Ordifile

한국어

Batch-convert and consolidate scientific instrument results into one clean, ordered and auditable Excel workbook.

Ordifile's proprietary-format direction is result-first: evidence-backed retention time and area tables from Agilent, Shimadzu and YoungIn should converge on the same Peaks / Peak_Matrix workbook model. Raw signals are an optional, independently validated capability: a result export does not require its raw file to be present. Each Agilent, Shimadzu, or YoungIn result adapter remains a separate exact-format reader, but its verified peak rows behave identically after canonical conversion. No vendor result parser is claimed before an actual result fixture proves its field boundaries and semantics.

Verified stable formats: CSV, TSV, semicolon-delimited TXT, and audited non-macro XLSX using Ordifile's documented schema. The current development source tree also includes seven narrowly bounded Experimental proprietary readers described below; this is not general vendor-format support. Published availability is shown by the PyPI badge.

sample_1.csv   sample_2.tsv   exported_peaks.xlsx
          \          |          /
           ordifile convert ...
                    |
                    v
          Ordifile_Result.xlsx
          ├── Manifest
          ├── Samples
          ├── Peak_Matrix
          ├── Peaks
          ├── Metadata
          └── Import_Log

Install

Install the latest published Ordifile release from PyPI. The PyPI badge above shows the currently available version.

python -m pip install --no-cache-dir ordifile

The Experimental desktop interface is first included in Ordifile v0.4.0. Until the PyPI badge shows v0.4.0 or newer, use a source checkout. The optional extra keeps existing CLI installations free of a Qt runtime dependency:

python -m pip install -e ".[gui]"
ordifile-gui

After v0.4.0 is published, the same interface can be installed with python -m pip install 'ordifile[gui]'. This is a Python-package GUI, not a standalone .exe or .app.

Quick start

python -c "from pathlib import Path; p=Path('ordifile_demo'); p.mkdir(exist_ok=True); [(p / f'sample_{n}.csv').write_text(f'sample_id,retention_time,area,compound\nsample_{n},{n / 10:.1f},{n * 10},demo\n', encoding='utf-8') for n in (1, 2, 10)]"
ordifile convert ordifile_demo --sort filename --output Ordifile_Result.xlsx

This package-independent synthetic example produces:

Input paths: 1
Discovered files: 3
Processed 1/3: success sample_1.csv
Processed 2/3: success sample_2.csv
Processed 3/3: success sample_10.csv
Export started: Ordifile_Result.xlsx
Output ready: Ordifile_Result.xlsx
Status: success
Output: Ordifile_Result.xlsx
Successful files: 3
Files with warnings: 0
Failed files: 0
Duplicate files: 0
Sort requested: filename
Sort used: filename
Sort reason: User requested filename ordering.
Sheets: Manifest, Samples, Peak_Matrix, Peaks, Metadata, Import_Log

The source files remain unchanged. Natural filename ordering keeps sample_2 before sample_10.

Experimental desktop interface

The optional desktop interface provides Add Files, Add Folder, and local file-manager drag and drop, followed by authoritative format inspection through the same public registry and pipeline used by the CLI. Choose one of the five existing sort modes and an .xlsx output, then convert in a background worker while progress and per-file success, warning, or failure remain visible.

The interface is offline-only: it has no upload, cloud, telemetry, embedded browser, or vendor-executable integration. It does not silently replace an existing workbook. Add buttons, visible labels, keyboard focus order, and accessible names provide a keyboard path equivalent to drag and drop. Forced cancellation is intentionally omitted until the public core can preserve workbook transaction safety during cancellation. Standalone .exe, .app, signing, and notarization remain tracked by Issue #6 and are not part of this Python-package interface.

Verified formats

“Generic” means the first row uses the documented column schema. It does not mean arbitrary vendor exports. An extension is supporting evidence only; Ordifile also checks content and schema. Run ordifile formats to see the adapters installed in the current environment.

Experimental proprietary adapters

These Experimental adapters have the exact capability boundaries below. Unsupported profiles are rejected rather than interpreted broadly.

The Agilent .CH adapter retains every decoded record in source order. Its x values are decoded_record_index, not retention time; its y values are decoded_raw_integer, not physically scaled intensity. Units, scientific point count, and the final record's role remain unresolved. It does not claim other .CH versions, .D directories, TCD, MS, peaks, calibrated values, or write support. See the exact capability and safety boundary.

