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https://github.com/galaxyproject/galaxy.git
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Remove a bunch of tool dependency utility code now unused.
This commit is contained in:
John Chilton
@@ -5,107 +5,10 @@ import shutil
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from sqlalchemy import and_
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from galaxy import util
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from galaxy.web.form_builder import SelectField
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log = logging.getLogger(__name__)
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def build_tool_dependencies_select_field(
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app, tool_shed_repository, name, multiple=True, display="checkboxes", uninstalled_only=False
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):
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"""
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Generate a SelectField consisting of the current list of tool dependency ids
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for an installed tool shed repository.
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"""
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tool_dependencies_select_field = SelectField(name=name, multiple=multiple, display=display)
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for tool_dependency in tool_shed_repository.tool_dependencies:
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if uninstalled_only:
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if tool_dependency.status not in [
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app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
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app.install_model.ToolDependency.installation_status.UNINSTALLED,
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]:
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continue
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else:
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if tool_dependency.status in [
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app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
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app.install_model.ToolDependency.installation_status.UNINSTALLED,
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]:
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continue
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option_label = f"{tool_dependency.name} version {tool_dependency.version}"
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option_value = app.security.encode_id(tool_dependency.id)
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tool_dependencies_select_field.add_option(option_label, option_value)
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return tool_dependencies_select_field
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def create_or_update_tool_dependency(app, tool_shed_repository, name, version, type, status, set_status=True):
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"""Create or update a tool_dependency record in the Galaxy database."""
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# Called from Galaxy (never the tool shed) when a new repository is being installed or when an uninstalled
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# repository is being reinstalled.
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context = app.install_model.context
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# First see if an appropriate tool_dependency record exists for the received tool_shed_repository.
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if version:
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tool_dependency = get_tool_dependency_by_name_version_type_repository(
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app, tool_shed_repository, name, version, type
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)
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else:
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tool_dependency = get_tool_dependency_by_name_type_repository(app, tool_shed_repository, name, type)
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if tool_dependency:
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# In some cases we should not override the current status of an existing tool_dependency, so do so only
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# if set_status is True.
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if set_status:
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set_tool_dependency_attributes(app, tool_dependency=tool_dependency, status=status)
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else:
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# Create a new tool_dependency record for the tool_shed_repository.
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debug_msg = f"Creating a new record for version {version} of tool dependency {name} for revision {tool_shed_repository.changeset_revision} of repository {tool_shed_repository.name}. "
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debug_msg += f"The status is being set to {status}."
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log.debug(debug_msg)
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tool_dependency = app.install_model.ToolDependency(tool_shed_repository.id, name, version, type, status)
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context.add(tool_dependency)
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context.flush()
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return tool_dependency
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def get_download_url_for_platform(url_templates, platform_info_dict):
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"""
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Compare the dict returned by get_platform_info() with the values specified in the url_template element. Return
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true if and only if all defined attributes match the corresponding dict entries. If an entry is not
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defined in the url_template element, it is assumed to be irrelevant at this stage. For example,
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<url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/faToTwoBit</url_template>
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where the OS must be 'darwin', but the architecture is filled in later using string.Template.
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"""
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os_ok = False
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architecture_ok = False
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for url_template in url_templates:
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os_name = url_template.get("os", None)
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architecture = url_template.get("architecture", None)
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if os_name:
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if os_name.lower() == platform_info_dict["os"]:
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os_ok = True
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else:
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os_ok = False
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else:
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os_ok = True
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if architecture:
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if architecture.lower() == platform_info_dict["architecture"]:
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architecture_ok = True
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else:
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architecture_ok = False
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else:
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architecture_ok = True
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if os_ok and architecture_ok:
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return url_template
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return None
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def get_platform_info_dict():
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"""Return a dict with information about the current platform."""
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platform_dict = {}
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sysname, nodename, release, version, machine = os.uname()
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platform_dict["os"] = sysname.lower()
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platform_dict["architecture"] = machine.lower()
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return platform_dict
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def get_tool_dependency(app, id):
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"""Get a tool_dependency from the database via id"""
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return app.install_model.context.query(app.install_model.ToolDependency).get(app.security.decode_id(id))
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@@ -176,39 +79,6 @@ def get_tool_dependency_ids(as_string=False, **kwd):
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return tool_dependency_ids
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def get_tool_dependency_install_dir(
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app,
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repository_name,
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repository_owner,
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repository_changeset_revision,
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tool_dependency_type,
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tool_dependency_name,
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tool_dependency_version,
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):
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if tool_dependency_type == "package":
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return os.path.abspath(
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os.path.join(
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app.tool_dependency_dir,
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tool_dependency_name,
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tool_dependency_version,
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repository_owner,
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repository_name,
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repository_changeset_revision,
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)
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)
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if tool_dependency_type == "set_environment":
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return os.path.abspath(
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os.path.join(
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app.tool_dependency_dir,
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"environment_settings",
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tool_dependency_name,
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repository_owner,
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repository_name,
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repository_changeset_revision,
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)
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)
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def parse_package_elem(package_elem, platform_info_dict=None, include_after_install_actions=True):
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"""
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Parse a <package> element within a tool dependency definition and return a list of action tuples.
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@@ -367,28 +237,3 @@ def remove_tool_dependency_installation_directory(dependency_install_dir):
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removed = True
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error_message = ""
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return removed, error_message
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def set_tool_dependency_attributes(app, tool_dependency, status, error_message=None):
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sa_session = app.install_model.context
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if status == app.install_model.ToolDependency.installation_status.UNINSTALLED:
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installation_directory = tool_dependency.installation_directory(app)
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remove_tool_dependency_installation_directory(installation_directory)
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tool_dependency.error_message = error_message
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if str(tool_dependency.status) != str(status):
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tool_shed_repository = tool_dependency.tool_shed_repository
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debug_msg = (
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"Updating an existing record for version %s of tool dependency %s for revision %s of repository %s "
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% (
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str(tool_dependency.version),
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str(tool_dependency.name),
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str(tool_shed_repository.changeset_revision),
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str(tool_shed_repository.name),
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)
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)
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debug_msg += f"by updating the status from {tool_dependency.status} to {status}."
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log.debug(debug_msg)
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tool_dependency.status = status
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sa_session.add(tool_dependency)
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sa_session.flush()
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return tool_dependency
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