|
| 1 | +{ |
| 2 | + "cells": [ |
| 3 | + { |
| 4 | + "cell_type": "markdown", |
| 5 | + "metadata": {}, |
| 6 | + "source": [ |
| 7 | + "# UCSC Toil Workflow Execution Service Demonstration\n", |
| 8 | + "\n", |
| 9 | + "<img src=\"https://github.com/dockstore/dockstore-ui2/raw/develop/src/assets/images/sponsors/coloured/ga4gh.png\" width=\"180\" align=\"right\"/>\n", |
| 10 | + "\n", |
| 11 | + "<img src=\"https://cgl.genomics.ucsc.edu/wp-content/uploads/2017/07/TOIL-Slug-Logo-862x1116.jpg\" width=\"200\" align=\"right\"/>\n", |
| 12 | + "\n", |
| 13 | + "This notebook is meant to contain all of the necessary parts needed to install and run the [Workflow Execution Service](https://github.com/ga4gh/workflow-execution-service-schemas) backed by [UCSC Toil](https://toil.readthedocs.io/en/3.15.0/) on a linux compliant system with Python installed!\n", |
| 14 | + "\n", |
| 15 | + "The Workflow Execution Service attempts to present the interface for workflow execution over HTTP methods. Simple JSON requests including the inputs and outputs for a workflow are sent to a service. This allows us to \"ship code to the data,\" since data privacy and egress costs require that data is not shared.\n", |
| 16 | + "\n", |
| 17 | + "UCSC Toil is software for executing workflows. It presents a Python native API, which will not be demonstrated here, as well as a CWL compliant CLI interface. For that reason, any CWLRunner can easily be exposed by the workflow-service, demonstrated here.\n", |
| 18 | + "\n", |
| 19 | + "## Installing the Dependencies\n", |
| 20 | + "\n", |
| 21 | + "[Docker](https://docs.docker.com/install/) is a required dependency to make workflow execution portable in this example. So install that first.\n", |
| 22 | + "\n", |
| 23 | + "Once you have docker installed, you can follow the below instructions, which will use Python's package manager to download the requirements." |
| 24 | + ] |
| 25 | + }, |
| 26 | + { |
| 27 | + "cell_type": "code", |
| 28 | + "execution_count": null, |
| 29 | + "metadata": {}, |
| 30 | + "outputs": [], |
| 31 | + "source": [ |
| 32 | + "!pip install toil git+git://github.com/common-workflow-language/workflow-service" |
| 33 | + ] |
| 34 | + }, |
| 35 | + { |
| 36 | + "cell_type": "markdown", |
| 37 | + "metadata": {}, |
| 38 | + "source": [ |
| 39 | + "If you have trouble executing that line, try putting it into a terminal. Depending on your Python installation, you may need to enter your password." |
| 40 | + ] |
| 41 | + }, |
| 42 | + { |
| 43 | + "cell_type": "markdown", |
| 44 | + "metadata": {}, |
| 45 | + "source": [ |
| 46 | + "## Starting the Server" |
| 47 | + ] |
| 48 | + }, |
| 49 | + { |
| 50 | + "cell_type": "markdown", |
| 51 | + "metadata": {}, |
| 52 | + "source": [ |
| 53 | + "Now that you have toil and the workflow-service installed, you just have to turn on the server, and it will be ready to accept requests!\n", |
| 54 | + "\n", |
| 55 | + "We'll have to tell the service which runner to use, the CWL runner which comes with the service, and the optional tool to use to run it, in this case `cwltoil`. Lastly, we lower the log output of toil so that the output JSON can be read by the wes-server (and returned to the client)." |
| 56 | + ] |
| 57 | + }, |
| 58 | + { |
| 59 | + "cell_type": "code", |
| 60 | + "execution_count": 5, |
| 61 | + "metadata": {}, |
| 62 | + "outputs": [ |
| 63 | + { |
| 64 | + "name": "stdout", |
| 65 | + "output_type": "stream", |
| 66 | + "text": [ |
| 67 | + " * Running on http://0.0.0.0:8080/ (Press CTRL+C to quit)\n", |
| 68 | + "^C\n" |
| 69 | + ] |
| 70 | + } |
| 71 | + ], |
| 72 | + "source": [ |
