bidsmri2nidm - "ERROR: initializing InterLex connection" without further info

[yarikoptic]

❯ bidsmri2nidm -d . -bidsignore
/home/yoh/proj/PyNIDM/venvs/dev3/lib/python3.11/site-packages/bids/config.py:38: FutureWarning: Setting 'extension_initial_dot' will be removed in pybids 0.16.
  warnings.warn("Setting 'extension_initial_dot' will be removed in pybids 0.16.",
ERROR: initializing InterLex connection...

It would be better if it informed a little more about that ERROR

• is URL (which?) not reached?
• is INTERLEX_API_KEY wrong?

so a user could get a clue on what to do next having got into this pickle

[madtitan02]

is this issue resolved , can you provide more details about this issue

[seanhatton]

Hi, I also have this error on a clean install of pynidm (Ubuntu 22.04). I have rolled back my rdflib to version 6.1.1.

[dbkeator]

Hi, Have you tried setting the environment variable INTERLEX_API_KEY with your key (see usage below)?

usage: bidsmri2nidm [-h] -d DIRECTORY [-jsonld] [-bidsignore] [-no_concepts] [-json_map JSON_MAP] [-log LOGFILE] [-o OUTPUTFILE]

This program will represent a BIDS MRI dataset as a NIDM RDF document and provide user with opportunity to annotate the dataset (i.e. create sidecar files) and associate selected variables with broader concepts to make datasets more FAIR.

Note, you must obtain an API key to Interlex by signing up for an account at scicrunch.org then going to My Account and API Keys. Then set the environment variable INTERLEX_API_KEY with your key.

optional arguments: -h, --help show this help message and exit -d DIRECTORY Full path to BIDS dataset directory -jsonld, --jsonld If flag set, output is json-ld not TURTLE -bidsignore, --bidsignore If flag set, tool will add NIDM-related files to .bidsignore file -no_concepts, --noconcepts If flag set, tool will no do concept mapping -log LOGFILE, --log LOGFILE Full path to directory to save log file. Log file name is bidsmri2nidm[basename(args.directory)].log -o OUTPUTFILE Outputs turtle file called nidm.ttl in BIDS directory by default..or whatever path/filename is set here

map variables to terms arguments: -json_map JSON_MAP, --json_map JSON_MAP Optional full path to user-suppled JSON file containing variable-term mappings.

[seanhatton]

Yes, my key is installed correctly.

On Wed, Feb 21, 2024, 3:03 PM David Keator @.***> wrote:

Hi, Have you tried setting the environment variable INTERLEX_API_KEY with your key (see usage below)?

usage: bidsmri2nidm [-h] -d DIRECTORY [-jsonld] [-bidsignore] [-no_concepts] [-json_map JSON_MAP] [-log LOGFILE] [-o OUTPUTFILE]

This program will represent a BIDS MRI dataset as a NIDM RDF document and provide user with opportunity to annotate the dataset (i.e. create sidecar files) and associate selected variables with broader concepts to make datasets more FAIR.

Note, you must obtain an API key to Interlex by signing up for an account at scicrunch.org http://scicrunch.org then going to My Account and API Keys. Then set the environment variable INTERLEX_API_KEY with your key.

optional arguments: -h, --help show this help message and exit -d DIRECTORY Full path to BIDS dataset directory -jsonld, --jsonld If flag set, output is json-ld not TURTLE -bidsignore, --bidsignore If flag set, tool will add NIDM-related files to .bidsignore file -no_concepts, --noconcepts If flag set, tool will no do concept mapping -log LOGFILE, --log LOGFILE Full path to directory to save log file. Log file name is bidsmri2nidm[basename(args.directory)].log -o OUTPUTFILE Outputs turtle file called nidm.ttl in BIDS directory by default..or whatever path/filename is set here

map variables to terms arguments: -json_map JSON_MAP, --json_map JSON_MAP Optional full path to user-suppled JSON file containing variable-term mappings.

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