turbomam
commented
3 years ago I see this error under Python 3.9 on an Apple Silicon MacBook and under 3.8 on an Intel Ubuntu 20 system.
Open turbomam opened 3 years ago
turbomam
commented
3 years ago I see this error under Python 3.9 on an Apple Silicon MacBook and under 3.8 on an Intel Ubuntu 20 system.
turbomam
commented
3 years ago rm -rf gen_diag_with_stage_obs_set.yaml
rm -rf Pipfile.lock
pipenv --rm
Removing virtualenv (/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ)...
pipenv install
Creating a virtualenv for this project...
Pipfile: /Users/mark/gitrepos/example-data/Pipfile
Using /opt/homebrew/bin/python3 (3.9.7) to create virtualenv...
⠹ Creating virtual environment...created virtual environment CPython3.9.7.final.0-64 in 149ms
creator CPython3Posix(dest=/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ, clear=False, no_vcs_ignore=False, global=False)
seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/Users/mark/Library/Application Support/virtualenv)
added seed packages: pip==21.3.1, setuptools==58.3.0, wheel==0.37.0
activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator
✔ Successfully created virtual environment!
Virtualenv location: /Users/mark/.local/share/virtualenvs/example-data-iClEazcJ
Pipfile.lock not found, creating...
Locking [dev-packages] dependencies...
Locking [packages] dependencies...
Building requirements...
Resolving dependencies...
✔ Success!
Updated Pipfile.lock (6421a4)!
Installing dependencies from Pipfile.lock (6421a4)...
🐍 ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 134/134 — 00:05:08
To activate this project's virtualenv, run pipenv shell.
Alternatively, run a command inside the virtualenv with pipenv run.
pipenv run pip list
Package Version
----------------------------- ---------
alabaster 0.7.12
antlr4-python3-runtime 4.9.3
appnope 0.1.2
argon2-cffi 21.1.0
attrs 21.2.0
Babel 2.9.1
backcall 0.2.0
bleach 4.1.0
cachetools 4.2.4
certifi 2021.10.8
cffi 1.15.0
CFGraph 0.2.1
charset-normalizer 2.0.7
click 7.1.2
crdch-model 1.1.5
debugpy 1.5.1
decorator 5.1.0
defusedxml 0.7.1
Deprecated 1.2.13
docutils 0.17.1
entrypoints 0.3
et-xmlfile 1.1.0
frozendict 2.0.7
graphviz 0.18
hbreader 0.9.1
idna 3.3
imagesize 1.3.0
iniconfig 1.1.1
ipykernel 6.5.0
ipython 7.29.0
ipython-genutils 0.2.0
ipywidgets 7.6.5
isodate 0.6.0
jedi 0.18.0
Jinja2 3.0.3
json-flattener 0.1.7
jsonasobj 1.3.1
jsonasobj2 1.0.4
jsonpatch 1.32
jsonpath-ng 1.5.3
jsonpointer 2.2
jsonschema 4.2.1
jupyter 1.0.0
jupyter-client 7.0.6
jupyter-console 6.4.0
jupyter-core 4.9.1
jupyterlab-pygments 0.1.2
jupyterlab-widgets 1.0.2
linkml 1.1.12
linkml-runtime 1.1.6
linkml-runtime-api 0.0.4
lxml 4.6.4
markdown-it-py 1.1.0
MarkupSafe 2.0.1
matplotlib-inline 0.1.3
mdit-py-plugins 0.2.8
mistune 0.8.4
myst-parser 0.15.2
nbclient 0.5.5
nbconvert 6.2.0
nbformat 5.1.3
nest-asyncio 1.5.1
notebook 6.4.5
numpy 1.21.4
openpyxl 3.0.9
packaging 21.2
pandas 1.3.4
pandocfilters 1.5.0
parse 1.19.0
parso 0.8.2
pexpect 4.8.0
pickleshare 0.7.5
pip 21.3.1
pluggy 1.0.0
ply 3.11
prefixcommons 0.1.9
prologterms 0.0.6
prometheus-client 0.12.0
prompt-toolkit 3.0.22
ptyprocess 0.7.0
py 1.11.0
pycparser 2.21
pydantic 1.8.2
Pygments 2.10.0
PyJSG 0.11.6
PyLD 2.0.3
PyLDmod 2.0.5
pyparsing 2.4.7
pyrsistent 0.18.0
PyShEx 0.7.20
PyShExC 0.8.3
pytest 6.2.5
python-dateutil 2.8.2
pytz 2021.3
PyYAML 5.4.1
pyzmq 22.3.0
qtconsole 5.2.0
QtPy 1.11.2
rdflib 5.0.0
rdflib-jsonld 0.6.1
rdflib-pyldmod-compat 0.1.2
requests 2.26.0
