Tool Landing API...

Author: jmchilton

client/src/api/schema/schema.ts

@@ -7832,7 +7832,7 @@ export interface components {
              * @default false
              */
             public: boolean;
-            request_state?: components["schemas"]["DataLandingRequestState"];
+            request_state: components["schemas"]["DataLandingRequestState"];
         };
         /** CreateEntryPayload */
         CreateEntryPayload: {

lib/galaxy/managers/landing.py

@@ -29,9 +29,21 @@
     WorkflowLandingRequest,
 )
 from galaxy.security.idencoding import IdEncodingHelper
-from galaxy.structured_app import StructuredApp
+from galaxy.structured_app import (
+    MinimalManagerApp,
+    StructuredApp,
+)
+from galaxy.tool_util.parameters import (
+    landing_decode,
+    LandingRequestInternalToolState,
+    LandingRequestToolState,
+)
 from galaxy.util import safe_str_cmp
 from .context import ProvidesUserContext
+from .tools import (
+    get_tool_from_toolbox,
+    ToolRunReference,
+)
 
 LandingRequestModel = Union[ToolLandingRequestModel, WorkflowLandingRequestModel]
 
@@ -43,16 +55,37 @@ def __init__(
         sa_session: galaxy_scoped_session,
         security: IdEncodingHelper,
         workflow_contents_manager: WorkflowContentsManager,
+        app: MinimalManagerApp,
     ):
         self.sa_session = sa_session
         self.security = security
         self.workflow_contents_manager = workflow_contents_manager
+        self.app = app
 
     def create_tool_landing_request(self, payload: CreateToolLandingRequestPayload, user_id=None) -> ToolLandingRequest:
+        tool_id = payload.tool_id
+        tool_version = payload.tool_version
+        request_state = payload.request_state
+
+        ref = ToolRunReference(tool_id=tool_id, tool_version=tool_version, tool_uuid=None)
+        tool = get_tool_from_toolbox(self.app.toolbox, ref)
+        landing_request_state = LandingRequestToolState(request_state or {})
+        # Okay this is a hack until tool request API commit is merged, tools don't yet have a parameter
+        # schema - so we can't do this properly.
+        if hasattr(tool, "parameters"):
+            internal_landing_request_state = landing_decode(landing_request_state, tool, self.security.decode_id)
+        else:
+            assert tool.id == "__DATA_FETCH__"
+            # we have validated the payload as part of the API request
+            # nothing else to decode ideally so just swap to internal model state object
+            internal_landing_request_state = LandingRequestInternalToolState(
+                input_state=landing_request_state.input_state
+            )
+
         model = ToolLandingRequestModel()
-        model.tool_id = payload.tool_id
-        model.tool_version = payload.tool_version
-        model.request_state = payload.request_state
+        model.tool_id = tool_id
+        model.tool_version = tool_version
+        model.request_state = internal_landing_request_state.input_state
         model.uuid = uuid4()
         model.client_secret = payload.client_secret
         model.public = payload.public

lib/galaxy/model/store/discover.py

@@ -985,10 +985,10 @@ def replace_request_syntax_sugar(obj):
             # item...
             new_hashes = []
             for key in HASH_NAME_MAP.keys():
-                if key in obj:
+                if key in obj and obj[key] is not None:
                     new_hashes.append({"hash_function": key, "hash_value": obj[key]})
                     del obj[key]
-                if key.lower() in obj:
+                if key.lower() in obj and obj[key.lower()] is not None:
                     new_hashes.append({"hash_function": key, "hash_value": obj[key.lower()]})
                     del obj[key.lower()]
             # hack around pydantic stick a None in here for data fetch models.

lib/galaxy/schema/fetch_data.py

@@ -13,6 +13,7 @@
     Field,
     field_validator,
     Json,
+    TypeAdapter,
 )
 from typing_extensions import (
     Literal,
@@ -205,7 +206,9 @@ class CompositeItems(FetchBaseModel):
 
 
 class NestedElement(BaseDataElement):
-    elements: list[Union["AnyElement", "NestedElement"]] = Field(..., alias="elements")
+    elements: list[Union["AnyElement", "NestedElement"]] = Field(
+        ..., validation_alias=AliasChoices("elements", "items")
+    )
 
 
 AnyElement = Annotated[
@@ -287,6 +290,9 @@ def targets_string_to_json(cls, v):
 ]
 
 
+TargetsAdapter = TypeAdapter(Targets)
+
+
 class FetchDataPayload(BaseDataPayload):
     targets: Targets
 
@@ -301,10 +307,8 @@ class DataLandingRequestState(Model):
 
 # Vaguely matches the schema.schema.ToolLandingState but we don't allow data_fetch to be called directly
 # via the tool API so we have a more specific model here.
-class DataLandingPayload(Model):
-    tool_id: str
-    tool_version: Optional[str] = None
-    request_state: DataLandingRequestState = None
+class CreateDataLandingPayload(Model):
+    request_state: DataLandingRequestState
     client_secret: Optional[str] = None
     public: bool = False
 

lib/galaxy/tool_util/client/landing.py

@@ -24,14 +24,18 @@
 
 
 def load_default_catalog():
-    catalog_yaml = resource_string(__name__, "landing_catalog.sample.yml")
+    name = __name__
+    if __name__ == "__main__":
+        name = "galaxy.tool_util.client.landing"
+    catalog_yaml = resource_string(name, "landing_library.catalog.yml")
     return yaml.safe_load(catalog_yaml)
 
 
 @dataclass
 class Request:
     template_id: str
     catalog: str
+    public: bool
     client_secret: Optional[str]
     galaxy_url: str
 
@@ -56,9 +60,16 @@ def generate_claim_url(request: Request) -> Response:
     else:
         catalog = load_default_catalog()
     template = catalog[template_id]
-    template_type = "tool" if "tool_id" in template else "workflow"
+    if "tool_id" in template:
+        template_type = "tool"
+    elif "workflow_id" in template:
+        template_type = "workflow"
+    else:
+        template_type = "data"
     if client_secret:
         template["client_secret"] = client_secret
+    if request.public:
+        template["public"] = True
 
     landing_request_url = f"{galaxy_url}/api/{template_type}_landings"
     raw_response = requests.post(
@@ -70,7 +81,8 @@ def generate_claim_url(request: Request) -> Response:
     except Exception:
         raise Exception("Request failed: %s", raw_response.text)
     response = raw_response.json()
-    url = f"{galaxy_url}/{template_type}_landings/{response['uuid']}"
+    response_type = "workflow" if template_type == "workflow" else "tool"
+    url = f"{galaxy_url}/{response_type}_landings/{response['uuid']}"
     if client_secret:
         url = url + f"?secret={client_secret}"
     return Response(url)
@@ -100,6 +112,14 @@ def arg_parser() -> argparse.ArgumentParser:
         default=None,
         help="An optional client secret to verify the request against, set to __GEN__ to generate one at random for this request.",
     )
+    parser.add_argument(
+        "-p",
+        "--public",
+        dest="public",
+        default=False,
+        action="store_true",
+        help="Declare the landing as public.",
+    )
     return parser
 
 
@@ -111,6 +131,7 @@ def main(argv=None) -> None:
     request = Request(
         args.template_id,
         args.catalog,
+        args.public,
         args.secret,
         args.galaxy_url,
     )