Fix casper

Author: rodriguez-facundo

.dockerignore

@@ -6,4 +6,8 @@ netpyne_ui/geppetto
 *.egg-info
 notebook.ipynb
 .git
-netpyne
+netpyne
+Dockerfile
+Dockerfile_base
+Dockerfile_dev
+netpyne_workspace

Dockerfile_dev

@@ -1,4 +1,5 @@
-FROM metacell/jupyter-neuron:latest
+# FROM metacell/jupyter-neuron:latest
+FROM frodriguez4600/jupyter-neuron:latest
 USER $NB_USER
 
 ARG netpyneuiBranch=development 
@@ -11,13 +12,12 @@ WORKDIR /home/jovyan/work
 COPY --chown=1000:1000 . NetPyNE-UI
 WORKDIR ${FOLDER}/utilities
 
-RUN /bin/bash -c "source activate snakes && python --version"
-RUN /bin/bash -c "source activate snakes && exec python install.py branch $netpyneuiBranch"
+RUN python install.py branch $netpyneuiBranch
 
-WORKDIR /home/jovyan
+WORKDIR /home/jovyan/work/NetPyNE-UI
 
-RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
-WORKDIR /home/jovyan/netpyne_workspace
+RUN git clone https://github.com/Neurosim-lab/netpyne_workspace && rm -rf netpyne_workspace/.git
+WORKDIR /home/jovyan/work/NetPyNE-UI/netpyne_workspace
 
-RUN ln -sfn /home/jovyan/work/NetPyNE-UI/netpyne_ui/tests tests
-CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"
+RUN ln -sfn /home/jovyan/work/NetPyNE-UI/netpyne_ui/tests ../tests
+CMD /bin/bash -c "cd .. && NetPyNE-UI"

netpyne_ui/api.py

@@ -8,14 +8,7 @@
 from tempfile import TemporaryDirectory
 from jupyter_geppetto.webapi import get, post
 from notebook.base.handlers import IPythonHandler
-
-ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg"]
-
-UPLOAD_FOLDER_NAME = "uploads"
-UPLOAD_FOLDER_PATH = os.path.join(os.getcwd(), UPLOAD_FOLDER_NAME)
-
-if not os.path.exists(UPLOAD_FOLDER_PATH):
-    os.makedirs(UPLOAD_FOLDER_PATH)
+from netpyne_ui.constants import NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME, ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH
 
 def allowed_file(filename, allowed_extensions=ALLOWED_EXTENSIONS):
     return '.' in filename and \

netpyne_ui/constants.py

@@ -0,0 +1,15 @@
+import os
+
+UPLOAD_FOLDER_NAME = 'uploads'
+NETPYNE_WORKDIR = 'netpyne_workspace'
+
+ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg"]
+
+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(UPLOAD_FOLDER_PATH):
+    os.makedirs(UPLOAD_FOLDER_PATH)
+
+if not os.path.exists(NETPYNE_WORKDIR_PATH):
+    os.makedirs(NETPYNE_WORKDIR_PATH)

netpyne_ui/netpyne_geppetto.py

@@ -30,8 +30,9 @@
 from jupyter_geppetto import jupyter_geppetto, synchronization, utils
 import imp
 from contextlib import redirect_stdout, redirect_stderr
+from netpyne_ui.constants import NETPYNE_WORKDIR_PATH
 
-
+os.chdir(NETPYNE_WORKDIR_PATH)
 class NetPyNEGeppetto():
 
     def __init__(self):
@@ -372,7 +373,7 @@ def getPlotSettings(self, plot):
     def getDirList(self, dir=None, onlyDirs = False, filterFiles=False):
         # Get Current dir
         if dir == None or dir == '':
-            dir = os.getcwd()
+            dir = os.path.join(os.getcwd(), NETPYNE_WORKDIR_PATH)
         dir_list = []
         file_list = []
         for f in sorted(os.listdir(str(dir)), key=str.lower):

utilities/install.py

@@ -36,6 +36,13 @@ def checkout(folder, default_branch, cwdp):
         subprocess.call(['git', 'checkout', default_branch], cwd='./')
     os.chdir(currentPath)
 
