Implement --no_cleanup option for test & serve commands.

jmchilton · jmchilton · commit 2e41e0a146b3 · 2015-02-21T22:39:41.000-05:00
Prevents deletion of temporary files created for/by Galaxy. Might be useful for debugging stuff (#80 (comment)) - probably would be a whole lot more useful for debugging if we also dropped a little shell script in that directory that allowed resuming Galaxy from that state.
diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst
@@ -36,6 +36,8 @@ instances.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
+      --no_cleanup                    Do not cleanup temp files created for and by
+                                      Galaxy.
       --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
       --dependency_resolvers_config_file PATH
diff --git a/docs/commands/test.rst b/docs/commands/test.rst
@@ -61,6 +61,8 @@ please careful and do not try this against production Galaxy instances.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
+      --no_cleanup                    Do not cleanup temp files created for and by
+                                      Galaxy.
       --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
       --tool_data_table PATH          tool_data_table_conf.xml file to for
diff --git a/docs/commands/tool_factory.rst b/docs/commands/tool_factory.rst
@@ -26,6 +26,8 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
+      --no_cleanup                    Do not cleanup temp files created for and by
+                                      Galaxy.
       --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
       --dependency_resolvers_config_file PATH
diff --git a/planemo/commands/cmd_serve.py b/planemo/commands/cmd_serve.py
@@ -9,6 +9,7 @@
 @options.optional_tools_arg()
 @options.galaxy_root_option()
 @options.install_galaxy_option()
+@options.no_cleanup_option()
 @options.test_data_option()
 @options.dependency_resolvers_option()
 @options.job_config_option()
diff --git a/planemo/commands/cmd_test.py b/planemo/commands/cmd_test.py
@@ -84,6 +84,7 @@
 )
 @options.galaxy_root_option()
 @options.install_galaxy_option()
+@options.no_cleanup_option()
 @options.test_data_option()
 @options.tool_data_table_option()
 @options.dependency_resolvers_option()
diff --git a/planemo/commands/cmd_tool_factory.py b/planemo/commands/cmd_tool_factory.py
@@ -9,6 +9,7 @@
 @click.command('tool_factory')
 @options.galaxy_root_option()
 @options.install_galaxy_option()
+@options.no_cleanup_option()
 @options.test_data_option()
 @options.dependency_resolvers_option()
 @options.job_config_option()
diff --git a/planemo/galaxy_config.py b/planemo/galaxy_config.py
@@ -200,7 +200,8 @@ def config_join(*args):
 
         yield GalaxyConfig(galaxy_root, config_directory, env, test_data_dir)
     finally:
-        if created_config_directory:
+        cleanup = not kwds.get("no_cleanup", False)
+        if created_config_directory and cleanup:
             shutil.rmtree(config_directory)
 
 
diff --git a/planemo/options.py b/planemo/options.py
@@ -149,6 +149,14 @@ def optional_project_arg(exists=True):
     )
 
 
+def no_cleanup_option():
+    return click.option(
+        "--no_cleanup",
+        is_flag=True,
+        help=("Do not cleanup temp files created for and by Galaxy.")
+    )
+
+
 def docker_cmd_option():
     return click.option(
         '--docker_cmd',

Original file line number	Diff line number	Diff line change
`@@ -84,6 +84,7 @@`
`84`	`84`	`)`
`85`	`85`	`@options.galaxy_root_option()`
`86`	`86`	`@options.install_galaxy_option()`
	`87`	`+@options.no_cleanup_option()`
`87`	`88`	`@options.test_data_option()`
`88`	`89`	`@options.tool_data_table_option()`
`89`	`90`	`@options.dependency_resolvers_option()`