apdavison/fairgraph

Experimental high-level Python API for the HBP Knowledge Graph

fairgraph's Issues

problem installing with pip

There seems to be a dependency problem when installing with PIP as mentioned in the readme:

$ pip install fairgraph
Collecting fairgraph
  Using cached https://files.pythonhosted.org/packages/8c/41/eb94767ac342fd80cbb1d381accf4cd4cf96b3c918861b53fe24bd7db0a1/fairgraph-0.5.1.tar.gz
ERROR: Packages installed from PyPI cannot depend on packages which are not also hosted on PyPI.
fairgraph depends on openid_http_client@ git+https://github.com/HumanBrainProject/openid_http_client.git#subdirectory=openid_http_client 

I tried with different Python versions (3.6, 3.7, 3.8), but since pip is the v19.3.1 for all of them it seems unlikely to be related.

$ pip --version
pip 19.3.1 from /.../lib/python3.8/site-packages/pip (python 3.8)

Is there a reason why pyxus and openid_http_connect are not available via pip?

Unexpected response when using "by_name"

import fairgraph
from fairgraph import KGClient

token = input("Enter token:")
client = KGClient(token)

biologicalSex = fairgraph.openminds.controlledterms.biological_sex.BiologicalSex.by_name("male", client)
print(biologicalSex)

Gives the following response (female, not male as expected):

BiologicalSex(name='female', definition='Biological sex that produces egg cells (ova).', description='A female organism typically has the capacity to produce relatively large, usually immobile gametes (reproductive cells), called egg cells (or ova). In the process of fertilization, an egg cell (ovum) fuses with a smaller, usually mobile male gametes, called sperm cells (or spermatozoa).', interlex_identifier=IRI(http://uri.interlex.org/base/ilx_0104150), preferred_ontology_identifier=IRI(http://purl.obolibrary.org/obo/PATO_0000383), space=controlled, id=https://kg.ebrains.eu/api/instances/7606df11-c8d9-4ca4-98e3-8167ce6f432b)