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  • Jan 31 2019 22:06
    blavoie starred zenodo/zenodo
  • Jan 31 2019 20:43
    dybedal commented #1583
  • Jan 31 2019 15:35
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    ChiaraBi synchronize #1652
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  • Jan 31 2019 12:59
    ChiaraBi synchronize #1652
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  • Jan 31 2019 10:49
    ChiaraBi synchronize #1692
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  • Jan 30 2019 18:10
    ChiaraBi synchronize #1652
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    ChiaraBi synchronize #1652
  • Jan 30 2019 10:45
    gwarf starred zenodo/zenodo
Graeme Winter
@graeme-winter
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
At around 07:13 UTC
Lars Holm Nielsen
@lnielsen
Checking
Graeme Winter
@graeme-winter
👍 thank you
Lars Holm Nielsen
@lnielsen
Do you have the deposit id that it happened to?
Graeme Winter
@graeme-winter
Located deposition: id = 3730327
Lars Holm Nielsen
@lnielsen
Usually this happens if e.g. a record was not put in editing mode, or is already in editing mode…..
e.g. the normal flow would be
/deposit/depositions/:id/actions/edit
Graeme Winter
@graeme-winter
Ah, record in editing mode would be the thing
Lars Holm Nielsen
@lnielsen
PUT /deposit/depositions/:id
POST /deposit/depositions/:id/actions/publish
Graeme Winter
@graeme-winter
I'm probably driving it wrong
This bit I missed - /deposit/depositions/:id/actions/edit
Somehow it accidentally worked for a couple 🙄 had probably been left in edit mode as a happy accident - will work this in now
Lars Holm Nielsen
@lnielsen
Yeah, it’s an artefact of having long running edit sessions that are not published until you make them…….API is not so clear in this respect
Graeme Winter
@graeme-winter
        # switch to edit mode
        r = requests.post(
            "%s/api/deposit/depositions/%s/actions/edit" % (self._server, self._dep_id),
            params={"access_token": self._token},
        )
yes?
(to save cluttering your error logs, for which I am probably about 80% responsible at the moment)
🤔 that would be a nope -
{'message': 'Invalid action', 'status': 403}
Traceback (most recent call last):
  File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 214, in <module>
    updater()
  File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 209, in updater
    zenodo_updater.update()
  File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 143, in update
    self._update()
  File "/Users/graeme/git/zenodo-uploader/zenodo_updater.py", line 106, in _update
    raise RuntimeError("in edit: HTTP status %d" % r.status_code)
RuntimeError: in edit: HTTP status 403
Lars Holm Nielsen
@lnielsen
I’m just in a daily standup meeting….will be back in 15-20 min
Graeme Winter
@graeme-winter
No problem
Lars Holm Nielsen
@lnielsen
“standup” sitting down remotely :-)
Graeme Winter
@graeme-winter
Well yes, I have a couple of the same things to look forward to later on ;-)
"look forward to"
OK, I think I may have accidentally left that one in manual edit mode via web interface... I clicked edit and discard changes and it then ran through just fine
Lars Holm Nielsen
@lnielsen
Out of meetings
Graeme Winter
@graeme-winter
Cool - actually I am all done 🙂 now in a "I should clean this code up" phase
Lars Holm Nielsen
@lnielsen
If you execute the edit on an already edited record, it will tell you 403, but then you should be able to continue editing the deposit as normal anyway…..and publish afterwards
i know that phase :-)