added getJobQueues function in Jobs module & some other fixes

NAMESPACE

@@ -6,5 +6,5 @@ export(SciDrive.createContainer,SciDrive.upload,SciDrive.publicUrl,SciDrive.down
 export(Config.isSciServerComputeEnvironment,Config.CasJobsRESTUri,Config.AuthenticationURL,Config.SciDriveHost,Config.SkyQueryUrl,Config.DataRelease,Config.SkyServerWSurl,Config.Version,Config.KeystoneTokenFilePath,Config.ComputeJobDirectoryFile,Config.RacmApiURL)
 export(SkyQuery.getJobStatus,SkyQuery.cancelJob,SkyQuery.listQueues,SkyQuery.getQueueInfo,SkyQuery.submitJob,SkyQuery.waitForJob,SkyQuery.listJobs,SkyQuery.listAllDatasets,SkyQuery.getDatasetInfo,SkyQuery.listDatasetTables,SkyQuery.getTableInfo,SkyQuery.listTableColumns,SkyQuery.getTable,SkyQuery.dropTable,SkyQuery.uploadTable)
 export(Files.getFileServices,Files.getFileServicesNames,Files.getFileServiceFromName,Files.__getFileServiceAPIUrl,Files.getRootVolumesInfo,Files.getDataVolumesInfo,Files.getUserVolumesInfo,Files.splitPath,Files.createUserVolume,Files.deleteUserVolume,Files.createDir,Files.delete,Files.upload,Files.download,Files.dirList,Files.move,Files.shareUserVolume)
-export(Jobs.getDockerComputeDomains,Jobs.getDockerComputeDomainsNames,Jobs.getDockerComputeDomainFromName,Jobs.getRDBComputeDomains,Jobs.getRDBComputeDomainsNames,Jobs.getRDBComputeDomainFromName,Jobs.getJobsList,Jobs.getDockerJobsListQuick,Jobs.getJobDescription,Jobs.getJobStatus,Jobs.submitNotebookJob,Jobs.submitShellCommandJob,Jobs.submitRDBQueryJob,Jobs.cancelJob,Jobs.waitForJob)
+export(Jobs.getDockerComputeDomains,Jobs.getDockerComputeDomainsNames,Jobs.getDockerComputeDomainFromName,Jobs.getRDBComputeDomains,Jobs.getRDBComputeDomainsNames,Jobs.getRDBComputeDomainFromName,Jobs.getJobsList,Jobs.getDockerJobsListQuick,Jobs.getJobDescription,Jobs.getJobStatus,Jobs.submitNotebookJob,Jobs.submitShellCommandJob,Jobs.submitRDBQueryJob,Jobs.cancelJob,Jobs.waitForJob,Jobs.getJobQueues)
 import(httr,jsonlite,utils,data.table)

R/Jobs.r

@@ -162,7 +162,7 @@ Jobs.getJobsList <- function(top=10, open=NULL, start=NULL, end=NULL, type="all"
       url = paste(Config.RacmApiURL,"/jobm/rest/dockerjobs?",sep="")
     }
 
-    url = paste(url,topString,startString,endString,"TaskName=",taskName,sep="")
+    url = paste(url,topString,startString,endString,openString,"TaskName=",taskName,sep="")
 
 
     r = GET(url,add_headers('X-Auth-Token'=token),accept("application/json"))
@@ -198,7 +198,7 @@ Jobs.getDockerJobsListQuick <- function(top=10, open=NULL, start=NULL, end=NULL,
 
 
     url = paste(Config.RacmApiURL,"/jobm/rest/dockerjobs/quick?",sep="")
-    url = paste(url,topString,startString,endString,"TaskName=",taskName,sep="")
+    url = paste(url,topString,startString,endString,labRegString,openString,"TaskName=",taskName,sep="")
 
     r = GET(url,add_headers('X-Auth-Token'=token),accept("application/json"))
 
@@ -212,6 +212,39 @@ Jobs.getDockerJobsListQuick <- function(top=10, open=NULL, start=NULL, end=NULL,
   }
 }
 
+Jobs.getJobQueues <- function(format="dataframe"){
+
+  token = Authentication.getToken()
+  if(!is.null(token) && token != "")
+  {
+
+    if(Config.isSciServerComputeEnvironment()){
+      taskName = "Compute.SciScript-R.Jobs.getJobQueues"
+    }else{
+      taskName = "SciScript-R.Jobs.getJobQueues"
+    }
+
+    url = paste(Config.RacmApiURL,"/jobm/rest/jobs/queues?","TaskName=",taskName,sep="")
+
+    r = GET(url,add_headers('X-Auth-Token'=token),accept("application/json"))
+
+    if(r$status_code != 200) {
+      stop(paste("Error when getting job queues from JOBM API.\nHttp Response from JOBM API returned status code ", r$status_code, ":\n",  content(r, as="text", encoding="UTF-8")))
+    } else {
+
+      if(format == "dataframe"){
+        r = fromJSON(content(r, "text", encoding="UTF-8"))
+        df <- data.frame(r$rows)
+        colnames(df) <- r$columns
+        return(df)
+      }else{
+        return(content(r))  
+      }
+    }
+  }else{
+    stop(paste("User token is not defined. First log into SciServer."))
+  }
+}
 