The separate Agilent Result XML adapter reads one exact ChemStation C.01.10 [201], single FID1/A, Percent/Area report profile without requiring a raw sibling. It maps the canonical ResultsGroup/Peak rows to source-order peaks, retains explicit min, pA*s and pA units, and checks every RT/area/height decimal string against its duplicate integration row. Peak boundaries are preserved, calibrated nonblank Name values map to compound, and source labels FID1/A map separately to canonical detector/channel FID/FID1A. Other revisions, multiple signals, detectors, quantitation modes, raw chromatograms and write support are rejected or unsupported. The external fixture remains controlled-CI only because it includes privacy-bearing run metadata. See the exact capability and safety boundary.

The Shimadzu adapter is limited to an exact LabSolutions 5.82, GC-2014, single-channel SFID1, uV, identity-factor profile. Its 66,255-point retention-time and signal series were compared point by point with a same-run LabSolutions ASCII reference. It does not claim other LabSolutions or GCsolution versions, detectors, channels, factors, GCD profiles, peaks, .QGD, .LCD, or write support. See the exact capability and safety boundary.

The separate Shimadzu result ASCII adapter reads one exact LabSolutions 5.82, GC-2014, single SFID1 / Ch1 export without requiring a raw sibling. It preserves all source Peak# values and independent source observation order, maps R.Time, I.Time, and F.Time to retention/start/end time in minutes, and retains area and height without inventing physical units. The exact fixture has no compound IDs or names, so no compound identity is emitted. Its embedded private metadata is omitted and its public source is a SHA-256 alias. Other software versions, instruments, detectors, channels, identified-compound tables, multiple peak sections and arbitrary LabSolutions text exports are unsupported. See the exact capability and safety boundary.

The separate QGD adapter is limited to one exact GCMSsolution 4.00 compound-file profile. It preserves all 16,800 TIC integers and the verified millisecond-derived retention-time axis. The physical TIC unit is unknown. MS1 blocks are checked for bounded scan structure and exact TIC-sum agreement, but spectra are not exported and encoded mass values are not called m/z. It does not claim other QGD versions, SIM/MRM, identifications, quantitation, or write support. See the exact capability and safety boundary.

The YoungIn adapter is a structural converter for one observed YL-Clarity 9.0.1.19 PRM profile. It preserves 563,240 finite stored binary32 records from 43 current blocks across 23 local-only files and separates the allowlisted FID/TCD labels stored in those files, while leaving the canonical detector field unset. Its x coordinate is record ordinal, not retention time. No physical scaling or unit is applied, and peaks are not exported. Runtime sample IDs are content-derived, and no filename-derived grouping is exported. It does not claim other PRM generations, recovery .RAW, Autochro, calibrated chromatograms, or write support. See the exact capability and safety boundary.

The separate YoungIn Result adapter reads the exact CP949-compatible, tab-delimited Result Table grammar established by two owner-generated exports. It preserves six source rows with explicit RT (min), area (mV.s), height (mV), signal number/name and source order without requiring PRM. One observed FID section explicitly has no peaks; the two populated TCD sections remain independent channels. Signal Name is not promoted to detector identity, W05 is not an integration boundary, and Total, percentage and empty compound-table rows are not peaks. The bytes contain no OEM or software-version marker, so broader YL-Clarity/Clarity CSV support is not claimed. See the exact capability and safety boundary.

CLI

Inspect one file without writing output:

ordifile inspect sample.csv
ordifile inspect exported.xlsx --sheet PeakTable --verbose

Convert files or folders:

ordifile convert sample_1.csv sample_2.tsv --output Ordifile_Result.xlsx
ordifile convert ./exports --recursive --sort acquired_at --include-signals \
  --output Ordifile_Result.xlsx
ordifile convert ./exports --extension .csv --extension .xlsx \
  --sheet-mode sidecar-csv --output Ordifile_Result.xlsx

Important behavior:

• existing output is not replaced unless --overwrite is present;
• folder discovery is non-recursive unless --recursive is present;
• --on-error continue preserves valid files and reports partial success;
• --on-error stop stops after the first file failure and writes no workbook;
• --adapter forces one installed adapter; --sheet selects one XLSX worksheet;
• signals are parsed when present but written only with --include-signals;
• --verbose adds detection evidence and detailed structured diagnostics.

