Unverified Commit 4dab5e1c authored by Dannon's avatar Dannon Committed by GitHub
Browse files

Merge pull request #16601 from mvdbeek/backport_tool_mem_fixes 

[23.1] Backport tool mem fixes
parents 607a4075 e0ba54e0

doc/source/admin/galaxy_options.rst

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@@ -1167,18 +1167,6 @@ 
:Type: str





~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

``delay_tool_initialization``

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



:Description:

    Set this to true to delay parsing of tool inputs and outputs until

    they are needed. This results in faster startup times but uses

    more memory when using forked Galaxy processes.

:Default: ``false``

:Type: bool





~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

``biotools_content_directory``

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/app.py

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@@ -619,6 +619,8 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication): 
            ("application stack", self._shutdown_application_stack),

        ]

        self._register_singleton(StructuredApp, self)  # type: ignore[type-abstract]

        if kwargs.get("is_webapp"):

            self.is_webapp = kwargs["is_webapp"]

        # A lot of postfork initialization depends on the server name, ensure it is set immediately after forking before other postfork functions

        self.application_stack.register_postfork_function(self.application_stack.set_postfork_server_name, self)

        self.config.reload_sanitize_allowlist(explicit="sanitize_allowlist_file" in kwargs)

lib/galaxy/app_unittest_utils/galaxy_mock.py

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@@ -104,6 +104,7 @@ class MockApp(di.Container, GalaxyDataTestApp): 
    history_manager: HistoryManager

    job_metrics: JobMetrics

    stop: bool

    is_webapp: bool = True



    def __init__(self, config=None, **kwargs) -> None:

        super().__init__()
@@ -227,7 +228,7 @@ class MockAppConfig(GalaxyDataTestConfig, CommonConfigurationMixin): 


        # set by MockDir

        self.enable_tool_document_cache = False

        self.delay_tool_initialization = True

        self.tool_cache_data_dir = os.path.join(self.root, "tool_cache")

        self.external_chown_script = None

        self.check_job_script_integrity = False

        self.check_job_script_integrity_count = 0

lib/galaxy/app_unittest_utils/tools_support.py

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@@ -109,7 +109,6 @@ class UsesTools(UsesApp): 
    def __setup_tool(self):

        tool_source = get_tool_source(self.tool_file)

        self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file)

        self.tool.assert_finalized()

        if getattr(self, "tool_action", None):

            self.tool.tool_action = self.tool_action

        return self.tool

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

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@@ -899,11 +899,6 @@ galaxy: 
  # this option will be resolved with respect to <data_dir>.

  #tool_search_index_dir: tool_search_index



  # Set this to true to delay parsing of tool inputs and outputs until

  # they are needed. This results in faster startup times but uses more

  # memory when using forked Galaxy processes.

  #delay_tool_initialization: false



  # Point Galaxy at a repository consisting of a copy of the bio.tools

  # database (e.g. https://github.com/bio-tools/content/) to resolve

  # bio.tools data for tool metadata.