python-odml
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G-Node
odML libraries
Currently there are two files, `odml/templates.py` and `odml/terminology.py`, that provide loading and handling of odml-templates and odml-terminologies. Since the code itself is very similar, it would be good to unify...
Hi! I have encountered myself doing the following many, many times: ``` import quantities as pq myQuantity = pq.Quantity(myOdml.properties['myProp'].value, myOdml.properties['myProp'].unit) ``` So I wondered this is probably something people would...
Deprecation warnings are emitted in Python 3.8 for invalid escape sequences. Escaping them or using raw strings will fix this issue. ``` find . -iname '*.py' | xargs -P 4...
In a previous version all odml files had the file extension `.odml`. After support for `JSON` and `YAML` was added, the `.odml` file extension was no longer supported. Some people...
Currently `odml/resources/odml-ontology.ttl` contains the basic ontology for mapping odML entities to RDF classes. It also includes some example `Section` subclasses e.g. `Cell` or `Hardware` as proof of concept. If we...
Subclassing the `dict` built-in is generally discouraged (and `collections.UserDict` exists for this purpose) but I think the reasons for that don't affect us here right now. I believe it's only...
Raising the question whether it would make sense to have a dedicated contact email attribute at document level.
odml version 1.4.1 INFO:rdflib:RDFLib Version: 4.2.2 ``` Traceback: writer.write_file('{0}.xml'.format("bla")) File "/usr/local/lib/python2.7/dist-packages/odml/tools/xmlparser.py", line 128, in write_file data = unicode(self).encode('utf-8') File "/usr/local/lib/python2.7/dist-packages/odml/tools/xmlparser.py", line 122, in __unicode__ return ET.tounicode(self.save_element(self.doc), pretty_print=True) File "/usr/local/lib/python2.7/dist-packages/odml/tools/xmlparser.py", line...
The terminologies, or specifically the terminology definitions should be updated and made a bit more generic. Example, the definition of Subject currently states: "_The investigated experimental subject (animal or person)....
Access and using terminologies (e.g., g-node terminologies) are cumbersome at the moment (cf. example in #74). It would be nice to have convenience functions in the terminology class for this,...