Closed Marie59 closed 10 months ago
Hi @Marie59 We can surely simply modify this for a simple try/except, and fallback on an "anonymous" fetched_by attribute. Would you need a new release for this or is the master branch ok ?
Hi @gmaze Thanks a lot for your answer and help ! I would need a new release in order to get the conda package up to date also (I am installing argopy with conda for the tool). Thank you !
Tests are running Before issuing a new release, can you make sure this will fix your issue downstream ? you can install argopy from the specific branch using pip
Hi @gmaze I just tested the changes and everything is working !!! Thank you ! If you could do a new release for the conda package it would be great !
Awesome, I'll issue a new release this afternoon then ! Could you please post here where to find this new argopy usage ? (not familiar with https://usegalaxy.eu/ stuff)
Great thanks ! Yes of course, I will give you the link to the tool once it's published here ! (for now it's only a PR)
Hi @gmaze ! Sorry to bother you again, I saw that you merged the branch but did not do the release, I just wanted to make sure that you did not forget :)
I'm on it, upstream tests are failing for some reasons I need to fix before the release
Ah ok no problem ! Good luck !
v0.1.15 is released on pypi and fix this bug
Hi @gmaze and happy new year! I forgot to send you the ling of the Argopy tool on the Galaxy Platform. So, there it is https://earth-system.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0 it's working pretty well ! Thanks a lot !!
awesome !
Hello, I would like to create a Galaxy (https://usegalaxy.eu/) tool using argopy in order to retrieve argo data and get them on Galaxy. I started the work here https://github.com/galaxyecology/tools-ecology/pull/81.
However when launching the galaxy test to get the tool up and running I'm having an error. Indeed, the tool is launched in a container and in the argopy code there's a line trying to get the user id which makes the tool stop. Here is the line https://github.com/euroargodev/argopy/blob/master/argopy/data_fetchers/erddap_data.py#L686
I was thinking maybe it would be possible to use a try except here to avoid the error. To analyze the error reported from Galaxy, I looked at the code. If being able to identify the origin of the data request is important, you can add a named parameter to the function
post_process()
to pass the value to be assigned tothis_ds.attrs["Fetched_by"]
. If a value is specified for this parameter, then the code does not attempt to retrieve the user from the OS session. In this case, it will be necessary to propagate this parameter to the calling functions.Do you think there is something that can be done here ?