damondouglas commented on code in PR #27516:
URL: https://github.com/apache/beam/pull/27516#discussion_r1266128537
##########
examples/notebooks/healthcare/beam_nlp.ipynb:
##########
@@ -0,0 +1,973 @@
+{
+ "nbformat": 4,
+ "nbformat_minor": 0,
+ "metadata": {
+ "colab": {
+ "provenance": [],
+ "include_colab_link": true
+ },
+ "kernelspec": {
+ "name": "python3",
+ "display_name": "Python 3"
+ },
+ "language_info": {
+ "name": "python"
+ }
+ },
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "view-in-github",
+ "colab_type": "text"
+ },
+ "source": [
+ "<a
href=\"https://colab.research.google.com/github/svetakvsundhar/beam/blob/healthcarenlp/examples/notebooks/healthcare/beam_nlp.ipynb\";
target=\"_parent\"><img
src=\"https://colab.research.google.com/assets/colab-badge.svg\"; alt=\"Open In
Colab\"/></a>"
Review Comment:
Will this URL remain if this PR merged?
##########
examples/notebooks/healthcare/beam_nlp.ipynb:
##########
@@ -0,0 +1,973 @@
+{
+ "nbformat": 4,
+ "nbformat_minor": 0,
+ "metadata": {
+ "colab": {
+ "provenance": [],
+ "include_colab_link": true
+ },
+ "kernelspec": {
+ "name": "python3",
+ "display_name": "Python 3"
+ },
+ "language_info": {
+ "name": "python"
+ }
+ },
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "view-in-github",
+ "colab_type": "text"
+ },
+ "source": [
+ "<a
href=\"https://colab.research.google.com/github/svetakvsundhar/beam/blob/healthcarenlp/examples/notebooks/healthcare/beam_nlp.ipynb\";
target=\"_parent\"><img
src=\"https://colab.research.google.com/assets/colab-badge.svg\"; alt=\"Open In
Colab\"/></a>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "# @title ###### Licensed to the Apache Software Foundation (ASF),
Version 2.0 (the \"License\")\n",
+ "\n",
+ "# Licensed to the Apache Software Foundation (ASF) under one\n",
+ "# or more contributor license agreements. See the NOTICE file\n",
+ "# distributed with this work for additional information\n",
+ "# regarding copyright ownership. The ASF licenses this file\n",
+ "# to you under the Apache License, Version 2.0 (the\n",
+ "# \"License\"); you may not use this file except in compliance\n",
+ "# with the License. You may obtain a copy of the License at\n",
+ "#\n",
+ "# http://www.apache.org/licenses/LICENSE-2.0\n";,
+ "#\n",
+ "# Unless required by applicable law or agreed to in writing,\n",
+ "# software distributed under the License is distributed on an\n",
+ "# \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY\n",
+ "# KIND, either express or implied. See the License for the\n",
+ "# specific language governing permissions and limitations\n",
+ "# under the License"
+ ],
+ "metadata": {
+ "id": "lBuUTzxD2mvJ"
+ },
+ "execution_count": 1,
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "# **Natural Language Processing Pipeline**\n",
+ "\n",
+ "**Note**: This example is used from
[here](https://github.com/rasalt/healthcarenlp/blob/main/nlp_public.ipynb).\n",
+ "\n",
+ "\n",
+ "\n",
+ "This example demonstrates how to set up an Apache Beam pipeline that
reads from a [Google Cloud Storage](https://https://cloud.google.com/storage)
file containing text from Shakespeare's work King Lear, tokenizes the text
lines into individual words, and performs a frequency count on each of those
words.\n",
Review Comment:
I see Healthcare NLP and a reference to Shakespeare's King Lear. May we
consider editing this?
