crim-ca · fmigneault · Dec 13, 2023 · May 19, 2023 · May 23, 2023 · May 23, 2023
diff --git a/.pylintrc b/.pylintrc
@@ -380,9 +380,11 @@ class-attribute-naming-style=any
 # Naming style matching correct class names.
 class-naming-style=PascalCase
 
-# Regular expression matching correct class names. Overrides class-naming-
-# style.
-#class-rgx=
+# Regular expression matching correct class names. Overrides class-naming-style.
+# Allow typing definitions that are matched as 'classes' to have slightly more versatile names.
+class-rgx=((_{0,2}[A-Z][a-zA-Z0-9]+)|((CWL|PKG|WPS|OAS|JSON|IO|ANY)_[a-zA-Z0-9_]+Types?))$
+
+typealias-rgx=_{0,2}(?!T[A-Z]|Type)((CWL|PKG|WPS|OAS|JSON|IO|ANY)_)?[A-Z]+[a-z0-9]+(?:[A-Z][a-z0-9]+)*$
 
 # Naming style matching correct constant names.
 const-naming-style=UPPER_CASE
@@ -406,7 +408,7 @@ function-naming-style=snake_case
 good-names=i,j,k,v,kv,ex,x,y,z,f,h,db,kw,dt,q,ns,id,s3,to,_
 
 # Include a hint for the correct naming format with invalid-name.
-include-naming-hint=no
+include-naming-hint=yes
 
 # Naming style matching correct inline iteration names.
 inlinevar-naming-style=any

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -12,11 +12,53 @@ Changes
 
 Changes:
 --------
-- No change.
-
-Fixes:
-------
-- No change.
+- Add ``weaver.formats.ContentEncoding`` with handlers for common encoding manipulation from input values.
+- Add |oap_echo|_ to the list of ``weaver.processes.builtin`` definitions with its `CWL` representation and
+  complementary `OGC API - Processes` reference implementation details. This `Process` will be automatically deployed
+  at `API` startup, and is employed to validate multiple parsing combinations of execution I/O values and encodings
+  (fixes `#379 <https://github.com/crim-ca/weaver/issues/379>`_).
+- Add support of `OGC` `BoundingBox` definition (``bbox`` and ``crs`` fields) as `Process` execution input value
+  with appropriate schema validation (fixes `#51 <https://github.com/crim-ca/weaver/issues/51>`_).
+- Add support of `Unit of Measure` (`UoM`) definition (``measurement`` and ``uom`` fields) as `Process` execution
+  input value with appropriate schema validation (fixes `#430 <https://github.com/crim-ca/weaver/issues/430>`_).
+- Add ``create_metalink`` utility function to facilitate generation of a ``.meta4`` or ``.metalink`` file definition
+  from a list of file link references (relates to `#25 <https://github.com/crim-ca/weaver/issues/25>`_).
+
+Fixes:
+------
+- Fix ``weaver.wps_restapi.swagger_definitions.ExecuteInputValues`` deserialization that sometimes silently dropped
+  invalid `JSON`-formatted inputs that did not fulfill schema validation. This was caused by a side effect regarding
+  how ``weaver.wps_restapi.colander_extras.VariableSchemaNode`` handled "unknown" `JSON` ``properties`` from submitted
+  content. In cases where *required* `Process` inputs were causing the invalid schema, `Job` execution would be aborted
+  and the error would be reported due to "missing" inputs. However, if the `JSON` failing schema validation happened to
+  be nested under an *optional* input definition, the `Job` execution could have resumed silently by omitting this
+  input's value propagation to the downstream `CWL`, `WPS` or `OGC API - Processes` implementation, which could make
+  it use an alternative default value than the real input that was submitted for the `Job`.
+- Fix schema name representation employed in generated ``colander.Invalid`` error when a schema validation failed, in
+  order to better represent deeply nested schema using multiple ``oneOf``, ``anyOf``, ``allOf`` schema nodes.
+  Using ``colander.Invalid.asdict``, each dictionary key now properly indicates the specific path of sub-nodes with
+  their relevant schema validation error.
+- Fix ``variable`` schema node names to provide a ``{SchemaName}<{VariableName}>`` representation, such that it can be
+  more easily identified. Schema nodes with a ``variable`` (i.e.: schema under ``additionalProperties``) previously only
+  indicated ``{VariableName}``, which made it complicated to follow reference schema classes that formed the error path.
+  Each of the evaluated fields against each possible ``variable`` schema will now report their corresponding nested
+  schema validation error as ``{SchemaName}<{VariableName}>({field})`` such that results can be understood.
+- Fix execution input reference (i.e.: using ``href``) dropping a ``schema`` URL reference if provided explicitly.
+  This parameter now remains within the produced content passed to the `Job`, and forwarded to a remote `Process` if
+  applicable, but no further schema validation is accomplished with the value in ``schema`` for the moment.
+- Fix ``ContentType.IMAGE_OGC_GEOTIFF`` using invalid media-type name (missing ``i`` in ``image``).
+- Fix `Job` input validation stripping additional parameters from provided Media-Type, potentially causing mismatching
+  Content-Type validation against the corresponding `Process` description inputs. Types should now match exactly the
+  original `Process` definition, including any additional parameters and sub-types.
+- Fix resolution of ``anyOf`` schema raising ``colander.Invalid`` even when the property was marked as optional
+  using ``missing=colander.drop``.
+- Fix ``$schema`` of `OGC` ``nameReferenceType`` being reported under every ``dataType`` of ``literalDataDomains`` for
+  literal `I/O` of `Process` descriptions. The reference is not only included in the `OpenAPI` definition as intended.
+- Fix override of `CWL` ``stderr`` and ``stdout`` definitions if specified by the original *Application Package* for
+  its own implementation. These stream handles are added to the `CWL` by Weaver to provide more contextual debugging
+  and traceability details of the internal application executed by the `Process`. However, a package making use of this
+  functionality of `CWL` to capture an output file would be broken unless naming the file exactly as ``stderr.log`` and
+  ``stdout.log``. Weaver will now employ the parameters provided by the *Application Package* if specified.
 
