Git failed to push dataset files on Jupyterlab

Renku (CLI)
1

Hi All,

Just come across this git problem and I wondered if you might be able to help please? I’m not sure what to try next or check from here…

I’m working on Jupterlab in the private repo: https://renkulab.io/gitlab/ACE-ASAID/cruise-track-legs0-4

I’ve imported a dataset and tried to add the files to git.

(Copied from Jupyterlab output)

work ❯ cruise-track-legs0-4 ▶ master ▶ 3? ▶ $ ▶ git add data/qualitychecked_onesec_10*

work ❯ cruise-track-legs0-4 ▶ master ▶ 8✔ ▶ 2? ▶ $ ▶ git commit -a
[master b5c9722] Added dataset quality checked one second resolution cruise track files.
git push orign m 8 files changed, 5976974 insertions(+)
 create mode 100644 data/qualitychecked_onesec_10/README.txt
 create mode 100644 data/qualitychecked_onesec_10/ace_cruise_track_1sec_2016-12.csv
 create mode 100644 data/qualitychecked_onesec_10/ace_cruise_track_1sec_2017-01.csv
 create mode 100644 data/qualitychecked_onesec_10/ace_cruise_track_1sec_2017-02.csv
 create mode 100644 data/qualitychecked_onesec_10/ace_cruise_track_1sec_2017-03.csv
 create mode 100644 data/qualitychecked_onesec_10/ace_cruise_track_1sec_2017-04.csv
 create mode 100644 data/qualitychecked_onesec_10/ace_cruise_track_trimble_example_deviation_2016-12-24.png
 create mode 100644 data/qualitychecked_onesec_10/data_file_header.txt

 work ❯ cruise-track-legs0-4 ▶ master ▶ ⬆ ▶ 2? ▶ $ ▶ git push origin master
Locking support detected on remote "origin". Consider enabling it with:
  $ git config lfs.https://oauth2:8509a6e80fe14fc384d7bce1c06c72d4f3782bd0997c5e58a6a342901cba2f20@renkulab.io/gitlab/ACE-ASAID/cruise-track-legs0-4.git/info/lfs.locksverify true
Counting objects: 9, done.
Delta compression using up to 8 threads.
error: pack-objects died of signal 9
error: pack-objects died of signal 9
fatal: The remote end hung up unexpectedly
fatal: The remote end hung up unexpectedly
fatal: The remote end hung up unexpectedly
error: failed to push some refs to 'https://oauth2:8509a6e80fe14fc384d7bce1c06c72d4f3782bd0997c5e58a6a342901cba2f20@renkulab.io/gitlab/ACE-ASAID/cruise-track-legs0-4.git'

 work ❯ cruise-track-legs0-4 ▶ master ▶ ⬆ ▶ 2? ▶ $ ▶ git config lfs.https://oauth2:8509a6e80fe14fc384d7bce1c06c72d4f3782bd0997c5e58a6a342901cba2f20@renkulab.io/gitlab/ACE-ASAID/cruise-track-legs0-4.git/info/lfs.locksverify true

work ❯ cruise-track-legs0-4 ▶ master ▶ ⬆ ▶ 2? ▶ $ ▶ git push origin masterCounting objects: 9, done.
Delta compression using up to 8 threads.
error: pack-objects died of signal 9
error: pack-objects died of signal 9
fatal: The remote end hung up unexpectedly
fatal: The remote end hung up unexpectedly
fatal: The remote end hung up unexpectedly
error: failed to push some refs to 'https://oauth2:8509a6e80fe14fc384d7bce1c06c72d4f3782bd0997c5e58a6a342901cba2f20@renkulab.io/gitlab/ACE-ASAID/cruise-track-legs0-4.git'

Thank you for your help and patience with all these questions :slight_smile:

2

It looks to me like you just checked in data directly to the repo (without adding them to LFS) - how big are those csv files?

3

The total is ~ 1 GB, so a few hundred MB each

4

And you didn’t add them to git-lfs beforehand, correct? Did you upload the files through the jupyterlab interface?

5

And you didn’t add them to git-lfs beforehand, correct?

No I didn’t, that is correct. Although since your message I have been trying and am now in a funny state of having some in lfs and others not…

Did you upload the files through the jupyterlab interface?

Yes

6

Ok, so we do actually now have a UI to do this :slight_smile:

If you go to the project and go to the datasets tab for the project, you can either modify existing datasets (and add files there) or create a new dataset. You can drag and drop files to add them.

To resolve your situation, here’s what I would do:

git reset <commit-id-before-git-add>
git lfs track <data files>
git add .gitattributes
git add <data files>
git commit -m "msg"

I think this should work.

7

ok thanks I’ll give it a go!

1 Like
8

Succeeded, thank you! Help much appreciated :grinning:

1 Like
9

whew I’m glad it was that easy :smiley: