add secrets into cwl and yml

galaxyproject · Oct 31, 2024 · 3873675 · 3873675
1 parent 44df605
commit 3873675
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 3 deletions.
diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
@@ -219,6 +219,9 @@ def software_requirements(self) -> List:
     def resource_requirements(self) -> List:
         return self.hints_or_requirements_of_class("ResourceRequirement")
 
+    def secrets(self) -> List:
+        return self.hints_or_requirements_of_class("Secrets")
+
 
 class CommandLineToolProxy(ToolProxy):
     _class = "CommandLineTool"

diff --git a/lib/galaxy/tool_util/deps/requirements.py b/lib/galaxy/tool_util/deps/requirements.py
@@ -339,13 +339,14 @@ def to_dict(self) -> Dict[str, Any]:
             "required": self.required,
         }
 
-    def from_dict(self, dict: Dict[str, Any]) -> "SecretsRequirement":
+    @classmethod
+    def from_dict(cls, dict: Dict[str, Any]) -> "SecretsRequirement":
         type = dict["type"]
         user_preferences_key = dict["user_preferences_key"]
         inject_as_env = dict["inject_as_env"]
         label = dict.get("label", "")
         required = dict.get("required", False)
-        return SecretsRequirement(
+        return cls(
             type=type,
             user_preferences_key=user_preferences_key,
             inject_as_env=inject_as_env,
@@ -358,11 +359,13 @@ def parse_requirements_from_lists(
     software_requirements: List[Union[ToolRequirement, Dict[str, Any]]],
     containers: Iterable[Dict[str, Any]],
     resource_requirements: Iterable[Dict[str, Any]],
-) -> Tuple[ToolRequirements, List[ContainerDescription], List[ResourceRequirement]]:
+    secrets: Iterable[Dict[str, Any]],
+) -> Tuple[ToolRequirements, List[ContainerDescription], List[ResourceRequirement], List[SecretsRequirement]]:
     return (
         ToolRequirements.from_list(software_requirements),
         [ContainerDescription.from_dict(c) for c in containers],
         resource_requirements_from_list(resource_requirements),
+        [SecretsRequirement.from_dict(s) for s in secrets],
     )
 
 

diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
@@ -162,10 +162,12 @@ def parse_requirements_and_containers(self):
 
         software_requirements = self.tool_proxy.software_requirements()
         resource_requirements = self.tool_proxy.resource_requirements()
+        secrets = self.tool_proxy.secrets()
         return requirements.parse_requirements_from_lists(
             software_requirements=[{"name": r[0], "version": r[1], "type": "package"} for r in software_requirements],
             containers=containers,
             resource_requirements=resource_requirements,
+            secrets=secrets,
         )
 
     def parse_profile(self):

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
@@ -111,6 +111,7 @@ def parse_requirements_and_containers(self):
             software_requirements=[r for r in mixed_requirements if r.get("type") != "resource"],
             containers=self.root_dict.get("containers", []),
             resource_requirements=[r for r in mixed_requirements if r.get("type") == "resource"],
+            secrets=self.root_dict.get("secrets", []),
         )
 
     def parse_input_pages(self) -> PagesSource: