add initial notebooks for guis

NIGMS · Oct 31, 2024 · ff62572 · ff62572
1 parent e3f55b4
commit ff62572
Show file tree

Hide file tree

Showing 4 changed files with 378 additions and 1 deletion.
diff --git a/reference_notebooks/start-bandage.sh b/reference_notebooks/start-bandage.sh
@@ -0,0 +1,14 @@
+#! /bin/bash
+apt-get update
+apt-get install ca-certificates curl -y
+install -m 0755 -d /etc/apt/keyrings
+curl -fsSL https://download.docker.com/linux/debian/gpg -o /etc/apt/keyrings/docker.asc
+chmod a+r /etc/apt/keyrings/docker.asc
+echo   "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/debian \
+  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
+export GCSFUSE_REPO=gcsfuse-`lsb_release -c -s` && echo "deb https://packages.cloud.google.com/apt $GCSFUSE_REPO main" | tee /etc/apt/sources.list.d/gcsfuse.list > /dev/null
+curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key add -
+apt-get update
+apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin fuse gcsfuse -y
+mkdir "/tmp/mount-folder" && chmod 777 /tmp/mount-folder && mount -t gcsfuse -o allow_other,file_mode=777,dir_mode=777 nigms-nosi-developers-us-notebooks "/tmp/mount-folder" 
+docker run --rm -v /tmp/mount-folder:/config/s3 -p 8080:3000 us-east4-docker.pkg.dev/nih-cl-shared-resources/nigms-sandbox/bandage-gui
diff --git a/reference_notebooks/start-gui-server.ipynb b/reference_notebooks/start-gui-server.ipynb
@@ -0,0 +1,350 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "4f80ce0b-c291-4d4a-aaa9-6a62f5cb61bd",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "subprocess.run('pip install google-cloud-compute notebook'.split(\" \"), text=True, capture_output=True)\n",
+    "import urllib.request\n",
+    "from __future__ import annotations\n",
+    "\n",
+    "import sys\n",
+    "from typing import Any\n",
+    "\n",
+    "from google.api_core.extended_operation import ExtendedOperation\n",
+    "from google.cloud import compute_v1\n",
+    "import time\n",
+    "import ipywidgets as widgets\n",
+    "from IPython.display import display, clear_output\n",
+    "from IPython.core.display import HTML\n",
+    "ts = time.time()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "7280cecd-7c37-414a-9f36-78b2e7eeb967",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "url = \"http://metadata.google.internal/computeMetadata/v1/project/project-id\"\n",
+    "req = urllib.request.Request(url)\n",
+    "req.add_header(\"Metadata-Flavor\", \"Google\")\n",
+    "project_id = urllib.request.urlopen(req).read().decode()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "cb07eb82-122b-40ad-aa51-631d4650a8ee",
+   "metadata": {
+    "jupyter": {
+     "source_hidden": true
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def wait_for_extended_operation(\n",
+    "    operation: ExtendedOperation, verbose_name: str = \"operation\", timeout: int = 300\n",
+    ") -> Any:\n",
+    "    \"\"\"\n",
+    "    Waits for the extended (long-running) operation to complete.\n",
+    "\n",
+    "    If the operation is successful, it will return its result.\n",
+    "    If the operation ends with an error, an exception will be raised.\n",
+    "    If there were any warnings during the execution of the operation\n",
+    "    they will be printed to sys.stderr.\n",
+    "\n",
+    "    Args:\n",
+    "        operation: a long-running operation you want to wait on.\n",
+    "        verbose_name: (optional) a more verbose name of the operation,\n",
+    "            used only during error and warning reporting.\n",
+    "        timeout: how long (in seconds) to wait for operation to finish.\n",
+    "            If None, wait indefinitely.\n",
+    "\n",
+    "    Returns:\n",
+    "        Whatever the operation.result() returns.\n",
+    "\n",
+    "    Raises:\n",
+    "        This method will raise the exception received from `operation.exception()`\n",
+    "        or RuntimeError if there is no exception set, but there is an `error_code`\n",
+    "        set for the `operation`.\n",
+    "\n",
+    "        In case of an operation taking longer than `timeout` seconds to complete,\n",
