[wip] workaround fix for CWL type [null, enum, array-enum] without ex…

…plicit name (relates to common-workflow-language/cwltool#1908)

CHANGES.rst

@@ -38,6 +38,10 @@ Fixes:
   Links will only be listed within the returned ``processSummary`` to respect the `OGC API - Processes` schema.
 - Fix `CLI` not removing embedded ``links`` in ``processSummary`` from ``deploy`` operation response
   when ``-nL``/``--no-links`` option is specified.
+- Fix `CWL` definitions combining nested ``enum`` types as ``["null", <enum>, {type: array, items: <enum>]`` without an
+  explicit ``name`` or ``SchemaDefRequirement`` causing failing ``schema_salad`` resolution under ``cwltool``. A patch
+  is applied for the moment to inject a temporary ``name`` to let the `CWL` engine succeed schema validation (relates
+  to `common-workflow-language/cwltool#1908 <https://github.com/common-workflow-language/cwltool/issues/1908>`_).
 
 .. _changes_4.31.0:
 

tests/functional/application-packages/Finch_EnsembleGridPointWetdays/deploy.yml

@@ -1,6 +1,293 @@
 processDescription:
   process:
     id: Finch_EnsembleGridPointWetdays
+#    inputs:
+#      lat:
+#        schema:
+#          oneOf:
+#            - type: string
+#            - type: array
+#              items: string
+#      lon:
+#        schema:
+#          oneOf:
+#            - type: string
+#            - type: array
+#              items: string
+#      start_date:
+#        schema:
+#          required: false
+#          type: string
+#      end_date:
+#        schema:
+#          required: false
+#          type: string
+#      ensemble_percentiles:
+#        schema:
+#          required: false
+#          type: string
+#          default: 10,50,90
+#      average:
+#        schema:
+#          required: false
+#          type: boolean
+#          default: false
+#      dataset:
+#        schema:
+#          required: false
+#          type: string
+#          enum:
+#          - humidex-daily
+#          - candcs-u5
+#          - candcs-u6
+#          - bccaqv2
+#          default: candcs-u5
+#      scenario:
+#        schema:
+#          required: false
+#          oneOf:
+#            - type: string
+#              enum:
+#              - ssp126
+#              - rcp85
+#              - rcp45
+#              - rcp26
+#              - ssp585
+#              - ssp245
+#            - type: array
+#              items:
+#                type: string
+#                enum:
+#                - ssp126
+#                - rcp85
+#                - rcp45
+#                - rcp26
+#                - ssp585
+#                - ssp245
+#      models:
+#        schema:
+#          required: false
+#          default: all
+#          oneOf:
+#            - type: string
+#              enum:
+#              - KACE-1-0-G
+#              - CCSM4
+#              - MIROC5
+#              - EC-Earth3-Veg
+#              - TaiESM1
+#              - GFDL-ESM4
+#              - GFDL-CM3
+#              - CanESM5
+#              - HadGEM3-GC31-LL
+#              - INM-CM4-8
+#              - IPSL-CM5A-MR
+#              - EC-Earth3
+#              - GFDL-ESM2G
+#              - humidex_models
+#              - GFDL-ESM2M
+#              - MIROC-ESM
+#              - CSIRO-Mk3-6-0
+#              - MPI-ESM-LR
+#              - NorESM1-M
+#              - CNRM-CM5
+#              - all
+#              - GISS-E2-1-G
+#              - 24models
+#              - MPI-ESM1-2-HR
+#              - CNRM-ESM2-1
+#              - CNRM-CM6-1
+#              - CanESM2
+#              - FGOALS-g3
+#              - NorESM1-ME
+#              - IPSL-CM6A-LR
+#              - CMCC-ESM2
+#              - pcic12
+#              - EC-Earth3-Veg-LR
+#              - ACCESS-ESM1-5
+#              - MRI-CGCM3
+#              - MIROC-ESM-CHEM
+#              - NorESM2-MM
+#              - bcc-csm1-1-m
+#              - BNU-ESM
+#              - UKESM1-0-LL
+#              - CESM1-CAM5
+#              - MIROC-ES2L
+#              - MRI-ESM2-0
+#              - HadGEM2-ES
+#              - MIROC6
+#              - MPI-ESM-MR
+#              - INM-CM5-0
+#              - bcc-csm1-1
+#              - BCC-CSM2-MR
+#              - ACCESS-CM2
+#              - NorESM2-LM
+#              - IPSL-CM5A-LR
+#              - FGOALS-g2
+#              - HadGEM2-AO
