Console: write method-file templates, and read relative paths from the method file in every mode

[YukiMatsuzawa]

Summary

Adds a template command to the MS-DIAL 5 Console that writes a method file for one processing mode, holding the built-in defaults. It also makes relative file paths in method files resolve the same way in every mode.

MSDIALCUI template lcms -o lcms_method.txt
MSDIALCUI template gcms --ionmode Negative

template <gcms|lcms|dims|imms|lcimms>

Options

• -o/--output: write to a file. Without it the template goes to standard output.
• -f/--force: replace an existing file. Without it an existing file is not replaced.
• --ionmode Positive|Negative: choose the ion mode.
• The mode name is not case-sensitive.

Where the values come from. Every value is taken from a freshly constructed parameter object for the mode, not typed by hand. Two exceptions state what a run actually uses:

• Acquisition type is written as DDA. The parameter starts as None, and CommonProcess turns that into DDA.
• Searched adduct ions is [M+H]+ or [M-H]-, following the ion mode. This is the PeakCharacterEstimator fallback, and works now that Make "Searched adduct ions" in a console method file take effect #815 has landed.

How keys are chosen

• Only keys the mode's processing uses are written.
• Each library path sits in the section of the annotation that uses it.
• Left out: isotope tracking, CorrDec, the isotope text DB, the target-detection compound list, and keys no process reads.
• Target CE and Sample average / blank average are kept deliberately, because they are about to be made to work. A code comment marks each.
• Choices are listed only as the reader accepts them.

Tests (MethodFileTemplateTests) cover all five modes and both ion modes:

• The template reads back with no unrecognised or unusable key.
• The parameter it reads back into equals the defaults in a whole-object JSON comparison.
• The comparison fails on any property it cannot serialize.
• A control test shows the comparison does see a changed value.

Relative paths: one rule for every mode

Before: only GC-MS resolved method-file paths against the method file's folder. That behaviour came with #779 (ResolveGcmsFilePaths). LC-MS, DIMS, IMMS and LC-IM-MS opened a relative path from the working directory, while the annotator settings tables in the same file were already read relative to the method file.

Now: every reader resolves these keys against the method file's folder, and environment variables are expanded:

• MSP, LBM, Text DB and isotope text DB paths
• target-detection and RT-correction compound lists
• RT correction peak selection
• the RI dictionary (GC-MS)

Transition behaviour

• Found only in the working directory: the file is used, and the run prints that it should be rewritten.
• Found in both folders and the two files differ: the file beside the method file is used, and the run names both.
• The same file reached by two spellings (8.3 name, junction, mapped drive): recognised from length and timestamps without reading it, and no message is printed.

Also

• Added accumulated rt range as the correct spelling of the LC-IM-MS key accumulated rt ragne. The old spelling still reads.
• Added "Method file" and "Method file template" to tests/MSDIAL5/MsdialCoreTestApp/CONTEXT.md.

Behaviour changes for existing method files

• Changes which library is read: in LC-MS, DIMS, IMMS and LC-IM-MS, a relative path now resolves against the method file's folder. A job run from another directory with the same file name there now reads the method file's copy, and says so.
• Changes an export field: a relative MSP or Text DB path now becomes absolute. This also changes the default annotator ID written to the Annotation method export field. This was judged acceptable.

Test plan

• dotnet test tests/MSDIAL5/MsdialCoreTestAppTests: 115 passed.
• MsdialCoreTestApp builds for net472, net48 and net8.
• CLI: each of the five templates, passed to its own command with -m, gives 0 unrecognised and 0 unusable keys in .keys.json.
• CLI: --ionmode Both is refused, and template LCMS --ionmode negative works.
• CLI: both transition messages appear, and a path found beside the method file prints nothing.
• Not run: a full analysis on real raw data. The repository has none; the CLI runs above stop at "No input file existed."

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