 .. _changes_4.38.0:
 
@@ -83,6 +125,9 @@ Changes:
 - Add more tests to validate core code paths of ``builtin`` `Process` ``jsonarray2netcdf``, ``metalink2netcdf`` and
   ``file_index_selector`` with validation of happy path and error handling conditions.
 
+.. _oap_echo: https://schemas.opengis.net/ogcapi/processes/part1/1.0/examples/json/ProcessDescription.json
+.. |oap_echo| replace:: ``EchoProcess``
+
 Fixes:
 ------
 - Fix invalid parsing of `XML` Metalink files in ``metalink2netcdf``. Metalink V3 and V4 will now properly consider the
@@ -1889,8 +1934,8 @@ Changes:
   where potentially inaccessible (according to settings). Definition of `CWL` package will need to add
   `InitialWorkDirRequirement <https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement>`_ as per
   defined by reference specification to stage those files if they need to be accessed with write permissions
-  (see: `example <https://www.commonwl.org/user_guide/15-staging/>`_). Addresses some issues listed in
-  `#155 <https://github.com/crim-ca/weaver/issues/155>`_.
+  (see: `example <https://www.commonwl.org/user_guide/topics/staging-input-files.html>`_).
+  Addresses some issues listed in `#155 <https://github.com/crim-ca/weaver/issues/155>`_.
 - Enforce removal of some invalid `CWL` hints/requirements that would break the behaviour offered by ``Weaver``.
 - Use ``weaver.request_options`` for `WPS GetCapabilities` and `WPS Check Status` requests under the running job.
 - Change default ``DOCKER_REPO`` value defined in ``Makefile`` to point to reference mentioned in ``README.md`` and

diff --git a/Makefile b/Makefile
@@ -281,7 +281,7 @@ install-npm:    ## install npm package manager and dependencies if they cannot b
 install-npm-stylelint: install-npm   	## install stylelint dependency for 'check-css' target using npm
 	@[ `npm ls 2>/dev/null | grep stylelint-config-standard | wc -l` = 1 ] || ( \
 		echo "Install required dependencies for CSS checks." && \
-		npm install stylelint stylelint-config-standard --save-dev \
+		npm install "stylelint@<16" "stylelint-config-standard@<35" --save-dev \
 	)
 
