Pin the RawDataHandler build that decodes the last mzML array element

[htsugawa]

Summary

This pins MsdialCore's Release reference to RawDataHandler 1.3.9769.328. That build has the mzML last-element fix from systemsomicslab/msrawdataworkbench#40 (commit 592b6db).

RawDataHandler 1.3.9699.469 never decodes the last element of an mzML binary data array. For data read from mzML, this means:

• every MS1 and MS/MS spectrum loses its highest-m/z peak, and a spectrum with one peak comes out empty;
• every chromatogram ends with an RT 0 / intensity 0 point in place of its real last point.

Change

One line in src/MSDIAL5/MsdialCore/MsdialCore.csproj: the Release PackageReference to RawDataHandler goes from 1.3.9699.469 to 1.3.9769.328. The Debug, vendor-unsupported and MS-DIAL 4 references are unchanged.

Must be done before merge

• The package exists only in a local feed for now. Publish it to the lab package source before merging. Until then, a Release restore on any other machine fails with NU1102.
• msrawdataworkbench#40 is still open. The package was built from its branch, not from merged master.
• The package is not obfuscated, unlike the published 1.3.* builds. If it is rebuilt with obfuscation for publication and gets a new version number, this pin has to move to that version.
• The package is built from RawDataHandler master (b34c857) plus the fix, not from 1.3.9699.469 plus the fix. So it also brings in the master commits that 1.3.9699.469 does not have. The Console output also ships lib/Reifycs/Reifycs.Hive.DataAccess.dll in place of Reifycs.Hive.Reader.dll.

Verification

Build. The Console was built from this commit with:

dotnet build tests/MSDIAL5/MsdialCoreTestApp/MsdialCoreTestApp.csproj --configuration Release --framework net48 --nologo

• Restore was limited to local sources: the local feed plus the machine's local package folders, with no nuget.org.
• Result: 0 errors.
• The output holds RawDataHandler.dll 1.3.9769.328+592b6db.
• MSDIALCUI.exe --help and --version start, reporting 5.5.260930 and commit f56d447.

Reading real mzML.

• Method: a small net48 harness reads a copy of MetaboLights MTBLS2207 M3T-Std_neg_DDA_1mz.mzML (2114 spectra) the way MS-DIAL does, with new RawDataAccess(path, 0, false, false, false).GetMeasurement(). It loads RawDataHandler.dll, Common.dll and zlib.net.dll from one Console output folder at a time.
• Builds compared: (a) the Console built at c471463, which has RawDataHandler 1.3.9699.469, and (b) the Console built from this branch, which has 1.3.9769.328.
• Reference: an independent Python decode of the same file (base64, zlib, struct).
• Comparison: per spectrum, the peak count, the last m/z and intensity, and a sha256 over every (m/z, intensity) pair.

spectra	(a) 1.3.9699.469	(b) 1.3.9769.328
first 50 (all MS1)	50/50 one peak short; the remaining peaks are identical to Python's	50/50 identical to Python
all 2114: 1753 MS1 + 361 MS2	2114/2114 one peak short, the rest identical	2114/2114 identical
the 2 MS2 spectra with one peak	read as empty	1 peak, identical

The first five rows:

index	Python n	Python last m/z	Python last int.	(a) n	(a) last m/z	(a) last int.	(b) n	(b) last m/z	(b) last int.
0	83	764.374512	407.407	82	747.042664	364.495	83	764.374512	407.407
1	51	793.347534	412.876	50	767.866943	401.104	51	793.347534	412.876
2	51	891.572266	424.587	50	824.392517	386.427	51	891.572266	424.587
3	53	652.298889	391.316	52	551.437317	375.022	53	652.298889	391.316
4	60	827.103882	437.434	59	769.841614	392.850	60	827.103882	437.434

No MS-DIAL analysis was run for this check.

🤖 Generated with Claude Code

Do not publish the package this build used

RawDataHandler 1.3.9769.328 in the local feed was built without Eazfuscator, which is not installed on the build machine. Two consequences:

• License key. The published 1.3.* assemblies are obfuscated, and their string encryption keeps the SCIEX Clearcore2 license key unreadable. In this build the key is readable plain text in RawDataHandler.dll.
• Where it may go. The package may be used only locally. It must not be copied to the lab package source, and no build that contains it may be distributed.

Before this PR can merge:

1. Build the release package from msrawdataworkbench master (after msrawdataworkbench#40) through the lab's normal obfuscated release process. That build will take a new version number.
2. Move this pin to that version.
3. Rebuild and re-verify.

The package is also msrawdataworkbench master b34c857 plus the fix, not 1.3.9699.469 plus the fix. It therefore includes the eight RawDataHandlerStandard commits since 1.3.9699.469:

• TSF support;
• mzML polarity from referenceableParamGroup;
• the Shimadzu IoModule scope;
• Hive 0.19 DataAccess in place of Hive 0.18 Reader.

🤖 Generated with Claude Code