Exit codes are stable for automation:

Sorting

--sort auto uses acquisition time only when every successful file has a reliable, timezone-aware timestamp. Otherwise it uses a complete sequence number, then natural filename order. Explicit modes are acquired_at, sequence, filename, and input_order. Missing or unreliable values receive a recorded filename fallback.

The effective mode, requested mode, reason, and per-file sort key are written to the workbook.

Workbook layout

Rows and columns are split into deterministic numbered sheets before Excel limits are reached. Data is never silently truncated. If workbook storage is impractical, --sheet-mode sidecar-csv can create explicit CSV sidecars; the Manifest records each relative path, row count, formula-escape count, and SHA-256.

Python API

The CLI calls the same public API intended for future interfaces:

from ordifile.api import convert, inspect_file, inspect_inputs, list_formats

inspection = inspect_file("sample.csv")
preview = inspect_inputs(["sample_1.csv", "sample_2.tsv"], sort="auto")
result = convert(
    ["sample_1.csv", "sample_2.tsv"],
    "Ordifile_Result.xlsx",
    sort="auto",
    include_signals=False,
)

print(preview.outcome, result.success_count, result.failure_count, result.sort.effective)

inspect_inputs() performs the same bounded discovery, detection, parsing, validation, and sorting without writing an artifact. convert() intentionally reads and validates the inputs again, and also accepts folders, recursion, extension filters, explicit adapters and XLSX sheets, error policy, overwrite policy, CSV sidecars, and a presentation-neutral progress callback.

Add an adapter

External packages can register a typed adapter through the ordifile.adapters Python entry-point group. Adapters detect and parse; they do not write worksheets or duplicate CLI logic. A new format needs bounded detection, format evidence, structured errors, a redistributable or synthetic fixture, capability-specific tests, and license review.

Start with Adding a format adapter. Installed third-party adapters execute Python code and must be treated as trusted software.

Good first contributions include an additional synthetic delimiter fixture, a clearer error-message test, a documentation translation, or a small adapter proposal backed by an openly redistributable fixture.

YoungIn Result export confirmed: two owner-generated YL-Clarity exports establish the exact Result Table RT/area/height grammar used by the Experimental standalone adapter. The maintainer bridge remains available for future local batch generation, but it is not a runtime or CI dependency. Native PRM inputs and actual exports remain local-only; public tests use independent synthetic values.

On a normally licensed Windows workstation, the one-command pilot-gated batch is:

py scripts/local/youngin_yl_clarity_export_bridge.py <prm-or-directory-or-zip> `
  --output <outside-git-or-ignored-local-output> --batch `
  [--executable <vendor-executable>]

If a future pilot reports that explicit RT and Area headers are absent, enable Result Table, Table Headers, Text File, and preferably In Fixed Format once in YL-Clarity's Export Data settings, then rerun the bridge. Do not add the vendor application, generated exports, or native inputs to the repository. The bridge rejects output inside a Git worktree unless it is below Ordifile's fixed .external-fixtures, .research-downloads, or fixture-cache ignored roots.

Integrity and security boundaries

• Inputs are opened read-only, SHA-256 is recorded, and content is checked again after parsing.
• Symbolic links are rejected. Duplicate paths and hard links are recorded instead of parsed twice; equal content hashes alone are not deduplicated.
• One ordinary parse failure is isolated from other inputs. Successful data can still produce a workbook and the failed file remains visible in Import_Log.
• Formula-like strings are written as literal text with formula and URL conversion disabled.
• Values that the verified XLSX writer/reader combination cannot represent exactly are rejected for that file instead of being silently changed.
• Generic source identities in XLSX audit cells use a reversible display encoder: unsafe code points become ~uXXXXXX; and a literal ~ is doubled. Privacy-sensitive adapters can instead request a core-owned source-<full SHA-256> alias; this also applies to API/CLI/progress and malformed-file issues. Input paths, bytes and hashes remain unchanged. See the source identity policy.
• CLI output renders terminal control and bidirectional-format characters as visible, single-line escapes while preserving normal Unicode and Windows paths.
• XLSX packages pass ZIP, relationship, Content-Type, XML namespace, coordinate, dimension, cell-type, and resource audits before openpyxl reads a selected sheet.
• Normal conversion is offline and does not upload instrument data.