| 73 | + "!wes-server --backend=wes_service.cwl_runner --opt runner=cwltoil --opt extra=--logLevel=CRITICAL" |
| 74 | + ] |
| 75 | + }, |
| 76 | + { |
| 77 | + "cell_type": "markdown", |
| 78 | + "metadata": {}, |
| 79 | + "source": [ |
| 80 | + "Background processes aren't supported directly in notebooks, so we close it here. But you can paste this command in a terminal and it will bring up your very own Workflow Execution Service!" |
| 81 | + ] |
| 82 | + }, |
| 83 | + { |
| 84 | + "cell_type": "markdown", |
| 85 | + "metadata": {}, |
| 86 | + "source": [ |
| 87 | + "## Using the Client\n", |
| 88 | + "\n", |
| 89 | + "The server is now running, but Toil hasn't started yet as we haven't issued any Workflow Execution requests. Here, using the provided CLI client, we demonstrate a simple workflow which calculates an md5sum.\n", |
| 90 | + "\n", |
| 91 | + "The workflow description is provided in the workflow-service test data, and we specify local inputs and outputs. `File` is currently the only supported file system protocol of the workflow-service." |
| 92 | + ] |
| 93 | + }, |
| 94 | + { |
| 95 | + "cell_type": "markdown", |
| 96 | + "metadata": {}, |
| 97 | + "source": [ |
| 98 | + "### Accessing a workflow via Dockstore Tool Registry Service\n", |
| 99 | + "\n", |
| 100 | + "We will start by accessing the metadata for a workflow from dockstore.\n", |
| 101 | + "\n", |
| 102 | + "#### List Tools\n" |
| 103 | + ] |
| 104 | + }, |
| 105 | + { |
| 106 | + "cell_type": "code", |
| 107 | + "execution_count": 17, |
| 108 | + "metadata": {}, |
| 109 | + "outputs": [ |
| 110 | + { |
| 111 | + "name": "stdout", |
| 112 | + "output_type": "stream", |
| 113 | + "text": [ |
| 114 | + "{u'verified': True, u'name': u'master', u'url': u'https://dockstore.org:8443/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/master', u'image': u'7f82fc51fa35d36bbd61297ee0c05170ab4ba67c969a9a66b28e5ed3c100034b', u'meta-version': u'2017-07-23 15:45:37.0', u'descriptor-type': [u'CWL', u'WDL'], u'dockerfile': True, u'id': u'quay.io/briandoconnor/dockstore-tool-md5sum:master', u'verified-source': u'Phase 1 GA4GH Tool Execution Challenge'}\n" |
| 115 | + ] |
| 116 | + } |
| 117 | + ], |
| 118 | + "source": [ |
| 119 | + "import requests\n", |
| 120 | + "response = requests.get('https://dockstore.org:8443/api/ga4gh/v1/tools/', params={\"name\": \"md5sum\"})\n", |
| 121 | + "print(response.json()[0]['versions'][0])\n", |
| 122 | + "md5sum_url = response.json()[0]['versions'][0]['url'] + '/plain-CWL/descriptor/%2FDockstore.cwl'" |
| 123 | + ] |
| 124 | + }, |
| 125 | + { |
| 126 | + "cell_type": "markdown", |
| 127 | + "metadata": {}, |
| 128 | + "source": [ |
| 129 | + "We now have a URL we can pass too WES for execution!" |
| 130 | + ] |
| 131 | + }, |
| 132 | + { |
| 133 | + "cell_type": "code", |
| 134 | + "execution_count": 18, |
| 135 | + "metadata": {}, |
| 136 | + "outputs": [ |
| 137 | + { |
| 138 | + "name": "stdout", |
| 139 | + "output_type": "stream", |
| 140 | + "text": [ |
| 141 | + "https://dockstore.org:8443/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/master/plain-CWL/descriptor/%2FDockstore.cwl\n" |
| 142 | + ] |
| 143 | + } |
| 144 | + ], |
| 145 | + "source": [ |
| 146 | + "print(md5sum_url)" |
| 147 | + ] |
| 148 | + }, |
| 149 | + { |
| 150 | + "cell_type": "markdown", |
| 151 | + "metadata": {}, |
| 152 | + "source": [ |
| 153 | + "### Using the WES CLI client to Execute" |
| 154 | + ] |
| 155 | + }, |
| 156 | + { |
| 157 | + "cell_type": "code", |
| 158 | + "execution_count": 19, |
| 159 | + "metadata": {}, |
| 160 | + "outputs": [ |
| 161 | + { |
| 162 | + "name": "stdout", |
| 163 | + "output_type": "stream", |
| 164 | + "text": [ |