+def clone_repo(project, repo_name, **kwargs):
+    normal = "\033[0;37;40m"
+    stroke = "\033[1;32;40m\n"
+    subprocess.run(["echo", f'{stroke}Cloning {repo_name} from {project}{stroke}'])
+    url = f'https://github.com/{project}/{repo_name}.git'
+    clone(url, **kwargs)
+
 def main(argv):
     global branch
     if(len(argv) > 0):
@@ -47,22 +54,54 @@ def main(argv):
 
 os.chdir(os.getcwd()+"/../")
 
-
-clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','ui')
-subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')
+# Fix terminado installation error
+terminado_path = '/opt/conda/lib/python3.7/site-packages/'
+subprocess.call(['rm', '-rf', terminado_path+'terminado', terminado_path+'terminado-0.8.3.dist-info', terminado_path+'terminado-0.8.3-py3.7.egg-info'])
 
 
+clone_repo(project='Neurosim-lab',
+           repo_name='netpyne',
+           folder='netpyne',
+           default_branch='ui'
+)
+subprocess.call(['python3', '-m', 'pip', 'install', '-e', '.'], cwd='./netpyne/')
 
 # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip
 # subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./')
-clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','v0.4.2-alpha','netpyne_ui/', False, 'geppetto')
-clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','development','netpyne_ui/geppetto/src/main/webapp/extensions/')
+clone_repo(project='openworm',
+           repo_name='org.geppetto.frontend',
+           folder='geppetto',
+           default_branch='v0.4.2-alpha',
+           cwdp='netpyne_ui/',
+           recursive=False,
+           destination_folder='geppetto'
+)
+
+clone_repo(project='MetaCell',
+           repo_name='geppetto-netpyne',
+           folder='geppetto-netpyne',
+           default_branch='development',
+           cwdp='netpyne_ui/geppetto/src/main/webapp/extensions/'
+)
 
 branch = None
 # Cloning Repos
-clone('https://github.com/openworm/pygeppetto.git','pygeppetto','development')
-subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/')
-clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','development')
+
+clone_repo(project='openworm',
+           repo_name='pygeppetto',
+           folder='pygeppetto',
+           default_branch='development'
+)
+subprocess.call(['python3', '-m', 'pip', 'install', '-e', '.'], cwd='./pygeppetto/')
+
+
+clone_repo(project='openworm',
+           repo_name='org.geppetto.frontend.jupyter',
+           folder='org.geppetto.frontend.jupyter',
+           default_branch='development'
+)
+
+
 with open('npm_frontend_jupyter_log', 'a') as stdout:
     subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js', stdout=stdout)
 subprocess.call(['npm', 'run', 'build-dev'], cwd='./org.geppetto.frontend.jupyter/js')
@@ -78,12 +117,12 @@ def main(argv):
 subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='./netpyne_ui/geppetto/src/main/webapp/')
 
 print("Installing jupyter_geppetto python package ...")
-subprocess.call(['pip', 'install', '-e', '.'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['python3', '-m', 'pip', 'install', '-e', '.'], cwd='./org.geppetto.frontend.jupyter')
 print("Installing jupyter_geppetto Jupyter Extension ...")
 subprocess.call(['jupyter', 'nbextension', 'install', '--py', '--symlink', '--sys-prefix', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
 subprocess.call(['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
 subprocess.call(['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'widgetsnbextension'], cwd='./org.geppetto.frontend.jupyter')
 subprocess.call(['jupyter', 'serverextension', 'enable', '--sys-prefix', '--py', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
 
 print("Installing NetPyNE UI python package ...")
-subprocess.call(['pip', 'install', '-e', '.'], cwd='.')
+subprocess.call(['python3', '-m', 'pip', 'install', '-e', '.'], cwd='.')