Added ability to use FastHPOCR instead of exact string matching. Refa… #116
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…ctored HPOConceptRecognizer inheritance. Added data and tests.
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For some reason, this is crashing on my end -- it is not finding the module:
ImportError while importing test module '/Users/robin/GIT/pyphetools/test/test_vital_status.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
test/test_vital_status.py:2: in
from pyphetools.creation import AgeOfDeathColumnMapper, Individual, MetaData
src/pyphetools/init.py:2: in
from . import creation
src/pyphetools/creation/init.py:10: in
from .create_template import TemplateCreator
src/pyphetools/creation/create_template.py:4: in
from .hpo_parser import HpoParser
src/pyphetools/creation/hpo_parser.py:8: in
from .hpo_fasthpocr_cr import HpoFastHPOCRConceptRecognizer
src/pyphetools/creation/hpo_fasthpocr_cr.py:3: in
from FastHPOCR.HPOAnnotator import HPOAnnotator
E ModuleNotFoundError: No module named 'FastHPOCR'
________________ ERROR collecting test/test_vital_status.py _________________
ImportError while importing test module '/Users/robin/GIT/pyphetools/test/test_vital_status.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
test/test_vital_status.py:2: in
from pyphetools.creation import AgeOfDeathColumnMapper, Individual, MetaData
src/pyphetools/init.py:2: in
from . import creation
src/pyphetools/creation/init.py:10: in
from .create_template import TemplateCreator
src/pyphetools/creation/create_template.py:4: in
from .hpo_parser import HpoParser
src/pyphetools/creation/hpo_parser.py:8: in
from .hpo_fasthpocr_cr import HpoFastHPOCRConceptRecognizer
src/pyphetools/creation/hpo_fasthpocr_cr.py:3: in
from FastHPOCR.HPOAnnotator import HPOAnnotator
E ModuleNotFoundError: No module named 'FastHPOCR'
========================== short test summary info ==========================
ERROR src/pyphetools/init.py
ERROR src/pyphetools/creation/init.py
ERROR src/pyphetools/creation/create_template.py
ERROR src/pyphetools/creation/disease_id_column_mapper.py
ERROR src/pyphetools/creation/hpo_fasthpocr_cr.py
ERROR src/pyphetools/creation/hpo_parser.py
ERROR src/pyphetools/creation/import_template.py
ERROR src/pyphetools/creation/option_column_mapper.py
ERROR src/pyphetools/creation/scm_generator.py
ERROR src/pyphetools/creation/structural_variant.py
ERROR src/pyphetools/creation/thresholded_column_mapper.py
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Did you install the module? |
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sorry it was very early in the morning, all is ok. Part of the CI is not building but that is not related to this PR so I will merge |
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Thank you. |
…ctored HPOConceptRecognizer inheritance. Added data and tests.