convert: add input object document

src/runcrate/convert.py

@@ -37,6 +37,7 @@
 
 
 WORKFLOW_BASENAME = "packed.cwl"
+INPUTS_FILE_BASENAME = "primary-job.json"
 
 CWL_TYPE_MAP = {
     "string": "Text",
@@ -256,6 +257,7 @@ def build(self):
         self.add_engine_run(crate)
         self.add_action(crate, self.workflow_run)
         self.patch_workflow_input_collection(crate)
+        self.add_inputs_file(crate)
         return crate
 
     def add_root_metadata(self, crate):
@@ -644,3 +646,11 @@ def patch_workflow_input_collection(self, crate, wf=None):
         for tool in wf.get("hasPart", []):
             if "ComputationalWorkflow" in as_list(tool.type):
                 self.patch_workflow_input_collection(crate, wf=tool)
+
+    def add_inputs_file(self, crate):
+        path = self.root / "workflow" / INPUTS_FILE_BASENAME
+        if path.is_file():
+            crate.add_file(path, properties={
+                "name": "input object document",
+                "encodingFormat": "application/json",
+            })

tests/test_cwlprov_crate_builder.py

@@ -32,6 +32,7 @@ def test_revsort(data_dir, tmpdir):
     output = tmpdir / "revsort-run-1-crate"
     license = "Apache-2.0"
     readme = data_dir / "README.md"
+    inputs_file = data_dir / "workflow" / "primary-job.json"
     workflow_name = "RevSort"
     builder = ProvCrateBuilder(root, workflow_name=workflow_name, license=license, readme=readme)
     crate = builder.build()
@@ -140,6 +141,11 @@ def test_revsort(data_dir, tmpdir):
     assert set(_connected(workflow)) == set([
         ("packed.cwl#sorttool.cwl/output", "packed.cwl#main/output"),
     ])
+    inputs_f = crate.get(inputs_file.name)
+    assert inputs_f
+    assert inputs_f.type == "File"
+    assert inputs_f["encodingFormat"] == "application/json"
+
     # file contents
     in_text = (root / "data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376").read_text()
     assert (output / wf_input_file.id).read_text() == in_text