Common Errors¶

.ndjson is out of date¶

Error: After git-drs adding and committing a file, when you go to submit your data, "DocumentReference.ndjson is out of date",

$ git add file.txt
$ git commit -m "adding file.txt"
$ git push
Please correct issues before pushing.
Command `git-drs status` failed with error code 1, stderr: WARNING: DocumentReference.ndjson is out of date 1969-12-31T16:00:00. The most recently changed file is MANIFEST/file.txt.dvc 2025-02-28T09:24:46.283870.  Please check DocumentReferences.ndjson
No data file changes.

Resolution: As well as checking that all files are committed, git-drs status also ensures that FHIR metadata in META/ is up to date. This means that you likely missed a crucial step in the process, updating the FHIR metadata using the file manifest! The general flow for adding file metadata is git-drs add > git-drs meta init > git-drs commit. To resolve this, update and commit the FHIR metadata:

$ git-drs meta init
Updated 2 metadata files.
resources={'summary': {'DocumentReference': 1, 'ResearchStudy': 1}} exceptions=[]

$ git-drs push

To better understand the process of adding file metadata through the manifest, see adding file metadata and adding FHIR metadata.

No new files to index¶

Error:

$ git-drs push
No new files to index.  Use --overwrite to force

Resolution: When pushing data, git-drs checks the manifest (MANIFEST/ directory) to see if there are any files to update, including new files or modified files. If no files have been modified, then the push will not go through. To push up the same file data or push up new FHIR metadata (META/), use git-drs push --overwrite

Uncommitted changes¶

Error: On the subsequent rounds of adding files, updating FHIR metadata, and committing the changes, you are unable to push up those new changes

$ git-drs add hello.txt
$ git-drs meta init
$ git-drs commit -m "add hello file"

$ git-drs push
Uncommitted changes found.  Please commit or stash them first.

$ git-drs status
No data file changes.
On branch main
Changes not staged for commit:
 ...
 modified:   META/DocumentReference.ndjson

Resolution: This happened because the update FHIR metadata created in the META init was not staged for commit. To stage and commit the FHIR metadata, do:

$ git add META/
$ git-drs commit -m "update DocumentReference.json"
$ git-drs push

Note that git add is used here rather than git-drs add because git add will update the project's FHIR metadata while git-drs add only updates the project's manifest. If you want to commit multiple file changes, you can also use git-drs commit -am "update all files", where all changes get committed to the project.