[t0mdavid-m]

Requested by Tom · project thread

Updates the deployment to the FLASH* tools on t0mdavid-m/OpenMS FDmerge and adds FLASHAnnotator as the source of fragment ion annotations. Version is now 1.1.0.

Pipeline (TagWorkflow.execution)

1. DecoyDatabase, only when needed: it is skipped when the FASTA already has DECOY_ entries or the database is PEFF. FLASHTnT now requires decoys.
2. FLASHDeconv.
3. FLASHTnT with -db and -in_raw. If FLASHTnT writes no protein or tag output, header-only TSVs are written so parsing and the viewer still work.
4. FLASHAnnotator on the raw mzML plus the FLASHTnT proteoform file (-out, -out_annotation), using FLASHTnT's ion_type.

Each TOPP call now checks run_topp's return value, and execution() returns False when inputs are missing.

Configure

• New FLASHAnnotator tab.
• FLASHTnT's fd: section is hidden because the FLASHDeconv tab already covers it. This relies on the section-prefix exclude_parameters from streamlit-template #413, cherry-picked as the first commit.
• Presets for the FLASHTnT workflow: Lysate (FLASHTnT native off, i.e. the default search) and Native (native on).
• FLASHTnT's and FLASHAnnotator's boolean parameters (native, keep_decoy, tag:allow_gap, …) are valueless flags. They are now declared as flag_parameters. Before, switching one on passed -native true, and FLASHTnT aborts with "Trailing text argument(s) '[true]'". On develop only three were declared; the other eight would fail the same way.

Parsing and viewer

• New src/parse/annotator.py. It converts FLASHAnnotator's terminal and internal envelopes into fragments in database-sequence coordinates, plus a per-proteoform summary. Both are stored in the sequence-data parquet as annotated_fragments / annotation_summary, and the schema is extended for them.
• Manual upload accepts the two FLASHAnnotator outputs as optional files.
• js-component/dist is rebuilt from Sequence view: FLASHAnnotator fragments and internal-ion visualization t0mdavid-m/openms-streamlit-vue-component#32, which adds the internal-ion visualization in the Sequence View. The Docker image builds the Vue bundle from FVdeploy, so that PR has to be merged before the deployed image includes it.

Deployment, version and data

• Dockerfile and Dockerfile.arm: OPENMS_BRANCH changed from FVdeploy to FDmerge.
• Version 1.0.1 → 1.1.0 in settings.json and in the Windows build name.
• Added 8 new E. coli example spectra (ADHE, AqpZ, GapA, MALE, OMPA, OMPF, OMPX, TSX) and removed the old AqpZ demo spectrum. With the bundled E. coli database, each one identifies its target protein.
• polars>=1.0,<2. Version 2.0 removed with_row_count, which broke parsing on a fresh install; the code now uses with_row_index.
• The user guide documents the database, the three configure tabs, FLASHAnnotator and the internal-ion view.

Not changed: example-data/workspaces/default/flashtnt/cache still holds old results. The viewer reads <workspace>/cache, not that folder, so nothing uses it.

Testing

• pytest tests/: 181 passed, including the new tests/test_annotator_parse.py.
• pylint --errors-only: no new errors. The remaining ones are in files this PR doesn't touch, or are pyopenms name lookups that depend on the environment.
• Ran the full pipeline on all 8 examples with tools built from FDmerge, and checked the FLASHTnT viewer (default layout) in headless Chromium.
• FLASHTnT … -native runs; -native true aborts, which is what the flag declaration fixes.

🤖 Generated with Claude Code

https://claude.ai/code/session_01P4MTpJCZMdSHNRFixkxcnz

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