+#              - 26models
+#              - MPI-ESM1-2-LR
+#              - KIOST-ESM
+#            - type: array
+#              items:
+#                type: string
+#                enum:
+#                - KACE-1-0-G
+#                - CCSM4
+#                - MIROC5
+#                - EC-Earth3-Veg
+#                - TaiESM1
+#                - GFDL-ESM4
+#                - GFDL-CM3
+#                - CanESM5
+#                - HadGEM3-GC31-LL
+#                - INM-CM4-8
+#                - IPSL-CM5A-MR
+#                - EC-Earth3
+#                - GFDL-ESM2G
+#                - humidex_models
+#                - GFDL-ESM2M
+#                - MIROC-ESM
+#                - CSIRO-Mk3-6-0
+#                - MPI-ESM-LR
+#                - NorESM1-M
+#                - CNRM-CM5
+#                - all
+#                - GISS-E2-1-G
+#                - 24models
+#                - MPI-ESM1-2-HR
+#                - CNRM-ESM2-1
+#                - CNRM-CM6-1
+#                - CanESM2
+#                - FGOALS-g3
+#                - NorESM1-ME
+#                - IPSL-CM6A-LR
+#                - CMCC-ESM2
+#                - pcic12
+#                - EC-Earth3-Veg-LR
+#                - ACCESS-ESM1-5
+#                - MRI-CGCM3
+#                - MIROC-ESM-CHEM
+#                - NorESM2-MM
+#                - bcc-csm1-1-m
+#                - BNU-ESM
+#                - UKESM1-0-LL
+#                - CESM1-CAM5
+#                - MIROC-ES2L
+#                - MRI-ESM2-0
+#                - HadGEM2-ES
+#                - MIROC6
+#                - MPI-ESM-MR
+#                - INM-CM5-0
+#                - bcc-csm1-1
+#                - BCC-CSM2-MR
+#                - ACCESS-CM2
+#                - NorESM2-LM
+#                - IPSL-CM5A-LR
+#                - FGOALS-g2
+#                - HadGEM2-AO
+#                - 26models
+#                - MPI-ESM1-2-LR
+#                - KIOST-ESM
+#      thresh:
+#        schema:
+#          required: false
+#          type: string
+#          default: "1.0 mm/day"
+#      freq:
+#        schema:
+#          required: false
+#          default: YS
+#          type: string
+#          enum:
+#          - YS
+#          - QS-DEC
+#          - AS-JUL
+#          - MS
+#      op:
+#        schema:
+#          type: string
+#          required: false
+#          default: '>='
+#          enum:
+#          - '>='
+#          - '>'
+#          - gt
+#          - ge
+#      month:
+#        schema:
+#          required: false
+#          oneOf:
+#            - type: integer
+#              enum: [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 ]
+#            - type: array
+#              items:
+#                type: integer
+#                enum: [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 ]
+#      season:
+#        schema:
+#          required: false
+#          type: string
+#          enum:
+#          - SON
+#          - MAM
+#          - JJA
+#          - DJF
+#      check_missing:
+#        schema:
+#          required: false
+#          type: string
+#          enum:
+#          - pct
+#          - at_least_n
+#          - wmo
+#          - skip
+#          - from_context
+#          - any
+#      missing_options:
+#        schema:
+#          required: false
+#          type: string
+#          contentMediaType: application/json
+#      cf_compliance:
+#        schema:
+#          required: false
+#          default: warn
+#          type: string
+#          enum:
+#          - raise
+#          - log
+#          - warn
+#      data_validation:
+#        schema:
+#          required: false
+#          default: raise
+#          type: string
+#          enum:
+#          - raise
+#          - log
+#          - warn
+#      output_name:
+#        schema:
+#          required: false
+#          type: string
+#      output_format:
+#        schema:
+#          required: false
+#          default: netcdf
+#          type: string
+#          enum:
+#          - csv
+#          - netcdf
+#      csv_precision:
+#        schema:
+#          required: false
+#          type: integer
+#  outputs:
+#    output:
+#      schema:
+#        type: string
+#        contentMediaType: text/plain
   jobControlOptions:
     - async-execute
   outputTransmission:

