Merge pull request #101 from cgiraldo/containers

Support directories and non .ipynb files in jupyter component application

Author: donaldh

api/src/main/resources/plugins/jupyter.py

@@ -25,6 +25,8 @@
 import json
 import os
 import logging
+import shutil
+import stat
 
 import deployer_utils
 from plugins.base_creator import Creator
@@ -67,25 +69,34 @@ def create_component(self, staged_component_path, application_name, user_name, c
         ## Create local git repo for application_user if not exist.
         repo_path = '{}/jupyter-{}'.format(self._config['git_repos_root'], application_user)
         if os.path.isdir(repo_path) == False:
-            os.system('mkdir -p {}'.format(repo_path))
+            os.makedirs(repo_path)
             os.system('git init {}'.format(repo_path))
-            os.system('cp {}/.git/hooks/post-update.sample {}/.git/hooks/post-update'.format(repo_path,repo_path))
-            os.system('chmod a+x {}/.git/hooks/post-update'.format(repo_path))
-            os.system('chmod a+w {} -R'.format(repo_path))
+            shutil.copyfile(repo_path+'/.git/hooks/post-update.sample', repo_path+'/.git/hooks/post-update')
+            os.chmod(repo_path+'/.git/hooks/post-update',0o755)
             this_dir = os.path.dirname(os.path.realpath(__file__))
-            os.system('cp {}/jupyter_README.md {}/README.md'.format(this_dir, repo_path))
-            os.system('cd {0} && git add README.md && git commit -m "Initial commit"'.format(repo_path))
+            shutil.copyfile(this_dir+'/jupyter_README.ipynb',repo_path+'/README.ipynb')
+            os.system('cd {0} && git add README.ipynb && git commit -m "Initial commit"'.format(repo_path))
         ## add notebooks to application_user github repo.
-        notebook_install_path = '{}/{}/'.format(repo_path, application_name)
-        os.system('mkdir -p {}'.format(notebook_install_path))
+        notebook_install_path = '{}/{}'.format(repo_path, application_name)
+        os.makedirs('{}'.format(notebook_install_path))
         file_list = component['component_detail']
         for file_name in file_list:
-            if file_name.endswith(r'.ipynb'):
-                self._fill_properties('%s/%s' % (staged_component_path, file_name), properties)
-
-                logging.debug('Copying {} to {}'.format(file_name, notebook_install_path))
-                os.system('cp {}/{} {}'.format( staged_component_path, file_name, notebook_install_path ))
-        # update local github repo:
+            # We copy all files in package to jupyter folder to let the user work with all kind of files/datasets.
+            #if file_name.endswith(r'.ipynb'):
+            if file_name != 'properties.json':
+                if os.path.isfile('{}/{}'.format(staged_component_path,file_name)):
+                    self._fill_properties('%s/%s' % (staged_component_path, file_name), properties)
+                    logging.debug('Copying {} to {}'.format(file_name, notebook_install_path))
+                    shutil.copyfile('{}/{}'.format(staged_component_path, file_name),
+                          '{}/{}'.format(notebook_install_path, file_name ))
+                else:
+                    logging.debug('creating {}/{} folder'.format(notebook_install_path, file_name))
+                    os.makedirs('{}/{}'.format(notebook_install_path, file_name))
+        # Create a properties.json file in notebooks to access application jupyter component properties.
+        with open('{}/properties.json'.format(notebook_install_path), 'w') as prop_file:
+            prop_dict = { k.replace('component_',''): v for k, v in properties.items() if k.startswith('component_')}
+            json.dump(prop_dict, prop_file)
+            # update local github repo:
 
         os.system('cd {0} && git add {1} && git commit -m "added {1} app notebooks"'.format(repo_path, application_name))
         delete_commands.append('rm -rf {}\n'.format( notebook_install_path))

api/src/main/resources/plugins/jupyter_README.ipynb

@@ -0,0 +1,39 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Notebooks of PNDA Applications\n",
+    "\n",
+    "This folder synchronizes the notebooks of the deployed PNDA Applications when your jupyter server starts. Each PNDA app is checkout in a folder with its name.\n",
+    "\n",
+    "> **WARNING**: WATCH OUT! modfications to notebooks or files in this folders will be removed when your jupyter server restarts.\n",
+    "> If you want to persist your changes, copy the files outside this folder.\n",
+    "\n",
+    "\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}