ResearchObject · simleo · May 9, 2025 · Apr 25, 2025 · Apr 25, 2025 · May 5, 2025
diff --git a/.gitignore b/.gitignore
@@ -103,3 +103,7 @@ ENV/
 
 # vim 
 *.swp
+
+# other
+.DS_Store
+/.vscode
diff --git a/CITATION.cff b/CITATION.cff
@@ -46,6 +46,10 @@ author:
   - family-names: Soiland-Reyes
     given-names: Stian
     orcid: https://orcid.org/0000-0001-9842-9718
+  - family-names: Thomas
+    given-names: Laurent
+    orcid: https://orcid.org/0000-0001-7686-3249
+
 title: "ro-crate-py"
 version: 0.13.0
 doi: 10.5281/zenodo.3956493

diff --git a/README.md b/README.md
@@ -468,6 +468,7 @@ Options:
 * Copyright 2024-2025 Data Centre, SciLifeLab, SE
 * Copyright 2024-2025 National Institute of Informatics (NII), JP
 * Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+* Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 
 Licensed under the
 Apache License, version 2.0 <https://www.apache.org/licenses/LICENSE-2.0>,

diff --git a/examples/fastapi/main.py b/examples/fastapi/main.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/examples/read_test_metadata.py b/examples/read_test_metadata.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 64"]
+build-backend = "setuptools.build_meta"
diff --git a/rocrate/__init__.py b/rocrate/__init__.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -44,7 +45,8 @@
     'Luca Pireddu',
     'Laura Rodríguez-Navas',
     'Raül Sirvent',
-    'Stian Soiland-Reyes'
+    'Stian Soiland-Reyes',
+    'Laurent Thomas'
 ))
 __copyright__ = """\
 Copyright 2019-2025 The University of Manchester, UK
@@ -55,6 +57,7 @@
 Copyright 2024-2025 Data Centre, SciLifeLab, SE
 Copyright 2024-2025 National Institute of Informatics (NII), JP
 Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 """
 __license__ = ("Apache License, version 2.0 "
                "<https://www.apache.org/licenses/LICENSE-2.0>")

diff --git a/rocrate/cli.py b/rocrate/cli.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/memory_buffer.py b/rocrate/memory_buffer.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/metadata.py b/rocrate/metadata.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/__init__.py b/rocrate/model/__init__.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/computationalworkflow.py b/rocrate/model/computationalworkflow.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/computerlanguage.py b/rocrate/model/computerlanguage.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/contextentity.py b/rocrate/model/contextentity.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/creativework.py b/rocrate/model/creativework.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/data_entity.py b/rocrate/model/data_entity.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/dataset.py b/rocrate/model/dataset.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/entity.py b/rocrate/model/entity.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/file.py b/rocrate/model/file.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/file_or_dir.py b/rocrate/model/file_or_dir.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/metadata.py b/rocrate/model/metadata.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/person.py b/rocrate/model/person.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/preview.py b/rocrate/model/preview.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/root_dataset.py b/rocrate/model/root_dataset.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/softwareapplication.py b/rocrate/model/softwareapplication.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/testdefinition.py b/rocrate/model/testdefinition.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/testinstance.py b/rocrate/model/testinstance.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/testservice.py b/rocrate/model/testservice.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/model/testsuite.py b/rocrate/model/testsuite.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -628,6 +629,47 @@ def add_action(self, instrument, identifier=None, object=None, result=None, prop
         self.root_dataset.append_to("mentions", action)
         return action
 
+    def add_formal_parameter(
+            self,
+            name,
+            additionalType,
+            identifier=None,
+            description=None,
+            valueRequired=False,
+            defaultValue=None,
+            properties=None
+    ):
+        """\
+        Add a FormalParameter to describe an input or output of a workflow.
+
+        A FormalParameter represents an input or output slot of a workflow, not
+        the actual value taken by a parameter. For further information see
+        https://w3id.org/ro/wfrun/workflow
+
+        Returns the created FormalParameter entity, which can be associated to
+        a workflow (e.g. as an input) using the syntax:
+          workflow_entity.append_to("input", formal_parameter_entity)
+        """
+        if properties is None:
+            properties = {}
+        props = {
+            "@type": "FormalParameter",
+            "name": name,
+            "additionalType": additionalType,
+            "valueRequired": valueRequired,
+            "conformsTo": {
+                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
+            }
+        }
+        if description:
+            props["description"] = description
+        if defaultValue:
+            props["defaultValue"] = defaultValue
+        props.update(properties)
+        return self.add(
+            ContextEntity(self, identifier=identifier, properties=props)
+        )
+
     def add_jsonld(self, jsonld):
         """Add a JSON-LD dictionary as a contextual entity to the RO-Crate.
 

diff --git a/rocrate/utils.py b/rocrate/utils.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/rocrate/vocabs.py b/rocrate/vocabs.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/setup.py b/setup.py
@@ -8,6 +8,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -72,7 +73,8 @@
         'Luca Pireddu',
         'Laura Rodríguez-Navas',
         'Raül Sirvent',
-        'Stian Soiland-Reyes'
+        'Stian Soiland-Reyes',
+        'Laurent Thomas'
     )),
     python_requires='>=3.9',
     author_email='stain@apache.org',

diff --git a/test/conftest.py b/test/conftest.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/test/test_cli.py b/test/test_cli.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/test/test_jsonld.py b/test/test_jsonld.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/test/test_metadata.py b/test/test_metadata.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/test/test_model.py b/test/test_model.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/test/test_read.py b/test/test_read.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/test/test_readwrite.py b/test/test_readwrite.py
@@ -6,6 +6,7 @@
 # Copyright 2024-2025 Data Centre, SciLifeLab, SE
 # Copyright 2024-2025 National Institute of Informatics (NII), JP
 # Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+# Copyright 2025 European Molecular Biology Laboratory (EMBL), Heidelberg, DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
-Original file line number
+Diff line change
@@ Expand Up / @@ -103,3 +103,7 @@ ENV/ @@
     # vim
     *.swp
+    # other
+    .DS_Store
+    /.vscode