csv2nidm -json_map

[maegancalvert]

I am running into a problem using csv2nidm. I created a json file from a csv file. My python code to use csv2nidm:

os.system('csv2nidm -csv /workspace/code/2022project-semanticcbcl/SemanticCBCL/NDA_Dictionaries/abcd_cbcl01_definitions.csv
-json_map /workspace/code/2022project-semanticcbcl/SemanticCBCL/NDA_Dictionaries/abcd_cbcl01_definitions.json
-out /workspace/code/2022project-semanticcbcl/SemanticCBCL/NDA_Dictionaries/abcd_cbcl01_definitions_outfile.json')

I can't get it to read the json file so it will only ask me the necessary concept prompts - it reads the CSV file and tries to take me through all the prompts, but the json file has many of the answers to the prompts. I can not run csv2nidm without the -csv CSV FILE. Does anyone have any thoughts?

[satra]

@dbkeator - any thoughts on this?

[dbkeator]

Hi, I would need to see the json file and the csv files if possible.
Thanks

[dnkennedy]

The csv would be like the one at https://github.com/ReproNim/SemanticCBCL/blob/main/fake_Data/abcd_cbcl01_simdata.txt. Will let someone else provide the example json file...

[satra]

here is a file: https://dl.dropbox.com/s/2hmlppx86rl0m5f/abcd_cbcl01_definitions.json?dl=0

[dbkeator]

@satra That JSON file isn't of the supported pynidm or BIDS forms. It's something else so if it's used directly in csv2nidm it don't recognize it....

[maegancalvert]

Thank you so much! That makes sense.

…

On Tue, Apr 26, 2022, 10:40 AM David Keator ***@***.***> wrote: @satra <https://github.com/satra> That JSON file isn't of the supported pynidm or BIDS forms. It's something else so if it's used directly in csv2nidm it don't recognize it.... — Reply to this email directly, view it on GitHub <#312 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQYVDGIJ23GTQBSG7KMIKADVHAE65ANCNFSM5UBK2D7A> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[dnkennedy]

So, how do we proceed with this? Convery satra's json to pynidm json? Or teach pynidm to read another json version?

[satra]

i suggest we write a few headings using csv2nidm and mimic it when we merge all our items.

[satra]

more generally, pynidm should inform the user why the json file is not being used. i.e. something like couldn't find appropriate keys or keys containing appropriate fields.

[dnkennedy]

Regarding an 'example run' to generate json we can mimic, if someone gets to that before me, please post it in the SemanticCBCL Slack!

[dbkeator]

Will add a message to both csv2nidm and bidsmri2nidm to indicate the JSON file supplied isn't of the appropriate format...