Improved "special" tool loading.

Instead of writing out the tools on startup (a more expensive operation than reading), just read the existing files in. Add new abstraction to the tool panel to reduce some otherwise duplicated code. Testing: The following two API tests should cover the modified behavior, they verify that metadata is still detectable and that history import and export still works. ``` ./run_tests.sh -api test/api/test_histories.py:HistoriesApiTestCase.test_import_export ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_rdata_not_decompressed ```
galaxyproject · Sep 29, 2015 · ac18cbe · ac18cbe
1 parent 3e0221c
commit ac18cbe
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Showing 6 changed files with 51 additions and 59 deletions.
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
@@ -634,32 +634,9 @@ def reload_display_applications( self, display_application_ids=None ):
     def load_external_metadata_tool( self, toolbox ):
         """Adds a tool which is used to set external metadata"""
         # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated
-        # tool.  We'll create a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective
-        # Properly building a tool without relying on parsing an XML file is near impossible...so we'll create a temporary file
-        tool_xml_text = """
-            <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata">
-              <type class="SetMetadataTool" module="galaxy.tools"/>
-              <requirements>
-                  <requirement type="package">samtools</requirement>
-              </requirements>
-              <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
-              <command>python "${set_metadata}" ${__SET_EXTERNAL_METADATA_COMMAND_LINE__}</command>
-              <inputs>
-                <param format="data" name="input1" type="data" label="File to set metadata on."/>
-                <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/>
-                <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value="">
-                  <sanitizer sanitize="False"/>
-                </param>
-              </inputs>
-              <configfiles>
-                <configfile name="set_metadata">from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()</configfile>
-              </configfiles>
-            </tool>
-            """
-        tmp_name = tempfile.NamedTemporaryFile()
-        tmp_name.write( tool_xml_text )
-        tmp_name.flush()
-        set_meta_tool = toolbox.load_hidden_tool( tmp_name.name )
+        # tool.  We'll load a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective
+        # Properly building a tool without relying on parsing an XML file is near difficult...so we bundle with Galaxy.
+        set_meta_tool = toolbox.load_hidden_lib_tool( "galaxy/datatypes/set_metadata_tool.xml" )
         self.set_external_metadata_tool = set_meta_tool
         self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id )
 

diff --git a/lib/galaxy/datatypes/set_metadata_tool.xml b/lib/galaxy/datatypes/set_metadata_tool.xml
@@ -0,0 +1,18 @@
+<tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata">
+  <type class="SetMetadataTool" module="galaxy.tools"/>
+  <requirements>
+      <requirement type="package">samtools</requirement>
+  </requirements>
+  <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
+  <command>python "${set_metadata}" ${__SET_EXTERNAL_METADATA_COMMAND_LINE__}</command>
+  <inputs>
+    <param format="data" name="input1" type="data" label="File to set metadata on."/>
+    <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/>
+    <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value="">
+      <sanitizer sanitize="False"/>
+    </param>
+  </inputs>
+  <configfiles>
+    <configfile name="set_metadata">from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()</configfile>
+  </configfiles>
+</tool>
diff --git a/lib/galaxy/tools/imp_exp/__init__.py b/lib/galaxy/tools/imp_exp/__init__.py
@@ -19,42 +19,16 @@
 
 log = logging.getLogger(__name__)
 
-EXPORT_HISTORY_TEXT = """
-        <tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history">
-          <type class="ExportHistoryTool" module="galaxy.tools"/>
-          <action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/>
-          <command>python $export_history $__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command>
-          <inputs>
-            <param name="__HISTORY_TO_EXPORT__" type="hidden"/>
-            <param name="compress" type="boolean"/>
-            <param name="__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__" type="hidden"/>
-          </inputs>
-          <configfiles>
-            <configfile name="export_history">from galaxy.tools.imp_exp.export_history import main; main()</configfile>
-          </configfiles>
-          <outputs>
-            <data format="gzip" name="output_file"/>
-          </outputs>
-        </tool>
-"""
-
 
 def load_history_imp_exp_tools( toolbox ):
     """ Adds tools for importing/exporting histories to archives. """
-    # Use same process as that used in load_external_metadata_tool; see that
-    # method for why create tool description files on the fly.
-    tool_xml_text = EXPORT_HISTORY_TEXT
 
