obj-tables command line tool throws an error

[liebermeister]

Hi Jonathan,

I'm trying out the obj-tables command line tool, command

obj-tables init-schema schema.csv schema.py

and get the error message

Traceback (most recent call last):
File "/usr/local/bin/obj-tables", line 10, in
sys.exit(main())
File "/usr/local/lib/python3.6/dist-packages/obj_tables/main.py", line 270, in main
app.run()
File "/usr/local/lib/python3.6/dist-packages/cement/core/foundation.py", line 916, in run
return_val = self.controller._dispatch()
File "/usr/local/lib/python3.6/dist-packages/cement/ext/ext_argparse.py", line 808, in _dispatch
return func()
File "/usr/local/lib/python3.6/dist-packages/obj_tables/main.py", line 125, in _default
utils.init_schema(args.in_file, out_filename=args.out_file)
File "/usr/local/lib/python3.6/dist-packages/obj_tables/utils.py", line 445, in init_schema
wb = wc_utils.workbook.io.read(filename)
File "/usr/local/lib/python3.6/dist-packages/wc_utils/workbook/io.py", line 889, in read
reader = reader_cls(path)
File "/usr/local/lib/python3.6/dist-packages/wc_utils/workbook/io.py", line 705, in init
path))
ValueError: path 'schema.csv' must have one glob pattern '*' in its base name

Can you make sense of it?

Thank you!

All the best,
Wolf

[jonrkarr]

I've made a bunch of changes to obj_tables and wc_utils to merge SBtab's concepts. I haven't yet pushed the changes to PyPI. Please use the latest revisions from GitHub. git clone https://github.com/karrlab/wc_utils.git git clone https://github.com/karrlab/ob_tables.git pip install -e wc_utils/ pip install -e obj_tables/

…

On Mon, Sep 30, 2019 at 2:49 PM Wolfram Liebermeister < ***@***.***> wrote: Hi Jonathan, I'm trying out the obj-tables command line tool, command obj-tables init-schema schema.csv schema.py and get the error message Traceback (most recent call last): File "/usr/local/bin/obj-tables", line 10, in sys.exit(main()) File "/usr/local/lib/python3.6/dist-packages/obj_tables/*main*.py", line 270, in main app.run() File "/usr/local/lib/python3.6/dist-packages/cement/core/foundation.py", line 916, in run return_val = self.controller._dispatch() File "/usr/local/lib/python3.6/dist-packages/cement/ext/ext_argparse.py", line 808, in _dispatch return func() File "/usr/local/lib/python3.6/dist-packages/obj_tables/*main*.py", line 125, in _default utils.init_schema(args.in_file, out_filename=args.out_file) File "/usr/local/lib/python3.6/dist-packages/obj_tables/utils.py", line 445, in init_schema wb = wc_utils.workbook.io.read(filename) File "/usr/local/lib/python3.6/dist-packages/wc_utils/workbook/io.py", line 889, in read reader = reader_cls(path) File "/usr/local/lib/python3.6/dist-packages/wc_utils/workbook/io.py", line 705, in *init* path)) ValueError: path 'schema.csv' must have one glob pattern '*' in its base name Can you make sense of it? Thank you! All the best, Wolf — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#97?email_source=notifications&email_token=AAVXMKIGW3Z57DDQOMOGUELQMJC3NA5CNFSM4I37CX3KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HOUKU2Q>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAVXMKPBIKWHVBU4MAIWCUTQMJC3NANCNFSM4I37CX3A> .

[liebermeister]

Great, thank you!