##########
examples/notebooks/healthcare/beam_nlp.ipynb:
##########
@@ -0,0 +1,973 @@
+{
+ "nbformat": 4,
+ "nbformat_minor": 0,
+ "metadata": {
+ "colab": {
+ "provenance": [],
+ "include_colab_link": true
+ },
+ "kernelspec": {
+ "name": "python3",
+ "display_name": "Python 3"
+ },
+ "language_info": {
+ "name": "python"
+ }
+ },
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "view-in-github",
+ "colab_type": "text"
+ },
+ "source": [
+ "<a
href=\"https://colab.research.google.com/github/svetakvsundhar/beam/blob/healthcarenlp/examples/notebooks/healthcare/beam_nlp.ipynb\";
target=\"_parent\"><img
src=\"https://colab.research.google.com/assets/colab-badge.svg\"; alt=\"Open In
Colab\"/></a>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "# @title ###### Licensed to the Apache Software Foundation (ASF),
Version 2.0 (the \"License\")\n",
+ "\n",
+ "# Licensed to the Apache Software Foundation (ASF) under one\n",
+ "# or more contributor license agreements. See the NOTICE file\n",
+ "# distributed with this work for additional information\n",
+ "# regarding copyright ownership. The ASF licenses this file\n",
+ "# to you under the Apache License, Version 2.0 (the\n",
+ "# \"License\"); you may not use this file except in compliance\n",
+ "# with the License. You may obtain a copy of the License at\n",
+ "#\n",
+ "# http://www.apache.org/licenses/LICENSE-2.0\n";,
+ "#\n",
+ "# Unless required by applicable law or agreed to in writing,\n",
+ "# software distributed under the License is distributed on an\n",
+ "# \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY\n",
+ "# KIND, either express or implied. See the License for the\n",
+ "# specific language governing permissions and limitations\n",
+ "# under the License"
+ ],
+ "metadata": {
+ "id": "lBuUTzxD2mvJ"
+ },
+ "execution_count": 1,
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "# **Natural Language Processing Pipeline**\n",
+ "\n",
+ "**Note**: This example is used from
[here](https://github.com/rasalt/healthcarenlp/blob/main/nlp_public.ipynb).\n",
+ "\n",
+ "\n",
+ "\n",
+ "This example demonstrates how to set up an Apache Beam pipeline that
reads from a [Google Cloud Storage](https://https://cloud.google.com/storage)
file containing text from Shakespeare's work King Lear, tokenizes the text
lines into individual words, and performs a frequency count on each of those
words.\n",
+ "\n",
+ "An Apache Beam pipeline is a pipeline that reads input data,
transforms that data, and writes output data. It consists of PTransforms and
PCollections. A PCollection represents a distributed data set that your Beam
pipeline operates on. A PTransform represents a data processing operation, or a
step, in your pipeline. It takes one or more PCollections as input, performs a
processing function that you provide on the elements of that PCollection, and
produces zero or more output PCollection objects.\n",
+ "\n",
+ "For details about Apache Beam pipelines, including PTransforms and
PCollections, visit the [Beam Programming
Guide](https://beam.apache.org/documentation/programming-guide/).\n",
+ "\n",
+ "You'll be able to use this notebook to explore the data in each
PCollection."
+ ],
+ "metadata": {
+ "id": "nEUAYCTx4Ijj"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "Instructions\n",
+ "1. Set the variables in the next cell based upon your project and
preferences\n",
+ "2. The files referred to in this notebook nlpsample*.csv are in the
format with one\n",
+ "blurb of clinical note."
