Merge pull request #2 from StuartWheater/master

Updated opal management functions and 'Azure Pipelines' files

Author: OllyButters

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: dsStatsClient
 Maintainer: <datashield@obiba.org>
 Author: <datashield@obiba.org>
-Version: 4.1.1
+Version: 4.1.2
 License: GPL-3
 Title: DataSHIELD client site stattistical functions
 Description: DataSHIELD client site stattistical functions
 Depends:
     opal,
     dsBaseClient
+RoxygenNote: 6.1.1

R/findLoginObjects.R

@@ -2,32 +2,44 @@
 #' @title searches for opal login object in the environment
 #' @description This is an internal function required by a client function
 #' @details if the user does not set the argument 'datasources', this function
-#' is called to searches for opal login objects in the environment. If more than one 
-#' login object is found a prompt asks the user to choose one and if none is found
-#' the process stops.
+#' is called to searches for opal login objects in the environment.
+#' If only one opal object is found, it automatically becomes the default selection.
+#' If more than one is found but one is called 'default.opals' then that is selected.
+#' If more than one is found with none is called 'default.opals' the user is 
+#' told that they can either specify a particular Opal using the 'datasources=' argument
+#' that exists in every relevant datashield client-side function or else they
+#' can use the 'ds.setDefaultOpals()' function to create a copy of a selected Opal objects
+#' which is called 'default.opals' and is then selected by default in future calls to findLoginObjects.
+#' If the default Opal object needs to be changed then 'ds.setDefaultOpals()' can be run again.
+#' A previous version of 'findLoginObjects()' asked the user to specify which Opal to choose
+#' if no default could be identified, but that did not work in all versions of R and so was removed.
 #' @keywords internal
 #' @return returns a list of opal login objects or stops the process
-#' @author Gaye, A.
+#' @author Amadou Gaye, Paul Burton (updated 15/10/18). THIS IS VERSION TO USE 8/2/19.
 #' 
 findLoginObjects <- function(){
 
   findLogin <- getOpals()
+
+  if (findLogin$flag == 0){
+    stop(" Are you logged in to any server? Please provide a valid opal login object! ", call.=FALSE)
+  } 
+
   if(findLogin$flag == 1){
     datasources <- findLogin$opals
-    return (datasources)
-  }else{
-    if(findLogin$flag == 0){
-      stop(" Are you logged in to any server? Please provide a valid opal login object! ", call.=FALSE)
-    }else{
-      message(paste0("More than one list of opal login object were found: '", paste(findLogin$opals,collapse="', '"), "'!"))
-      userInput <- readline("Please enter the name of the login object you want to use: ")
-      datasources <- eval(parse(text=userInput))
-      if(class(datasources[[1]]) == 'opal'){
-        return (datasources)
-      }else{
-        stop("End of process: you failed to enter a valid login object", call.=FALSE)
-      }
-    }
+    return(datasources)
   }
 
-}
+  if(findLogin$flag > 1) {
+    for(j in 1:findLogin$flag){
+      if(findLogin$opals[[j]]=="default.opals"){
+        datasources<-eval(parse(text=findLogin$opals[[j]]),envir=0)
+        return(datasources)
+	  }
+	}
+    message(paste0(" More than one list of opal login objects was found with no default specified:\n '", paste(findLogin$opals.list,collapse="', '"), "'!!"))
+    stop(" \n\n Please specify a default Opal object using the following call syntax:\n ds.setDefaultOpals(opal.name='name of opal in inverted commas')\n\n",call.=FALSE) 
+  }
+	
+}
+#findLoginObjects

R/getOpals.R

@@ -6,9 +6,9 @@
 #' This way no matter what the user calls his opal login object it will be captured. 
 #' @keywords internal
 #' @return a list of opal object obtained after login into the servers
-#' @author Gaye,A.
-#' 
+#' @author Amadou Gaye, Paul Burton (updated 15/10/18). THIS IS VERSION TO USE 8/2/19.
 getOpals <- function(){
+  
   # get the names of all the objects in the current work environment
   objs <- ls(name=.GlobalEnv)
 
@@ -24,28 +24,31 @@ getOpals <- function(){
         list2check <- eval(parse(text=objs[i]))
         if(length(list2check) > 0){
           cl2 <- class(list2check[[1]])
-          if(cl2 == 'opal'){
-            cnt <- cnt + 1
-            opalist[[cnt]] <- objs[i]
-            flag <- 1
+          for(s in 1:length(cl2)){
+            if(cl2[s] == 'opal'){
+              cnt <- cnt + 1
+              opalist[[cnt]] <- objs[i]
+              flag <- 1
+            }
           }
         }
       }
     }
     if(flag == 1){ 
       if(length(opalist) > 1){
          flag <- 2
-         return(list("flag"=flag, "opals"=unlist(opalist)))
+         return(list("flag"=flag, "opals"=unlist(opalist), "opals.list"=unlist(opalist)))
       }else{
         pp <- opalist[[1]] 
         opals <- eval(parse(text=pp))
-        return(list("flag"=flag, "opals"=opals))
+        return(list("flag"=flag, "opals"=opals, "opals.list"=unlist(opalist)))
       }
     }else{
-      return(list("flag"=flag, "opals"=NULL))
+      return(list("flag"=flag, "opals"=NULL, "opals.list"=NULL))
     }
   }else{
-    return(list("flag"=flag, "opals"=NULL))
+    return(list("flag"=flag, "opals"=NULL, "opals.list"=NULL))
   }
 
