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 c50760df01 Showing image data in cell output
c50760df01 is described below
commit c50760df01e900a68f4fd83d7d11b7cc6e897326
Author: Dimuthu Wannipurage <[email protected]>
AuthorDate: Sat Jul 20 00:25:06 2024 -0400
Showing image data in cell output
---
modules/agent-framework/airavata-agent/agent.go | 47 ++++++-
.../airavata-agent/jupyter/kernel.py | 9 +-
.../airavata-agent/jupyter/magic.ipynb | 145 +++++++++++++--------
3 files changed, 139 insertions(+), 62 deletions(-)
diff --git a/modules/agent-framework/airavata-agent/agent.go
b/modules/agent-framework/airavata-agent/agent.go
index 86696adb28..75088578b8 100644
--- a/modules/agent-framework/airavata-agent/agent.go
+++ b/modules/agent-framework/airavata-agent/agent.go
@@ -12,6 +12,7 @@ import (
"io/ioutil"
"encoding/json"
"bytes"
+ "bufio"
protos "airavata-agent/protos"
"golang.org/x/crypto/ssh"
@@ -51,12 +52,52 @@ func main() {
go func() {
log.Printf("Starting jupyter kernel")
cmd := exec.Command("python", "/opt/jupyter/kernel.py")
- _, err := cmd.Output()
+ //cmd := exec.Command("jupyter/venv/bin/python",
"jupyter/kernel.py")
+ stdout, err := cmd.StdoutPipe()
+
+ if err != nil {
+ fmt.Println("Error creating StdoutPipe:", err)
+ return
+ }
+
+ // Get stderr pipe
+ stderr, err := cmd.StderrPipe()
if err != nil {
- log.Printf(err.Error())
- close(kernelChannel)
+ fmt.Println("Error creating StderrPipe:", err)
return
}
+
+ // Start the command
+ if err := cmd.Start(); err != nil {
+ fmt.Println("Error starting command:", err)
+ return
+ }
+
+ // Create channels to read from stdout and stderr
+ stdoutScanner := bufio.NewScanner(stdout)
+ stderrScanner := bufio.NewScanner(stderr)
+
+ // Stream stdout
+ go func() {
+ for stdoutScanner.Scan() {
+ fmt.Printf("stdout: %s\n", stdoutScanner.Text())
+ }
+ }()
+
+ // Stream stderr
+ go func() {
+ for stderrScanner.Scan() {
+ fmt.Printf("stderr: %s\n", stderrScanner.Text())
+ }
+ }()
+
+ // Wait for the command to finish
+ if err := cmd.Wait(); err != nil {
+ fmt.Println("Error waiting for command:", err)
+ return
+ }
+
+ fmt.Println("Command finished")
}()
go func() {
diff --git a/modules/agent-framework/airavata-agent/jupyter/kernel.py
b/modules/agent-framework/airavata-agent/jupyter/kernel.py
index c3f9f19569..5188105732 100644
--- a/modules/agent-framework/airavata-agent/jupyter/kernel.py
+++ b/modules/agent-framework/airavata-agent/jupyter/kernel.py
@@ -20,7 +20,7 @@ def start_kernel():
global kernel_running
if kernel_running:
- return
+ return "Kernel already running"
# Create a new kernel manager
km = KernelManager(kernel_name='python3')
km.start_kernel()
@@ -53,6 +53,9 @@ def execute():
while True:
try:
msg = kc.get_iopub_msg(timeout=1)
+ print("------------------")
+ print(msg)
+ print("-================-")
content = msg["content"]
parent_header = msg["parent_header"]
@@ -62,6 +65,8 @@ def execute():
if msg["msg_type"] == "stream" and content["name"] == "stdout":
print(content["text"])
content_text = content_text + content["text"]
+ if msg["msg_type"] == "display_data":
+ return jsonify({'display': content}), 200
if msg["msg_type"] == "error":
return jsonify({'error': content}), 200
if msg["msg_type"] == "status" and execution_noticed:
@@ -83,7 +88,7 @@ def stop():
global kernel_running
if not kernel_running:
