Merge branch 'interactive_url' into 'dev' (dff53995) · Commits · NDIP / Galaxy

lib/galaxy/app_unittest_utils/galaxy_mock.py

+4 −1

Original line number	Diff line number	Diff line
		@@ -143,7 +143,10 @@ class MockApp(di.Container, GalaxyDataTestApp):
		self.auth_manager = AuthManager(self.config)
		self.user_manager = UserManager(cast(BasicSharedApp, self))
		self.execution_timer_factory = Bunch(get_timer=StructuredExecutionTimer)
		self.interactivetool_manager = Bunch(create_interactivetool=lambda args, *kwargs: None)
		self.interactivetool_manager = Bunch(
		create_interactivetool=lambda args, *kwargs: None,
		get_job_subdomain=lambda args, *kwargs: None
		)
		self.is_job_handler = False
		self.biotools_metadata_source = None
		set_thread_app(self)

lib/galaxy/jobs/init.py

+5 −3

Original line number	Diff line number	Diff line
		@@ -1243,6 +1243,11 @@ class MinimalJobWrapper(HasResourceParameters):
		self.__prepare_upload_paramfile(job)

		tool_evaluator = self._get_tool_evaluator(job)
		if hasattr(self.app, "interactivetool_manager"):
		self.interactivetools = tool_evaluator.populate_interactivetools()
		self.app.interactivetool_manager.create_interactivetool(job, self.tool, self.interactivetools)
		job.interactive_url = self.app.interactivetool_manager.get_job_subdomain(job)

		compute_environment = compute_environment or self.default_compute_environment(job)
		tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
		(
		@@ -1252,9 +1257,6 @@ class MinimalJobWrapper(HasResourceParameters):
		self.environment_variables,
		) = tool_evaluator.build()
		job.command_line = self.command_line
		if hasattr(self.app, "interactivetool_manager"):
		self.interactivetools = tool_evaluator.populate_interactivetools()
		self.app.interactivetool_manager.create_interactivetool(job, self.tool, self.interactivetools)

		# Ensure galaxy_lib_dir is set in case there are any later chdirs
		self.galaxy_lib_dir # noqa: B018

lib/galaxy/managers/interactivetool.py

+15 −7

Original line number	Diff line number	Diff line
		@@ -175,6 +175,11 @@ class InteractiveToolManager:
		with transaction(self.sa_session):
		self.sa_session.commit()

		def get_job_subdomain(self, job):
		# returns the url for the first entry point
		for ep in job.interactivetool_entry_points:
		return self.calculate_entry_point(self.app.security.encode_id, ep)

		def configure_entry_point(self, job, tool_port=None, host=None, port=None, protocol=None):
		return self.configure_entry_points(
		job, {tool_port: dict(tool_port=tool_port, host=host, port=port, protocol=protocol)}
		@@ -296,6 +301,15 @@ class InteractiveToolManager:
		self.sa_session.commit()
		self.propagator.remove_entry_point(entry_point)

		def calculate_entry_point(self, encode_id, entry_point):
		entry_point_encoded_id = encode_id(entry_point.id)
		entry_point_class = entry_point.__class__.__name__.lower()
		entry_point_prefix = self.app.config.interactivetools_prefix
		entry_point_token = entry_point.token
		if self.app.config.interactivetools_shorten_url:
		return f"{entry_point_encoded_id}-{entry_point_token[:10]}.{entry_point_prefix}"
		return f"{entry_point_encoded_id}-{entry_point_token}.{entry_point_class}.{entry_point_prefix}"

		def target_if_active(self, trans, entry_point):
		if entry_point.active and not entry_point.deleted:
		request_host = trans.request.host
		@@ -313,13 +327,7 @@ class InteractiveToolManager:
		return rval

		def get_entry_point_subdomain(self, trans, entry_point):
		entry_point_encoded_id = trans.security.encode_id(entry_point.id)
		entry_point_class = entry_point.__class__.__name__.lower()
		entry_point_prefix = self.app.config.interactivetools_prefix
		entry_point_token = entry_point.token
		if self.app.config.interactivetools_shorten_url:
		return f"{entry_point_encoded_id}-{entry_point_token[:10]}.{entry_point_prefix}"
		return f"{entry_point_encoded_id}-{entry_point_token}.{entry_point_class}.{entry_point_prefix}"
		return self.calculate_entry_point(trans.security.encode_id, entry_point)

		def get_entry_point_path(self, trans, entry_point):
		entry_point_encoded_id = trans.security.encode_id(entry_point.id)

lib/galaxy/tools/evaluation.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -14,6 +14,7 @@ from typing import (
		Optional,
		Union,
		)
		from urllib.parse import urlparse

		from galaxy import model
		from galaxy.authnz.util import provider_name_to_backend
		@@ -195,6 +196,9 @@ class ToolEvaluator:
		if self._history:
		param_dict["__history_id__"] = self.app.security.encode_id(self._history.id)
		param_dict["__galaxy_url__"] = self.compute_environment.galaxy_url()
		if hasattr(self.job, "interactive_url") and isinstance(self.job.interactive_url, str):
		param_dict["__tool_url_prefix__"] = ''.join([self.job.interactive_url, ".", urlparse(self.compute_environment.galaxy_url()).hostname])

		param_dict.update(self.tool.template_macro_params)
		# All parameters go into the param_dict
		param_dict.update(incoming)