File path resolution and validation

file-path-resolution-and-validation

Summary

Resolve and validate file paths for session data files (workflow.csv, sequence.csv) co-located in a session directory, and verify their integrity before loading into SmartPeak for metabolomics workflow execution. This skill ensures that critical configuration and data files are correctly located, readable, and schema-compliant before downstream processing begins.

When to use

When initializing a SmartPeak session from a sequence file, you need to load and validate the workflow.csv and sequence.csv files that are co-located in the session directory. Apply this skill at session startup to detect missing, mislocated, or malformed configuration files before attempting to parse or execute workflow steps.

When NOT to use

• Workflow configuration has already been loaded and validated in memory — skip re-validation.
• User is working with a custom programmatic workflow definition (not CSV-based) — this skill applies only to CSV-driven workflows.
• Session is being resumed from a persisted state where file paths and integrity have been previously verified and cached.

Inputs

• Session directory path (string)
• workflow.csv file (CSV text file with workflow_step column)
• sequence.csv file (CSV text file co-located in session directory)

Outputs

• Ordered list of validated workflow command names (list of strings)
• Resolved absolute file paths for workflow.csv and sequence.csv (file paths)
• Integrity check report (boolean: pass/fail, with list of errors if any)

How to apply

First, resolve the session directory path from the user-selected sequence file location or from the session metadata. Locate the workflow.csv file co-located in the same directory as sequence.csv. Read the workflow.csv file line-by-line and parse each row to extract the workflow_step command name (e.g., LOAD_RAW_DATA, EXTRACT_CHROMATOGRAM_WINDOWS, PICK_MRM_FEATURES). Validate each extracted command against the known set of supported workflow commands maintained by SmartPeak. If a command is not recognized, flag it as an integrity error and halt file validation. Construct an ordered list of commands preserving the row sequence from the file. Use SmartPeak's built-in integrity checks (accessible via GUI: Actions | Integrity checks) to verify that all referenced files and paths are accessible and well-formed. Return the validated, ordered command list and resolved file paths for downstream workflow executor invocation.

Related tools

• SmartPeak (Orchestrates workflow parsing and execution; provides integrity check API and file validation mechanisms) — https://github.com/AutoFlowResearch/SmartPeak
• SmartPeakCLI (Command-line interface for session loading and file path resolution without GUI; callable via docker or direct binary) — https://github.com/AutoFlowResearch/SmartPeak
• SmartPeakGUI (Graphical file browser and integrity check viewer; exposes file resolution and validation via Actions | Integrity checks menu) — https://github.com/AutoFlowResearch/SmartPeak
• OpenMS (Underlying toolkit providing file I/O and validation primitives used by SmartPeak for CSV and data file handling)

Evaluation signals

• All workflow command names extracted from workflow.csv match the documented set of supported commands (LOAD_RAW_DATA, MAP_CHROMATOGRAMS, EXTRACT_CHROMATOGRAM_WINDOWS, ZERO_CHROMATOGRAM_BASELINE, PICK_MRM_FEATURES, SELECT_FEATURES, STORE_FEATURES, etc.)
• Row order in the parsed command list exactly matches the row sequence in the source workflow.csv file
• SmartPeak integrity check reports pass with zero file-not-found or schema-validation errors for workflow.csv and sequence.csv
• File paths resolve to readable, non-empty files accessible by the SmartPeak process; no permission or I/O errors occur during file open/read
• Parsed CSV rows contain no empty or null workflow_step values; malformed rows are flagged and reported to the user

Limitations

• The skill assumes workflow.csv and sequence.csv are co-located in a single session directory; workflows split across multiple directories are not supported.
• File path validation is filesystem-dependent; network paths or cloud storage may have latency or transient access issues not caught at validation time.
• The integrity check does not validate the semantic correctness or inter-dependency of workflow commands — only syntactic presence in the supported command set. A valid command sequence that violates data flow requirements (e.g., STORE_FEATURES before PICK_MRM_FEATURES) will pass validation but fail at execution.
• No changelog or version-specific command support information is available; if SmartPeak is updated with new workflow commands, the validation set must be manually updated.

Evidence

• [other] Read the workflow.csv file from the session directory (co-located with sequence.csv). Parse each row to extract the workflow_step command name.: "Read the workflow.csv file from the session directory (co-located with sequence.csv). Parse each row to extract the workflow_step command name."
• [other] Validate each command against the known set of supported workflow commands (e.g., LOAD_RAW_DATA, MAP_CHROMATOGRAMS, EXTRACT_CHROMATOGRAM_WINDOWS, ZERO_CHROMATOGRAM_BASELINE, PICK_MRM_FEATURES, SELECT_FEATURES, STORE_FEATURES).: "Validate each command against the known set of supported workflow commands (e.g., LOAD_RAW_DATA, MAP_CHROMATOGRAMS, EXTRACT_CHROMATOGRAM_WINDOWS, ZERO_CHROMATOGRAM_BASELINE, PICK_MRM_FEATURES,"
• [readme] The integrity of the loaded data can be checked with Actions | Integrity checks. The results of the integrity checks can be viewed with View | Info.: "The integrity of the loaded data can be checked with Actions | Integrity checks. The results of the integrity checks can be viewed with View | Info."
• [readme] Start the session with File | Load session from sequence. Choose the corresponding directory with Change dir. The path to example folder can be shortened to f.e. /data/GCMS_SIM_Unknowns. Select the sequence file.: "Start the session with File | Load session from sequence. Choose the corresponding directory with Change dir."
• [other] Construct an ordered list preserving the row sequence from the file. Return the ordered command list for downstream workflow executor to invoke each step in sequence.: "Construct an ordered list preserving the row sequence from the file. Return the ordered command list for downstream workflow executor to invoke each step in sequence."