Merge branch 'feature/changes-v6' into develop

.github/workflows/pytest.yml

@@ -1,9 +1,8 @@
 name: Python Test
 
-on: 
+on:
   push:
     branches:
-      - master  
       - develop
   pull_request:
     branches:

.github/workflows/tox.yml

@@ -0,0 +1,30 @@
+name: Python Test
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.7]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install tox
+    - name: Test with tox
+      run: |
+        tox

README.md

@@ -1,6 +1,6 @@
 # pyomop
 
-OMOP CDM utils. This repo may be similar to [@jbadger3's](https://github.com/jbadger3) [inspectomop](https://github.com/jbadger3/inspectomop), but this is not a fork. 
+OMOP CDM utils. This repo may be similar to [@jbadger3's](https://github.com/jbadger3) [inspectomop](https://github.com/jbadger3/inspectomop), but this is not a fork.
 
 ## Description
 
@@ -29,6 +29,12 @@ import datetime
 
 cdm = CdmEngineFactory()  # Creates SQLite database by default
 
+# Postgres example (db='mysql' also supported)
+# cdm = CdmEngineFactory(db='pgsql', host='', port=5432,
+#                       user='', pw='',
+#                       name='', schema='cdm6')
+
+
 engine = cdm.engine
 # Create Tables if required
 metadata.create_all(engine)
@@ -38,8 +44,8 @@ vocab = CdmVocabulary(cdm)
 
 # SQLAlchemy as ORM
 session =  cdm.session
-session.add(Cohort(cohort_definition_id=2, subject_id=100, 
-            cohort_end_date=datetime.datetime.now(), 
+session.add(Cohort(cohort_definition_id=2, subject_id=100,
+            cohort_end_date=datetime.datetime.now(),
             cohort_start_date=datetime.datetime.now()))
 session.commit()
 

src/pyomop/cdm6_tables.py

@@ -1,18 +1,18 @@
 """
  Copyright (C) 2020 Bell Eapen
- 
+
  This file is part of PyOMOP.
- 
+
  PyOMOP is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.
- 
+
  PyOMOP is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
- 
+
  You should have received a copy of the GNU General Public License
  along with PyOMOP.  If not, see <http://www.gnu.org/licenses/>.
 """
@@ -454,7 +454,9 @@ class Person(Base):
     year_of_birth = Column(Integer, nullable=False)
     month_of_birth = Column(Integer)
     day_of_birth = Column(Integer)
-    time_of_birth = Column(String(10))
+    #time_of_birth = Column(String(10))
+    birth_datetime = Column(String(10))
+    death_datetime = Column(String(10))
     race_concept_id = Column(Integer, nullable=False)
     ethnicity_concept_id = Column(Integer, nullable=False)
     location_id = Column(Integer)

tox.ini

@@ -4,14 +4,19 @@
 
 [tox]
 minversion = 2.4
-envlist = default
+envlist = py37, integration
 
 [testenv]
 setenv = TOXINIDIR = {toxinidir}
-passenv =
-    HOME
+deps =
+    pytest
 commands =
     py.test {posargs}
 extras =
     all
     testing
+
+[testenv:integration]
+setenv = TOXINIDIR = {toxinidir}
+commands =
+    python t_install.py