Genemania cyrest access - check if any dataset has been installed

[nivedas...@gmail.com]

Hi,

I'm interested in programmatically checking if any species dataset has been installed locally (i.e. in offline mode)

To do so, I use the CyREST command line API call: 

body = dict(offline=True)
response = requests.post("http://localhost:1234/v1/commands/genemania/organisms", json=body)

If no organism is found, this call immediately opens up a pop-up window enabling the user to install a species dataset. Is there a way to prevent this window from opening up? The script I'm currently running checks for species and if present proceeds to perform other functions. I want to prevent any stall/error with the subsequent steps of my script that may occur in the time taken for the user to install a genemania dataset should the pop-up occur. 

Alternatively, is there a way to check my local machine to see if a species dataset is installed? I see that installing datasets creates a folder in Documents\genemania_plugin. Can I retrieve species information from somewhere in the folder?

Thanks!

[Ruth Isserlin]

Hi,

The fact that the dialog is popping up sounds like a bug to me.  I have submitted it to Genemania's bug tracker.

In order to get around it you can check the Documents\genemania_plugin directory.  Unfortunately the directories aren't named with their taxonomy identifiers.  

They have the following mapping

1   is A. Thaliana (arabidopsis)
2   is C. Elegans (worm)
3   is D. Melanogaster (fruit fly)
4   is H. Sapiens (human)
5   is M. Musculus (mouse)
6   is S. Cerevisiae (yeast)

7   is R. Norvegicus (rat)

8   is D. renio (Zebrafish)

9   is E. coli

So if there is a directory Documents\genemania_plugin\{name of data release i.e gmdata-2017-07-13-core}\4 - then the human dataset is installed. 

Unfortunately it is very much a hack.  I have also put into the genemania tracker to add a simple cyrest function to check which datasets are installed (https://github.com/GeneMANIA/genemania/issues/135).  It looks like "genemania organism" also returns the entire set of networks as well.   If you come across any other cyrest commands that are useful please feel free to add it the genemania issue tracker here: https://github.com/GeneMANIA/genemania/issues

Thanks, 

Ruth 

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[nivedas...@gmail.com]

Thanks, this helps!

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