Removed the option of setting the worker temp directory directly in the Runnable

The implementation was not aware that a worker can take on multiple
analyses. Being implemented at the Runnable level, there was also the risk
that the method would use job parameters to make the directory name,
unaware that the name is set for all jobs of all analyses the worker takes.

The impact is anyway minimal, as the only Ensembl Runnable that was using
this feature is a Compara Runnable, which can be ported to the new
resource-class based system.

And if Runnables still need to change the worker's temp directory, there
are still free to override worker_temp_directory() and
cleanup_worker_temp_directory().

docs/advanced_usage/mpi.rst

@@ -204,16 +204,9 @@ In our case, Examl uses MPI and wants to share data via the filesystem too.
 In this specific Runnable, Examl is set to run in eHive's managed temporary
 directory, which by default is under /tmp which is not shared across nodes on
 our compute cluster.
-We have to override the eHive method to use a shared directory (``$self->param('examl_dir')``) instead.
+We have to override the eHive method to use a shared directory (``$self->o('examl_dir')``) instead.
 
-::
-
-      use Path::Tiny;
-
-      sub worker_temp_directory_name {
-          my $self = shift @_;
-          my $default_temp_directory_name = $self->SUPER::worker_temp_directory_name(@_);
-          my $name = path($default_temp_directory_name)->basename;
-          return $self->param('examl_dir')."/$name/";
-      }
+This can be done at the resource class level, by adding
+``"-worker_base_tmp_dir ".$self->o('examl_dir')`` to the
+``worker_cmd_args`` attribute of the resource-class
 

docs/creating_runnables/runnable_api.rst

@@ -84,7 +84,8 @@ Job (by removing some files, for instance), or to clean it up completely
 with ``$self->cleanup_worker_temp_directory``.
 
 By default, this directory will be put under /tmp, but it can be overriden
-by adding a ``worker_temp_directory_name`` method to the runnable. This can
+by setting the ``-worker_base_tmp_dir`` option for workers through their
+resource classes. This can
 be used to:
 
 - use a faster filesystem (although /tmp is usually local to the machine),

modules/Bio/EnsEMBL/Hive/GuestProcess.pm

@@ -79,7 +79,7 @@ response from GuestProcess):
     ---> dbIDs of the jobs that have been created
 
     <--- WORKER_TEMP_DIRECTORY
-         // The content is the "worker_temp_directory_name" as defined in the runnable (or null otherwise)
+         // No content needed (ignored)
     ---> returns the temporary directory of the worker
 
     <--- JOB_END
@@ -135,7 +135,7 @@ use base ('Bio::EnsEMBL::Hive::Process');
 
 # -------------------------------------- <versioning of the GuestProcess interface> -------------------------------------------------------
 
-our $GUESTPROCESS_PROTOCOL_VERSION = '3';       # Make sure you change this number whenever an incompatible change is introduced
+our $GUESTPROCESS_PROTOCOL_VERSION = '4';       # Make sure you change this number whenever an incompatible change is introduced
 
 
 =head2 get_protocol_version
@@ -561,7 +561,6 @@ sub life_cycle {
             $self->send_response($d);
 
         } elsif ($event eq 'WORKER_TEMP_DIRECTORY') {
-            $self->{worker_temp_directory_name} = $content;
             my $wtd = $self->worker_temp_directory;
             $self->send_response($wtd);
 
@@ -598,33 +597,12 @@ sub life_cycle {
     }
 }
 
-=head2 worker_temp_directory_name
-
-  Example     : $process->worker_temp_directory_name();
-  Description : Returns the name of the temp directory for this module
-                The value in $self is initialized at the WORKER_TEMP_DIRECTORY
-                event above and returned to the caller if defined. This allows
-                runnables to redefine the name
-  Returntype  : string
-  Exceptions  : none
-
-=cut
-
-sub worker_temp_directory_name {
-    my $self = shift;
-    return $self->{worker_temp_directory_name} if $self->{worker_temp_directory_name};
-    return $self->SUPER::worker_temp_directory_name();
-}
-
-
-
 
