Support use of lustre/gscratch pilot space

Author: bbimber

cluster/api-src/org/labkey/api/cluster/ClusterResourceAllocator.java

@@ -6,7 +6,9 @@
 import org.labkey.api.pipeline.RemoteExecutionEngine;
 import org.labkey.api.pipeline.TaskId;
 
+import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 /**
  * CluterResourceAllocator typically serves two functions.  First, it allows code to be written to automatically adjust job resource settings
@@ -59,4 +61,10 @@ default void processJavaOpts(PipelineJob job, RemoteExecutionEngine engine, @Not
     {
 
     }
+
+    @NotNull
+    default Map<String, Object> getEnvironmentVars(PipelineJob job, RemoteExecutionEngine engine)
+    {
+        return Collections.emptyMap();
+    }
 }

cluster/src/org/labkey/cluster/pipeline/HTCondorExecutionEngine.java

@@ -17,6 +17,7 @@
 import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -181,6 +182,7 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                     Integer maxCpus = null;
                     Integer maxRam = null;
                     List<String> extraLines = new ArrayList<>(getConfig().getExtraSubmitLines());
+                    Map<String, Object> extraEnvironmentVars = new HashMap<>();
 
                     if (job.getActiveTaskId() != null)
                     {
@@ -204,6 +206,8 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                             }
 
                             allocator.addExtraSubmitScriptLines(job, this, extraLines);
+
+                            extraEnvironmentVars.putAll(allocator.getEnvironmentVars(job, this));
                         }
                     }
 
@@ -245,6 +249,10 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                         environment.addAll(getConfig().getEnvironmentVars());
                     }
 
+                    extraEnvironmentVars.forEach((name, val) -> {
+                        environment.add(name + "=" + val);
+                    });
+
                     if (!environment.isEmpty())
                     {
                         writer.write("environment = \"" + StringUtils.join(environment, " ") + "\"\n");

cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java

@@ -19,6 +19,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
@@ -308,6 +309,7 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                     Integer maxCpus = null;
                     Integer maxRam = null;
                     List<String> extraLines = new ArrayList<>(getConfig().getExtraSubmitLines());
+                    Map<String, Object> extraEnvironmentVars = new HashMap<>();
 
                     if (job.getActiveTaskId() != null)
                     {
@@ -332,6 +334,8 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                             }
 
                             allocator.addExtraSubmitScriptLines(job, this, extraLines);
+
+                            extraEnvironmentVars.putAll(allocator.getEnvironmentVars(job, this));
                         }
                     }
 
@@ -375,6 +379,10 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                         environment.addAll(getConfig().getEnvironmentVars());
                     }
 
+                    extraEnvironmentVars.forEach((name, val) -> {
+                        environment.add(name + "=" + val);
+                    });
+
                     if (!environment.isEmpty())
                     {
                         writer.write("#SBATCH --export=" + StringUtils.join(environment, ",") + "\n");