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BICF
KCE
kce_etl
Commits
6bc28655
Commit
6bc28655
authored
Dec 12, 2019
by
Venkat Malladi
Browse files
Merge branch '23-imaging_tests' into 'master'
Resolve "Add tests for imaging" Closes
#23
See merge request
!8
parents
d99b54f6
d5c343d7
Pipeline
#5275
failed with stage
in 1 second
Changes
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.gitlab-ci.yml
View file @
6bc28655
before_script
:
-
module add python/2.7.14-anaconda
-
env
-
module load python/3.7.x-anaconda
-
conda env create --file environment.yml
stages
:
-
unit
u
ser_configuration
:
u
nit_tests
:
stage
:
unit
script
:
-
source activate kce_etl
-
pytest -m unit
-
conda activate kce_etl
-
pytest -m unit --cov=./scripts
after_script
:
-
conda deactivate
-
conda env remove --name kce_etl -y
environment.yml
View file @
6bc28655
name
:
kce_etl
channels
:
-
conda-forge
-
bioconda
-
defaults
dependencies
:
-
conda-forge::pandas=0.24.2
pip
:
-
pytest-pythonpath==0.7.1
-
pytest-cov==2.5.1
-
_libgcc_mutex=0.1=main
-
ca-certificates=2019.11.28=hecc5488_0
-
certifi=2019.11.28=py38_0
-
ld_impl_linux-64=2.33.1=h53a641e_7
-
libblas=3.8.0=14_openblas
-
libcblas=3.8.0=14_openblas
-
libffi=3.2.1=he1b5a44_1006
-
libgcc-ng=9.2.0=hdf63c60_0
-
libgfortran-ng=7.3.0=hdf63c60_2
-
liblapack=3.8.0=14_openblas
-
libopenblas=0.3.7=h5ec1e0e_5
-
libstdcxx-ng=9.2.0=hdf63c60_0
-
ncurses=6.1=hf484d3e_1002
-
numpy=1.17.3=py38h95a1406_0
-
openssl=1.1.1d=h516909a_0
-
pandas=0.24.2=py38hb3f55d8_1
-
pip=19.3.1=py38_0
-
python=3.8.0=h357f687_5
-
python-dateutil=2.8.1=py_0
-
pytz=2019.3=py_0
-
readline=8.0=hf8c457e_0
-
setuptools=42.0.2=py38_0
-
six=1.13.0=py38_0
-
sqlite=3.30.1=hcee41ef_0
-
tk=8.6.10=hed695b0_0
-
wheel=0.33.6=py38_0
-
xz=5.2.4=h14c3975_1001
-
zlib=1.2.11=h516909a_1006
-
pip
:
-
attrs==19.3.0
-
coverage==4.5.4
-
more-itertools==8.0.2
-
packaging==19.2
-
pluggy==0.13.1
-
py==1.8.0
-
pyparsing==2.4.5
-
pytest==5.3.1
-
pytest-cov==2.5.1
-
pytest-pythonpath==0.7.1
-
wcwidth==0.1.7
tests/test_transform_imaging.py
0 → 100644
View file @
6bc28655
#!/usr/bin/env python3
import
pytest
import
os
import
pandas
as
pd
from
StringIO
import
StringIO
import
transform_imaging
IMAGE_STRING
=
"""MRN,CPT,TYPE,C_NAME,START_DATE,OBSERVATION_BLOB
45,CPT:74160,CT,"(CPT:74160)Computed tomography, abdomen; with contrast material(s)",9/20/17 0:00,"AVM_VISIT_NUMBER:13348936;ICD9CODE:789.5; IDX PROCEDURE_NAME:CT, ABD, W/CONTRAST"
"""
@
pytest
.
fixture
def
image
():
image_file
=
StringIO
(
IMAGE_STRING
)
image_df
=
pd
.
read_csv
(
image_file
)
return
image_df
@
pytest
.
mark
.
unit
def
test_check_reformmat
(
image
):
transform_immage
=
transform_imaging
.
reformat_record
(
image
)
assert
transform_immage
.
shape
[
1
]
==
4
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