+ ],
+ "metadata": {
+ "id": "ZLBB0PTG5CHw"
+ }
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "pip install apache-beam[gcp]"
+ ],
+ "metadata": {
+ "colab": {
+ "base_uri": "https://localhost:8080/";
+ },
+ "id": "O7hq2sse8K4u",
+ "outputId": "c6f559a6-1419-43f2-b88d-49fedca1c686"
+ },
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "Requirement already satisfied: apache-beam[gcp] in
/usr/local/lib/python3.10/dist-packages (2.49.0)\n",
+ "Requirement already satisfied: crcmod<2.0,>=1.7 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.7)\n",
+ "Requirement already satisfied: orjson<4.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.9.2)\n",
+ "Requirement already satisfied: dill<0.3.2,>=0.3.1.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.3.1.1)\n",
+ "Requirement already satisfied: cloudpickle~=2.2.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.2.1)\n",
+ "Requirement already satisfied: fastavro<2,>=0.23.6 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.8.0)\n",
+ "Requirement already satisfied: fasteners<1.0,>=0.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.18)\n",
+ "Requirement already satisfied: grpcio!=1.48.0,<2,>=1.33.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.56.0)\n",
+ "Requirement already satisfied: hdfs<3.0.0,>=2.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.7.0)\n",
+ "Requirement already satisfied: httplib2<0.23.0,>=0.8 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.21.0)\n",
+ "Requirement already satisfied: numpy<1.25.0,>=1.14.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.22.4)\n",
+ "Requirement already satisfied: objsize<0.7.0,>=0.6.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.6.1)\n",
+ "Requirement already satisfied: pymongo<5.0.0,>=3.8.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (4.4.1)\n",
+ "Requirement already satisfied: proto-plus<2,>=1.7.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.22.3)\n",
+ "Requirement already satisfied: protobuf<4.24.0,>=3.20.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.20.3)\n",
+ "Requirement already satisfied: pydot<2,>=1.2.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.4.2)\n",
+ "Requirement already satisfied: python-dateutil<3,>=2.8.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.8.2)\n",
+ "Requirement already satisfied: pytz>=2018.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2022.7.1)\n",
+ "Requirement already satisfied: regex>=2020.6.8 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2022.10.31)\n",
+ "Requirement already satisfied: requests<3.0.0,>=2.24.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.27.1)\n",
+ "Requirement already satisfied: typing-extensions>=3.7.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (4.7.1)\n",
+ "Requirement already satisfied: zstandard<1,>=0.18.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.21.0)\n",
+ "Requirement already satisfied: pyarrow<12.0.0,>=3.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (9.0.0)\n",
+ "Requirement already satisfied: cachetools<6,>=3.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (5.3.1)\n",
+ "Requirement already satisfied: google-apitools<0.5.32,>=0.5.31 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.5.31)\n",
+ "Requirement already satisfied: google-auth<3,>=1.18.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.17.3)\n",
+ "Requirement already satisfied: google-auth-httplib2<0.2.0,>=0.1.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.1.0)\n",
+ "Requirement already satisfied: google-cloud-datastore<3,>=2.0.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.15.2)\n",
+ "Requirement already satisfied: google-cloud-pubsub<3,>=2.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.18.0)\n",
+ "Requirement already satisfied: google-cloud-pubsublite<2,>=1.2.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.8.3)\n",
+ "Requirement already satisfied: google-cloud-bigquery<4,>=2.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.10.0)\n",
+ "Requirement already satisfied:
google-cloud-bigquery-storage<3,>=2.6.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.22.0)\n",
+ "Requirement already satisfied: google-cloud-core<3,>=2.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.3.3)\n",
+ "Requirement already satisfied: google-cloud-bigtable<3,>=2.19.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.19.0)\n",
+ "Requirement already satisfied: google-cloud-spanner<4,>=3.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.36.0)\n",
+ "Requirement already satisfied: google-cloud-dlp<4,>=3.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.12.2)\n",