- return
+ return "Kernel is not running to shut down"
kc.stop_channels()
km.shutdown_kernel()
diff --git a/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
b/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
index 5f80e5782c..c667375f30 100644
--- a/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
+++ b/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 40,
+ "execution_count": 1,
"id": "e520a5ea-847a-4237-a0a8-e52deb0b2c0d",
"metadata": {},
"outputs": [],
@@ -18,20 +18,23 @@
},
{
"cell_type": "code",
- "execution_count": 41,
+ "execution_count": 53,
"id": "c5c591cb-7f0f-47ab-a9fa-4700161439c2",
"metadata": {},
"outputs": [],
"source": [
+ "from IPython.display import display, Image\n",
+ "import base64\n",
+ "\n",
"@register_cell_magic\n",
"def run_remote(line, cell):\n",
- " url = 'http://localhost:18880/api/v1/agent/executejupyterrequest'\n",
+ " url =
'http://scigap02.sciencegateways.iu.edu:18880/api/v1/agent/executejupyterrequest'\n",
"\n",
" data = {\n",
" \"sessionId\": \"session1\",\n",
" \"keepAlive\": True,\n",
" \"code\": cell,\n",
- " \"agentId\": \"agent3\"\n",
+ " \"agentId\": \"agent1991\"\n",
" }\n",
"\n",
" json_data = json.dumps(data) \n",
@@ -43,7 +46,7 @@
" 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",
+ " url =
\"http://scigap02.sciencegateways.iu.edu: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",
@@ -56,12 +59,35 @@
" print(result['error']['ename'])\n",
" print(result['error']['evalue'])\n",
" print(result['error']['traceback'])\n",
+ " elif 'display' in result:\n",
+ " display_obj = result['display']\n",
+ " if 'data' in display_obj:\n",
+ " data_obj = display_obj['data']\n",
+ " if 'image/png' in data_obj:\n",
+ " image_data = data_obj['image/png']\n",
+ "
display(Image(data=base64.b64decode(image_data), format='png'))\n",
" break\n",
" time.sleep(1)\n",
"\n",
"@register_line_magic\n",
"def init_remote(line):\n",
" print(f\"Your input: {line}\")\n",
+ " pairs = line.split()\n",
+ "\n",
+ " # Initialize variable to store the cluster value\n",
+ " cluster_value = None\n",
+ " \n",
+ " # Iterate through the pairs to find the cluster value\n",
+ " for pair in pairs:\n",
+ " if pair.startswith(\"cluster=\"):\n",
+ " cluster_value = pair.split(\"=\")[1]\n",
+ " break\n",
+ " \n",
+ " # Print the cluster value\n",
+ " if cluster_value:\n",
+ " print(f\"Cluster value: {cluster_value}\")\n",
+ "\n",
+ " \n",
"\n",
"@register_line_magic\n",
"def terminate_remote(line):\n",
@@ -70,109 +96,114 @@
},
{
"cell_type": "code",
- "execution_count": 6,
- "id": "5c43ee08-39fc-4e44-a3f6-9f7ba372d201",
+ "execution_count": 51,
+ "id": "9e969c05-fbf9-4eca-9b83-d1c62429a13b",
"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"
+ "Your input: cluster=jetstream cpu=2 memory=2GB\n",
+ "Cluster value: jetstream\n"
]
}
],
"source": [
- "! pip install airavata-jupyter-magic==0.5"
+ "%init_remote cluster=jetstream cpu=2 memory=2GB queue=shared walltime=60"
]
},
{
"cell_type": "code",
- "execution_count": 7,
- "id": "4c04f9ef-161c-4eb5-bd60-78a68ef614ac",
+ "execution_count": 59,
+ "id": "4e60d84a-2a81-4b04-9dcb-dea48c4228b8",
"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"
+ "10\n",
+ "\n"
]
}
],
"source": [
- "%init_remote cluster=jetstream cpu=2 memory=2GB"
+ "%%run_remote\n",
+ "# Your code here\n",