ruamel.yaml 0.17.17
ruamel.yaml.clib 0.2.6
Send2Trash 1.8.0
setuptools 58.5.3
ShExJSG 0.7.1
six 1.16.0
snowballstemmer 2.1.0
sparqlslurper 0.4.1
SPARQLWrapper 1.8.5
Sphinx 4.3.0
sphinx-click 3.0.2
sphinx-rtd-theme 1.0.0
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy 1.4.26
terminado 0.12.1
testfixtures 6.18.3
testpath 0.5.0
toml 0.10.2
tornado 6.1
traitlets 5.1.1
typing-extensions 3.10.0.2
urllib3 1.26.7
watchdog 2.1.6
wcwidth 0.2.5
webencodings 0.5.1
wheel 0.37.0
widgetsnbextension 3.5.2
wrapt 1.13.3
pipenv run python gen_diag_with_stage_obs_set.py
cat gen_diag_with_stage_obs_set.yaml
stage:
- method_type:
- coding:
- code: C125738
system: http://ncithesaurus.nci.nih.gov/
label: FIGO Stage
tag:
- harmonized
observations:
- observation_type:
coding:
- code: C25605
system: http://ncithesaurus.nci.nih.gov/
label: Overall
tag:
- harmonized
value_codeable_concept:
coding:
- code: C96258
system: http://ncithesaurus.nci.nih.gov/
label: FIGO Stage IIIC
tag:
- harmonized
pipenv run python instantiate_diag_with_stage_obs_set.py
Traceback (most recent call last):
File "/Users/mark/gitrepos/example-data/instantiate_diag_with_stage_obs_set.py", line 6, in <module>
diag = yaml_loader.load(diagnosis_fn, Diagnosis)
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/linkml_runtime/loaders/yaml_loader.py", line 22, in load
return self.load_source(source, loader, target_class, accept_header="text/yaml, application/yaml;q=0.9",
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/linkml_runtime/loaders/loader_root.py", line 62, in load_source
target_class(**as_dict(data_as_dict)) if data_as_dict is not None else None
File "<string>", line 20, in __init__
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/crdch_model.py", line 579, in __post_init__
self.stage = [v if isinstance(v, CancerStageObservationSet) else CancerStageObservationSet(**as_dict(v)) for v in self.stage]
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/crdch_model.py", line 579, in <listcomp>
self.stage = [v if isinstance(v, CancerStageObservationSet) else CancerStageObservationSet(**as_dict(v)) for v in self.stage]
File "<string>", line 10, in __init__
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/crdch_model.py", line 443, in __post_init__
self._normalize_inlined_as_list(slot_name="observations", slot_type=CancerStageObservation, key_name="observation_type", keyed=False)
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/linkml_runtime/utils/yamlutils.py", line 97, in _normalize_inlined_as_list
self._normalize_inlined(slot_name, slot_type, key_name, keyed, True)
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/linkml_runtime/utils/yamlutils.py", line 181, in _normalize_inlined
order_up(cooked_obj[key_name], cooked_obj)
File "/Users/mark/.local/share/virtualenvs/example-data-iClEazcJ/lib/python3.9/site-packages/linkml_runtime/utils/yamlutils.py", line 132, in order_up
cooked_keys.add(key)
TypeError: unhashable type: 'CodeableConcept'
make: *** [instantiate] Error 1
I don't know if this is a LinkML error or something specific to the CRDC-H model, so I will cross post an issue in linkml/linkml
Run
make allfrom this branchissue-27-codable-concept-notebooksin the example-data repomake allclears and recreates the somewhat top-heavy piping virtual environment used elsewhere in this repo, so that could take a few minutes.See gen_diag_with_stage_obs_set.py for the code that creates the problematic YAML data file.