 .PHONY: install-npm-remarklint
@@ -850,3 +850,7 @@ stop: 		## kill application instance(s) started with gunicorn (pserve)
 .PHONY: stat
 stat: 		## display processes with PID(s) of gunicorn (pserve) instance(s) running the application
 	@lsof -i :4001 || echo "No instance running"
+
+# Reapply config if overrides were defined.
+# Ensure overrides take precedence over targets and auto-resolution logic of variables.
+-include Makefile.config
diff --git a/docs/source/appendix.rst b/docs/source/appendix.rst
@@ -20,7 +20,7 @@ Glossary
 
     API
         | Application Programming Interface
-        | Most typically, referring to the use of HTTP requests following an :term:`OpenAPI` specification.
+        | Most typically, referring to the use of HTTP(S) requests following an :term:`OpenAPI` specification.
 
     Application Package
         General term that refers to *"what and how to execute"* the :term:`Process`. Application Packages provide the
@@ -103,7 +103,8 @@ Glossary
           Alternative operation modes are described in :ref:`Configuration Settings`.
 
     I/O
-        Inputs and/or Outputs of CWL and/or WPS depending on context.
+        Inputs and/or Outputs of :term:`CWL`, :term:`OAP`, :term:`WPS` or :term:`OAS` representation
+        depending on context.
 
     IANA
         Ontology that regroups multiple definitions, amongst which `Weaver` looks up most of its known and supported
@@ -142,6 +143,7 @@ Glossary
     OGC
         |ogc|_
 
+    OAP
     OGC API - Processes
         The new :term:`API` that defines :term:`JSON` REST-binding representation
         of :term:`WPS` :term:`Process` collection.
@@ -205,6 +207,25 @@ Glossary
           transferred to the :term:`Process` as specified, and it is up to the underlying :term:`Application Package`
           definition to interpret it as deemed fit.
 
+    URI
+        | Uniform Resource Identifier
+        | Superset of :term:`URL` and :term:`URN` that uses a specific string format to identify a resource.
+
+    URL
+        | Uniform Resource Locator
+        | Subset of :term:`URI` that follows the ``<scheme>://<scheme-specific-part>`` format, as per :rfc:`1738`.
+          Specifies where an identified resource is available and the protocol mechanism employed for retrieving it.
+          This is employed in `Weaver` for ``http(s)://``, ``s3://`` and ``file://`` locations by :term:`I/O`, or in
+          general to refer to :term:`API` locations.
+
+    URN
+        | Uniform Resource Name
+        | Subset of :term:`URI` that follows the ``urn:<namespace>:<specific-part>`` format, as per :rfc:`8141`.
+          It is used to register a unique reference to a named entity such as a :term:`UoM` or other common definitions.
+
+        .. seealso::
+            - `IANA URN Namespaces <https://www.iana.org/assignments/urn-namespaces/urn-namespaces.xhtml>`_
+
     Vault
         Secured storage employed to upload files that should be temporarily stored on the `Weaver` server for
         later retrieval using an access token.

diff --git a/docs/source/package.rst b/docs/source/package.rst
@@ -1174,7 +1174,7 @@ Below is a list of compatible elements.
 | Parameters in :term:`WPS` Context       | Parameters in :term:`CWL` Context                        |
 +=========================================+==========================================================+
 | ``keywords``                            | ``s:keywords`` (expecting ``s`` in ``$namespace``        |
-|                                         | referring to http://schema.org [#schemaorg]_)            |
+|                                         | referring to http://schema.org [#cwl_schemaorg]_)        |
 +-----------------------------------------+----------------------------------------------------------+
 | ``metadata``                            | ``$schemas``/``$namespace``                              |
 | (using ``title`` and ``href`` fields)   | (using namespace name and HTTP references)               |
@@ -1186,8 +1186,8 @@ Below is a list of compatible elements.
 