+ "Requirement already satisfied: google-cloud-language<3,>=2.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.9.1)\n",
+ "Requirement already satisfied:
google-cloud-videointelligence<3,>=2.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.11.3)\n",
+ "Requirement already satisfied: google-cloud-vision<4,>=2 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.4.4)\n",
+ "Requirement already satisfied:
google-cloud-recommendations-ai<0.11.0,>=0.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.10.4)\n",
+ "Requirement already satisfied:
google-cloud-aiplatform<2.0,>=1.26.0 in /usr/local/lib/python3.10/dist-packages
(from apache-beam[gcp]) (1.28.0)\n",
+ "Requirement already satisfied: oauth2client>=1.4.12 in
/usr/local/lib/python3.10/dist-packages (from
google-apitools<0.5.32,>=0.5.31->apache-beam[gcp]) (4.1.3)\n",
+ "Requirement already satisfied: six>=1.12.0 in
/usr/local/lib/python3.10/dist-packages (from
google-apitools<0.5.32,>=0.5.31->apache-beam[gcp]) (1.16.0)\n",
+ "Requirement already satisfied: pyasn1-modules>=0.2.1 in
/usr/local/lib/python3.10/dist-packages (from
google-auth<3,>=1.18.0->apache-beam[gcp]) (0.3.0)\n",
+ "Requirement already satisfied: rsa<5,>=3.1.4 in
/usr/local/lib/python3.10/dist-packages (from
google-auth<3,>=1.18.0->apache-beam[gcp]) (4.9)\n",
+ "Requirement already satisfied:
google-api-core[grpc]!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.*,!=2.4.*,!=2.5.*,!=2.6.*,!=2.7.*,<3.0.0dev,>=1.32.0
in /usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (2.11.1)\n",
+ "Requirement already satisfied: packaging>=14.3 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (23.1)\n",
+ "Requirement already satisfied:
google-cloud-storage<3.0.0dev,>=1.32.0 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (2.8.0)\n",
+ "Requirement already satisfied:
google-cloud-resource-manager<3.0.0dev,>=1.3.3 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (1.10.2)\n",
+ "Requirement already satisfied: shapely<2.0.0 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (1.8.5.post1)\n",
+ "Requirement already satisfied:
google-resumable-media<3.0dev,>=0.6.0 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-bigquery<4,>=2.0.0->apache-beam[gcp]) (2.5.0)\n",
+ "Requirement already satisfied:
grpc-google-iam-v1<1.0.0dev,>=0.12.4 in /usr/local/lib/python3.10/dist-packages
(from google-cloud-bigtable<3,>=2.19.0->apache-beam[gcp]) (0.12.6)\n",
+ "Requirement already satisfied: grpcio-status>=1.33.2 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-pubsub<3,>=2.1.0->apache-beam[gcp]) (1.48.2)\n",
+ "Requirement already satisfied: overrides<7.0.0,>=6.0.1 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-pubsublite<2,>=1.2.0->apache-beam[gcp]) (6.5.0)\n",
+ "Requirement already satisfied: sqlparse>=0.4.4 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-spanner<4,>=3.0.0->apache-beam[gcp]) (0.4.4)\n",
+ "Requirement already satisfied: docopt in
/usr/local/lib/python3.10/dist-packages (from
hdfs<3.0.0,>=2.1.0->apache-beam[gcp]) (0.6.2)\n",
+ "Requirement already satisfied:
pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in
/usr/local/lib/python3.10/dist-packages (from
httplib2<0.23.0,>=0.8->apache-beam[gcp]) (3.1.0)\n",
+ "Requirement already satisfied: dnspython<3.0.0,>=1.16.0 in
/usr/local/lib/python3.10/dist-packages (from
pymongo<5.0.0,>=3.8.0->apache-beam[gcp]) (2.4.0)\n",
+ "Requirement already satisfied: urllib3<1.27,>=1.21.1 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (1.26.16)\n",
+ "Requirement already satisfied: certifi>=2017.4.17 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (2023.5.7)\n",
+ "Requirement already satisfied: charset-normalizer~=2.0.0 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (2.0.12)\n",
+ "Requirement already satisfied: idna<4,>=2.5 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (3.4)\n",
+ "Requirement already satisfied: httpcore>=0.17.3 in
/usr/local/lib/python3.10/dist-packages (from
dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp]) (0.17.3)\n",
+ "Requirement already satisfied: sniffio<2.0,>=1.1 in
/usr/local/lib/python3.10/dist-packages (from
dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp]) (1.3.0)\n",
+ "Requirement already satisfied:
googleapis-common-protos<2.0.dev0,>=1.56.2 in
/usr/local/lib/python3.10/dist-packages (from
google-api-core[grpc]!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.*,!=2.4.*,!=2.5.*,!=2.6.*,!=2.7.*,<3.0.0dev,>=1.32.0->google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp])
(1.59.1)\n",
+ "Requirement already satisfied: google-crc32c<2.0dev,>=1.0 in
/usr/local/lib/python3.10/dist-packages (from
