This is an automated email from the ASF dual-hosted git repository.
dimuthuupe pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata.git
The following commit(s) were added to refs/heads/master by this push:
new 657897d2b4 Initial magic extension bundle
657897d2b4 is described below
commit 657897d2b4b14d4c98e9bddea7e9734dfd04c0d2
Author: Dimuthu Wannipurage <[email protected]>
AuthorDate: Thu Jul 18 07:12:03 2024 -0400
Initial magic extension bundle
---
modules/agent-framework/airavata-agent/agent.go | 4 +-
.../airavata-agent/jupyter/README.md | 28 ++-
.../extension/airavata_jupyter_magic/LICENSE | 202 +++++++++++++++++
.../extension/airavata_jupyter_magic/README.md | 33 +++
.../airavata_jupyter_magic/__init__.py | 1 +
.../airavata_jupyter_magic.py | 50 +++++
.../build/lib/airavata_jupyter_magic/__init__.py | 1 +
.../airavata_magic_extension.py | 47 ++++
.../extension/airavata_jupyter_magic/setup.py | 23 ++
.../airavata-agent/jupyter/magic.ipynb | 249 +++++++++++++++++++++
10 files changed, 635 insertions(+), 3 deletions(-)
diff --git a/modules/agent-framework/airavata-agent/agent.go
b/modules/agent-framework/airavata-agent/agent.go
index b2e82c1f40..b2e7a2a80c 100644
--- a/modules/agent-framework/airavata-agent/agent.go
+++ b/modules/agent-framework/airavata-agent/agent.go
@@ -144,9 +144,9 @@ func main() {
log.Printf("Failed to read
response for run jupyter kernel: %v", err)
}
- log.Println("Jupyter execution
response")
+
jupyterResponse := string(body)
-
+ log.Println("Jupyter execution
response: " + jupyterResponse)
if err :=
stream.Send(&protos.AgentMessage{Message:
&protos.AgentMessage_JupyterExecutionResponse{
diff --git a/modules/agent-framework/airavata-agent/jupyter/README.md
b/modules/agent-framework/airavata-agent/jupyter/README.md
index 3f012526e8..565673eadc 100644
--- a/modules/agent-framework/airavata-agent/jupyter/README.md
+++ b/modules/agent-framework/airavata-agent/jupyter/README.md
@@ -15,4 +15,30 @@ python3 kernel.py
curl -X GET http://127.0.0.1:15000/start
curl -X POST http://127.0.0.1:15000/execute -H "Content-Type:
application/json" -d '{"code": "print(4)"}'
curl -X GET http://127.0.0.1:15000/stop
-```
\ No newline at end of file
+```
+
+
+### Build and upload the magic extension
+
+* Make sure you have `setuptools` and `wheel` installed:
+
+```
+pip install setuptools wheel
+```
+
+* Build the extension
+```
+cd jupyter/extension/airavata_jupyter_magic
+python setup.py sdist bdist_wheel
+```
+
+* Upload the distribution to pypi
+```
+pip install twine
+twine upload dist/*
+```
+
+* Extension is available at https://pypi.org/project/airavata-jupyter-magic
+
+
+
diff --git
a/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/LICENSE
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/LICENSE
new file mode 100644
index 0000000000..d645695673
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/LICENSE
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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diff --git
a/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/README.md
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/README.md
new file mode 100644
index 0000000000..e903231f7d
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/README.md
@@ -0,0 +1,33 @@
+# Airavata Magic Extension to run local Jupyter Notebooks on Clusters
+
+
+## Installation
+
+```
+pip install airavata_jupyter_magic
+```
+
+## Usage
+
+### Load the extension in the notebook
+```
+%load_ext airavata_jupyter_magic
+```
+
+### Initialize the remote cluster job
+```
+%init_remote cluster=jetstream cpu=2 memory=2GB
+```
+
+### Run remote cell
+```
+%%run_remote
+# Your code here
+a = 10 + a
+print(a)
+```
+
+### Terminate the remote cluster job and the connection
+```
+%terminate_remote
+```
diff --git
a/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/airavata_jupyter_magic/__init__.py
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/airavata_jupyter_magic/__init__.py
new file mode 100644
index 0000000000..174863c815
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/airavata_jupyter_magic/__init__.py
@@ -0,0 +1 @@
+from .airavata_jupyter_magic import load_ipython_extension,
unload_ipython_extension
\ No newline at end of file
diff --git
a/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/airavata_jupyter_magic/airavata_jupyter_magic.py
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/airavata_jupyter_magic/airavata_jupyter_magic.py
new file mode 100644
index 0000000000..1d30e9781b
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/airavata_jupyter_magic/airavata_jupyter_magic.py
@@ -0,0 +1,50 @@
+from IPython.core.magic import register_line_magic, register_cell_magic
+
+def load_ipython_extension(ipython):
+
+ @register_cell_magic
+ def run_remote(line, cell):
+ url = 'http://localhost:18880/api/v1/agent/executejupyterrequest'
+
+ data = {
+ "sessionId": "session1",
+ "keepAlive": True,
+ "code": cell,
+ "agentId": "agent3"
+ }
+
+ json_data = json.dumps(data)
+ response = requests.post(url, headers={'Content-Type':
'application/json'}, data=json_data)
+ execution_resp = response.json()
+ execution_id = execution_resp["executionId"]
+ error = execution_resp["error"]
+ if error:
+ print("Cell execution failed. Error: " + error)
+ if execution_id:
+ while True:
+ url =
"http://localhost:18880/api/v1/agent/executejupyterresponse/"; + execution_id
+ response = requests.get(url, headers={'Accept':
'application/json'})
+ json_response = response.json()
+ #print(json_response)
+ if json_response['available']:
+ result_str = json_response['responseString']
+ result = json.loads(result_str)
+ if 'result' in result:
+ print(result['result'])
+ elif 'error' in result:
+ print(result['error']['ename'])
+ print(result['error']['evalue'])
+ print(result['error']['traceback'])
+ break
+ time.sleep(1)
+
+ @register_line_magic
+ def init_remote(line):
+ print(f"Your input: {line}")
+
+ @register_line_magic
+ def terminate_remote(line):
+ print(f"Your input: {line}")
+
+def unload_ipython_extension(ipython):
+ pass
\ No newline at end of file
diff --git
a/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/build/lib/airavata_jupyter_magic/__init__.py
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/build/lib/airavata_jupyter_magic/__init__.py
new file mode 100644
index 0000000000..174863c815
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/build/lib/airavata_jupyter_magic/__init__.py
@@ -0,0 +1 @@
+from .airavata_jupyter_magic import load_ipython_extension,
unload_ipython_extension
\ No newline at end of file
diff --git
a/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/build/lib/airavata_jupyter_magic/airavata_magic_extension.py
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/build/lib/airavata_jupyter_magic/airavata_magic_extension.py
new file mode 100644
index 0000000000..59beeabb6e
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/build/lib/airavata_jupyter_magic/airavata_magic_extension.py
@@ -0,0 +1,47 @@
+from IPython.core.magic import register_line_magic, register_cell_magic
+
+def load_ipython_extension(ipython):
+
+ @register_cell_magic
+ def run_remote(line, cell):
+ url = 'http://localhost:18880/api/v1/agent/executejupyterrequest'
+
+ data = {
+ "sessionId": "session1",
+ "keepAlive": True,
+ "code": cell,
+ "agentId": "agent3"
+ }
+
+ json_data = json.dumps(data)
+ response = requests.post(url, headers={'Content-Type':
'application/json'}, data=json_data)
+ execution_resp = response.json()
+ execution_id = execution_resp["executionId"]
+ error = execution_resp["error"]
+ if error:
+ print("Cell execution failed. Error: " + error)
+ if execution_id:
+ while True:
+ url =
"http://localhost:18880/api/v1/agent/executejupyterresponse/"; + execution_id
+ response = requests.get(url, headers={'Accept':
'application/json'})
+ json_response = response.json()
+ #print(json_response)
+ if json_response['available']:
+ result_str = json_response['responseString']
+ result = json.loads(result_str)
+ if 'result' in result:
+ print(result['result'])
+ elif 'error' in result:
+ print(result['error']['ename'])
+ print(result['error']['evalue'])
+ print(result['error']['traceback'])
+ break
+ time.sleep(1)
+
+ @register_line_magic
+ def init_remote(line):
+ print(f"Your input: {line}")
+
+ @register_line_magic
+ def terminate_remote(line):
+ print(f"Your input: {line}")
\ No newline at end of file
diff --git
a/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/setup.py
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/setup.py
new file mode 100644
index 0000000000..7cbcf810b8
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/extension/airavata_jupyter_magic/setup.py
@@ -0,0 +1,23 @@
+from setuptools import setup, find_packages
+
+setup(
+ name='airavata_jupyter_magic',
+ version='0.5',
+ packages=find_packages(),
+ install_requires=[
+ # Add any dependencies your extension needs here
+ ],
+ include_package_data=True,
+ description='A custom IPython magic extension for Airavata to recute local
notebooks on clusters',
+ long_description=open('README.md').read(),
+ long_description_content_type='text/markdown',
+ author='Dimuthu Wannipurage',
+ author_email='[email protected]',
+ url='https://github.com/apache/airavata', # Update with your repo link
+ classifiers=[
+ 'Programming Language :: Python :: 3',
+ 'License :: OSI Approved :: Apache Software License',
+ 'Operating System :: OS Independent',
+ ],
+ license='Apache License 2.0',
+)
\ No newline at end of file
diff --git a/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
b/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
new file mode 100644
index 0000000000..5f80e5782c
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
@@ -0,0 +1,249 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 40,
+ "id": "e520a5ea-847a-4237-a0a8-e52deb0b2c0d",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from IPython.core.magic import register_cell_magic\n",
+ "from IPython.core.magic import register_line_magic\n",
+ "\n",
+ "import time\n",
+ "import requests\n",
+ "import json\n",