 ### Summary of Process methods ###
 
 ## Have to be redefined
 # life_cycle
 # param_defaults
-# worker_temp_directory_name
 
 ## Needed, can be reused from the base class
 # worker_temp_directory

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -678,19 +678,13 @@ sub worker_temp_directory {
     my $self = shift @_;
 
     unless(defined($self->{'_tmp_dir'}) and (-e $self->{'_tmp_dir'})) {
-        $self->{'_tmp_dir'} = $self->worker_temp_directory_name();
+        $self->{'_tmp_dir'} = $self->worker->temp_directory_name();
         make_path( $self->{'_tmp_dir'}, { mode => 0777 } );
         throw("unable to create a writable directory ".$self->{'_tmp_dir'}) unless(-w $self->{'_tmp_dir'});
     }
     return $self->{'_tmp_dir'};
 }
 
-sub worker_temp_directory_name {
-    my $self = shift @_;
-
-    return $self->worker->temp_directory_name;
-}
-
 
 =head2 cleanup_worker_temp_directory
 

wrappers/java/build.xml

@@ -8,7 +8,7 @@
 	<property name="build" location="build" />
 	<property name="lib" location="lib" />
 	<property name="doc" location="doc" />
-	<property name="version" value="3.1" />
+	<property name="version" value="4.0" />
 
 	<path id="wrapper_classpath">
 		<fileset dir="${lib}/">

wrappers/java/src/org/ensembl/hive/BaseRunnable.java

@@ -73,7 +73,7 @@ public abstract class BaseRunnable {
 	private static final String JOB_END_TYPE = "JOB_END";
 	private static final String OK = "OK";
 
-	public final static String VERSION = "3.1";
+	public final static String VERSION = "4.0";
 
 	protected final static Map<String, Object> DEFAULT_PARAMS = new HashMap<>();
 
@@ -317,23 +317,13 @@ public abstract class BaseRunnable {
 	 */
 	protected String workerTempDirectory() {
 		if (workerTempDirectory == null) {
-			sendEventMessage(WORKER_TEMP_DIRECTORY_TYPE,
-					getWorkerTemplateName());
+			sendEventMessage(WORKER_TEMP_DIRECTORY_TYPE, null);
 			workerTempDirectory = (String) (readMessageAndRespond()
 					.get(RESPONSE_KEY));
 		}
 		return workerTempDirectory;
 	}
 
-	/**
-	 * Override to provide a special template for the worker temporary directory
-	 * 
-	 * @return A String representing the template location for worker directories or null
-	 */
-	protected String getWorkerTemplateName() {
-		return null;
-	}
-
 	/**
 	 * Send a message and wait for OK from the parent
 	 * 

wrappers/python3/eHive/Process.py

@@ -24,7 +24,7 @@ import unittest
 import warnings
 import traceback
 
-__version__ = "3.0"
+__version__ = "4.0"
 
 __doc__ = """
 This module mainly implements python's counterpart of GuestProcess. Read
@@ -219,12 +219,9 @@ class BaseRunnable(object):
 
     def worker_temp_directory(self):
         """Returns the full path of the temporary directory created by the worker.
-        Runnables can implement "worker_temp_directory_name()" to return the name
-        they would like to use
         """
         if self.__created_worker_temp_directory is None:
-            template_name = self.worker_temp_directory_name() if hasattr(self, 'worker_temp_directory_name') else None
-            self.__send_message('WORKER_TEMP_DIRECTORY', template_name)
+            self.__send_message('WORKER_TEMP_DIRECTORY', None)
             self.__created_worker_temp_directory = self.__read_message()['response']
         return self.__created_worker_temp_directory
 

wrappers/python3/eHive/examples/TestRunnable.py

@@ -14,6 +14,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+# standaloneJob.pl eHive.examples.TestRunnable -language python3
+
+import os
+import subprocess
+
 import eHive
 
 class TestRunnable(eHive.BaseRunnable):
@@ -29,15 +34,20 @@ class TestRunnable(eHive.BaseRunnable):
         self.warning("Fetch the world !")
         print("alpha is", self.param_required('alpha'))
         print("beta is", self.param_required('beta'))
+        self.temp_dir = self.worker_temp_directory()
+        print("my directory name is", self.temp_dir)
 
     def run(self):
         self.warning("Run the world !")
         s = self.param('alpha') + self.param('beta')
         print("set gamma to", s)
         self.param('gamma', s)
+        self.greeting_path = os.path.join(self.temp_dir, "hello")
+        subprocess.check_call(["touch", self.greeting_path])
 
     def write_output(self):
         self.warning("Write to the world !")
         print("gamma is", self.param('gamma'))
         self.dataflow( {'gamma': self.param('gamma')}, 2 )
+        print("Greetings in place:", os.path.exists(self.greeting_path))