#273: Added jupyterenv/bin to environment variable PATH inside the Entrypoint

doc/changes/changes_2.1.0.md

@@ -18,6 +18,7 @@ Version: 2.1.0
 * #279: Made the notebooks tests running in SaaS as well as in the Docker-DB.
 * #19: Added SLC notebook
 * #301: Added CloudFront distribution for example data S3 bucket
+* #273: Added `jupyterenv/bin` to environment variable `PATH` inside the DockerContainer
 
 ## Security
 
@@ -41,4 +42,4 @@ Version: 2.1.0
 * #193: Ignored warnings in notebook tests
 * #297: Reduced log level for transitive libraries in notebook tests
 * #307: Made the notebook tests running in parallel;
-        moved common steps from test jobs to a composite action 
+        moved common steps from test jobs to a composite action

exasol/ds/sandbox/lib/dss_docker/create_image.py

@@ -47,6 +47,7 @@ def jupyter():
         user_home = get_fact(facts, "jupyter", "home")
         password = get_fact(facts, "jupyter", "password")
         logfile = get_fact(facts, "jupyter", "logfile")
+        virtualenv = get_fact(facts, "jupyter", "virtualenv")
         return [
             "--home", user_home,
             "--jupyter-server", command,
@@ -56,6 +57,7 @@ def jupyter():
             "--docker-group", docker_group,
             "--password", password,
             "--jupyter-logfile", logfile,
+            "--venv", virtualenv,
         ]
 
     entrypoint = get_fact(facts, "entrypoint")
@@ -166,6 +168,7 @@ def _commit_container(
         port = get_fact(facts, "jupyter", "port")
         notebook_folder_final = get_fact(facts, "notebook_folder", "final")
         notebook_folder_initial = get_fact(facts, "notebook_folder", "initial")
+
         conf = {
             "Entrypoint": entrypoint(facts),
             "Cmd": [],
@@ -175,7 +178,7 @@ def _commit_container(
             "Env": [
                 f"VIRTUAL_ENV={virtualenv}",
                 f"NOTEBOOK_FOLDER_FINAL={notebook_folder_final}",
-                f"NOTEBOOK_FOLDER_INITIAL={notebook_folder_initial}"
+                f"NOTEBOOK_FOLDER_INITIAL={notebook_folder_initial}",
             ],
         }
         img = container.commit(repository=self.image_name, conf=conf)

exasol/ds/sandbox/runtime/ansible/roles/entrypoint/files/entrypoint.py

@@ -36,6 +36,10 @@ def arg_parser():
         "--notebooks", type=Path,
         help="destination location for notebook files to copy",
     )
+    parser.add_argument(
+        "--venv", type=Path, metavar="<PATH-TO-VIRTUAL-ENVIRONMENT>",
+        help="Prepend subdirectory bin to environment variable PATH before starting Jupyter server",
+    )
     parser.add_argument(
         "--jupyter-server", metavar="<PATH-TO-JUPYTER-BINARY>",
         help="start server for Jupyter notebooks",
@@ -75,6 +79,11 @@ def arg_parser():
     return parser
 
 
+def command_with_venv(venv_activate: Path, command: List[str]) -> List[str]:
+    bash_cmd = [ "source", str(venv_activate), ";" ] + command
+    return [ "bash", "-c", " ".join(bash_cmd) ]
+
+
 def start_jupyter_server(
         home_directory: str,
         binary_path: str,
@@ -83,6 +92,7 @@ def start_jupyter_server(
         logfile: Path,
         user: str,
         password: str,
+        venv: Path,
         poll_sleep: float = 1,
 ):
     """
@@ -107,6 +117,11 @@ def exit_on_error(rc):
 
     env = os.environ.copy()
     env["HOME"] = home_directory
+    if venv:
+        venv_bin = str(venv / "bin")
+        path = env.get("PATH")
+        env["PATH"] = f"{venv_bin}:{path}" if path else venv_bin
+        _logger.info(f'Changed environment variable PATH to {env["PATH"]}')
     with open(logfile, "w") as f:
         p = subprocess.Popen(command_line, stdout=f, stderr=f, env=env)
 
@@ -350,6 +365,7 @@ def main():
             args.jupyter_logfile,
             args.user,
             args.password,
+            args.venv,
         )
     else:
         sleep_infinity()

test/unit/entrypoint/test_main.py

@@ -83,10 +83,12 @@ def test_jupyter(mocker):
     port = "1234"
     notebook_folder = Path("/root/notebooks")
     logfile = Path("/root/jupyter-server.log")
+    venv = Path("/root/jupyterenv")
     mocker.patch("sys.argv", [
         "app",
         "--home", "home-directory",
         "--notebooks", str(notebook_folder),
+        "--venv", str(venv),
         "--jupyter-server", jupyter,
         "--port", port,
         "--user", "usr",
@@ -106,6 +108,7 @@ def test_jupyter(mocker):
         logfile,
         "usr",
         "pwd",
+        venv,
     )
     assert entrypoint.start_jupyter_server.call_args == expected
     assert not entrypoint.sleep_infinity.called

test/unit/entrypoint/test_start_jupyter_server.py

@@ -40,6 +40,7 @@ def run(self):
             self.logfile,
             "user",
             "password",
+            Path("venv"),
             poll_sleep = 0.1,
         )
         return self
@@ -62,5 +63,6 @@ def test_late_error(tmp_path, caplog):
     with pytest.raises(SystemExit) as ex:
         testee = Testee(tmp_path).create_script(after="exit 23").run()
     assert ex.value.code == 23
+    assert "Changed environment variable PATH to venv/bin:" in caplog.text
     assert "Server for Jupyter has been started successfully." in caplog.text
     assert "Jupyter Server terminated with error code 23" in caplog.text

test/unit/test_dss_docker_image.py

@@ -79,6 +79,7 @@ def test_entrypoint_with_copy_args():
         "dss_facts": {
             "docker_group": "docker-group-name",
             "jupyter": {
+                "virtualenv": "/home/jupyter/jupyterenv",
                 "command": "/home/jupyter/jupyterenv/bin/jupyter-lab",
                 "port": "port",
                 "user": "jupyter-user-name",
@@ -101,6 +102,7 @@ def fact(*args):
         "--notebook-defaults": fact("notebook_folder", "initial"),
         "--notebooks": fact("notebook_folder", "final"),
         "--home": fact("jupyter", "home"),
+        "--venv": fact("jupyter", "virtualenv"),
         "--jupyter-server": fact("jupyter", "command"),
         "--port": fact("jupyter", "port"),
         "--user": fact("jupyter", "user"),