+    "        a `concurrent.futures.TimeoutError` will be raised.\n",
+    "    \"\"\"\n",
+    "    result = operation.result(timeout=timeout)\n",
+    "\n",
+    "    if operation.error_code:\n",
+    "        print(\n",
+    "            f\"Error during {verbose_name}: [Code: {operation.error_code}]: {operation.error_message}\",\n",
+    "            file=sys.stderr,\n",
+    "            flush=True,\n",
+    "        )\n",
+    "        print(f\"Operation ID: {operation.name}\", file=sys.stderr, flush=True)\n",
+    "        raise operation.exception() or RuntimeError(operation.error_message)\n",
+    "\n",
+    "    if operation.warnings:\n",
+    "        print(f\"Warnings during {verbose_name}:\\n\", file=sys.stderr, flush=True)\n",
+    "        for warning in operation.warnings:\n",
+    "            print(f\" - {warning.code}: {warning.message}\", file=sys.stderr, flush=True)\n",
+    "\n",
+    "    return result\n",
+    "\n",
+    "\n",
+    "def delete_instance(zone: str, machine_name: str) -> None:\n",
+    "    \"\"\"\n",
+    "    Send an instance deletion request to the Compute Engine API and wait for it to complete.\n",
+    "\n",
+    "    Args:\n",
+    "        project_id: project ID or project number of the Cloud project you want to use.\n",
+    "        zone: name of the zone you want to use. For example: “us-west3-b”\n",
+    "        machine_name: name of the machine you want to delete.\n",
+    "    \"\"\"\n",
+    "    instance_client = compute_v1.InstancesClient()\n",
+    "\n",
+    "    print(f\"Deleting {machine_name} from {zone}...\")\n",
+    "    operation = instance_client.delete(project=project_id, zone=zone, instance=machine_name\n",
+    "    )\n",
+    "    wait_for_extended_operation(operation, \"instance deletion\")\n",
+    "    print(f\"Instance {machine_name} deleted.\")\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c7d33171-3a65-482e-a28a-31b2fdc0649d",
+   "metadata": {},
+   "source": [
+    "Please paste the following cell output and run it"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "id": "5bc64703-823c-4b51-9e40-a3c2ed09998d",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "application/javascript": [
+       "// Send data\n",
+       "\n",
+       "fetch( 'https://api64.ipify.org/')\n",
+       "  .then(\n",
+       "    response => response.text()\n",
+       "  ).then(\n",
+       "    text => element.append(\"ip='\"+text+\"'\")\n",
+       "  );\n"
+      ],
+      "text/plain": [
+       "<IPython.core.display.Javascript object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "%%javascript\n",
+    "// Send data\n",
+    "\n",
+    "fetch( 'https://api64.ipify.org/')\n",
+    "  .then(\n",
+    "    response => response.text()\n",
+    "  ).then(\n",
+    "    text => element.append(\"ip='\"+text+\"'\")\n",
+    "  );"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "2f528cb1-7c20-4daa-9dd6-726eccecf566",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "ip='128.231.234.47'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "561e3647-94cd-41c2-b950-b9404e12cb98",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "firewall_rule_capture = subprocess.run('gcloud compute firewall-rules list'.split(\" \"), text=True, capture_output=True) \n",
+    "rules = firewall_rule_capture.stdout.split(\"\\n\")\n",
+    "rule_found = False\n",
+    "for x in rules:\n",
+    "    if 'allow-gui-access-'+str(int(ts)) in x:\n",
+    "        rule_found = True\n",
+    "        print(\"rule already exist\")\n",
+    "if not rule_found:\n",
+    "    subprocess.run(['gcloud','compute','firewall-rules','create','allow-gui-access-'+str(int(ts)),'--allow=tcp:8080','--source-ranges='+ip+'/32','--description=\"allow-gui-access\"'])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6b7a9e9f-2698-462e-aefc-36755c39dbea",
+   "metadata": {},
+   "source": [
