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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
    slint review_requested #1690
  • Jan 31 2019 15:31
    slint labeled #1599
  • Jan 31 2019 15:31
    slint labeled #1599
  • Jan 31 2019 15:31
    slint labeled #1599
  • Jan 31 2019 15:31
    slint commented #1599
  • Jan 31 2019 15:29
    ChiaraBi synchronize #1652
  • Jan 31 2019 13:37
    slint unassigned #617
  • Jan 31 2019 13:37
    slint unassigned #1639
  • Jan 31 2019 12:59
    ChiaraBi synchronize #1652
  • Jan 31 2019 11:09
    ChiaraBi assigned #1646
  • Jan 31 2019 10:49
    ChiaraBi synchronize #1692
  • Jan 31 2019 10:44
    ChiaraBi assigned #1657
  • Jan 31 2019 10:43
    ChiaraBi synchronize #1692
  • Jan 31 2019 10:31
    ChiaraBi opened #1692
  • Jan 31 2019 08:40
    kpalin commented #1599
  • Jan 30 2019 18:10
    ChiaraBi synchronize #1652
  • Jan 30 2019 17:26
    ChiaraBi synchronize #1652
  • Jan 30 2019 10:45
    gwarf starred zenodo/zenodo
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
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},
        )