google-resumable-media<3.0dev,>=0.6.0->google-cloud-bigquery<4,>=2.0.0->apache-beam[gcp])
(1.5.0)\n",
+ "Requirement already satisfied: pyasn1>=0.1.7 in
/usr/local/lib/python3.10/dist-packages (from
oauth2client>=1.4.12->google-apitools<0.5.32,>=0.5.31->apache-beam[gcp])
(0.5.0)\n",
+ "Requirement already satisfied: h11<0.15,>=0.13 in
/usr/local/lib/python3.10/dist-packages (from
httpcore>=0.17.3->dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp])
(0.14.0)\n",
+ "Requirement already satisfied: anyio<5.0,>=3.0 in
/usr/local/lib/python3.10/dist-packages (from
httpcore>=0.17.3->dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp])
(3.7.1)\n",
+ "Requirement already satisfied: exceptiongroup in
/usr/local/lib/python3.10/dist-packages (from
anyio<5.0,>=3.0->httpcore>=0.17.3->dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp])
(1.1.2)\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "#Change this variable to True if you want to debug the Interactive
Runner Pipeline else it uses Dataflow\n",
+ "debug = False\n",
+ "DATASET=\"<YOUR_DATASET_NAME>\"\n",
+ "TEMP_LOCATION=\"<YOUR_TEMP_LOCATION>\"\n",
+ "PROJECT='<YOUR_PROJECT_ID>'\n",
+ "LOCATION='us-central1'\n",
+ "URL='https://healthcare.googleapis.com/v1/projects/'+PROJECT+
'/locations/'+LOCATION+'/services/nlp:analyzeEntities'\n",
+
"NLP_SERVICE='projects/'+PROJECT+'/locations/'+LOCATION+'/services/nlp'\n",
Review Comment:
Could you use python's f-string syntax instead of concatenating using '+'?
##########
examples/notebooks/healthcare/beam_nlp.ipynb:
##########
@@ -0,0 +1,973 @@
+{
+ "nbformat": 4,
+ "nbformat_minor": 0,
+ "metadata": {
+ "colab": {
+ "provenance": [],
+ "include_colab_link": true
+ },
+ "kernelspec": {
+ "name": "python3",
+ "display_name": "Python 3"
+ },
+ "language_info": {
+ "name": "python"
+ }
+ },
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "view-in-github",
+ "colab_type": "text"
+ },
+ "source": [
+ "<a
href=\"https://colab.research.google.com/github/svetakvsundhar/beam/blob/healthcarenlp/examples/notebooks/healthcare/beam_nlp.ipynb\";
target=\"_parent\"><img
src=\"https://colab.research.google.com/assets/colab-badge.svg\"; alt=\"Open In
Colab\"/></a>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "# @title ###### Licensed to the Apache Software Foundation (ASF),
Version 2.0 (the \"License\")\n",
+ "\n",
+ "# Licensed to the Apache Software Foundation (ASF) under one\n",
+ "# or more contributor license agreements. See the NOTICE file\n",
+ "# distributed with this work for additional information\n",
+ "# regarding copyright ownership. The ASF licenses this file\n",
+ "# to you under the Apache License, Version 2.0 (the\n",
+ "# \"License\"); you may not use this file except in compliance\n",
+ "# with the License. You may obtain a copy of the License at\n",
+ "#\n",
+ "# http://www.apache.org/licenses/LICENSE-2.0\n";,
+ "#\n",
+ "# Unless required by applicable law or agreed to in writing,\n",
+ "# software distributed under the License is distributed on an\n",
+ "# \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY\n",
+ "# KIND, either express or implied. See the License for the\n",
+ "# specific language governing permissions and limitations\n",
+ "# under the License"
+ ],
+ "metadata": {
+ "id": "lBuUTzxD2mvJ"
+ },
+ "execution_count": 1,
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "# **Natural Language Processing Pipeline**\n",
+ "\n",
+ "**Note**: This example is used from
[here](https://github.com/rasalt/healthcarenlp/blob/main/nlp_public.ipynb).\n",
+ "\n",
+ "\n",
+ "\n",
+ "This example demonstrates how to set up an Apache Beam pipeline that
reads from a [Google Cloud Storage](https://https://cloud.google.com/storage)
file containing text from Shakespeare's work King Lear, tokenizes the text
lines into individual words, and performs a frequency count on each of those
words.\n",
+ "\n",
+ "An Apache Beam pipeline is a pipeline that reads input data,
transforms that data, and writes output data. It consists of PTransforms and
PCollections. A PCollection represents a distributed data set that your Beam
pipeline operates on. A PTransform represents a data processing operation, or a
step, in your pipeline. It takes one or more PCollections as input, performs a
processing function that you provide on the elements of that PCollection, and
produces zero or more output PCollection objects.\n",
+ "\n",
+ "For details about Apache Beam pipelines, including PTransforms and
PCollections, visit the [Beam Programming
Guide](https://beam.apache.org/documentation/programming-guide/).\n",
+ "\n",
+ "You'll be able to use this notebook to explore the data in each
PCollection."