+ "import time"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 41,
+ "id": "c5c591cb-7f0f-47ab-a9fa-4700161439c2",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "@register_cell_magic\n",
+ "def run_remote(line, cell):\n",
+ " url = 'http://localhost:18880/api/v1/agent/executejupyterrequest'\n",
+ "\n",
+ " data = {\n",
+ " \"sessionId\": \"session1\",\n",
+ " \"keepAlive\": True,\n",
+ " \"code\": cell,\n",
+ " \"agentId\": \"agent3\"\n",
+ " }\n",
+ "\n",
+ " json_data = json.dumps(data) \n",
+ " response = requests.post(url, headers={'Content-Type':
'application/json'}, data=json_data)\n",
+ " execution_resp = response.json()\n",
+ " execution_id = execution_resp[\"executionId\"]\n",
+ " error = execution_resp[\"error\"]\n",
+ " if error:\n",
+ " print(\"Cell execution failed. Error: \" + error)\n",
+ " if execution_id:\n",
+ " while True:\n",
+ " url =
\"http://localhost:18880/api/v1/agent/executejupyterresponse/\"; +
execution_id\n",
+ " response = requests.get(url, headers={'Accept':
'application/json'})\n",
+ " json_response = response.json()\n",
+ " #print(json_response)\n",
+ " if json_response['available']:\n",
+ " result_str = json_response['responseString']\n",
+ " result = json.loads(result_str)\n",
+ " if 'result' in result:\n",
+ " print(result['result'])\n",
+ " elif 'error' in result:\n",
+ " print(result['error']['ename'])\n",
+ " print(result['error']['evalue'])\n",
+ " print(result['error']['traceback'])\n",
+ " break\n",
+ " time.sleep(1)\n",
+ "\n",
+ "@register_line_magic\n",
+ "def init_remote(line):\n",
+ " print(f\"Your input: {line}\")\n",
+ "\n",
+ "@register_line_magic\n",
+ "def terminate_remote(line):\n",
+ " print(f\"Your input: {line}\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "5c43ee08-39fc-4e44-a3f6-9f7ba372d201",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Collecting airavata-jupyter-magic==0.5\n",
+ " Obtaining dependency information for airavata-jupyter-magic==0.5 from
https://files.pythonhosted.org/packages/12/1b/f7214be1a74520d1af8f7810ade38b0346f74b8ccf998eb0586a77b4e636/airavata_jupyter_magic-0.5-py3-none-any.whl.metadata\n";,
+ " Downloading airavata_jupyter_magic-0.5-py3-none-any.whl.metadata (994
bytes)\n",
+ "Downloading airavata_jupyter_magic-0.5-py3-none-any.whl (7.6 kB)\n",
+ "Installing collected packages: airavata-jupyter-magic\n",
+ " Attempting uninstall: airavata-jupyter-magic\n",
+ " Found existing installation: airavata-jupyter-magic 0.4\n",
+ " Uninstalling airavata-jupyter-magic-0.4:\n",
+ " Successfully uninstalled airavata-jupyter-magic-0.4\n",
+ "Successfully installed airavata-jupyter-magic-0.5\n",
+ "\n",
+
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
A new release of pip is available:
\u001b[0m\u001b[31;49m23.2.1\u001b[0m\u001b[39;49m ->
\u001b[0m\u001b[32;49m24.1.2\u001b[0m\n",
+
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n"
+ ]
+ }
+ ],
+ "source": [
+ "! pip install airavata-jupyter-magic==0.5"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "id": "4c04f9ef-161c-4eb5-bd60-78a68ef614ac",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "The airavata_jupyter_magic module is not an IPython extension.\n"
+ ]
+ }
+ ],
+ "source": [
+ "%load_ext airavata_jupyter_magic"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "9e969c05-fbf9-4eca-9b83-d1c62429a13b",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "UsageError: Line magic function `%init_remote` not found.\n"
+ ]
+ }
+ ],
+ "source": [
+ "%init_remote cluster=jetstream cpu=2 memory=2GB"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 48,
+ "id": "4e60d84a-2a81-4b04-9dcb-dea48c4228b8",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "70\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%run_remote\n",
+ "# Your code here\n",
+ "a = 10 + a\n",
+ "print(a)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 35,
+ "id": "ebd549f1-3a5d-47e3-876d-beb91d971ac2",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%run_remote\n",
+ "b = 20"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 38,
+ "id": "01b350f1-dc56-4434-86c1-0ff024cc589d",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Requirement already satisfied: numpy in
./jupyter/venv/lib/python3.11/site-packages (2.0.0)\n",
+ "\n",
+
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
A new release of pip is available:
\u001b[0m\u001b[31;49m23.2.1\u001b[0m\u001b[39;49m ->
\u001b[0m\u001b[32;49m24.1.2\u001b[0m\n",
+
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%run_remote cluster=jetstream cpu=2 memory=2GB\n",
+ "!pip install numpy"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 43,
+ "id": "4acff051-2148-45d6-bb4e-c3cabb1a162c",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Your input: \n"
+ ]
+ }
+ ],
+ "source": [
+ "%terminate_remote"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "ad0cb710-d4f7-490e-a7b6-a8d97a3f45ed",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "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": "3.11.5"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