Limits

• One input file represents one sample.
• Generic delimited-text input is UTF-8 or UTF-8 with BOM. Exact proprietary text adapters use only their documented fixture-backed encoding. Delimiters are fixed per adapter; guessing is not supported.
• Extension filters are normalized to lowercase dotted ASCII before discovery. At most 32 unique filters are accepted; each has at most 32 ASCII characters after the leading dot, and the Manifest form is capped at 1,024 characters.
• Only exact documented headers are mapped. Units are copied, not converted.
• Compound identity is never inferred from retention time. RT-tolerance matching and duplicate-compound aggregation are not enabled.
• XLSX support is limited to an audited transitional, non-macro .xlsx workbook with explicit uppercase row and cell coordinates. Templates, macros, implicit coordinates, and other OOXML variants are rejected.
• XLSX formula text is preserved, but cached formula results are never treated as measured values.
• Numeric Excel date-style cells have no timezone and remain unreliable for automatic acquisition-time sorting. An OOXML t="d" ISO timestamp is parsed from its audited raw lexeme; an explicit offset can make that timestamp reliable.
• OOXML numeric lexemes must use ASCII sign, decimal, and exponent characters without whitespace. A cell type incompatible with its documented field is preserved as raw Metadata with a warning, not converted through Python stringification.
• Files at or above 256 MiB receive a warning; files above 2 GiB are hashed but not parsed. Delimited inputs and declared XLSX uncompressed content are capped at 512 MiB.
• The XLSX audit additionally caps 10,000 archive members, 8 MiB control XML parts, 250,000 physical rows, 1,000,000 physical cells, a 250,000 logical row, 5,000,000 projected cells, XML depth 128, and raw cell lexemes at 32,767 characters. Raw formula text is capped at 32,766 because the exported literal includes a leading =.
• Canonical integers are limited to 1,000 decimal digits; integer source lexemes are limited to 4,096 characters. Excel numbers beyond 15 exact integer digits are written as literal strings and counted.
• Mandatory audit cells are limited to 32,767 characters. A file that cannot fit its own Samples/Import_Log identity or issue summary is isolated before workbook planning; batch summaries are bounded and report omitted-code counts.
• The practical workbook cap is 512 sheets and the conservative portable output-path cap is 218 Unicode code points.
• Proprietary readers are limited to the exact Experimental profiles above. The optional Experimental GUI exposes only those same registry capabilities and does not broaden format support.

These practical bounds are Ordifile safety policies, not claims about every valid Excel file. See the exact generic format contract and the architecture decision.

Development

Ordifile targets Python 3.11–3.14. Required tests, release builds, wheel smoke tests, and external real-fixture workflows target Python 3.14 on a shared Linux DGX self-hosted runner. TestPyPI/PyPI publishing, byte verification, attestations, and GitHub Release publication use GitHub-hosted Ubuntu. There is no current Windows or macOS CI matrix. Public-fork workflows require maintainer approval before they run on that machine and receive read-only repository permission without publishing secrets or OIDC permission. Runner availability is an operational setting visible in GitHub Actions; this describes the configured target, not a guarantee that the runner is currently online.

python -m pip install -e ".[dev]"
ruff format --check .
ruff check .
mypy
pytest
python -m build
ordifile --help
pip-audit

See CONTRIBUTING.md, SECURITY.md, the release runbook, GC fixture research, external-fixture policy, and the evidence register. Do not attach proprietary raw files or fixtures without confirmed redistribution permission to a public issue.

Project name and trademarks

Ordifile was selected after a technical collision screen on 2026-08-16. No exact-name record was found in the checked GitHub and package-registry searches at that time, but search absence is not a reservation or legal trademark clearance. See the renaming research. Vendor names, if mentioned in future compatibility notes, remain the property of their owners and do not imply affiliation or endorsement.

Agilent, ChemStation, Shimadzu, LabSolutions, GCsolution, YOUNG IN Chromass, ChroZen, YL-Clarity, AUTOCHRO, and related product names are trademarks or product names of their respective owners. Ordifile is not affiliated with or endorsed by Agilent, Shimadzu, or YOUNG IN Chromass.

License

Ordifile is licensed under Apache License 2.0. See LICENSE, NOTICE, and THIRD_PARTY_NOTICES.md.