 Jobs.getJobDescription <- function(jobId){
 
@@ -316,7 +349,7 @@ Jobs.submitNotebookJob <- function(notebookPath, dockerComputeDomain=NULL, docke
           if(uVol$name == vol$name && uVol$rootVolumeName == vol$rootVolumeName && uVol$owner == vol$owner){
 
             found = TRUE
-            if(uVol$needsWriteAccess){
+            if(!is.null(uVol$needsWriteAccess)){
 
               if(uVol$needsWriteAccess == TRUE && ('write' %in% vol$allowedActions) ){
                 uVols[[length(uVols)+1]] <- list(userVolumeId= vol$id, needsWriteAccess= TRUE)
@@ -346,7 +379,7 @@ Jobs.submitNotebookJob <- function(notebookPath, dockerComputeDomain=NULL, docke
     if( is.null(dataVolumes)){
       for( i in 1:length(dockerComputeDomain$volumes)){
         vol = dockerComputeDomain$volumes[[i]]
-        if("write" %in% vol$allowedActions){
+        if(vol$writable){
           dataVols[[length(dataVols)+1]] <- list(id=vol$id, name= vol$name, writable=TRUE)
         }else{
           dataVols[[length(dataVols)+1]] <- list(id=vol$id, name= vol$name, writable=FALSE)
@@ -360,17 +393,17 @@ Jobs.submitNotebookJob <- function(notebookPath, dockerComputeDomain=NULL, docke
           vol = dockerComputeDomain$volumes[[j]]
           if( vol$name == dVol$name ){
             found = TRUE;
-            if(dVol$needsWriteAccess){
+            if(!is.null(dVol$needsWriteAccess)){
 
-              if(dVol$needsWriteAccess == TRUE && ('write' %in% vol$allowedActions) ){
+              if(dVol$needsWriteAccess == TRUE){
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= TRUE)
               }else{
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= FALSE)
               }
 
             }else{
 
-              if('write' %in% vol$allowedActions ){
+              if(vol$writable){
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= TRUE)
               }else{
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= FALSE)
@@ -465,7 +498,7 @@ Jobs.submitShellCommandJob <- function(shellCommand, dockerComputeDomain = NULL,
           if(uVol$name == vol$name && uVol$rootVolumeName == vol$rootVolumeName && uVol$owner == vol$owner){
 
             found = TRUE
-            if(uVol$needsWriteAccess){
+            if(!is.null(uVol$needsWriteAccess)){
 
               if(uVol$needsWriteAccess == TRUE && ('write' %in% vol$allowedActions) ){
                 uVols[[length(uVols)+1]] <- list(userVolumeId= vol$id, needsWriteAccess= TRUE)
@@ -495,7 +528,7 @@ Jobs.submitShellCommandJob <- function(shellCommand, dockerComputeDomain = NULL,
     if( is.null(dataVolumes)){
       for( i in 1:length(dockerComputeDomain$volumes)){
         vol = dockerComputeDomain$volumes[[i]]
-        if("write" %in% vol$allowedActions){
+        if(vol$writable){
           dataVols[[length(dataVols)+1]] <- list(id=vol$id, name= vol$name, writable=TRUE)
         }else{
           dataVols[[length(dataVols)+1]] <- list(id=vol$id, name= vol$name, writable=FALSE)
@@ -509,24 +542,24 @@ Jobs.submitShellCommandJob <- function(shellCommand, dockerComputeDomain = NULL,
           vol = dockerComputeDomain$volumes[[j]]
           if( vol$name == dVol$name ){
             found = TRUE;
-            if(dVol$needsWriteAccess){
+            if(!is.null(dVol$needsWriteAccess)){
 
-              if(dVol$needsWriteAccess == TRUE && ('write' %in% vol$allowedActions) ){
+              if(dVol$needsWriteAccess == TRUE){
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= TRUE)
               }else{
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= FALSE)
               }
-              
+
             }else{
 
-              if('write' %in% vol$allowedActions ){
+              if(vol$writable){
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= TRUE)
               }else{
                 dataVols[[length(dataVols)+1]] <- list(id= vol$id, name=vol$name, writable= FALSE)
               }
 
