#277 fix/clean tests, improve containerization

Author: filippomc

.dockerignore

@@ -2,19 +2,24 @@ org.geppetto.frontend.jupyter
 pygeppetto
 .vscode
 .ipynb_checkpoints
-netpyne_ui/geppetto
+
 *.egg-info
 notebook.ipynb
 .git
-netpyne
+
 Dockerfile
 Dockerfile_base
 Dockerfile_dev
-webapp/node_modules
+node_modules
 webapp/build
 webapp/geppetto-client
 workspace
-tests
+.idea
 k8s
-src
-x86_64
+/src
+x86_64
+app.log
+/.pytest_cache
+.jupyter-config
+**/*.pyc
+**/__pycache__

Dockerfile

@@ -28,4 +28,7 @@ RUN python install.py ${BUILD_ARGS}
 
 WORKDIR ${INSTALLATION_FOLDER}
 
+RUN pip install -r requirements-test.txt
+RUN pip install -e .
+RUN pytest tests/backend
 CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"

netpyne_ui/constants.py

@@ -4,9 +4,16 @@
 NETPYNE_WORKDIR = 'workspace'
 
 ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg", "hoc"]
+HERE = os.path.dirname(os.path.abspath(__file__))
+ROOT = os.path.dirname(HERE)
+UPLOAD_FOLDER_PATH = os.path.join(ROOT, NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME)
+NETPYNE_WORKDIR_PATH = os.path.join(ROOT, NETPYNE_WORKDIR)
 
-UPLOAD_FOLDER_PATH = os.path.join(os.getcwd(), NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME)
-NETPYNE_WORKDIR_PATH = os.path.join(os.getcwd(), NETPYNE_WORKDIR)
+if not os.path.exists(NETPYNE_WORKDIR_PATH):
+    NETPYNE_WORKDIR_PATH = os.path.join(os.getcwd(), NETPYNE_WORKDIR)
+
+if not os.path.exists(NETPYNE_WORKDIR_PATH):
+    raise Exception(f"Workdir path {NETPYNE_WORKDIR_PATH} does not exist")
 
 if not os.path.exists(UPLOAD_FOLDER_PATH):
     os.makedirs(UPLOAD_FOLDER_PATH)

netpyne_ui/netpyne_geppetto.py

@@ -26,9 +26,10 @@
 from netpyne_ui.constants import NETPYNE_WORKDIR_PATH, NUM_CONN_LIMIT
 from netpyne_ui.mod_utils import compileModMechFiles
 
+
 os.chdir(NETPYNE_WORKDIR_PATH)
 
-neuron.nrn_dll_loaded.append("/home/user/NetPyNE-UI/workspace/mod") # Avoids to load workspace modfiles twice
+neuron.nrn_dll_loaded.append(os.path.join(NETPYNE_WORKDIR_PATH, 'mod')) # Avoids to load workspace modfiles twice
 
 class NetPyNEGeppetto: