Programatic access to entities with new upload dialog broken


I might have misunderstood something but it looks as if the new "UPLOAD" restriction interferes with the programatic clients. I am trying to update an a project entity from the python client (in the new build 48) and get:

WARNING: This entity has access restrictions. Please visit the web page for this entity (syn.onweb("syn2344890")). Click the downward pointing arrow next to the file's name to review and fulfill its download requirement(s).

Repro (in python):

ent= syn.get('syn300013')




Larsson Omberg
July 14, 2014, 2:14 PM

Not able to reproduce anymore. It might be worth to create a new project with UPLOAD restrictions when testing this in the two clients however as all issues I saw at the time of the upgrade were not present the next day (which is also after I hade updated each project at least once.)

Bruce Hoff
July 11, 2014, 7:17 PM

The problems I can verify are problems with the clients. I opened issues and to track them. Larsson, if you agree that those issues track the problem will you close this issue? If not, please say what is/are the remaining issue(s).

Bruce Hoff
July 11, 2014, 7:05 PM

Two updates:
1) Although Larsson mentions entity syn300013 ("TCGA_pancancer" project) several times it doesn't appear that any access restriction exists or has ever existed for this entity. First, I checked the access restrictions on syn300013 and verified there are none. Second, I checked with Jay who created the UPLOAD access restrictions. He gave me a list of 13 entities, none of which is this one: "syn1725886","syn2344890","syn2344108","syn2480680","syn2024473","syn1960986","syn2426653","syn1935546","syn2296810","syn2284679","syn2289118","syn1973664","syn2318326". There is an upload access restriction on the other project mentioned by Larsson (syn2344890, "TCGA_Cervical_AWG" project) and that access restriction applies to the 13 IDs given to me by Jay.
2) I verified that it is possible to update annotations on a project having UPLOAD access restrictions, from R:

Therefore the problem may be in the Python client. I opened an issue to check the Python client.

Larsson Omberg
June 27, 2014, 4:21 PM

Thanks Bruce:

1) Not blocked.
2) Not sure how I approved myself unless the attempted access with the client did it.

Bruce Hoff
June 27, 2014, 1:57 PM

> Did something change in the last 35 minutes?
Yes, it looks like you 'agreed to' the access requirement on syn2344890

It looks like there are a couple of issues here, possibly with the clients' behavior (Py and Web – we should check R too) and possibly with the way access restrictions are inherited. We should straighten this all out, but it seems like for the moment you are not blocked. If you ARE still blocked, please let us know.



Bruce Hoff


Larsson Omberg


Larsson Omberg





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