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  • Jan 31 2019 22:06
    blavoie starred zenodo/zenodo
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  • Jan 30 2019 10:45
    gwarf starred zenodo/zenodo
Lordjette Leigh Lecaros
@lordjette
I have 3 published article in a community but still doesn't show in front https://ibb.co/5T174NT
Lars Holm Nielsen
@lnielsen
Lordjette Leigh Lecaros
@lordjette
@lnielsen thanks.
Kai Woerner
@Herrner
Deleting records and files through the api is only allowed for unpublished depositions (so say the docs) - is there any other way to delete published records and their files programatically (for an admin user)?
<context>we have a sandbox(staging machine that we would like to "clean up" from time to time - so no DOI harm done.</context>
Lordjette Leigh Lecaros
@lordjette
Hello, I have found there is no "stats":{} shows in page after published and accept record in a community. I tried to run celery along zenodo run - h 1.2.3.4
Lordjette Leigh Lecaros
@lordjette
I tried 3 different users to download and view record but it does not appear in page.
Graeme Winter
@graeme-winter
Hi Folks - talked to Lars last week - Graeme from Diamond Light Source who is working on a tool to allow folks to automatically upload COVID-19 related data sets - for small files works fine using the new stream-type API, but for larger files I am getting network errors sometimes - ``` File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20200323/conda_base/lib/python3.6/site-packages/requests/api.py", line 134, in put
return request('put', url, data=data, kwargs)
File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20200323/conda_base/lib/python3.6/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url,
kwargs)
File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20200323/conda_base/lib/python3.6/site-packages/requests/sessions.py", line 530, in request
resp = self.send(prep, send_kwargs)
File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20200323/conda_base/lib/python3.6/site-packages/requests/sessions.py", line 643, in send
r = adapter.send(request,
kwargs)
File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20200323/conda_base/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', OSError("(32, 'EPIPE')",))
Lars Holm Nielsen
@lnielsen
Hi @graeme-winter
Does it happen immediately
?
or
Graeme Winter
@graeme-winter
No, after quite a while - makes me think a lot of the data has been uploaded
I acknowledge that this is quite a lot of data to HTTP PUT
Lars Holm Nielsen
@lnielsen
can you provide me with one of the following: user-agent string, bucket id and filename (e.g. file upload url) or ip address
then i can locate the requests in the webserer logs more easily
Graeme Winter
@graeme-winter
sure thing, will see what I can do
OK, so this was the upload which included a failed file https://zenodo.org/deposit/3724425
I think the file was "INS1_3.tar"
Lars Holm Nielsen
@lnielsen
Ok….tahnks…..
will check
Graeme Winter
@graeme-winter
I was running inside a screen session so the logging vanished off the top 🙄
I should add some actual logging to the application...
Lars Holm Nielsen
@lnielsen
Ok….I’ve found the failed request in the logs
Graeme Winter
@graeme-winter
Cool - there is a very good chance that the issue was on the interconnect or at my end... but adding some more resilience would be a good thing I think
Lars Holm Nielsen
@lnielsen
I can see it send a 502 bad gateway from our end
and that it managed to go to ~5GB uploaded first
does it fit that it was uploading for some 15-20 minutes before failing?
Graeme Winter
@graeme-winter
Yeh that fits
anything I can do at my end to be more resilient e.g. restart the upload at the failed point?
Lars Holm Nielsen
@lnielsen
unfortunately we don’t do resumable uploads :S
we’re looking into it and trying to debug it…..right now,it’s just to try again….which is not very nice for a 20 minute upload :(
Graeme Winter
@graeme-winter
I'll leave with you for a little while then - for the moment it seems to be fine with files <= ~ 1GB or so which should cover most of our use case. Thanks for looking into it :)
Graeme Winter
@graeme-winter
@lnielsen we are going now - looks like people are appreciating this too https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind2003&L=CCP4BB&D=0&P=190211 - thanks again for your help. Quick question, probably for Monday - currently reading API is in development according to your pages - would it be possible for you to give me some hints how I could make a script which will perform a keyword search and then grab the title / doi / file list for each? This will mean I can liaise with the other data archive people (the protein data bank) to allow linking back to the data sources...
Lars Holm Nielsen
@lnielsen
great news!!! Thanks for keeping us in the loop. If I get a moment during the weekend, I’ll try to send you info on the api
Our entire front end goes through this interface
The q Parma is the query from the search guide
Graeme Winter
@graeme-winter
👍 thanks for the starting point - I can figure things out from here I think 🙂 appreciate the quick feedback too!
Will try this out a bit later - got other things on right now ...
Lars Holm Nielsen
@lnielsen
Actually, the easiest is - make your search query on zenodo
and you got your search query…...
Graeme Winter
@graeme-winter
OK, followed up on this finally - all good, got what I was looking for 🙂 thank you
Graeme Winter
@graeme-winter
Good morning 🙂 now trying to update automatically some of these records to (i) fix a typo in a keyword and (ii) add a couple of extra words to the descriptions - weird thing I am finding is that it works sometimes but now appears to be failing with an invalid action
{'message': 'Invalid action', 'status': 403}
Traceback (most recent call last):
File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 203, in <module>
updater()
File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 198, in updater
zenodo_updater.update()
File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 132, in update
self._update()
File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 106, in _update
raise RuntimeError("in update: HTTP status %d" % r.status_code)
RuntimeError: in update: HTTP status 403