Parameter validation

[RobbinBouwmeester]

No description provided.

[RobbinBouwmeester]

Should implement #993

[Copilot]

Pull request overview

This PR introduces a framework-agnostic submission-validation layer (proteobench.validation) and wires it into the Streamlit submission flow to validate uploaded results/parameters (and optionally protein IDs against a module reference FASTA) before creating a public datapoint.

Changes:

• Added a core validation package (proteobench.validation) with structured reporting, reference FASTA handling, and per-check validators.
• Integrated validation into the Streamlit submission tab: render the report, block submission on validation errors, and append a validation summary to the PR description.
• Added module-level [reference_database] FASTA URLs to multiple module_settings.toml files and added unit/integration tests plus a small FASTA test fixture.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
webinterface/pages/base_pages/utils/validation_ui.py	New Streamlit “glue” to build a standardized DF, fetch/cache FASTA, call core validator, and render issues.
webinterface/pages/base_pages/tabs/tab6_submit_results.py	Runs validation before PR creation; blocks on errors and appends a validation summary to PR text.
test/test_validation.py	Unit + lightweight integration tests for validation helpers, checks, report semantics, and real-parser integration.
test/data/validation/ProteoBench_validation_reference.fasta	Small reference FASTA fixture for protein-id validation tests.
proteobench/validation/init.py	Exposes the new validation public API.
proteobench/validation/validator.py	Orchestrates checks into a single ValidationReport with fault-tolerant check execution.
proteobench/validation/report.py	Defines Severity, ValidationIssue, and ValidationReport (+ summary/serialization helpers).
proteobench/validation/checks.py	Implements individual validation checks (protein IDs, charge, length, enzyme heuristic, modifications heuristic, run consistency).
proteobench/validation/config.py	Adds module-level validation configuration, including reading [reference_database] from module settings.
proteobench/validation/fasta.py	Implements FastaReference parsing/loading (path/bytes/url; zip/gz/plain) and header identifier extraction.
proteobench/validation/protein_ids.py	Protein group splitting + identifier extraction and decoy/contaminant detection helpers.
proteobench/validation/exceptions.py	Adds SubmissionValidationError convenience exception wrapping a ValidationReport.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DIA/ion/ZenoTOF/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DIA/ion/singlecell/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DIA/ion/plasma/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DIA/ion/diaPASEF/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DIA/ion/Astral/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DIA/ion/AIF/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DDA/peptidoform/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DDA/ion/QExactive/module_settings.toml	Adds [reference_database] with FASTA URL for validation.
proteobench/io/parsing/io_parse_settings/Quant/lfq/DDA/ion/Astral/module_settings.toml	Adds [reference_database] with FASTA URL for validation.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 26 out of 27 changed files in this pull request and generated 4 comments.