 }
+#getOpals

azure-pipelines.yml

@@ -0,0 +1,56 @@
+pool:
+  vmImage: 'Ubuntu 16.04'
+
+steps:
+- bash: |
+    sudo service mysql stop
+    sudo apt-get update
+    sudo apt-get remove --purge mysql-client mysql-server mysql-common -y
+    sudo apt-get purge mysql-client mysql-server mysql-common -y
+    sudo apt-get autoremove -y
+    sudo apt-get autoclean -y
+    sudo rm -rf /var/lib/mysql/
+
+    wget -nv https://apt.puppetlabs.com/puppet5-release-xenial.deb
+    sudo dpkg -i puppet5-release-xenial.deb
+    sudo apt-get install -qq -f
+    sudo apt-get update
+    sudo rm -f puppet5-release-xenial.deb
+
+    sudo apt-get install puppet-agent -y
+
+    sudo apt-get clean all
+    sudo apt-get update
+    sudo apt-get autoremove -y
+    sudo apt-get clean all
+
+    sudo /opt/puppetlabs/puppet/bin/gem install r10k
+
+    echo -n "Puppet version: "
+    /opt/puppetlabs/bin/puppet --version
+    /opt/puppetlabs/puppet/bin/r10k version
+
+    git clone -b ubuntu16 https://github.com/datashield/datashield-infrastructure.git ../datashield-infrastructure
+    pushd ../datashield-infrastructure/puppet/environments/datashield_azurepipelines && sudo /opt/puppetlabs/puppet/bin/r10k puppetfile install && popd
+    sudo /opt/puppetlabs/bin/puppet apply azure-pipelines_site.pp --environment datashield_azurepipelines --environmentpath ../datashield-infrastructure/puppet/environments
+  displayName: 'Install DataSHIELD server'
+
+- bash: |
+    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+    sudo add-apt-repository 'deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu xenial/'
+    sudo apt-get update
+    sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev -y
+    sudo apt-get install -qq r-base -y
+    sudo R -e "install.packages('devtools', dependencies=TRUE)"
+  displayName: 'Install R client'
+
+- bash: |
+    R -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout
+    grep --quiet "0 error" azure-pipelines_check.Rout
+  displayName: 'Devtools checks'
+  condition: always()
+
+- bash: |
+    ./checkDocumentationUpdated.sh
+  displayName: 'Check documents'
+  condition: always()

azure-pipelines_site.pp

@@ -0,0 +1,23 @@
+# Datashield for Azure Pipelines testing.
+#
+# Install mysql and mongodb, include test data but don't install the firewall.
+# This is an example please change to meet the needs of your install. Consider changing any passwords in this file!
+#
+
+class { ::datashield:
+  test_data      => true,         # Install the test data
+  firewall       => false,        # Do not install the firewall
+  mysql          => true,         # Install mysql server
+  mongodb        => true,         # Install mongodb server
+  remote_mongodb => false,        # There is not a remote mongodb server
+  remote_mysql   => false,        # There is not a remote mysql server
+
+  dsbase_githubusername      => 'datashield',
+  dsbase_ref                 => 'master',
+  dsstats_githubusername     => 'datashield', 
+  dsstats_ref                => 'master',
+  dsgraphics_githubusername  => 'datashield',
+  dsgraphics_ref             => 'master',
+  dsmodelling_githubusername => 'datashield',
+  dsmodelling_ref            => 'master'
+}

checkDocumentationUpdated.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+# Check if the documentation in the man directory matches what should be in it
+# based on what is in the headers of the R scripts.
+echo "Starting documentation check."
+
+# Concatenate all the files in the man dir into one long string and md5sum it.
+orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
+
+# Rebuild the documentation.
+R -e "devtools::document()"
+
+# Concatenate all the files in the man dir into one long string and md5sum it.
+new_sum=$(find man -type f | sort -u | xargs cat | md5sum)
+
+# echo $orig_sum
+# echo $new_sum
+
+if [ "$orig_sum" != "$new_sum" ]; then
+  echo "Your committed manual files (man/*.Rd) are out of sync with the documentation in the R files."
+  echo "Run roxygenise() locally then commit again."
+  exit 1
+else
+  echo "Documentation up to date."
+  exit 0
+fi