weaver/processes/convert.py

@@ -122,14 +122,14 @@
         AnySettingsContainer,
         AnyValueType,
         CWL,
-        CWL_Input_Type,
         CWL_IO_ComplexType,
         CWL_IO_DataType,
         CWL_IO_EnumSymbols,
         CWL_IO_FileValue,
         CWL_IO_LiteralType,
+        CWL_IO_Type,
         CWL_IO_Value,
-        CWL_Output_Type,
+        CWL_SchemaNames,
         ExecutionInputs,
         ExecutionInputsList,
         ExecutionInputsMap,
@@ -176,7 +176,6 @@
         "supported_formats": NotRequired[List[JSON_Format]],
     }, total=False)
     JSON_IO_ListOrMap = Union[List[JSON], Dict[str, Union[JSON, str]]]
-    CWL_IO_Type = Union[CWL_Input_Type, CWL_Output_Type]
     PKG_IO_Type = Union[JSON_IO_Type, WPS_IO_Type]
     ANY_IO_Type = Union[CWL_IO_Type, JSON_IO_Type, WPS_IO_Type, OWS_IO_Type]
     ANY_Format_Type = Union[Dict[str, Optional[str]], Format]
@@ -1175,6 +1174,28 @@ def get_cwl_io_type_name(io_type):
     return io_type
 
 
+def resolve_cwl_io_type_schema(io_info, cwl_schema_names=None):
+    # type: (CWL_IO_Type, Optional[CWLSchemaNames]) -> CWL_IO_Type
+    """
+    Reverse :term:`CWL` schema references by name back to their full :term:`CWL` I/O definition.
+
+    .. seealso::
+        - :meth:`weaver.processes.wps_package.WpsPackage.make_inputs`
+        - :meth:`weaver.processes.wps_package.WpsPackage.update_cwl_schema_names`
+    """
+    if not isinstance(io_info, dict) or not cwl_schema_names:
+        return io_info
+    io_type = io_info.get("type")
+    io_item = io_info.get("items")
+    if io_type == "array" and isinstance(io_item, str) and io_item in cwl_schema_names:
+        io_info = io_info.copy()  # avoid undoing CWL tool parsing/resolution
+        io_info["items"] = cwl_schema_names[io_item]._props
+    elif isinstance(io_type, str) and io_type in cwl_schema_names:
+        io_info = io_info.copy()  # avoid undoing CWL tool parsing/resolution
+        io_info["type"] = cwl_schema_names[io_type]._props
+    return io_info
+
+
 @dataclass
 class CWLIODefinition(object):
     """
@@ -1272,8 +1293,8 @@ def __iter__(self):
     """
 
 
-def get_cwl_io_type(io_info, strict=True):
-    # type: (CWL_IO_Type, bool) -> CWLIODefinition
+def get_cwl_io_type(io_info, strict=True, cwl_schema_names=None):
+    # type: (CWL_IO_Type, bool, Optional[CWL_SchemaNames]) -> CWLIODefinition
     """
     Obtains the basic type of the CWL input and identity if it is optional.
 
@@ -1290,6 +1311,7 @@ def get_cwl_io_type(io_info, strict=True):
 
     :param io_info: :term:`CWL` definition to parse.
     :param strict: Indicates if only pure :term:`CWL` definition is allowed, or allow implicit data-type conversions.
+    :param cwl_schema_names: Mapping of CWL type schema references to resolve in long form if used in a definition.
     :return: tuple of guessed base type and flag indicating if it can be null (optional input).
     """
     io_type = get_cwl_io_type_name(io_info["type"])
@@ -1316,6 +1338,7 @@ def get_cwl_io_type(io_info, strict=True):
             io_base_type = None
             for i, typ in enumerate(io_type, start=int(is_null)):
                 typ = get_cwl_io_type_name(typ)
+                typ = resolve_cwl_io_type_schema(typ, cwl_schema_names)
                 io_name = io_info["name"]
                 sub_type = {"type": typ, "name": f"{io_name}[{i}]"}  # type: CWL_IO_Type
                 array_io_def = parse_cwl_array_type(sub_type, strict=strict)