partial support of CWL for single app process (relates to #56)

CHANGES.rst

@@ -25,6 +25,9 @@ Changes:
   ``application/ogcapppkg+yaml`` for the |ogc-app-pkg|_ schema, or using ``application/cwl+yaml`` for
   a `CWL`-only definition. The definition will be loaded and converted to ``JSON`` for schema validation. Otherwise,
   ``JSON`` contents is assumed to be directly provided in the request payload for validation as previously accomplished.
+- Add partial support of `CWL` with ``$graph`` representation for the special case where the graph is composed of a list
+  of exactly one `Application Package`. Multi/nested-`CWL` definitions are **NOT** supported
+  (relates to `#56 <https://github.com/crim-ca/weaver/issues/56>`_).
 
 Fixes:
 ------

weaver/processes/utils.py

@@ -61,7 +61,7 @@
 
 LOGGER = logging.getLogger(__name__)
 if TYPE_CHECKING:
-    from typing import Any, List, Optional, Tuple, Union
+    from typing import List, Optional, Tuple, Union
 
     from pyramid.request import Request
 
@@ -143,7 +143,6 @@ def _check_deploy(payload):
     """
     Validate minimum deploy payload field requirements with exception handling.
     """
-    # FIXME: handle colander invalid directly in tween (https://github.com/crim-ca/weaver/issues/112)
     message = "Process deployment definition is invalid."
     try:
         results = sd.Deploy().deserialize(payload)
@@ -207,6 +206,7 @@ def _check_deploy(payload):
                 generate_diff(p_exec_unit, r_exec_unit, val_name="original payload", ref_name="parsed result")
             )
         return results
+    # FIXME: handle colander invalid directly in tween (https://github.com/crim-ca/weaver/issues/112)
     except colander.Invalid as exc:
         LOGGER.debug("Failed deploy body schema validation:\n%s", exc)
         raise HTTPBadRequest(json={
@@ -287,6 +287,7 @@ def _load_payload(payload, content_type):
     return payload
 
 
+# FIXME: supported nested and $graph multi-deployment (https://github.com/crim-ca/weaver/issues/56)
 def deploy_process_from_payload(payload, container, overwrite=False):
     # type: (Union[JSON, str], Union[AnySettingsContainer, AnyRequestType], bool) -> HTTPException
     """
@@ -312,7 +313,7 @@ def deploy_process_from_payload(payload, container, overwrite=False):
     payload = _check_deploy(payload)
 
     # validate identifier naming for unsupported characters
-    process_description = payload.get("processDescription")
+    process_description = payload.get("processDescription", {})  # empty possible if CWL directly passed
     process_info = process_description.get("process", process_description)
     process_href = process_description.pop("href", None)
 
@@ -335,9 +336,14 @@ def deploy_process_from_payload(payload, container, overwrite=False):
         package = None
         reference = content.get("href")
         found = isinstance(reference, str)
-    elif c_type in (ContentType.ANY_CWL + [ContentType.APP_JSON]) and "cwlVersion" in payload:
-        package = payload
+    elif c_type in (list(ContentType.ANY_CWL) + [ContentType.APP_JSON]) and "cwlVersion" in payload:
         process_info = {}
+        package = payload
+        if "$graph" in package and isinstance(package["$graph"], list) and len(package["$graph"]) == 1:
+            # consider package as if provided in non-graph representation
+            # must preserve top level fields (e.g.: 'cwlVersion') and nested graph item
+            package.update(package.pop("$graph")[0])
+        found = True
     else:  # ogc-apppkg type, but no explicit check since used by default (backward compat)
         if deployment_profile_name:  # optional hint
             allowed_profile_suffix = [ProcessType.APPLICATION, ProcessType.WORKFLOW]
@@ -363,6 +369,7 @@ def deploy_process_from_payload(payload, container, overwrite=False):
             "ProcessDescription.href",
             "ProcessDescription.owsContext.content.href",
             "executionUnit[*].(unit|href)",
+            "{ <CWL> }",
         ]
         raise HTTPBadRequest(
             f"Missing one of required parameters {params} to obtain package/process definition or reference."

weaver/wps_restapi/processes/processes.py

@@ -141,7 +141,7 @@ def add_local_process(request):
     """
     Register a local process.
     """
-    return deploy_process_from_payload(request.body, request)
+    return deploy_process_from_payload(request.text, request)  # use text to allow parsing as JSON or YAML
 
 
 @sd.process_service.get(tags=[sd.TAG_PROCESSES, sd.TAG_DESCRIBEPROCESS], renderer=OutputFormat.JSON,

weaver/wps_restapi/swagger_definitions.py

@@ -20,7 +20,7 @@
 
 import duration
 import yaml
-from colander import DateTime, Email, Money, OneOf, Range, Regex, drop, null, required
+from colander import DateTime, Email, Length, Money, OneOf, Range, Regex, drop, null, required
 from dateutil import parser as date_parser
 
 from weaver import __meta__
@@ -4149,15 +4149,19 @@ class CWLGraphList(ExtendedSequenceSchema):
     cwl = CWLGraphItem()
 
 
+# FIXME: supported nested and $graph multi-deployment (https://github.com/crim-ca/weaver/issues/56)
 class CWLGraphBase(ExtendedMappingSchema):
     graph = CWLGraphList(
         name="$graph", description=(
-            "Graph definition that combines one or many CWL application packages within a single payload. "
-            "If an single application is given (list of one item), it will be deployed as normal CWL by itself. "
-            "If multiple applications are defined, the first MUST be the top-most Workflow process. "
-            "Other items deployment will be performed, and the full deployment will be persisted only if all are "
-            "valid. The resulting Workflow will be registered as a package by itself (i.e: not as a graph)."
-        )
+            "Graph definition that defines *exactly one* CWL application package represented as list. "
+            "Multiple definitions simultaneously deployed is NOT supported at the moment."
+            # "Graph definition that combines one or many CWL application packages within a single payload. "
+            # "If an single application is given (list of one item), it will be deployed as normal CWL by itself. "
+            # "If multiple applications are defined, the first MUST be the top-most Workflow process. "
+            # "Deployment of other items will be performed, and the full deployment will be persisted only if all are "
+            # "valid. The resulting Workflow will be registered as a package by itself (i.e: not as a graph)."
+        ),
+        validator=Length(min=1, max=1)
     )
 
 
@@ -4170,6 +4174,10 @@ class DeployCWL(NotKeywordSchema, CWL):
         CWLGraphBase()
     ]
     id = CWLIdentifier()  # required in this case
+    inputs = CWLInputsDefinition(
+        missing=drop,  # empty definition permitted during deployment
+        description="All inputs available to the Application Package.",
+    )
 
 
 class Deploy(OneOfKeywordSchema):