Merge branch 'debug' into main

r-notebook/README.md

@@ -4,4 +4,4 @@ Custom notebook based on RHODS standard data science notebook, adding:
 
 * R
 * R Kernel
-* Elyra plugins
+* R Studio

r-notebook/container/Dockerfile

@@ -34,25 +34,25 @@ RUN wget https://download2.rstudio.org/server/rhel8/x86_64/rstudio-server-rhel-2
 # Specific RStudio config and fixes
 RUN chmod 1777 /var/run/rstudio-server && \
     mkdir -p /usr/share/doc/R
-
 COPY rsession.conf /etc/rstudio/rsession.conf
 
-# Copying custom packages
+# Copying additional packages
 COPY requirements.txt /tmp/
+COPY ./jupyter-rsession-proxy /tmp/jupyter-rsession-proxy
 
-# Install custom packages
-RUN micropipenv install --deploy 
-RUN pip install --no-cache-dir --use-deprecated legacy-resolver elyra[all]==3.6.0 && \
+# Install additional packages
+RUN micropipenv install --deploy && \
+    pip install --no-cache-dir /tmp/jupyter-rsession-proxy && \
     jupyter labextension install @techrah/text-shortcuts && \
     jupyter labextension install @jupyterlab/server-proxy && \
     jupyter lab build && \
     jupyter lab clean && \
     npm cache clean --force && \
-    rm -rf $HOME/.cache/yarn && \
-    rm -rf $HOME/.node-gyp && \
+    rm -rf /usr/local/share/.cache/yarn && \
     fix-permissions /opt/app-root
 
