permissions about covid-em-project HOT 12 CLOSED

Yes, that was the int/float type check in the converter's parameters. Ichacnged the code but not the command line call when I launched the script ;-)

Will do the changes and then upload to s3 and push the changes.

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OK, trying to do the merge locally and then commit to master...

git commit -am 'new data'
error: insufficient permission for adding an object to repository database .git/objects
error: insufficient permission for adding an object to repository database .git/objects
error: Error building trees

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@constantinpape
Any news? The datasets are still screwed and I cannot update them...

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Oh sorry, I didn't see this one. Give me a second, I will check.

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OK, pushing should be sorted.
Could you check the local dir?
I have looked at file permissions but cannot spot any problem here.
Can you maybe commit the changes and check what we need to manually update to incorporate the new datasets?

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Ok, I have pushed. I will update the data layout now.
@martinschorb have you uploaded it to s3 already?

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ok, I have updated everything in the dataset and it should work, but I couldn't test it yet, because the dataset is not on s3 yet, and I can't pull to the git repo on the emcf share due to permission issues, so I also can't test it locally.
@martinschorb Could you use your sudo rights to chmod everything to g+rwx in the folder?

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I can't... even though I am member of the group.
We need to involve IT.

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should I pull?
I think that worked yesterday...

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Yes, please pull.
Then I can check if it worked locally

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That's the master...

$ git pull
Updating 436a66e..69d9a6e
Fast-forward
 data/Covid19-S4-cell1plus_5nm/images/images.json                                           | 12 +++++++-----
 data/Covid19-S4-cell1plus_5nm/images/remote/sbem-6dpf-1-whole-raw.xml                      |  1 +
 data/Covid19-S4-cell1plus_5nm/misc/bookmarks/default.json                                  | 12 ++++++++++++
 data/Covid19-S4-cell1plus_5nm/misc/{bookmarks.json => bookmarks/manuscript_bookmarks.json} |  0
 data/datasets.json                                                                         |  5 +++--
 5 files changed, 23 insertions(+), 7 deletions(-)
 create mode 100644 data/Covid19-S4-cell1plus_5nm/misc/bookmarks/default.json
 rename data/Covid19-S4-cell1plus_5nm/misc/{bookmarks.json => bookmarks/manuscript_bookmarks.json} (100%)

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Yes, it works now:

But there is still an issue with the resolution: it's set to 5 micrometer instead of 5 nanometer, see
https://github.com/mobie-org/covid-em-datasets/blob/master/data/Covid19-S4-cell1plus_5nm/images/local/sbem-6dpf-1-whole-raw.xml#L20
This needs to be changed in 3 different files:

• https://github.com/mobie-org/covid-em-datasets/blob/master/data/Covid19-S4-cell1plus_5nm/images/local/sbem-6dpf-1-whole-raw.xml
• https://github.com/mobie-org/covid-em-datasets/blob/master/data/Covid19-S4-cell1plus_5nm/images/remote/sbem-6dpf-1-whole-raw.xml
• /g/emcf/common/5792_Sars-Cov-2/covid-em/data/Covid19-S4-cell1plus_5nm/images/local/sbem-6dpf-1-whole-raw.n5/setup0/timepoint0/attributes.json

For the xmls, it needs to be changed in the voxel size and in the affine.

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