Merge pull request #11349 from jmchilton/tool_environment_vars_puslar

[21.01] Add tool environment variables to Pulsar client.

lib/galaxy/jobs/__init__.py

@@ -2586,6 +2586,10 @@ class SharedComputeEnvironment(SimpleComputeEnvironment):
     def working_directory(self):
         return self.job_wrapper.working_directory
 
+    def env_config_directory(self):
+        """Working directory (possibly as environment variable evaluation)."""
+        return "$_GALAXY_JOB_DIR"
+
     def new_file_path(self):
         return os.path.abspath(self.app.config.new_file_path)
 

lib/galaxy/jobs/runners/pulsar.py

@@ -382,6 +382,16 @@ class PulsarJobRunner(AsynchronousJobRunner):
             if os.path.exists(tool_script):
                 log.debug("Registering tool_script for Pulsar transfer [%s]" % tool_script)
                 job_directory_files.append(tool_script)
+            # Following is job destination environment variables
+            env = client.env
+            # extend it with tool defined environment variables
+            tool_envs = job_wrapper.environment_variables
+            env.extend(tool_envs)
+            for tool_env in tool_envs:
+                job_directory_path = tool_env.get("job_directory_path")
+                if job_directory_path:
+                    config_files.append(job_directory_path)
+
             client_job_description = ClientJobDescription(
                 command_line=command_line,
                 input_files=input_files,
@@ -392,7 +402,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 tool=job_wrapper.tool,
                 config_files=config_files,
                 dependencies_description=dependencies_description,
-                env=client.env,
+                env=env,
                 rewrite_paths=rewrite_paths,
                 arbitrary_files=path_rewrites_unstructured,
                 touch_outputs=output_names,
@@ -1056,6 +1066,9 @@ class PulsarComputeEnvironment(ComputeEnvironment):
     def working_directory(self):
         return self._working_directory
 
+    def env_config_directory(self):
+        return self.config_directory()
+
     def config_directory(self):
         return self._config_directory
 

lib/galaxy/tools/evaluation.py

@@ -540,13 +540,14 @@ class ToolEvaluator:
                 is_template = False
             else:
                 is_template = True
-            with tempfile.NamedTemporaryFile(dir=directory, delete=False) as temp:
+            with tempfile.NamedTemporaryFile(dir=directory, prefix="tool_env_", delete=False) as temp:
                 config_filename = temp.name
             self.__write_workdir_file(config_filename, environment_variable_template, param_dict, is_template=is_template, strip=environment_variable_def.get("strip", False))
             config_file_basename = os.path.basename(config_filename)
             # environment setup in job file template happens before `cd $working_directory`
-            environment_variable["value"] = '`cat "$_GALAXY_JOB_DIR/%s"`' % config_file_basename
+            environment_variable["value"] = '`cat "%s/%s"`' % (self.compute_environment.env_config_directory(), config_file_basename)
             environment_variable["raw"] = True
+            environment_variable["job_directory_path"] = config_filename
             environment_variables.append(environment_variable)
 
         home_dir = self.compute_environment.home_directory()

test/integration/test_pulsar_embedded.py

@@ -25,4 +25,5 @@ test_tools = integration_util.integration_tool_runner([
     "multi_data_param",
     "output_filter",
     "vcf_bgzip_test",
+    "environment_variables",
 ])