 .. rubric:: Footnotes
 
-.. [#schemaorg]
-    See example: https://www.commonwl.org/user_guide/17-metadata/index.html
+.. [#cwl_schemaorg]
+    See example: `cwl-metadata`_
 
 .. |br| raw:: html
 

diff --git a/docs/source/references.rst b/docs/source/references.rst
@@ -34,7 +34,7 @@
 .. _cwl-workflow: https://www.commonwl.org/v1.1/Workflow.html
 .. |cwl-workdir-req| replace:: InitialWorkDirRequirement
 .. _cwl-workdir-req: https://www.commonwl.org/v1.1/CommandLineTool.html#InitialWorkDirRequirement
-.. _cwl-workdir-ex: https://www.commonwl.org/user_guide/15-staging/
+.. _cwl-workdir-ex: https://www.commonwl.org/user_guide/topics/staging-input-files.html
 .. |cwl-docker-req| replace:: DockerRequirement
 .. _cwl-docker-req: https://www.commonwl.org/v1.1/CommandLineTool.html#DockerRequirement
 .. FIXME apply official CWL specification location
@@ -49,7 +49,7 @@
 .. _cwl-io-map: https://www.commonwl.org/v1.1/CommandLineTool.html#map
 .. |cwl-io-type| replace:: CWLType Symbols
 .. _cwl-io-type: https://www.commonwl.org/v1.1/CommandLineTool.html#CWLType
-.. _cwl-metadata: https://www.commonwl.org/user_guide/17-metadata/index.html
+.. _cwl-metadata: https://www.commonwl.org/user_guide/topics/metadata-and-authorship.html
 .. _docker: https://docs.docker.com/develop/
 .. |docker| replace:: Docker
 .. |ems| replace:: Execution Management Service

diff --git a/requirements.txt b/requirements.txt
@@ -44,7 +44,8 @@ geotiff>=0.2.8
 # use pserve to continue supporting config.ini with paste settings
 gunicorn>=20.0.4
 # reduced dependencies contrains to let packages update to latest (https://github.com/vinitkumar/json2xml/issues/157)
-json2xml>=3.20.0
+# even more reduced dependency constraints (https://github.com/vinitkumar/json2xml/pull/195)
+json2xml>=4.1.0
 jsonschema>=3.0.1
 # FIXME: kombu for pymongo>=4 not yet released as 5.3.0 (only pre-releases available)
 # - https://github.com/crim-ca/weaver/issues/386
@@ -60,8 +61,9 @@ mypy_boto3_s3
 numpy>=1.22.2
 # esgf-compute-api (cwt) needs oauthlib but doesn't add it in their requirements
 oauthlib
-owslib==0.28.1
+owslib==0.29.3
 PasteDeploy>=3.1.0; python_version >= "3.12"
+pint
 psutil
 # FIXME: pymongo>=4 breaks with kombu corresponding to pinned Celery
 # - https://github.com/crim-ca/weaver/issues/386
@@ -78,7 +80,7 @@ python-dateutil
 pyramid_rewrite
 pyramid_storage
 pytz
-pywps==4.5.2
+pywps==4.6.0
 pyyaml>=5.2
 rdflib>=5  # pyup: ignore
 requests

