gocra

gocra

gocra is a port to Cipres Restful API (CRA) using golang.

When using gocra alway consut the CRA User Guide along with gocra documentation.

gocra is capable of submmiting jobs, monitoring jobs status, download results and delete jobs.

You need a cra_auth.json file (the source code contais an example that can be edited) in your user home folder containing you credentials used to login to Cipres API.

{
    "url": "https://cipresrest.sdsc.edu/cipresrest/v1",
    "appid": "Your application ID",
    "username": "Your Username",
    "password": "Your Password"
}

Here is an example of gocran package usage:

package main

import (
    "fmt"
    "log"
    "os"
    "time"

    "github.com/Godrigos/gocra"
)

func main() {

    var jr gocra.JobResults
    var total float64
    jl := gocra.ListJobs()
    count := len(jl.Jobs.Jobstatus)

    // Ends the execution if there is no job on server.
    if count == 0 {
        fmt.Println("There are no jobs on Cipres servers.")
        os.Exit(0)
    }

    for i := range jl.Jobs.Jobstatus {
        job := gocra.JobStat(jl.Jobs.Jobstatus[i].SelfURI.URL)
        wdir := gocra.WorkDir(job)
        jr = gocra.JobResult(job)
        // Destination folder for the downloaded files
        destDir := "/home/user/Downloads"

        /* Based on job state passed by jobStage field from a JobStatus structure
           prints to stdout the actual job stage and download its results if the
           job is completed. */
        switch {
        case job.JobStage == "QUEUE":
            fmt.Printf("The job \033[41;1;37m%s\033[0m has been validated"+
                " and placed in CIPRES's queue.\n", job.Metadata.Entry.Value)
            fmt.Printf("  \u25CF Job Handle: %s.\n", job.JobHandle)

        case job.JobStage == "COMMANDRENDERING":
            fmt.Printf("The job \033[41;1;37m%s\033[0m has reached the head"+
                " of the queue and CIPRES has created the command line that"+
                " will be run.\n", job.Metadata.Entry.Value)
            fmt.Printf("  \u25CF Job Handle: %s.\n", job.JobHandle)

        case job.JobStage == "INPUTSTAGING":
            fmt.Printf("CIPRES has created a temporary working directory"+
                " for the job \033[41;1;37m%s\033[0m on the execution host"+
                " and copied the input files over.\n",
                job.Metadata.Entry.Value)
            fmt.Printf("  \u25CF Job Handle: %s.\n", job.JobHandle)

        case job.JobStage == "SUBMITTED":
            fmt.Printf("The job \033[41;1;37m%s\033[0m has been submited"+
                " to the scheduler on the execution host.\n",
                job.Metadata.Entry.Value)
            fmt.Printf("  \u25CF Job Handle: %s.\n", job.JobHandle)
            fmt.Println("  \u25cf Working Directory Files List:")
            for j := range wdir.Jobfiles.Jobfile {
                fmt.Printf("      %-25s %12.2f kB\n",
                    wdir.Jobfiles.Jobfile[j].Filename,
                    float64(wdir.Jobfiles.Jobfile[j].Length)/1000)
                total += float64(wdir.Jobfiles.Jobfile[j].Length) / 1000
            }
            fmt.Printf("  \u25CF Total size %29.2f kB\n\n", total)

        case job.JobStage == "LOAD_RESULTS":
            fmt.Printf("The job \033[41;1;37m%s\033[0m has finished running"+
                " on the execution host and CIPRES has begun to transfer the"+
                " results.\n", job.Metadata.Entry.Value)
            fmt.Printf("  \u25CF Job Handle: %s.\n", job.JobHandle)

        case job.JobStage == "COMPLETED":
            fmt.Printf("Job \033[41;1;37m%s\033[0m results successfully"+
                " transferred and available.\n", job.Metadata.Entry.Value)
            fmt.Printf("  \u25CF Job Handle: %s.\n", job.JobHandle)
            fmt.Println("  \u25cf Results Files List:")
            for j := range jr.Jobfiles.Jobfile {
                fmt.Printf("      %-25s %12.2f kB\n",
                    jr.Jobfiles.Jobfile[j].Filename,
                    float64(jr.Jobfiles.Jobfile[j].Length)/1000)
                total += float64(jr.Jobfiles.Jobfile[j].Length) / 1000
            }
            fmt.Printf("\nDownloading files of job %s (%.2f MB)...\n",
                job.Metadata.Entry.Value, total/1000)
            // Parallel downloading
            gocra.DownloadAll(jr, job, destDir)
            gocra.Delete(job.SelfURI.URL)

        default:
            fmt.Println("Can not define job state. Try again later!")
        }

        /* When there is more than one job on CIPRES server, applies a delay
           between jobs access, acconding to the MinPollIntervalSeconds
           field from a JobStatus structure */
        if count > 1 {
            time.Sleep(time.Duration(job.MinPollIntervalSeconds) * time.Second)
            count--
        }
    }
}