fix test supporting collection input (fixes #682) - cwltool patch loadContents (relates to common-workflow-language/cwltool#2036)

Author: fmigneault

CHANGES.rst

@@ -12,7 +12,12 @@ Changes
 
 Changes:
 --------
-- No change.
+- Add support of *OGC API - Processes: Part 3* ``collection`` as input to a `Process`
+  (fixes `#682 <https://github.com/crim-ca/weaver/issues/682>`_).
+- Update ``cwltool`` with fork
+  `fmigneault/cwltool @ fix-load-contents-array <https://github.com/fmigneault/cwltool/tree/fix-load-contents-array>`_
+  until ``loadContents`` behavior is resolved for ``type: File[]``
+  (relates to `common-workflow-language/cwltool#2036 <https://github.com/common-workflow-language/cwltool/pull/2036>`_).
 
 Fixes:
 ------

requirements.txt

@@ -35,7 +35,8 @@ cryptography
 # use cwltool gpu-enabled support until integrated within the original tool
 # (https://github.com/common-workflow-language/common-workflow-language/issues/587)
 ### git+https://github.com/crim-ca/cwltool@docker-gpu#egg=cwltool
-cwltool==3.1.20230906142556
+##cwltool==3.1.20230906142556
+cwltool @ git+https://github.com/fmigneault/cwltool.git@fix-load-contents-array
 docker>=7.1
 duration
 esgf-compute-api @ git+https://github.com/ESGF/[email protected]
@@ -58,7 +59,7 @@ lxml
 mako
 # force use of later mistune (https://github.com/common-workflow-language/schema_salad/pull/619#issuecomment-1346025607)
 # employed by cwltool -> schema-salad -> mistune
-mistune>=2.0.3,<2.1
+#mistune>=2.0.3,<2.1
 mypy_boto3_s3
 numpy>=1.22.2,<2; python_version < "3.10"
 numpy>=1.22.2; python_version >= "3.10"

tests/functional/application-packages/EchoFeatures/echo_features.cwl

@@ -22,14 +22,15 @@ inputs:
         }
         return "http://www.opengis.net/def/glossary/term/FeatureCollection";
       }
+    loadContents: true
     inputBinding:
       valueFrom: |
         ${
           if (Array.isArray(inputs.features)) {
-            return {
+            return JSON.stringify({
               "type": "FeatureCollection",
-              "features": inputs.features.every(item => item.contents)
-            };
+              "features": inputs.features.map(item => JSON.parse(item.contents))
+            });
           }
           return inputs.features.contents;
         }
@@ -38,8 +39,8 @@ outputs:
     type: File
     format: "ogc-term:FeatureCollection"
     outputBinding:
-      glob: "features.json"
-stdout: "features.json"
+      glob: "features.geojson"
+stdout: "features.geojson"
 $namespaces:
   iana: "https://www.iana.org/assignments/media-types/"
   ogc-term: "http://www.opengis.net/def/glossary/term/"

tests/functional/test_wps_package.py

@@ -2277,23 +2277,21 @@ def test_execute_job_with_collection_input_geojson_feature_collection(self):
             tmp_dir = stack.enter_context(tempfile.TemporaryDirectory())  # pylint: disable=R1732
             stack.enter_context(mocked_file_server(tmp_dir, tmp_host, settings=self.settings, mock_browse_index=True))
 
-            col_file = os.path.join(tmp_dir, "test.geojson")
             exec_body_val = self.retrieve_payload(name, "execute", local=True)
+            col_file = os.path.join(tmp_dir, "test.json")
+            col_feats = exec_body_val["inputs"]["features"]["value"]  # type: JSON
             with open(col_file, mode="w", encoding="utf-8") as tmp_feature_collection_geojson:
-                json.dump(
-                    exec_body_val["inputs"]["features"]["value"],
-                    tmp_feature_collection_geojson,
-                )
+                json.dump(col_feats, tmp_feature_collection_geojson)
 
             col_exec_body = {
                 "mode": ExecuteMode.ASYNC,
                 "response": ExecuteResponse.DOCUMENT,
                 "inputs": {
                     "features": {
                         # accessed directly as a static GeoJSON FeatureCollection
-                        "collection": "https://mocked-file-server.com/test.geojson",
+                        "collection": "https://mocked-file-server.com/test.json",
                         "format": ExecuteCollectionFormat.GEOJSON,
-                        "type": ContentType.APP_GEOJSON,
+                        "schema": "http://www.opengis.net/def/glossary/term/FeatureCollection",
                     },
                 }
             }
@@ -2307,9 +2305,16 @@ def test_execute_job_with_collection_input_geojson_feature_collection(self):
 
             status_url = resp.json["location"]
             results = self.monitor_job(status_url)
-            assert "outputs" in results
-
-        raise NotImplementedError  # FIXME: implement! (see above bbox case for inspiration)
+            assert "features" in results
+
+        job_id = status_url.rsplit("/", 1)[-1]
+        wps_dir = get_wps_output_dir(self.settings)
+        job_dir = os.path.join(wps_dir, job_id)
+        job_out = os.path.join(job_dir, "features", "features.geojson")
+        assert os.path.isfile(job_out), f"Invalid output file not found: [{job_out}]"
+        with open(job_out, mode="r", encoding="utf-8") as out_fd:
+            out_data = json.load(out_fd)
+        assert out_data["features"] == col_feats["features"]
 
     def test_execute_job_with_collection_input_ogc_features(self):
         name = "EchoFeatures"