Execute-in-terminal/Polly-CLI

Execute-in-terminal/Polly-CLI

1. Install/update Polly CLI Polly CLI - Polly Documentation or open up a notebook on polly with the smallest machine possible (as it already has Polly CLI pre-installed)

   Quick installation guide

   
   

   Installation

   Dependencies Required for Polly CLI

   The following dependencies are required to be installed before installing Polly CLI:

   • Node and npm:

     • Linux: For installation on Linux, follow the steps mentioned here.

     • Mac: For installation on Mac, follow the steps mentioned here.

   Commands to install

   To install Polly CLI, run the following commands on Terminal / Command prompt:

   • Linux:

     sudo npm install -g @elucidatainc/pollycli
     

   • Mac:

     npm install -g @elucidatainc/pollycli
     

2. Open your terminal or polly notebook code using bash:

   Currently a small step has to be done for configuring your polly CLI. Please copy paste these codes on a terminal.

   echo 'const axios = require("axios");
   const chalk = require("chalk");
   const pollyEnv = require("./env.json");
   const pollymsg = require("./message");
   const { getHeaders } = require("./pollyheaders");
   
   const getWorkflowClient = async () => {
       const{ headers } = await getHeaders();
       const workflowClient = axios.create({
           baseURL: `${pollyEnv.computeApi}/workflow`,
           headers
       });
   
       return workflowClient;
   }
   
   export const submitWorkflow = async (workspace_id, config) => {
       try {
           const workflowClient = await getWorkflowClient();
           let { pipeline, main_script, container } = config;
   
           if(!pipeline.endsWith("/")) {
               pipeline = pipeline + "/";
           }
   
           const body = {
               workspace_id,
               pipeline,
           }
   
           if(!!container) {
               body.container = container;
           }
   
           if(!!main_script) {
               body.main_script = main_script
           }
   
           const res = await workflowClient.post("/", body);
           pollymsg.pollySuccess(`${res.data.message}, run_id = ${res.data.id}`);
           console.log(chalk.bold(`status: polly workflows status --run-id=${res.data.id}`));
           console.log(chalk.bold(`logs  : polly workflows logs --run-id=${res.data.id}`));
           console.log(chalk.bold(`cancel: polly workflows cancel --run-id=${res.data.id}`));
       } catch(e) {
           if(e.response && e.response.data) {
               pollymsg.pollyError(e.response.data.detail);
           }
           pollymsg.pollyError(e.message);
       }
   }
   
   export const deleteWorkflow = async (run_id) => {
       try {
           const workflowClient = await getWorkflowClient();
           const res = await workflowClient.delete(`/${run_id}`);
           pollymsg.pollySuccess("workflow execution terminated");
       } catch(e) {
           if(e.response && e.response.data) {
               pollymsg.pollyError(e.response.data.detail);
           }
           pollymsg.pollyError(e.message);
       }
   }
   
   export const getWorkflow = async (run_id) => {
       try {
           const workflowClient = await getWorkflowClient();
           const res = await workflowClient.get(`/${run_id}`);
           if(res.data.status === "failed") {
               console.log(chalk.bold.red(`workflow ${res.data.status}`));
           } else {
               console.log(chalk.bold.green(`workflow ${res.data.status}`))
           }
       } catch(e) {
           if(e.response && e.response.data) {
               pollymsg.pollyError(e.response.data.detail);
           }
           pollymsg.pollyError(e.message);
       }
   }
   
   export const getWorkflowLogs = async (run_id) => {
       try {
           const workflowClient = await getWorkflowClient();
           const res = await workflowClient.get(`/${run_id}/logs`);
           if(res.data.logs.length === 0) {
               console.log("logs not yet generated");
               return;
           }
   
           console.log(chalk.bold.italic("logs:"));
           console.log(res.data.logs);
       } catch(e) {
           if(e.response && e.response.data) {
               pollymsg.pollyError(e.response.data.detail);
           }
           pollymsg.pollyError(e.message);
       }
   }'>./workflows.js
   sudo mv ./workflows.js /usr/lib/node_modules/@elucidatainc/pollycli/src/workflows.js
   cat /usr/lib/node_modules/@elucidatainc/pollycli/src/workflows.js
   

3. Now open up your terminal and type:

   polly workflows submit \
   --workspace-id <******> \
   --pipeline <name of the folder> \
   --main-script main.nf \
   --container <docker image>
   

   Eg:

   polly workflows submit \
   --workspace-id 9810 \
   --pipeline Demo \
   --main-script main.nf \
   --container docker.polly.elucidata.io/elucidata/ic_exp:nf
   

   - Run the command 4. You will get 3 commands to see the status or check the logs or to cancel the workflow.

4. Just copy paste and run each of these command from the output and you’ll be able to check the status, log or cancel the run.

   

5. 

Reading the output has been explained in detail at the end

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