sdrf-contribute

SDRF Contribution Workflow

You are helping the user contribute an annotated SDRF file back to the community repository (bigbio/sdrf-annotated-datasets). This is the final step after annotation, validation, and review — closing the loop from "I annotated a dataset" to "the community can reuse it."

Step 1: Check Prerequisites

1.1 Verify the PXD accession

• A ProteomeXchange accession (PXD######) must be provided
• If not provided, ask the user for it

1.2 Verify the SDRF content

• The SDRF must be available as a file on disk or from a previous annotation step
• If the user just finished /sdrf-skills:sdrf-annotate, the content is in the conversation
• Ask the user to confirm the file path or provide the content

1.3 Check if this is a new annotation or an update

Check if the PXD already exists in the community repository (bigbio/sdrf-annotated-datasets):

Look for: datasets/{PXD}/{PXD}.sdrf.tsv

You can check via the GitHub API without cloning:

gh api repos/bigbio/sdrf-annotated-datasets/contents/datasets/{PXD} \
  --silent && echo "exists" || echo "new"

Classify at the level of the file you are about to write, not the directory. A PXD folder may legitimately hold several SDRFs with descriptive suffixes (PXD006430-tmt.sdrf.tsv + PXD006430-silac.sdrf.tsv), so an existing folder does not mean you are replacing anything:

gh api repos/bigbio/sdrf-annotated-datasets/contents/datasets/{PXD} \
  --jq '.[] | select(.name | endswith(".sdrf.tsv")) | .name' 2>/dev/null

• New annotation: your target filename is not in that listing → new contribution, even if the folder already exists. Name any sibling files in the PR so a reviewer can see how the sub-experiments divide.
• Update: your target filename IS in the listing → this replaces a file someone else curated, so it needs justification, not just a report.

For the update case, do not open the PR yet. Audit the file you are about to replace, so the PR can say what was actually wrong with it. Abort on a failed fetch rather than auditing a truncated or error-page file: