Added .bamboo folder

updated test_downloadable to properly check if regimen already tracked

.bamboo/run_tests.sh

@@ -0,0 +1,12 @@
+export PATH=${bamboo_build_working_directory}/miniconda/bin:$PATH
+export HOME=${bamboo_build_working_directory}/.home
+export TMPDIR=${bamboo_build_working_directory}
+export CONDA_PATH_BACKUP=${CONDA_PATH_BACKUP:-$PATH}
+export CONDA_PREFIX=${CONDA_PREFIX:-}
+export CONDA_PS1_BACKUP=${CONDA_PS1_BACKUP:-}
+
+source activate ${bamboo_build_working_directory}/.conda/conda_test_env
+cd ${bamboo_build_working_directory}
+coverage run --source ./ -m pytest --junitxml=test-reports/tests.xml --html=test-reports/report.html --self-contained-html
+coverage html --omit="tests/*,setup.py" --directory=htmlcov
+source deactivate

.bamboo/setup_env.sh

@@ -0,0 +1,16 @@
+set -eu
+
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+bash miniconda.sh -b -p ${bamboo_build_working_directory}/miniconda
+export PATH=${bamboo_build_working_directory}/miniconda/bin:$PATH
+export HOME=${bamboo_build_working_directory}/.home
+export TMPDIR=${bamboo_build_working_directory}
+export CONDA_PATH_BACKUP=${CONDA_PATH_BACKUP:-$PATH}
+export CONDA_PREFIX=${CONDA_PREFIX:-}
+export CONDA_PS1_BACKUP=${CONDA_PS1_BACKUP:-}
+conda create -y -v --prefix ${bamboo_build_working_directory}/.conda/conda_test_env python=3.6
+source activate ${bamboo_build_working_directory}/.conda/conda_test_env
+cd ${bamboo_build_working_directory}
+pip install -r requirements.txt
+pip install -r requirements_dev.txt
+source deactivate

requirements.txt

@@ -0,0 +1,2 @@
+pyyaml
+requests

requirements_dev.txt

@@ -0,0 +1,7 @@
+pytest
+bumpversion
+flake8
+pytest-cov
+pytest-html
+coverage
+pandas

tests/utils.py → tests/conftest.py

@@ -1,7 +1,9 @@
+import pytest
 import os
 import yaml
 
-def load_regimen():
+@pytest.fixture
+def regimen_dict():
     regimen_path = os.path.join(
         os.path.dirname(__file__),
         '..',

tests/test_downloadable.py

@@ -3,13 +3,47 @@
 import hashlib
 import warnings
 import requests
-from .utils import load_regimen
+import sys
+import itertools
+import pandas as pd
 
-regimen_data = load_regimen()
+'''
+Copy-pasted get_page and get_df; This is code duplication, but I dont want this to be an installed package, and both tests and scripts need this code
+'''
 
-def test_script_files_download():
+def get_page(table_name, api_base='http://prodmtrain1:5000', get_obj=None, **kwargs):
 
-    for stage_name, stage_dict in regimen_data['stages'].items():
+    if get_obj is None:
+        get_obj = requests
+
+    data = {'total_pages':'--'}
+    for ii in itertools.count(1):
+        print('Downloading page: %s/%s ' % (ii , data['total_pages']), end='')
+        sys.stdout.flush()
+
+        tmp = get_obj.get(os.path.join(api_base, "api/v1/%s?page=%i" % (table_name, ii)), **kwargs)
+        try:
+            data = tmp.json()
+        except TypeError:
+            data = tmp.json
+        print('... ', end='')
+        if 'message' not in data:
+            df = pd.DataFrame(data["objects"])
+            print('done')
+            sys.stdout.flush()
+            yield df
+
+        if 'total_pages' not in data or data['total_pages'] == ii:
+            print('done')
+            return
+
+def get_df(table_name, api_base='http://prodmtrain1:5000', get_obj=None, **kwargs):
+    return pd.concat([df for df in get_page(table_name, api_base=api_base, get_obj=get_obj, **kwargs)], axis=0)
+
+
+def test_script_files_download(regimen_dict):
+
+    for stage_name, stage_dict in regimen_dict['stages'].items():
         if stage_dict['script'] == 'NotImplemented':
             warnings.warn('Stage "%s" Not Implemented' % stage_name)
         else:
@@ -25,12 +59,9 @@ def test_script_files_download():
                 downloaded_md5 = hashlib.md5(result.content).hexdigest()
                 assert downloaded_md5 == stage_dict['script_md5'], "{}:{}".format(stage_name,downloaded_md5)
 
-def test_add_already_tracked_regimen():
+def test_add_already_tracked_regimen(regimen_dict):
 
-    api_endpoint = 'http://prodmtrain1:5000/api/v1/regimens'
-    result = requests.get(api_endpoint)
-    assert result.status_code == 200
-    data = result.json()
-    assert data['total_pages'] >= 1
-    if regimen_data['name'] in [x['name'] for x in data['objects']]:
-        warnings.warn('Regimen name %s already tracked on server %s' % (regimen_data['name'], api_endpoint))
+    api_base = 'http://prodmtrain1:5000'
+    regimen_list = get_df('regimens', api_base=api_base)['name'].values
+    if regimen_dict['name'] in regimen_list:
+        raise Exception('Regimen name %s already tracked on server %s' % (regimen_dict['name'], api_base))

tests/test_stage_name_in_params.py

@@ -1,8 +1,16 @@
-from .utils import load_regimen
 
-regimen_data = load_regimen()
-
-def test_stage_name_in_params():
-    for stage_name, stage_dict in regimen_data['stages'].items():
+def test_stage_name_in_params(regimen_dict):
+    for stage_name, stage_dict in regimen_dict['stages'].items():
         stage_param = stage_dict['parameters']['stage']
         assert stage_param==stage_name, "stage: {}, param: {}".format(stage_name,stage_param)
+
+def test_transitions_stages_match(regimen_dict):
+
+    # Double-check regimen stages and transitions match:
+    transition_source_target_set = set()
+    for t in regimen_dict['transitions']:
+        transition_source_target_set.add(t['source'])
+        transition_source_target_set.add(t['dest'])
+    stage_set = set(regimen_dict['stages'].keys())
+    if not all([curr_stage in stage_set for curr_stage in transition_source_target_set]):
+        raise Exception('Stages and source/dest of transitions are not consistent')