Merge branch '23-imaging_tests' into 'master'

Resolve "Add tests for imaging"

Closes #23

See merge request !8

.gitlab-ci.yml

 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
 
-user_configuration:
+unit_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

 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

+#!/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