+ ],
+ "metadata": {
+ "id": "nEUAYCTx4Ijj"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "Instructions\n",
+ "1. Set the variables in the next cell based upon your project and
preferences\n",
+ "2. The files referred to in this notebook nlpsample*.csv are in the
format with one\n",
+ "blurb of clinical note."
+ ],
+ "metadata": {
+ "id": "ZLBB0PTG5CHw"
+ }
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "pip install apache-beam[gcp]"
+ ],
+ "metadata": {
+ "colab": {
+ "base_uri": "https://localhost:8080/";
+ },
+ "id": "O7hq2sse8K4u",
+ "outputId": "c6f559a6-1419-43f2-b88d-49fedca1c686"
+ },
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "Requirement already satisfied: apache-beam[gcp] in
/usr/local/lib/python3.10/dist-packages (2.49.0)\n",
+ "Requirement already satisfied: crcmod<2.0,>=1.7 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.7)\n",
+ "Requirement already satisfied: orjson<4.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.9.2)\n",
+ "Requirement already satisfied: dill<0.3.2,>=0.3.1.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.3.1.1)\n",
+ "Requirement already satisfied: cloudpickle~=2.2.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.2.1)\n",
+ "Requirement already satisfied: fastavro<2,>=0.23.6 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.8.0)\n",
+ "Requirement already satisfied: fasteners<1.0,>=0.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.18)\n",
+ "Requirement already satisfied: grpcio!=1.48.0,<2,>=1.33.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.56.0)\n",
+ "Requirement already satisfied: hdfs<3.0.0,>=2.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.7.0)\n",
+ "Requirement already satisfied: httplib2<0.23.0,>=0.8 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.21.0)\n",
+ "Requirement already satisfied: numpy<1.25.0,>=1.14.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.22.4)\n",
+ "Requirement already satisfied: objsize<0.7.0,>=0.6.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.6.1)\n",
+ "Requirement already satisfied: pymongo<5.0.0,>=3.8.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (4.4.1)\n",
+ "Requirement already satisfied: proto-plus<2,>=1.7.1 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.22.3)\n",
+ "Requirement already satisfied: protobuf<4.24.0,>=3.20.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.20.3)\n",
+ "Requirement already satisfied: pydot<2,>=1.2.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.4.2)\n",
+ "Requirement already satisfied: python-dateutil<3,>=2.8.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.8.2)\n",
+ "Requirement already satisfied: pytz>=2018.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2022.7.1)\n",
+ "Requirement already satisfied: regex>=2020.6.8 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2022.10.31)\n",
+ "Requirement already satisfied: requests<3.0.0,>=2.24.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.27.1)\n",
+ "Requirement already satisfied: typing-extensions>=3.7.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (4.7.1)\n",
+ "Requirement already satisfied: zstandard<1,>=0.18.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.21.0)\n",
+ "Requirement already satisfied: pyarrow<12.0.0,>=3.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (9.0.0)\n",
+ "Requirement already satisfied: cachetools<6,>=3.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (5.3.1)\n",
+ "Requirement already satisfied: google-apitools<0.5.32,>=0.5.31 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.5.31)\n",
+ "Requirement already satisfied: google-auth<3,>=1.18.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.17.3)\n",
+ "Requirement already satisfied: google-auth-httplib2<0.2.0,>=0.1.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.1.0)\n",
+ "Requirement already satisfied: google-cloud-datastore<3,>=2.0.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.15.2)\n",
