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Pull Request Overview
This PR updates the MassQL integration endpoint, enhances JSON parsing to handle arrays and single objects, extends qualifier support, and refactors the fragment‐search logic.
- Switches the MassQL API URL and adds robust JSON array/single‐object deserialization with error handling.
- Maps new qualifier fields (intensity, time, drift time, charge) into PeakFeatureSearchValue and adds
ConditionType. - Refactors
FragmentSearcherto eliminate duplicated MS1 query logic, introducesEvaluateCondition, and implementsIsMs1FeatureMatched/IsMs1SpotMatched.
Reviewed Changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
| src/MSDIAL5/MsdialGuiApp/Model/Setting/MassqlSettingModel.cs | Updated MassQL URL, JSON parsing branches, extended qualifiers. |
| src/MSDIAL5/MsdialCore/DataObj/PeakFeatureSearchValue.cs | Added Charge and non-nullable ConditionType keys. |
| src/MSDIAL5/MsdialCore/Algorithm/FragmentSearcher.cs | Removed duplicate MS1 checks, added EvaluateCondition and new matching methods. |
Comments suppressed due to low confidence (2)
src/MSDIAL5/MsdialCore/Algorithm/FragmentSearcher.cs:93
- [nitpick] Method names in C# should use PascalCase. Rename
isPeakDetectedByBasicMsPropertyQuerytoIsPeakDetectedByBasicMsPropertyQueryfor consistency.
private static bool isPeakDetectedByBasicMsPropertyQuery(ChromatogramPeakFeature feature, double maxIntensity, List<PeakFeatureSearchValue> queries) {
src/MSDIAL5/MsdialGuiApp/Model/Setting/MassqlSettingModel.cs:46
- Add unit tests for both array and single-object JSON responses to ensure both branches (
StartsWith("[")and the fallback) work correctly.
if (json.TrimStart().StartsWith("[")) {
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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