support custom Bpipe home in agent configuration

ssadedin · Aug 23, 2024 · 0ff1ca2 · 0ff1ca2
1 parent 53e8e4b
commit 0ff1ca2
Show file tree

Hide file tree

Showing 4 changed files with 23 additions and 7 deletions.
diff --git a/src/main/groovy/bpipe/agent/Agent.groovy b/src/main/groovy/bpipe/agent/Agent.groovy
@@ -59,8 +59,8 @@ abstract class Agent extends TimerTask {
      * for that command type. These are either objects extending BpipeCommand or Closures 
      * that are executed directly.
      */
-    public static Map COMMANDS = [
-        "retry" : { dir, args, writer -> bpipe(dir, ['retry'], writer)},
+    public Map COMMANDS = [
+        "retry" : { dir, args, writer -> bpipe(bpipeHome, dir, ['retry'], writer)},
         "stop" : Stop,
         "log" : LogCommand,
         "run" : RunPipelineCommand,
@@ -96,6 +96,8 @@ abstract class Agent extends TimerTask {
 
     Semaphore concurrency = null
 
+    String bpipeHome = bpipe.Runner.BPIPE_HOME 
+
     int executed = 0
 
     int errors = 0
@@ -155,7 +157,13 @@ abstract class Agent extends TimerTask {
         try {
             ++this.executed
             BpipeCommand command = createCommandFromAttributes(commandAttributes)
-            command.dir = commandAttributes.directory ?: ((PipelineInfo)pipelines[((Map)(commandAttributes.run)).id]).path
+            command.bpipeHome = this.bpipeHome
+
+            command.dir = commandAttributes.directory
+            if(!command.dir) {
+                command.dir = ((PipelineInfo)pipelines[((Map)(commandAttributes.run))?.id])?.path
+            }
+
             validateCommand(command)
             AgentCommandRunner runner = new AgentCommandRunner(createConnection(), (Long)commandAttributes.id, command, outputMode, onRun)
             runner.concurrency = this.concurrency
@@ -241,7 +249,7 @@ abstract class Agent extends TimerTask {
         return command
     }
 
-    static void bpipe(String dir, List bpipeArgs, Writer out) {
+    static void bpipe(String home, String dir, List bpipeArgs, Writer out) {
         if(dir == null) 
             throw new IllegalArgumentException("Directory parameter not set. Directory for command to run in must be specified")
 
@@ -250,7 +258,7 @@ abstract class Agent extends TimerTask {
             throw new IllegalArgumentException("Directory supplied $dir is not in an existing path. The directory parent must already exist.")
 
         log.info "Args are: " + bpipeArgs
-        List<String> cmd = [ bpipe.Runner.BPIPE_HOME + "/bin/bpipe" ] 
+        List<String> cmd = [ home + "/bin/bpipe" ] 
         cmd.addAll(bpipeArgs)
         log.info "Running command : " + cmd;
         ExecutedProcess result = Utils.executeCommand(cmd, out:out, err: out) {

diff --git a/src/main/groovy/bpipe/agent/AgentRunner.groovy b/src/main/groovy/bpipe/agent/AgentRunner.groovy
@@ -62,6 +62,11 @@ class AgentRunner {
                 agent.concurrency = new Semaphore(concurrency.toInteger())
             }
             agent.singleShot = agentConfig.getOrDefault('singleshot', opts.s)
+
+            if(agentConfig.containsKey('bpipeHome')) {
+                agent.bpipeHome = agentConfig.bpipeHome
+                log.info("Using custom Bpipe home $agent.bpipeHome for agent $agent.name")
+            }
 
             if(opts.t) {
                 log.info "Scheduling timeout in $opts.t ms"

diff --git a/src/main/groovy/bpipe/cmd/BpipeCommand.groovy b/src/main/groovy/bpipe/cmd/BpipeCommand.groovy
@@ -6,6 +6,7 @@ import bpipe.agent.PipelineInfo
 import groovy.transform.CompileStatic;
 import groovy.util.logging.Log;;
 
+@CompileStatic
 @Log
 abstract class BpipeCommand {
 
@@ -21,6 +22,8 @@ abstract class BpipeCommand {
 
     String dir
 
+    String bpipeHome = bpipe.Runner.BPIPE_HOME 
+
     BpipeCommand(String commandLine, List<String> args) {
         this.commandLine = commandLine
         this.args = args
@@ -55,7 +58,7 @@ abstract class BpipeCommand {
         if(!COMMAND_TMP.exists())
             COMMAND_TMP.mkdirs()
 
-        String command = bpipe.Runner.BPIPE_HOME + "/bin/$exe $commandLine"
+        String command = this.bpipeHome + "/bin/$exe $commandLine"
         if(args) {
             command = "$command " + args.collect { "'" + it + "'" }.join(" ")
         }

diff --git a/src/main/groovy/bpipe/cmd/RunPipelineCommand.groovy b/src/main/groovy/bpipe/cmd/RunPipelineCommand.groovy
@@ -68,7 +68,7 @@ class RunPipelineCommand extends BpipeCommand {
 
         this.runDirectory = dirFile
 
-        List<String> cmd = [ bpipe.Runner.BPIPE_HOME + "/bin/bpipe", "run" ] 
+        List<String> cmd = [ bpipeHome + "/bin/bpipe", "run" ] 
         cmd.addAll(args)
         result = Utils.executeCommand(cmd, out:out, err: out) {
             directory(dirFile)