+ "Requirement already satisfied: google-cloud-pubsub<3,>=2.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.18.0)\n",
+ "Requirement already satisfied: google-cloud-pubsublite<2,>=1.2.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (1.8.3)\n",
+ "Requirement already satisfied: google-cloud-bigquery<4,>=2.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.10.0)\n",
+ "Requirement already satisfied:
google-cloud-bigquery-storage<3,>=2.6.3 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.22.0)\n",
+ "Requirement already satisfied: google-cloud-core<3,>=2.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.3.3)\n",
+ "Requirement already satisfied: google-cloud-bigtable<3,>=2.19.0
in /usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.19.0)\n",
+ "Requirement already satisfied: google-cloud-spanner<4,>=3.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.36.0)\n",
+ "Requirement already satisfied: google-cloud-dlp<4,>=3.0.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.12.2)\n",
+ "Requirement already satisfied: google-cloud-language<3,>=2.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.9.1)\n",
+ "Requirement already satisfied:
google-cloud-videointelligence<3,>=2.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (2.11.3)\n",
+ "Requirement already satisfied: google-cloud-vision<4,>=2 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (3.4.4)\n",
+ "Requirement already satisfied:
google-cloud-recommendations-ai<0.11.0,>=0.1.0 in
/usr/local/lib/python3.10/dist-packages (from apache-beam[gcp]) (0.10.4)\n",
+ "Requirement already satisfied:
google-cloud-aiplatform<2.0,>=1.26.0 in /usr/local/lib/python3.10/dist-packages
(from apache-beam[gcp]) (1.28.0)\n",
+ "Requirement already satisfied: oauth2client>=1.4.12 in
/usr/local/lib/python3.10/dist-packages (from
google-apitools<0.5.32,>=0.5.31->apache-beam[gcp]) (4.1.3)\n",
+ "Requirement already satisfied: six>=1.12.0 in
/usr/local/lib/python3.10/dist-packages (from
google-apitools<0.5.32,>=0.5.31->apache-beam[gcp]) (1.16.0)\n",
+ "Requirement already satisfied: pyasn1-modules>=0.2.1 in
/usr/local/lib/python3.10/dist-packages (from
google-auth<3,>=1.18.0->apache-beam[gcp]) (0.3.0)\n",
+ "Requirement already satisfied: rsa<5,>=3.1.4 in
/usr/local/lib/python3.10/dist-packages (from
google-auth<3,>=1.18.0->apache-beam[gcp]) (4.9)\n",
+ "Requirement already satisfied:
google-api-core[grpc]!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.*,!=2.4.*,!=2.5.*,!=2.6.*,!=2.7.*,<3.0.0dev,>=1.32.0
in /usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (2.11.1)\n",
+ "Requirement already satisfied: packaging>=14.3 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (23.1)\n",
+ "Requirement already satisfied:
google-cloud-storage<3.0.0dev,>=1.32.0 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (2.8.0)\n",
+ "Requirement already satisfied:
google-cloud-resource-manager<3.0.0dev,>=1.3.3 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (1.10.2)\n",
+ "Requirement already satisfied: shapely<2.0.0 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp]) (1.8.5.post1)\n",
+ "Requirement already satisfied:
google-resumable-media<3.0dev,>=0.6.0 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-bigquery<4,>=2.0.0->apache-beam[gcp]) (2.5.0)\n",
+ "Requirement already satisfied:
grpc-google-iam-v1<1.0.0dev,>=0.12.4 in /usr/local/lib/python3.10/dist-packages
(from google-cloud-bigtable<3,>=2.19.0->apache-beam[gcp]) (0.12.6)\n",
+ "Requirement already satisfied: grpcio-status>=1.33.2 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-pubsub<3,>=2.1.0->apache-beam[gcp]) (1.48.2)\n",
+ "Requirement already satisfied: overrides<7.0.0,>=6.0.1 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-pubsublite<2,>=1.2.0->apache-beam[gcp]) (6.5.0)\n",
+ "Requirement already satisfied: sqlparse>=0.4.4 in
/usr/local/lib/python3.10/dist-packages (from
google-cloud-spanner<4,>=3.0.0->apache-beam[gcp]) (0.4.4)\n",
+ "Requirement already satisfied: docopt in
/usr/local/lib/python3.10/dist-packages (from
hdfs<3.0.0,>=2.1.0->apache-beam[gcp]) (0.6.2)\n",
+ "Requirement already satisfied:
pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in
/usr/local/lib/python3.10/dist-packages (from
httplib2<0.23.0,>=0.8->apache-beam[gcp]) (3.1.0)\n",
+ "Requirement already satisfied: dnspython<3.0.0,>=1.16.0 in
/usr/local/lib/python3.10/dist-packages (from
pymongo<5.0.0,>=3.8.0->apache-beam[gcp]) (2.4.0)\n",
+ "Requirement already satisfied: urllib3<1.27,>=1.21.1 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (1.26.16)\n",
+ "Requirement already satisfied: certifi>=2017.4.17 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (2023.5.7)\n",
+ "Requirement already satisfied: charset-normalizer~=2.0.0 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (2.0.12)\n",
+ "Requirement already satisfied: idna<4,>=2.5 in
/usr/local/lib/python3.10/dist-packages (from
requests<3.0.0,>=2.24.0->apache-beam[gcp]) (3.4)\n",
+ "Requirement already satisfied: httpcore>=0.17.3 in
/usr/local/lib/python3.10/dist-packages (from
dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp]) (0.17.3)\n",
+ "Requirement already satisfied: sniffio<2.0,>=1.1 in
/usr/local/lib/python3.10/dist-packages (from
dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp]) (1.3.0)\n",
+ "Requirement already satisfied:
googleapis-common-protos<2.0.dev0,>=1.56.2 in
/usr/local/lib/python3.10/dist-packages (from
google-api-core[grpc]!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.*,!=2.4.*,!=2.5.*,!=2.6.*,!=2.7.*,<3.0.0dev,>=1.32.0->google-cloud-aiplatform<2.0,>=1.26.0->apache-beam[gcp])
(1.59.1)\n",
+ "Requirement already satisfied: google-crc32c<2.0dev,>=1.0 in
/usr/local/lib/python3.10/dist-packages (from
google-resumable-media<3.0dev,>=0.6.0->google-cloud-bigquery<4,>=2.0.0->apache-beam[gcp])
(1.5.0)\n",
+ "Requirement already satisfied: pyasn1>=0.1.7 in
/usr/local/lib/python3.10/dist-packages (from
oauth2client>=1.4.12->google-apitools<0.5.32,>=0.5.31->apache-beam[gcp])
(0.5.0)\n",
+ "Requirement already satisfied: h11<0.15,>=0.13 in
/usr/local/lib/python3.10/dist-packages (from
httpcore>=0.17.3->dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp])
(0.14.0)\n",
+ "Requirement already satisfied: anyio<5.0,>=3.0 in
/usr/local/lib/python3.10/dist-packages (from
httpcore>=0.17.3->dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp])
(3.7.1)\n",
+ "Requirement already satisfied: exceptiongroup in
/usr/local/lib/python3.10/dist-packages (from
anyio<5.0,>=3.0->httpcore>=0.17.3->dnspython<3.0.0,>=1.16.0->pymongo<5.0.0,>=3.8.0->apache-beam[gcp])
(1.1.2)\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "#Change this variable to True if you want to debug the Interactive
Runner Pipeline else it uses Dataflow\n",
+ "debug = False\n",
+ "DATASET=\"<YOUR_DATASET_NAME>\"\n",
+ "TEMP_LOCATION=\"<YOUR_TEMP_LOCATION>\"\n",
+ "PROJECT='<YOUR_PROJECT_ID>'\n",
+ "LOCATION='us-central1'\n",
+ "URL='https://healthcare.googleapis.com/v1/projects/'+PROJECT+
'/locations/'+LOCATION+'/services/nlp:analyzeEntities'\n",
+
"NLP_SERVICE='projects/'+PROJECT+'/locations/'+LOCATION+'/services/nlp'\n",
+ "GCS_BUCKET=PROJECT"
+ ],
+ "metadata": {
+ "id": "s9lhe5CZ5F3o"
+ },
+ "execution_count": null,
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "**BigQuery Setup**\n",
+ "\n",
+ "We will be using BigQuery to warehouse the structured data revealed
in the output of the Healthcare NLP API. For this purpose I create 3 tables to
organize the data"
Review Comment:
In tutorial speech, might this say "For this purpose we create ..."
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: [email protected]
For queries about this service, please contact Infrastructure at:
[email protected]
![https://colab.research.google.com/assets/colab-badge.svg\"](https://colab.research.google.com/assets/colab-badge.svg\"){kind=link}