             }
-
+            
           }
         }
 

man/Jobs.getJobQueues.Rd

@@ -0,0 +1,29 @@
+\name{Jobs.getJobQueues}
+\alias{Jobs.getJobQueues}
+\title{
+Get Jobs Queues
+}
+\description{
+Gets information about queues of jobs submitted to all compute domains, including the ranking jobs that users have already submitted to the queue for execution, as well as the ranking that a new job would get if submitted to a queue.
+}
+\usage{Jobs.getJobQueues()}
+\arguments{
+  \item{format}{Format (string) of the returned object. If equal to "dataframe" (default setting), then the reult is a dataframe, else it is a list.}
+}
+\value{a dataframe or list containing job queues information.}
+\author{
+Manuchehr Taghizadeh-Popp \cr
+Maintainer: Manuchehr Taghizadeh-Popp <mtaghiza@jhu.edu>
+}
+\seealso{
+\code{\link[SciServer]{Jobs.getJobsList}},\code{\link[SciServer]{Jobs.submitNotebookJob}},\code{\link[SciServer]{Jobs.submitShellCommandJob}},\code{\link[SciServer]{Jobs.getJobStatus}},\code{\link[SciServer]{Jobs.getDockerComputeDomains}},\code{\link[SciServer]{Jobs.cancelJob}}
+}
+\references{
+\href{http://www.sciserver.org}{http://www.sciserver.org}\cr
+\href{http://apps.sciserver.org/}{http://apps.sciserver.org}\cr
+\href{http://www.github.com/sciserver/SciScript-R}{http://www.github.com/sciserver/SciScript-R}
+}
+\examples{
+jobs = Jobs.getJobQueues()
+}
+\keyword{SciServer}

man/Jobs.submitNotebookJob.Rd

@@ -13,7 +13,7 @@ Submits a Jupyter Notebook for execution (as an asynchronous job) inside a Docke
   \item{dockerImageName}{name (string) of the Docker image for executing the notebook. E.g.,  dockerImageName="Python (astro)". An array of available Docker images is defined as the 'images' property in the dockerComputeDomain object.}
   \item{userVolumes}{a list with the names of user volumes (with optional write permissions) that will be mounted to the docker Image. E.g.: 
   userVolumes = list( list(name="JobsTestVolume", rootVolumeName="Storage", owner="myUserName", needsWriteAccess=TRUE), list(name="scratch", rootVolumeName="Temporary", owner="myUserName", needsWriteAccess=TRUE) ). A list of available user volumes can be found as the 'userVolumes' property in the dockerComputeDomain object. If userVolumes=Null, then all available user volumes are mounted, with 'needsWriteAccess' = TRUE if the user has Write permissions on the volume.}
-  \item{dataVolumes}{a list with the names of data volumes that will be mounted to the docker Image. E.g.: dataVolumes=list(list(name='SDSS DAS')). A list of available data volumes can be found as the 'volumes' property in the dockerComputeDomain list. If dataVolumes=NULL, then all available data volumes are mounted.}
+  \item{dataVolumes}{a list with the names of data volumes (with optional write permissions) that will be mounted to the docker Image. E.g.: dataVolumes=list(list(name='SDSS DAS', needsWriteAccess=TRUE)). A list of available data volumes can be found as the 'volumes' property in the dockerComputeDomain list. If dataVolumes=NULL, then all available data volumes are mounted.}
   \item{resultsFolderPath}{full path to results folder (string) where the original notebook is copied to and executed. E.g.: /home/idies/workspace/rootVolume/username/userVolume/jobsFolder. If not set, then a default folder will be set automatically.}
   \item{parameters}{string containing parameters that the notebook might need during its execution. This string is written in the 'parameters.txt' file in the same directory level where the notebook is being executed.}
   \item{jobAlias}{alias (string) of job, defined by the user.}

man/Jobs.submitShellCommandJob.Rd

@@ -13,7 +13,7 @@ Submits a shell command for execution (as an asynchronous job) inside a Docker c
   \item{dockerImageName}{name (string) of the Docker image for executing the notebook. E.g.,  dockerImageName="Python (astro)". An array of available Docker images is defined as the 'images' property in the dockerComputeDomain object.}
   \item{userVolumes}{a list with the names of user volumes (with optional write permissions) that will be mounted to the docker Image. E.g.: 
   userVolumes = list( list(name="JobsTestVolume", rootVolumeName="Storage", owner="myUserName", needsWriteAccess=TRUE), list(name="scratch", rootVolumeName="Temporary", owner="myUserName", needsWriteAccess=TRUE) ). A list of available user volumes can be found as the 'userVolumes' property in the dockerComputeDomain object. If userVolumes=Null, then all available user volumes are mounted, with 'needsWriteAccess' = TRUE if the user has Write permissions on the volume.}
-  \item{dataVolumes}{a list with the names of data volumes that will be mounted to the docker Image. E.g.: dataVolumes=list(list(name='SDSS DAS')). A list of available data volumes can be found as the 'volumes' property in the dockerComputeDomain list. If dataVolumes=NULL, then all available data volumes are mounted.}
+  \item{dataVolumes}{a list with the names of data volumes (with optional write permissions) that will be mounted to the docker Image. E.g.: dataVolumes=list(list(name='SDSS DAS', needsWriteAccess=FALSE)). A list of available data volumes can be found as the 'volumes' property in the dockerComputeDomain list. If dataVolumes=NULL, then all available data volumes are mounted.}
   \item{resultsFolderPath}{full path to results folder (string) where the original notebook is copied to and executed. E.g.: /home/idies/workspace/rootVolume/username/userVolume/jobsFolder. If not set, then a default folder will be set automatically.}
   \item{jobAlias}{alias (string) of job, defined by the user.}
 }