| 165 | + "INFO:root:Workflow id is 1b7cbeac80e84740a450f2c6bc12b7f2\n", |
| 166 | + "INFO:root:State is COMPLETE\n", |
| 167 | + "INFO:root:\n", |
| 168 | + "{\n", |
| 169 | + " \"output_file\": {\n", |
| 170 | + " \"format\": \"http://edamontology.org/data_3671\", \n", |
| 171 | + " \"checksum\": \"sha1$5cd16de143136d95a0307bc1db27d88b57b033e9\", \n", |
| 172 | + " \"basename\": \"md5sum.txt\", \n", |
| 173 | + " \"nameext\": \".txt\", \n", |
| 174 | + " \"nameroot\": \"md5sum\", \n", |
| 175 | + " \"http://commonwl.org/cwltool#generation\": 0, \n", |
| 176 | + " \"location\": \"file:///home/david/git/workflow-service/workflows/1b7cbeac80e84740a450f2c6bc12b7f2/outdir/md5sum.txt\", \n", |
| 177 | + " \"class\": \"File\", \n", |
| 178 | + " \"size\": 33\n", |
| 179 | + " }\n", |
| 180 | + "}" |
| 181 | + ] |
| 182 | + } |
| 183 | + ], |
| 184 | + "source": [ |
| 185 | + "!wes-client --host localhost:8080 --proto http $md5sum_url testdata/md5sum.cwl.json" |
| 186 | + ] |
| 187 | + }, |
| 188 | + { |
| 189 | + "cell_type": "markdown", |
| 190 | + "metadata": {}, |
| 191 | + "source": [ |
| 192 | + "As you can see, the wes-client routed a request and polled the service until the its state was `COMPLETE`. It then shows us the location of the outputs, so we can read them." |
| 193 | + ] |
| 194 | + }, |
| 195 | + { |
| 196 | + "cell_type": "code", |
| 197 | + "execution_count": 20, |
| 198 | + "metadata": {}, |
| 199 | + "outputs": [ |
| 200 | + { |
| 201 | + "name": "stdout", |
| 202 | + "output_type": "stream", |
| 203 | + "text": [ |
| 204 | + "b1946ac92492d2347c6235b4d2611184\r\n" |
| 205 | + ] |
| 206 | + } |
| 207 | + ], |
| 208 | + "source": [ |
| 209 | + "!cat /home/david/git/workflow-service/workflows/1b7cbeac80e84740a450f2c6bc12b7f2/outdir/md5sum.txt" |
| 210 | + ] |
| 211 | + }, |
| 212 | + { |
| 213 | + "cell_type": "markdown", |
| 214 | + "metadata": {}, |
| 215 | + "source": [ |
| 216 | + "## Future Work\n", |
| 217 | + "\n", |
| 218 | + "Because toil implements the cwl CLI interface, it can be easily exchanged for a number of CWL runners. Although this demonstration works only for local files, it should be possible to demonstrate provisioners like those in Toil.\n", |
| 219 | + "\n", |
| 220 | + "Both the workflow-service and Toil are Python native applications, and this suggests a deeper integration is possible. Future demonstrations like these could use native Python code to interact with WES.\n", |
| 221 | + "\n", |
| 222 | + "Dockstore and the Tool Registry Service API could be used to first find the workflow that will be run, demonstrating interoperability in these services.\n", |
| 223 | + "\n", |
| 224 | + "By provisioning using DOS URLs, it should be possible for systems to reason about file locations whether they are system local or on a cloud." |
| 225 | + ] |
| 226 | + }, |
| 227 | + { |
| 228 | + "cell_type": "code", |
| 229 | + "execution_count": null, |
| 230 | + "metadata": {}, |
| 231 | + "outputs": [], |
| 232 | + "source": [] |
| 233 | + } |
| 234 | + ], |
| 235 | + "metadata": { |
| 236 | + "kernelspec": { |
| 237 | + "display_name": "env3", |
| 238 | + "language": "python", |
| 239 | + "name": "env3" |
| 240 | + }, |
| 241 | + "language_info": { |
| 242 | + "codemirror_mode": { |
| 243 | + "name": "ipython", |
| 244 | + "version": 2 |
| 245 | + }, |
| 246 | + "file_extension": ".py", |
| 247 | + "mimetype": "text/x-python", |
| 248 | + "name": "python", |
| 249 | + "nbconvert_exporter": "python", |
| 250 | + "pygments_lexer": "ipython2", |
| 251 | + "version": "2.7.12+" |
| 252 | + } |
| 253 | + }, |
| 254 | + "nbformat": 4, |
| 255 | + "nbformat_minor": 2 |
| 256 | +} |
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