diff --git a/tests/functional/application-packages/EchoBoundingBox/deploy.yml b/tests/functional/application-packages/EchoBoundingBox/deploy.yml
@@ -0,0 +1,43 @@
+# YAML representation supported by WeaverClient
+processDescription:
+  process:
+    id: EchoBoundingBox
+    title: Test Echo Bounding Box
+    version: "1.0"  # must be string, avoid interpretation as float
+    description: Dummy process that simply echo's back the input bbox for testing purposes.
+    keywords:
+      - test
+    inputs:
+      bboxInput:
+        schema:
+          type: object
+          format: ogc-bbox
+          required: ["bbox"]
+          properties:
+            bbox:
+              type: array
+              items:
+                type: number
+            crs:
+              type: string
+    outputs:
+      bboxOutput:
+        schema:
+          type: object
+          format: ogc-bbox
+          required: ["bbox"]
+          properties:
+            bbox:
+              type: array
+              items:
+                type: number
+            crs:
+              type: string
+  jobControlOptions:
+    - async-execute
+  outputTransmission:
+    - reference
+executionUnit:
+  # note: This does not work by itself! The test suite injects the file dynamically.
+  - href: "tests/functional/application-packages/EchoBoundingBox/echo_bbox.cwl"
+deploymentProfileName: "http://www.opengis.net/profiles/eoc/dockerizedApplication"
diff --git a/tests/functional/application-packages/EchoBoundingBox/echo_bbox.cwl b/tests/functional/application-packages/EchoBoundingBox/echo_bbox.cwl
@@ -0,0 +1,23 @@
+cwlVersion: "v1.0"
+class: CommandLineTool
+baseCommand: cat
+requirements:
+  DockerRequirement:
+    dockerPull: "debian:stretch-slim"
+inputs:
+  bboxInput:
+    # for CWL, bbox is simply a JSON file!
+    type: File
+    format: "iana:application/json"
+    inputBinding:
+      position: 1
+outputs:
+  bboxOutput:
+    # for CWL, bbox is simply a JSON file!
+    type: File
+    format: "iana:application/json"
+    outputBinding:
+      glob: "bbox.json"
+stdout: "bbox.json"
+$namespaces:
+  iana: "https://www.iana.org/assignments/media-types/"
diff --git a/tests/functional/application-packages/EchoBoundingBox/execute.yml b/tests/functional/application-packages/EchoBoundingBox/execute.yml
@@ -0,0 +1,11 @@
+bboxInput:
+  # note: values can be integer, but use float here to make testing easier (values are auto-converted)
+  bbox: [1., 2., 3., 4.]
+  # note:
+  #   OGC-API BBOX definition is strict about needing an URI.
+  #   A simple namespaced CRS (eg: "urn:ogc:def:crs:EPSG::4326" or "EPSG:4326") is not sufficient.
+  #   Definitions can be loosened when using a nested qualified value, since bbox essentially becomes a generic object.
+  #   see:
+  #   - https://schemas.opengis.net/ogcapi/processes/part1/1.0/openapi/schemas/bbox.yaml
+  #   - https://github.com/opengeospatial/ogcapi-processes/blob/master/openapi/schemas/processes-core/bbox.yaml
+  crs: "http://www.opengis.net/def/crs/OGC/1.3/CRS84"
diff --git a/tests/functional/application-packages/EchoProcess/describe.yml b/tests/functional/application-packages/EchoProcess/describe.yml
@@ -26,7 +26,7 @@ inputs:
       allOf:
         - format: ogc-bbox
         # - $ref: ../../openapi/schemas/bbox.yaml
-        - $ref: https://raw.githubusercontent.com/opengeospatial/ogcapi-processes/d52579/core/openapi/schemas/bbox.yaml
+        - $ref: https://schemas.opengis.net/ogcapi/processes/part1/1.0/openapi/schemas/bbox.yaml
     title: Bounding Box Input Example
   complexObjectInput:
     description: This is an example of a complex object input.
@@ -156,7 +156,7 @@ outputs:
       allOf:
         - format: ogc-bbox
           # - $ref: ../../openapi/schemas/bbox.yaml
-        - $ref: https://raw.githubusercontent.com/opengeospatial/ogcapi-processes/d52579/core/openapi/schemas/bbox.yaml
+        - $ref: https://schemas.opengis.net/ogcapi/processes/part1/1.0/openapi/schemas/bbox.yaml
   complexObjectOutput:
     schema:
       properties: