Merge pull request #11186 from mvdbeek/disable_tool_cache_optionally

[21.01] Add setting that lets admins enable/disable the tool document cache

doc/source/admin/galaxy_options.rst

@@ -1049,6 +1049,21 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_tool_document_cache``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Set this to false to disable the tool document cache. This cache
+    stores expanded xml strings. Disabling the tool cache results in
+    slower startup times. The tool cache is backed by sqlite database,
+    which cannot be stored on certain network disks. The cache
+    location is configurable using the ``tool_cache_data_dir``
+    setting, but can be disabled completely here.
+:Default: ``true``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~
 ``tool_cache_data_dir``
 ~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/config/sample/galaxy.yml.sample

@@ -617,6 +617,14 @@ galaxy:
   # generated commands run in sh.
   #default_job_shell: /bin/bash
 
+  # Set this to false to disable the tool document cache. This cache
+  # stores expanded xml strings. Disabling the tool cache results in
+  # slower startup times. The tool cache is backed by sqlite database,
+  # which cannot be stored on certain network disks. The cache location
+  # is configurable using the ``tool_cache_data_dir`` setting, but can
+  # be disabled completely here.
+  #enable_tool_document_cache: true
+
   # Tool related caching. Fully expanded tools and metadata will be
   # stored at this path. Per tool_conf cache locations can be configured
   # in (``shed_``)tool_conf.xml files using the tool_cache_data_dir

lib/galaxy/tools/__init__.py

@@ -305,13 +305,14 @@ class ToolBox(BaseGalaxyToolBox):
         return self._tools_by_id
 
     def get_cache_region(self, tool_cache_data_dir):
-        if tool_cache_data_dir not in self.cache_regions:
-            self.cache_regions[tool_cache_data_dir] = ToolDocumentCache(cache_dir=tool_cache_data_dir)
-        return self.cache_regions[tool_cache_data_dir]
+        if self.app.config.enable_tool_document_cache:
+            if tool_cache_data_dir not in self.cache_regions:
+                self.cache_regions[tool_cache_data_dir] = ToolDocumentCache(cache_dir=tool_cache_data_dir)
+            return self.cache_regions[tool_cache_data_dir]
 
     def create_tool(self, config_file, tool_cache_data_dir=None, **kwds):
         cache = self.get_cache_region(tool_cache_data_dir or self.app.config.tool_cache_data_dir)
-        if config_file.endswith('.xml') and not cache.disabled:
+        if config_file.endswith('.xml') and cache and not cache.disabled:
             tool_document = cache.get(config_file)
             if tool_document:
                 tool_source = self.get_expanded_tool_source(

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -765,6 +765,17 @@ mapping:
           should be disabled. Containerized jobs always use /bin/sh - so more maximum
           portability tool authors should assume generated commands run in sh.
 
+      enable_tool_document_cache:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Set this to false to disable the tool document cache. This cache stores
+          expanded xml strings. Disabling the tool cache results in slower startup
+          times. The tool cache is backed by sqlite database, which cannot
+          be stored on certain network disks. The cache location is configurable
+          using the ``tool_cache_data_dir`` setting, but can be disabled completely here.
+
       tool_cache_data_dir:
         type: str
         default: tool_cache

test/unit/unittest_utils/galaxy_mock.py

@@ -170,6 +170,7 @@ class MockAppConfig(Bunch):
 
         # set by MockDir
         self.root = root
+        self.enable_tool_document_cache = False
         self.tool_cache_data_dir = os.path.join(root, 'tool_cache')
         self.delay_tool_initialization = True
         self.external_chown_script = None