… load a convention from a local YAML file?

… load a convention from a local YAML file?#

Yes you can. To demonstrate this, let’s take a convention file, which comes with the h5RDMtoolbox

import h5rdmtoolbox as h5tbx
from h5rdmtoolbox import tutorial

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[1], line 1
----> 1 import h5rdmtoolbox as h5tbx
      2 from h5rdmtoolbox import tutorial

File ~/checkouts/readthedocs.org/user_builds/h5rdmtoolbox/checkouts/v1.7.0/h5rdmtoolbox/__init__.py:129
    125     with File(src) as h5:
    126         return h5.dumps()
--> 129 from h5rdmtoolbox.wrapper.ld.hdf.file import get_ld as hdf_get_ld
    130 from h5rdmtoolbox.wrapper.ld.user.file import get_ld as user_get_ld
    133 def get_ld(
    134         hdf_filename: Union[str, pathlib.Path],
    135         structural: bool = True,
    136         semantic: bool = True,
    137         blank_node_iri_base: Optional[str] = None,
    138         **kwargs) -> rdflib.Graph:

File ~/checkouts/readthedocs.org/user_builds/h5rdmtoolbox/checkouts/v1.7.0/h5rdmtoolbox/wrapper/ld/__init__.py:1
----> 1 import ssnolib.ssno.standard_name
      2 from ontolutils.namespacelib import M4I
      3 from ontolutils.namespacelib import SCHEMA

ModuleNotFoundError: No module named 'ssnolib'

yaml_filename = tutorial.get_convention_yaml_filename()

cv = h5tbx.convention.Convention.from_yaml(yaml_filename)
h5tbx.use(cv)

Convention "h5rdmtoolbox-tutorial-convention" filename: C:\Users\da4323\Documents\programming\GitHub\h5RDMtoolbox\h5rdmtoolbox\data\tutorial_convention.yaml
creating directory for the convention
No special functions defined
Found 0 function(s) in C:\Users\da4323\AppData\Local\h5rdmtoolbox\h5rdmtoolbox\conventions\h5rdmtoolbox_tutorial_convention\h5rdmtoolbox_tutorial_convention.py

using("h5rdmtoolbox-tutorial-convention")

The convention requires a standard name table. It comes with a default one, but let’s also load a local one:

snt_yaml_filename = tutorial.get_standard_name_table_yaml_file()

with h5tbx.File(data_type='experimental', contact=h5tbx.__author_orcid__,
               standard_name_table=snt_yaml_filename) as h5:
    snt = h5.standard_name_table
    c = h5.contact
    h5.dump()
    • __h5rdmtoolbox_version__ : 0.9.0a0
    • contact : ORCID logohttps://orcid.org/0000-0001-8729-0482
    • data_type : experimental
    • standard_name_table :
    • StandardNameTable: (institution: my_institution, contact: https://orcid.org/0000-0001-8729-0482, valid_characters: [^a-zA-Z0-9_], pattern: ^[0-9 ].*, last_modified: 2023-08-16_11:05:00, version: v1.1)