     # Load export tool.
-    tmp_name = tempfile.NamedTemporaryFile()
-    tmp_name.write( tool_xml_text )
-    tmp_name.flush()
-    history_exp_tool = toolbox.load_hidden_tool( tmp_name.name )
+    history_exp_tool = toolbox.load_hidden_lib_tool( "galaxy/tools/imp_exp/exp_history_to_archive.xml" )
     log.debug( "Loaded history export tool: %s", history_exp_tool.id )
 
     # Load import tool.
-    tool_xml = os.path.join( os.getcwd(), "lib/galaxy/tools/imp_exp/imp_history_from_archive.xml" )
-    history_imp_tool = toolbox.load_hidden_tool( tool_xml )
+    history_imp_tool = toolbox.load_hidden_lib_tool( "galaxy/tools/imp_exp/imp_history_from_archive.xml" )
     log.debug( "Loaded history import tool: %s", history_imp_tool.id )
 
 

diff --git a/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml b/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
@@ -0,0 +1,16 @@
+<tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history">
+  <type class="ExportHistoryTool" module="galaxy.tools"/>
+  <action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/>
+  <command>python $export_history $__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command>
+  <inputs>
+    <param name="__HISTORY_TO_EXPORT__" type="hidden"/>
+    <param name="compress" type="boolean"/>
+    <param name="__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__" type="hidden"/>
+  </inputs>
+  <configfiles>
+    <configfile name="export_history">from galaxy.tools.imp_exp.export_history import main; main()</configfile>
+  </configfiles>
+  <outputs>
+    <data format="gzip" name="output_file"/>
+  </outputs>
+</tool>
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
@@ -741,6 +741,10 @@ def load_tool( self, config_file, guid=None, repository_id=None, **kwds ):
             self._tool_watcher.watch_file( config_file, tool.id )
         return tool
 
+    def load_hidden_lib_tool( self, path ):
+        tool_xml = os.path.join( os.getcwd(), "lib", path )
+        return self.load_hidden_tool( tool_xml )
+
     def load_hidden_tool( self, config_file, **kwds ):
         """ Load a hidden tool (in this context meaning one that does not
         appear in the tool panel) and register it in _tools_by_id.

diff --git a/test/unit/tools/test_parsing.py b/test/unit/tools/test_parsing.py
@@ -1,11 +1,11 @@
 from math import isinf
 
+import os
 import os.path
 import tempfile
 import shutil
 
 from galaxy.tools.parser.factory import get_tool_source
-from galaxy.tools.imp_exp import EXPORT_HISTORY_TEXT
 
 import unittest
 
@@ -111,8 +111,11 @@ def _get_tool_source(self, source_file_name=None, source_contents=None):
             source_file_name = self.source_file_name
         if source_contents is None:
             source_contents = self.source_contents
-        path = os.path.join(self.temp_directory, source_file_name)
-        open(path, "w").write(source_contents)
+        if not os.path.isabs(source_file_name):
+            path = os.path.join(self.temp_directory, source_file_name)
+            open(path, "w").write(source_contents)
+        else:
+            path = source_file_name
         tool_source = get_tool_source(path)
         return tool_source
 
@@ -404,8 +407,8 @@ def test_hidden(self):
 
 
 class SpecialToolLoaderTestCase(BaseLoaderTestCase):
-    source_file_name = "export.xml"
-    source_contents = EXPORT_HISTORY_TEXT
+    source_file_name = os.path.join(os.getcwd(), "lib/galaxy/tools/imp_exp/exp_history_to_archive.xml")
+    source_contents = None
 
     def test_tool_type(self):
         tool_module = self._tool_source.parse_tool_module()