feat(components): Added the Run notebook using papermill component. F…

…ixes kubeflow#497 (kubeflow#4578)

* Components - Added the Run notebook using papermill component

Fixes kubeflow#497

* Added a notebook to be used in samples

* Added the sample pipeline

components/notebooks/Run_notebook_using_papermill/component.yaml

@@ -0,0 +1,50 @@
+name: Run notebook using papermill
+description: |
+  Run Jupyter notebook using papermill.
+  The notebook will receive the parameter values passed to it as well as the INPUT_DATA_PATH and OUTPUT_DATA_PATH variables that will be set to the input data path (if provided) and directory for the optional output data.
+inputs:
+- {name: Notebook, type: JupyterNotebook, description: 'Notebook to execute.'}
+- {name: Parameters, type: JsonObject, default: '{}', description: 'Map with notebook paramater values.'}
+- {name: Packages to install, type: JsonArray, default: '', description: 'Python packages to install'}
+- {name: Input data, optional: true, description: 'Optional data that can be passed to notebook. In notebook, the INPUT_DATA_PATH variable will point to the data (if passed).'}
+outputs:
+- {name: Notebook, type: JupyterNotebook, description: 'Executed notebook.'}
+- {name: Output data, description: 'Directory with any output data. In notebook, the OUTPUT_DATA_PATH variable will point to this directory, so that the notebook can write output data there.'}
+metadata:
+  annotations:
+    author: Alexey Volkov <alexey.volkov@ark-kun.com>
+implementation:
+  container:
+    image: python:3.7
+    command:
+    - sh
+    - -exc
+    - |
+      input_notebook_path="$0"
+      output_notebook_path="$1"
+      arguments="$2"
+      packages_to_install="$3"
+      input_data_path="$4"
+      output_data_path="$5"
+      mkdir -p "$(dirname "$output_notebook_path")"
+      mkdir -p "$output_data_path"
+
+      # Converting packages_to_install from JSON to command-line arguments
+      packages_to_install=$(echo "$packages_to_install" | sed -E -e 's/^\[//' -e 's/]$//' -e 's/",/" /g' -e "s/\"/'/g")
+      # Installing packages
+      sh -c "python3 -m pip install --upgrade --quiet jupyter papermill==2.2.0 ${packages_to_install}"
+      # Running the notebook using papermill
+      papermill --parameters_yaml "$arguments" --parameters INPUT_DATA_PATH "$input_data_path" --parameters OUTPUT_DATA_PATH "$output_data_path" "$input_notebook_path" "$output_notebook_path"
+      
+    - {inputPath: Notebook}
+    - {outputPath: Notebook}
+    - {inputValue: Parameters}
+    - if:
+        cond: {isPresent: Packages to install}
+        then: [{inputValue: Packages to install}]
+        else: "{}"
+    - if:
+        cond: {isPresent: Input data}
+        then: [{inputPath: Input data}]
+        else: ""
+    - {outputPath: Output data}

components/notebooks/samples/sample_pipeline.py

@@ -0,0 +1,20 @@
+kfp_endpoint = None
+
+import kfp
+from kfp import components
+
+download_op = components.load_component_from_url('https://raw.githubusercontent.com/kubeflow/pipelines/240543e483076ae718f82c6f280441daa2f041fd/components/web/Download/component.yaml')
+run_notebook_op = components.load_component_from_url('https://raw.githubusercontent.com/kubeflow/pipelines/4ebce5f643b6af5639053ea7eaed52b02bf7e928/components/notebooks/Run_notebook_using_papermill/component.yaml')
+
+def notebook_pipeline():
+    notebook = download_op('https://raw.githubusercontent.com/kubeflow/pipelines/93fc34474bf989998cf19445149aca2847eee763/components/notebooks/samples/test_notebook.ipynb').output    
+
+    run_notebook_op(
+        notebook=notebook,
+        parameters={'param1': 'value 1'},
+        input_data="Optional. Pass output of any component here. Can be a directory.",
+        packages_to_install=["matplotlib"],
+    )
+
+if __name__ == '__main__':
+    pipelin_run = kfp.Client(host=kfp_endpoint).create_run_from_pipeline_func(notebook_pipeline, arguments={})

components/notebooks/samples/test_notebook.ipynb

@@ -0,0 +1,82 @@
+{
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.6.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2,
+ "cells": [
+  {
+   "source": [
+    "# Parameters\n",
+    "INPUT_DATA_PATH = INPUT_DATA_PATH or \"\"\n",
+    "OUTPUT_DATA_PATH = OUTPUT_DATA_PATH or \"\""
+   ],
+   "cell_type": "code",
+   "metadata": {},
+   "execution_count": null,
+   "outputs": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "# Show the parameter values\n",
+    "print('INPUT_DATA_PATH = ' + INPUT_DATA_PATH)\n",
+    "print('OUTPUT_DATA_PATH = ' + OUTPUT_DATA_PATH)\n",
+    "print('locals() = ' + str(locals()))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Checking the input data\n",
+    "import os\n",
+    "\n",
+    "if INPUT_DATA_PATH:\n",
+    "    if os.path.isdir(INPUT_DATA_PATH):\n",
+    "        print('os.listdir(INPUT_DATA_PATH):')\n",
+    "        print(os.listdir(INPUT_DATA_PATH))\n",
+    "    if os.path.isfile(INPUT_DATA_PATH):\n",
+    "        print('os.stat(INPUT_DATA_PATH):')\n",
+    "        print(os.stat(INPUT_DATA_PATH))\n",
+    "else:\n",
+    "    print('INPUT_DATA_PATH is empty')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Writing some output data\n",
+    "from pathlib import Path\n",
+    "\n",
+    "(Path(OUTPUT_DATA_PATH) / 'output.txt').write_text(\"Hello world!\")"
+   ]
+  }
+ ]
+}