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Apollo Export and Delete Organism tools fail for Admin users unless they have specifically granted READ/WRITE permissions #56

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MoffMade opened this issue Aug 25, 2020 · 1 comment

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@MoffMade
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Steps to reproduce:

  • Using a user account with the Admin role in Apollo, run export.py or delete_features.py or delete_organism.py on an organism without specific permissions assigned

Tool fails with something similar to:

Traceback (most recent call last):
  File "/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/gga/apollo_export/0d4234488bd0/apollo_export/export.py", line 49, in <module>
    raise Exception("You do not have read permission on organism %s" % org_cn)
Exception: You do not have read permission on organism <name>

I find that the utility of these tools is much reduced by requiring I must manually assign myself these permissions through Apollo before I can use the tools to remove or retrieve the data, when I could just do so through the Apollo UI as I am already there for the permissions. Could we expand the accessible_organism call for specific permissions to also accept "ADMIN" permissions similar to when it is called without the specified variable?

@abretaud
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Sure, modifying accessible_organism as you wrote would be great, I'll look into it, thanks for reporting!

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