 WORKDIR /opt/app-root/src
+
 USER 1001
 
 CMD /opt/app-root/bin/start-singleuser.sh --ip=0.0.0.0 --port=8080

r-notebook/container/jupyter-rsession-proxy/jupyter_rsession_proxy/__init__.py

@@ -0,0 +1,155 @@
+import getpass
+import os
+import pathlib
+import shutil
+import subprocess
+import tempfile
+from textwrap import dedent
+from urllib.parse import urlparse, urlunparse
+
+
+def get_rstudio_executable(prog):
+    # Find prog in known locations
+    other_paths = [
+        # When rstudio-server deb is installed
+        os.path.join('/usr/lib/rstudio-server/bin', prog),
+        # When just rstudio deb is installed
+        os.path.join('/usr/lib/rstudio/bin', prog),
+    ]
+    if shutil.which(prog):
+        return prog
+
+    for op in other_paths:
+        if os.path.exists(op):
+            return op
+
+    raise FileNotFoundError(f'Could not find {prog} in PATH')
+
+def get_icon_path():
+    return os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), 'icons', 'rstudio.svg'
+    )
+
+def rewrite_auth(response, request):
+    '''
+       As of rstudio-server 1.4ish, it would send the client to /auth-sign-in
+       rather than what the client sees as the full URL followed by
+       /auth-sign-in. See rstudio/rstudio#8888. We rewrite the response by
+       sending the client to the right place.
+    '''
+    correct_root_url = request.host
+    for header, v in response.headers.get_all():
+        if header == "Location" and correct_root_url not in v:
+            # Visit the correct page
+            u = urlparse(v)
+            response.headers[header] = urlunparse(u._replace(netloc=correct_root_url))
+
+def setup_rserver():
+    def _get_env(port):
+        return dict(USER=getpass.getuser())
+
+    def db_config(db_dir):
+        '''
+        Create a temporary directory to hold rserver's database, and create
+        the configuration file rserver uses to find the database.
+
+        https://docs.rstudio.com/ide/server-pro/latest/database.html
+        https://github.com/rstudio/rstudio/tree/v1.4.1103/src/cpp/server/db
+        '''
+        # create the rserver database config
+        db_conf = dedent("""
+            provider=sqlite
+            directory={directory}
+        """).format(directory=db_dir)
+        f = tempfile.NamedTemporaryFile(mode='w', delete=False, dir=db_dir)
+        db_config_name = f.name
+        f.write(db_conf)
+        f.close()
+        return db_config_name
+
+    def _support_arg(arg):
+        ret = subprocess.check_output([get_rstudio_executable('rserver'), '--help'])
+        return ret.decode().find(arg) != -1
+
+    def _get_cmd(port):
+        ntf = tempfile.NamedTemporaryFile()
+
+        # use mkdtemp() so the directory and its contents don't vanish when
+        # we're out of scope
+        server_data_dir = tempfile.mkdtemp()
+        database_config_file = db_config(server_data_dir)
+
+        cmd = [
+            get_rstudio_executable('rserver'),
+            '--auth-none=1',
+            '--www-frame-origin=same',
+            '--www-port=' + str(port),
+            '--www-verify-user-agent=0',
+            '--secure-cookie-key-file=' + ntf.name,
+            '--server-user=' + getpass.getuser(),
+        ]
+        # Support at least v1.2.1335 and up
+
+        if _support_arg('www-root-path'):
+            cmd.append('--www-root-path={base_url}rstudio/')
+        if _support_arg('server-data-dir'):
+            cmd.append(f'--server-data-dir={server_data_dir}')
+        if _support_arg('database-config-file'):
+            cmd.append(f'--database-config-file={database_config_file}')
+
+        print("cmd=")
+        print(*cmd, sep = ", ")
+
+        return cmd
+
+    server_process = {
+        'command': _get_cmd,
+        'environment': _get_env,
+        'rewrite_response': rewrite_auth,
+        'launcher_entry': {
+            'title': 'RStudio',
+            'icon_path': get_icon_path()
+        },
+        'absolute_url': False
+    }
+    return server_process
+
+def setup_rsession():
+    def _get_env(port):
+        # Detect various environment variables rsession requires to run
+        # Via rstudio's src/cpp/core/r_util/REnvironmentPosix.cpp
+        cmd = ['R', '--slave', '--vanilla', '-e',
+                'cat(paste(R.home("home"),R.home("share"),R.home("include"),R.home("doc"),getRversion(),sep=":"))']
+
+        r_output = subprocess.check_output(cmd)
+        R_HOME, R_SHARE_DIR, R_INCLUDE_DIR, R_DOC_DIR, version = \
+            r_output.decode().split(':')
+
+        return {
+            'R_DOC_DIR': R_DOC_DIR,
+            'R_HOME': R_HOME,
+            'R_INCLUDE_DIR': R_INCLUDE_DIR,
+            'R_SHARE_DIR': R_SHARE_DIR,
+            'RSTUDIO_DEFAULT_R_VERSION_HOME': R_HOME,
+            'RSTUDIO_DEFAULT_R_VERSION': version,
+        }
+
+    def _get_cmd(port):
+        return [
+            get_rstudio_executable('rsession'),
+            '--standalone=1',
+            '--program-mode=server',
+            '--log-stderr=1',
+            '--session-timeout-minutes=0',
+            '--user-identity=' + getpass.getuser(),
+            '--www-port=' + str(port)
+        ]
+
+    return {
+        'command': _get_cmd,
+        'environment': _get_env,
+        'launcher_entry': {
+            'title': 'RStudio',
+            'icon_path': get_icon_path()
+        }
+    }

r-notebook/container/jupyter-rsession-proxy/setup.cfg

@@ -0,0 +1 @@
+[metadata]

r-notebook/container/jupyter-rsession-proxy/setup.py

@@ -0,0 +1,23 @@
+import setuptools
+
+setuptools.setup(
+    name="jupyter-rsession-proxy",
+    version='2.0.1',
+    url="https://github.com/jupyterhub/jupyter-rsession-proxy",
+    author="Ryan Lovett & Yuvi Panda",
+    description="Jupyter extension to proxy RStudio",
+    packages=setuptools.find_packages(),
+	keywords=['Jupyter'],
+	classifiers=['Framework :: Jupyter'],
+    install_requires=[
+        'jupyter-server-proxy>=3.2.0'
+    ],
+    entry_points={
+        'jupyter_serverproxy_servers': [
+            'rstudio = jupyter_rsession_proxy:setup_rserver'
+        ]
+    },
+    package_data={
+        'jupyter_rsession_proxy': ['icons/rstudio.svg'],
+    },
+)

r-notebook/container/requirements.in

@@ -2,6 +2,7 @@
 #
 # Default dependencies
 #
+## Forced to update packages due to JL issue with RStudio
 ipython<8.0.0
 notebook==6.4.6
 jupyterhub==1.3.0
@@ -13,4 +14,3 @@ supervisor==4.1.0
 jupyterlab-git==0.30
 jupyterlab-spellchecker==0.7.2
 jupyter-server-proxy==3.2.1
-jupyter-rsession-proxy==2.0.1