+    "## Now we will create a Compute instance to run our GUI program"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "id": "7adfc414-112a-4d32-8fb2-4ff2c6fabd0d",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "61e65e7e214047e8ad514008110a96c0",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Dropdown(description='GUI:', options=('bandage', 'pymol', 'molbobity'), value='bandage')"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "7d0f5644e07b4ecfaf4ce51ad6528c1f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Button(description='Start Gui', style=ButtonStyle())"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "eae09f2d13cd41e9a04bd301d2b80435",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Output()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "\n",
+    "w = widgets.Dropdown(\n",
+    "    options=['bandage', 'pymol', 'molbobity'],\n",
+    "    value='bandage',\n",
+    "    description='GUI:',\n",
+    ")\n",
+    "script_key = 'bandage'\n",
+    "script={\n",
+    "    'bandage':'start-bandage.sh',\n",
+    "    'pymol':'start-pymol.sh',\n",
+    "    'molbobity':'start-molbobity.sh',\n",
+    "}\n",
+    "def on_change(change):\n",
+    "    if change['type'] == 'change' and change['name'] == 'value':\n",
+    "        script_key = change['new']\n",
+    "        print(\"changed to %s\" % change['new'])\n",
+    "\n",
+    "out = widgets.Output()\n",
+    "\n",
+    "\n",
+    "def on_button_clicked(b):\n",
+    "    with out:\n",
+    "        clear_output()\n",
+    "        server_out = subprocess.run(['gcloud','compute','instances','create','bandage-gui-'+str(int(ts)),'--zone=us-east4-a','--boot-disk-size=200','--metadata-from-file=startup-script='+script[script_key],'--image-project=debian-cloud','--image-family=debian-12'], text=True, capture_output=True)\n",
+    "        server_name = 'bandage-gui-'+str(int(ts))\n",
+    "        if len(server_out.stdout) >0:\n",
+    "            print(\"Please access the GUI at http://\"+server_out.stdout.split(\"\\n\")[1].split(\" \")[-3]+\":8080\")\n",
+    "            print(\"Note, it may take 3-4 minutes for it to fully start\")\n",
+    "        else:\n",
+    "            display(HTML(server_out.stderr))\n",
+    "            print(server_out.stderr)\n",
+    "\n",
+    "\n",
+    "button = widgets.Button(description=\"Start Gui\")\n",
+    "button.on_click(on_button_clicked)\n",
+    "w.observe(on_change)\n",
+    "display(w)\n",
+    "display(button)\n",
+    "display(out)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "55229d32-607d-4b90-8947-54f43abeb8e8",
+   "metadata": {},
+   "source": [
+    "Run the below to clean up the GUI once done"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "23702d79-3dee-45e4-9401-c6614c66fce8",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "delete_instance(zone='us-east4-a',machine_name=server_name)"
+   ]
+  }
+ ],
+ "metadata": {
+  "environment": {
+   "kernel": "conda-base-py",
+   "name": "workbench-notebooks.m125",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m125"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel) (Local)",
+   "language": "python",
+   "name": "conda-base-py"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.15"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/reference_notebooks/start-pymol.sh b/reference_notebooks/start-pymol.sh
@@ -0,0 +1,14 @@
+#! /bin/bash
+apt-get update
+apt-get install ca-certificates curl -y
+install -m 0755 -d /etc/apt/keyrings
+curl -fsSL https://download.docker.com/linux/debian/gpg -o /etc/apt/keyrings/docker.asc
+chmod a+r /etc/apt/keyrings/docker.asc
+echo   "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/debian \
+  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
+export GCSFUSE_REPO=gcsfuse-`lsb_release -c -s` && echo "deb https://packages.cloud.google.com/apt $GCSFUSE_REPO main" | tee /etc/apt/sources.list.d/gcsfuse.list > /dev/null
+curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key add -
+apt-get update
+apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin fuse gcsfuse -y
+mkdir "/tmp/mount-folder" && chmod 777 /tmp/mount-folder && mount -t gcsfuse -o allow_other,file_mode=777,dir_mode=777 nigms-nosi-developers-us-notebooks "/tmp/mount-folder" 
+docker run --rm -v /tmp/mount-folder:/config/s3 -p 8080:3000 us-east4-docker.pkg.dev/nih-cl-shared-resources/nigms-sandbox/bandage-gui
diff --git a/reusable-workflow-repo b/reusable-workflow-repo