Merge branch 'proxy_https' into 'dev' (2a709cb7) · Commits · NDIP / Galaxy

lib/galaxy/managers/interactivetool.py

+11 −7

Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@ class InteractiveToolSqlite:
		conn = sqlite3.connect(self.sqlite_filename)
		try:
		c = conn.cursor()
		select = f"""SELECT token, host, port, info
		select = f"""SELECT token, host, port, info, protocol
		FROM {DATABASE_TABLE_NAME}
		WHERE key=? and key_type=?"""
		c.execute(
		@@ -36,15 +36,15 @@ class InteractiveToolSqlite:
		),
		)
		try:
		token, host, port, info = c.fetchone()
		token, host, port, info, protocol = c.fetchone()
		except TypeError:
		log.warning("get(): invalid key: %s key_type %s", key, key_type)
		return None
		return dict(key=key, key_type=key_type, token=token, host=host, port=port, info=info)
		return dict(key=key, key_type=key_type, token=token, host=host, port=port, info=info, protocol=protocol)
		finally:
		conn.close()

		def save(self, key, key_type, token, host, port, info=None):
		def save(self, key, key_type, token, host, port, info=None, protocol=None):
		"""
		Writeout a key, key_type, token, value store that is can be used for coordinating
		with external resources.
		@@ -66,6 +66,7 @@ class InteractiveToolSqlite:
		host text,
		port integer,
		info text,
		protocol text,
		PRIMARY KEY (key, key_type)
		)"""
		% (DATABASE_TABLE_NAME)
		@@ -81,8 +82,8 @@ class InteractiveToolSqlite:
		),
		)
		insert = """INSERT INTO %s
		(key, key_type, token, host, port, info)
		VALUES (?, ?, ?, ?, ?, ?)""" % (
		(key, key_type, token, host, port, info, protocol)
		VALUES (?, ?, ?, ?, ?, ?, ?)""" % (
		DATABASE_TABLE_NAME
		)
		c.execute(
		@@ -94,6 +95,7 @@ class InteractiveToolSqlite:
		host,
		port,
		info,
		protocol
		),
		)
		conn.commit()
		@@ -135,6 +137,7 @@ class InteractiveToolSqlite:
		entry_point.host,
		entry_point.port,
		None,
		entry_point.protocol,
		)

		def remove_entry_point(self, entry_point):
		@@ -164,6 +167,7 @@ class InteractiveToolManager:
		entry_url=entry["url"],
		name=entry["name"],
		requires_domain=entry["requires_domain"],
		protocol=entry["protocol"],
		short_token=self.app.config.interactivetools_shorten_url,
		)
		self.sa_session.add(ep)
		@@ -188,10 +192,10 @@ class InteractiveToolManager:
		else:
		ep.host = port_dict["host"]
		ep.port = port_dict["port"]
		self.save_entry_point(ep)
		ep.protocol = port_dict["protocol"]
		ep.configured = True
		self.sa_session.add(ep)
		self.save_entry_point(ep)
		configured.append(ep)
		if configured:
		with transaction(self.sa_session):

lib/galaxy/tool_util/parser/xml.py

+4 −1

Original line number	Diff line number	Diff line
		@@ -304,7 +304,10 @@ class XmlToolSource(ToolSource):
		if name:
		name = name.strip()
		requires_domain = string_as_bool(ep_el.attrib.get("requires_domain", False))
		rtt.append(dict(port=port, url=url, name=name, requires_domain=requires_domain))
		protocol = ep_el.attrib.get("protocol", "http")
		if protocol:
		protocol = protocol.strip()
		rtt.append(dict(port=port, url=url, name=name, requires_domain=requires_domain, protocol=protocol))
		return rtt

		def parse_hidden(self):

lib/galaxy/tools/evaluation.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -521,7 +521,7 @@ class ToolEvaluator:
		it = []
		for ep in getattr(self.tool, "ports", []):
		ep_dict = {}
		for key in "port", "name", "url", "requires_domain":
		for key in "port", "name", "url", "requires_domain", "protocol":
		val = ep.get(key, None)
		if val is not None and not isinstance(val, bool):
		val = fill_template(