Emit Diagnostics

This example shows how to compose diagnostics and emit them to the terminal.

sprocket_bio/examples/emit_diagnostics.py

import os

from sprocket_bio.diagnostics import Mode, emit_diagnostics
from sprocket_bio.grammar import Diagnostic, Span

diagnostics = [
    # Annotate the `command` section with an error.
    Diagnostic.error("this is an error").with_highlight(Span(77, 54)),
    # Annotate the `version` statement with a warning.
    Diagnostic.warning("this is a warning")
    .with_label("additional details on the warning", Span(0, 11))
    .with_help("this is the help message"),
]


def main() -> None:
    # Get the full path of `example.wdl` from this script's location.
    workflow_path = os.path.join(
        os.path.dirname(os.path.realpath(__file__)), "example.wdl"
    )

    with open(workflow_path, mode="rt", encoding="utf-8") as f:
        workflow_source = f.read()

    emit_diagnostics(
        workflow_path,
        workflow_source,
        diagnostics,
        report_mode=Mode.FULL,
        colorize=True,
    )


if __name__ == "__main__":
    main()

If you have the Python bindings installed, you can run the example yourself:

$ python -m sprocket_bio.examples.emit_diagnostics
error: this is an error
   ┌─ /Users/bd/dev/gsoc/sprocket/python/sprocket_bio/examples/example.wdl:8:5
   │
 8 │ ╭     command <<<
 9 │ │         echo "~{greeting}, world!"
10 │ │     >>>
   │ ╰───────^

warning: this is a warning
  ┌─ /Users/bd/dev/gsoc/sprocket/python/sprocket_bio/examples/example.wdl:1:1
  │
1 │ version 1.3
  │ ^^^^^^^^^^^ additional details on the warning
  │
  = help: this is the help message