Images retrieved from Galaxy server are malformed

tripal / tripal_galaxy

This module is for integration of Tripal and a remote Galaxy Instance.

https://tripal-galaxy.readthedocs.io/en/latest/

GNU General Public License v2.0

2 stars 4 forks source link

Images retrieved from Galaxy server are malformed #160

Closed Ferrisx4 closed 4 years ago

Ferrisx4 commented 4 years ago

Images created by a workflow on Galaxy get returned to Tripal Galaxy but they are not able to open. Currently seeing broken PNG files, testing other image types.

Files appear to be correct in Galaxy history, and also appear to be correct when transferring to Tripal Galaxy (correct size, correct type).

Example .png attached Galaxy14- 01-sample_dendrogram -1

almasaeed2010 commented 4 years ago

Looks like there are 4 spaces prepended to the file when being streamed by Galaxy or when being saved by Tripal_Galaxy. In either case, we can fix it by trimming the content of the file trim(file_get_contents('file_path')).

You can inspect the image using xxd filenam.png | less

Once the spaces are removed, the image will render correctly: 80219695-d63ad500-8610-11ea-8b80-7e0839026a54

Ferrisx4 commented 4 years ago

Issue appears to be related to the Tripal Sequence Similarity Search module putting four extra spaces on every page. Disabling that module removes the four extra spaces from every page.

Closing for now.

Ferrisx4 commented 4 years ago

This has been fixed by https://github.com/tripal/tripal_sequence_similarity_search/issues/8