zenodo/zenodo

Zenodo - Research. Shared. Problem running Zenodo? https://github.com/zenodo/zenodo/wiki/Troubleshooting

Lars Holm Nielsen

@lnielsen

https://help.zenodo.org/guides/search/

https://zenodo.org/api/records?q=

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

e.g. https://zenodo.org/search?page=1&size=20&q=%22COVID-19%22

change https://zenodo.org/search to https://zenodo.org/api/records

https://zenodo.org/api/records/?page=1&size=20&q=%22COVID-19%22

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 :-)

FYI: we’re gonna change the frontpage to focus on COVID-19 related uploads in Zenodo and we’ll feature your uploads…..hopefully online by tomorrow

Graeme Winter

@graeme-winter

But, this has got me thinking, that there may be value in writing up a very short "how we did this" type paper which could be circulated amongst the crystallography community - just a couple of pages on what the logic was for creating / uploading etc. as this has been a frequent topic. You fancy being an author?

Lars Holm Nielsen

@lnielsen

Sure, I’ll be happy to help

Graeme Winter

@graeme-winter

👍

Apropos zenodo / covid uploads - if you need / would like / feel anything is missing please shout

Thanks by the way for all your help - am happy to respond in kind on documentation etc. once all the dust has settled

ugswork

@ugswork

@Herrner I see that you had posted earlier that you were getting the following error accessing admin in Zenodo.

in _handle_view
    setattr(invenio_app.talisman.local_options,
AttributeError: 'NoneType' object has no attribute 'local_options'

I deleted and created all the docker images. I have APP_ENABLE_SECURE_HEADERS = False in config. I would like to know what (else) needs to be done to get to 'admin' page in Zenodo. Thank you.

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