+ "a = 10\n",
+ "print(a)"
]
},
{
"cell_type": "code",
- "execution_count": 48,
- "id": "4e60d84a-2a81-4b04-9dcb-dea48c4228b8",
+ "execution_count": 60,
+ "id": "ebd549f1-3a5d-47e3-876d-beb91d971ac2",
"metadata": {},
"outputs": [
{
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "70\n",
- "\n"
- ]
+ "data": {
+ "image/png":
"iVBORw0KGgoAAAANSUhEUgAAAjIAAAHHCAYAAACle7JuAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjkuMSwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy/TGe4hAAAACXBIWXMAAA9hAAAPYQGoP6dpAABKOElEQVR4nO3dd3QU5eLG8e+mB1JIIIQASQgdUuhwKYoFqSKIYENFr165gAgiIFhBRVRQUEFsgHoVC9VCUVCKAgoIpNBL6IFQk5CQtju/P6L5ESCQhCSzmzyfc3KOOzuz+7wOZB/efXfWYhiGgYiIiIgDcjI7gIiIiEhRqciIiIiIw1KREREREYelIiMiIiIOS0VGREREHJaKjIiIiDgsFRkRERFxWCoyIiIi4rBUZERERMRhqciIlAO1atXi4YcfNuW5x40bh8ViKdXnPHDgABaLhU8//bRUn7cwPv30UywWCwcO
[...]
+ "text/plain": [
+ "<IPython.core.display.Image object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
}
],
"source": [
"%%run_remote\n",
- "# Your code here\n",
- "a = 10 + a\n",
- "print(a)"
+ "import matplotlib.pyplot as plt\n",
+ "\n",
+ "# Sample data\n",
+ "x = [1, 2, 3, 4, 5]\n",
+ "y = [2, 3, 5, 7, 11]\n",
+ "\n",
+ "# Create the plot\n",
+ "plt.plot(x, y)\n",
+ "\n",
+ "# Add a title and labels\n",
+ "plt.title('Simple Line Plot')\n",
+ "plt.xlabel('X Axis')\n",
+ "plt.ylabel('Y Axis')\n",
+ "\n",
+ "# Show the plot\n",
+ "plt.show()"
]
},
{
"cell_type": "code",
- "execution_count": 35,
- "id": "ebd549f1-3a5d-47e3-876d-beb91d971ac2",
+ "execution_count": 57,
+ "id": "a946bee5-384b-4883-9753-e5d2bf162d39",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
+ "Requirement already satisfied: matplotlib in
/usr/local/lib/python3.12/site-packages (3.9.1)\n",
+ "Requirement already satisfied: contourpy>=1.0.1 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (1.2.1)\n",
+ "Requirement already satisfied: cycler>=0.10 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (0.12.1)\n",
+ "Requirement already satisfied: fonttools>=4.22.0 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (4.53.1)\n",
+ "Requirement already satisfied: kiwisolver>=1.3.1 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (1.4.5)\n",
+ "Requirement already satisfied: numpy>=1.23 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (2.0.0)\n",
+ "Requirement already satisfied: packaging>=20.0 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (24.1)\n",
+ "Requirement already satisfied: pillow>=8 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (10.4.0)\n",
+ "Requirement already satisfied: pyparsing>=2.3.1 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (3.1.2)\n",
+ "Requirement already satisfied: python-dateutil>=2.7 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (2.9.0.post0)\n",
+ "Requirement already satisfied: six>=1.5 in
/usr/local/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib)
(1.16.0)\n",
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken
permissions and conflicting behaviour with the system package manager. It is
recommended to use a virtual environment instead:
https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n";,
+ "\u001b[0m\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;49m24.0\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\n",
- "b = 20"
+ "!pip3 install matplotlib\n"
]
},
{
