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A Deterministic GDAL CLI Context for Reproducible Workflows

Chris Reudenbach

2025-12-28

Source: vignettes/link2GI6.Rmd
link2GI6.Rmd

Motivation

GDAL is available in R through high-level packages such as sf and terra, and through wrapper packages like gdalUtilities. These approaches work well for many use cases, but they share a fundamental limitation:

They bind against a specific GDAL build, not necessarily the GDAL binaries actually used on the system.

In practice, this leads to several recurring problems:

  • Different GDAL versions on different machines
  • Mismatch between linked libraries and CLI binaries
  • Silent changes in available drivers, options, or defaults
  • Poor traceability of what actually ran in batch or HPC contexts

The goal of the link2GI GDAL context is not to replace existing packages, but to expose and control the system GDAL CLI deterministically.

Design Goals

The GDAL context introduced here follows a small set of strict principles:

  1. Use the linked GDAL binaries explicitly
    No implicit reliance on PATH, no guessing, no fallback to other builds.

  2. Be system-honest
    The context reflects what the system can actually do, not what a package was compiled against.

  3. Remain thin and non-intrusive
    No re-implementation of GDAL semantics, no competing wrapper API.

  4. Enable reproducibility
    Every run can be fingerprinted and logged, including environment and versions.

  5. Support interactive and batch workflows equally
    From exploratory work to large batch runs or CI pipelines.

Core Concept: The GDAL Context

At the heart of the approach is a GDAL CLI context:

  • A fixed binDir containing GDAL executables
  • A per-call environment (PATH, GDAL_DATA, PROJ_LIB, …)
  • A resolved set of available GDAL utilities
  • Optional logging and help caching

This context is immutable for a run and can be reused safely.

Creating a Context from linkGDAL()

The recommended entry point is linkGDAL():

gdal_link <- linkGDAL()

This locates a valid GDAL installation on the system. From this result, a deterministic CLI context is created:

ctx <- gdal_context_from_link(gdal_link)

At this point:

  • The exact GDAL binaries are fixed
  • The effective environment is known
  • No global state has been modified

Inspecting Capabilities (Fingerprinting)

To document what this GDAL can do, a fingerprint can be collected:

fp <- gdal_fingerprint(ctx)

This records, among other things:

  • GDAL version string
  • Available raster and vector formats
  • Spatial reference behaviour (axis order probe)
  • Context identifier

Optionally, the fingerprint can be written to an NDJSON log for auditability.

Running GDAL Commands Deterministically

A GDAL utility can now be executed explicitly:

res <- run_gdal(
  ctx,
  cmd  = "gdalinfo",
  args = c("--formats")
)

Key properties:

  • The resolved executable path is used
  • The environment is passed explicitly
  • Output and exit status are captured
  • No reliance on global PATH

This makes the call reproducible across machines as long as the same binaries are used.

Help-Driven Skeleton Generation

One recurring pain point when using the GDAL CLI is remembering valid flags and argument structure.

The context provides a help-based skeleton:

sk <- gdal_skeleton(ctx, "gdalwarp")

This skeleton is derived directly from gdalwarp --help and contains:

  • The primary Usage: line
  • A flat list of supported flags
  • A minimal argument template

Importantly:

The skeleton does not guess semantics or defaults. It reflects exactly what this GDAL build exposes.

Building Arguments Programmatically

Skeletons can be combined with structured options:

args <- gdal_build_args(
  sk,
  opts = list(
    t_srs = "EPSG:25832",
    r     = "bilinear"
  ),
  positional = c("in.tif", "out.tif")
)

This avoids error-prone copy-paste and keeps CLI usage explicit.

NDJSON Logging for Reproducibility

Every GDAL call can optionally be logged as one JSON object per line:

  • Command and arguments
  • Resolved executable
  • Environment variables
  • Runtime, exit code, stdout/stderr
  • Host and system metadata

This format is:

  • Append-only
  • Stream-friendly
  • Easy to post-process or archive

It enables answering questions like:

Which GDAL, with which environment, produced this output?

Relationship to Existing Packages

This approach is complementary, not competitive:

  • sf / terra Excellent for in-memory workflows and analysis; rely on linked libraries.

  • gdalUtilities Provides R wrappers for many CLI tools, but still depends on system setup.

  • link2GI GDAL context Focuses on deterministic execution, capability introspection and traceability.

You can freely mix these approaches in one project.

When Is This Useful?

Typical use cases include:

  • Batch processing pipelines
  • HPC or containerised workflows
  • Teaching and documentation
  • Cross-platform projects
  • Debugging GDAL behaviour differences
  • Long-term reproducibility requirements

If you already rely heavily on the GDAL CLI, this approach removes ambiguity without adding conceptual overhead.

Summary

The GDAL CLI context in link2GI provides:

  • Explicit control over GDAL binaries
  • Minimal but reliable skeleton generation
  • Deterministic execution
  • Optional, structured logging
  • Zero interference with existing R geospatial packages

It is intentionally small, honest, and system-centric.