abcd -e `key=value` doesn't get processed corretly

[gelzinyte]

e.g. abcd upload -i -e "dset_type=train" train.xyz gets parsed into {'dset_type': Tree('value', []), 'train': True} and Tree cannot be hashed. Full Traceback:

Traceback (most recent call last):
  File "/opt/womble/miniconda3/user_envs/eg475/wo/bin/abcd", line 33, in <module>
    sys.exit(load_entry_point('abcd', 'console_scripts', 'abcd')())
  File "/home/eg475/programs/abcd/abcd/frontends/commandline/parser.py", line 121, in main
    callback_func(**kwargs)
  File "/home/eg475/programs/abcd/abcd/frontends/commandline/decorators.py", line 15, in wrapper
    func(*args, config=config, **kwargs)
  File "/home/eg475/programs/abcd/abcd/frontends/commandline/decorators.py", line 48, in wrapper
    func(*args, db=db, query=query, **kwargs)
  File "/home/eg475/programs/abcd/abcd/frontends/commandline/decorators.py", line 59, in wrapper
    func(*args, **kwargs)
  File "/home/eg475/programs/abcd/abcd/frontends/commandline/commands.py", line 69, in upload
    db.upload(path, extra_infos, store_calc=calculator)
  File "/home/eg475/programs/abcd/abcd/backends/atoms_pymongo.py", line 230, in upload
    self.push(data, extra_info, store_calc=store_calc)
  File "/home/eg475/programs/abcd/abcd/backends/atoms_pymongo.py", line 214, in push
    data = AtomsModel.from_atoms(self.collection, item, extra_info=extra_info, store_calc=store_calc)
  File "/home/eg475/programs/abcd/abcd/backends/atoms_pymongo.py", line 46, in from_atoms
    obj = super().from_atoms(atoms, extra_info, store_calc)
  File "/home/eg475/programs/abcd/abcd/model.py", line 202, in from_atoms
    item.pre_save()
  File "/home/eg475/programs/abcd/abcd/model.py", line 276, in pre_save
    m.update(self[key])
  File "/home/eg475/programs/abcd/abcd/model.py", line 47, in update
    raise ValueError("The {} type cannot be hashed! (Value: {})", format(type(value), value))
TypeError: format() argument 2 must be str, not Tree

[gabor1]

Because string values need to be in quotes (I.e 'dset_type="train"') if this is a massive pain we can think about special casing it. But in queries, it's a nightmare if you don't do this

-- Gábor

On 6 Apr 2021, at 09:43, gelzinyte @.***> wrote:

 e.g. abcd upload -i -e "dset_type=train" train.xyz gets parsed into {'dset_type': Tree('value', []), 'train': True} and Tree cannot be hashed. Full Traceback:

Traceback (most recent call last): File "/opt/womble/miniconda3/user_envs/eg475/wo/bin/abcd", line 33, in sys.exit(load_entry_point('abcd', 'console_scripts', 'abcd')()) File "/home/eg475/programs/abcd/abcd/frontends/commandline/parser.py", line 121, in main callback_func(kwargs) File "/home/eg475/programs/abcd/abcd/frontends/commandline/decorators.py", line 15, in wrapper func(*args, config=config, *kwargs) File "/home/eg475/programs/abcd/abcd/frontends/commandline/decorators.py", line 48, in wrapper func(args, db=db, query=query, kwargs) File "/home/eg475/programs/abcd/abcd/frontends/commandline/decorators.py", line 59, in wrapper func(*args, **kwargs) File "/home/eg475/programs/abcd/abcd/frontends/commandline/commands.py", line 69, in upload db.upload(path, extra_infos, store_calc=calculator) File "/home/eg475/programs/abcd/abcd/backends/atoms_pymongo.py", line 230, in upload self.push(data, extra_info, store_calc=store_calc) File "/home/eg475/programs/abcd/abcd/backends/atoms_pymongo.py", line 214, in push data = AtomsModel.from_atoms(self.collection, item, extra_info=extra_info, store_calc=store_calc) File "/home/eg475/programs/abcd/abcd/backends/atoms_pymongo.py", line 46, in from_atoms obj = super().from_atoms(atoms, extra_info, store_calc) File "/home/eg475/programs/abcd/abcd/model.py", line 202, in from_atoms item.pre_save() File "/home/eg475/programs/abcd/abcd/model.py", line 276, in pre_save m.update(self[key]) File "/home/eg475/programs/abcd/abcd/model.py", line 47, in update raise ValueError("The {} type cannot be hashed! (Value: {})", format(type(value), value)) TypeError: format() argument 2 must be str, not Tree — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[gelzinyte]

Ah ok, just forgot about it (even though it's mentioned further down in the examples). Thanks!