +import java.util.regex.Matcher; import java.util.regex.Pattern; public class Utilities { @@ -183,6 +184,37 @@ public static String removeProgramKeyAndUnknownAdditionalData(String original, S return stripped; } + /** + * Extracts the germplasm identifier (GID) from a germplasm name string that contains + * a key in the format "[PROGKEY-NUMBER]". + * + *

This method searches for a pattern matching "[anything-digits]" in the input string + * and returns the numeric portion if found. The prefix before the hyphen can be any sequence + * of characters.

+ * + * @param germplasmNameWithKey The germplasm name string containing the identifier in the format + * "[PROGKEY-NUMBER]", e.g., "TestDup [DEMO-12]" + * @return The numeric portion after the hyphen as a String if the pattern is found, + * or null if the pattern is not found in the input string + * @throws NullPointerException If the input string is null + * + * @example + * 
+     * String gid = extractGid("TestDup [DEMO-12]"); // Returns "12"
+     * String gid = extractGid("Wheat [BRC-789]");   // Returns "789"
+     * String gid = extractGid("NoPattern");         // Returns null
+     *
+ */ + public static String extractGid(String germplasmNameWithKey) { + Pattern pattern = Pattern.compile("\\[(.*?)-(\\d+)\\]"); + Matcher matcher = pattern.matcher(germplasmNameWithKey); + + if (matcher.find()) { + return matcher.group(2); + } + return null; + } + public static String generateApiExceptionLogMessage(ApiException e) { return new StringBuilder("BrAPI Exception: \n\t").append("message: ") .append(e.getMessage()) From d982380e83ae791af5a8ed1c3f7a6e1ee6cbba58 Mon Sep 17 00:00:00 2001 From: Nick <53413353+nickpalladino@users.noreply.github.com> Date: Wed, 9 Apr 2025 15:50:57 -0400 Subject: [PATCH 2/2] Removed unused code --- .../brapi/v2/services/BrAPIGermplasmService.java | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java index e0602e046..7e4a01e67 100644 --- a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java +++ b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java @@ -196,11 +196,6 @@ public List getGermplasmByList(UUID programId, String listDbId) germplasmByGid.put(g.getAccessionNumber(), g); } - // Get the program key. - String programKey = programService.getById(programId) - .orElseThrow(ApiException::new) - .getKey(); - // Extract gids from list names List gids = germplasmNames.stream().map(Utilities::extractGid).collect(Collectors.toList());