Merge pull request #212 from dnlbauer/stream_crate

Stream RO-Crate Zip

Author: simleo

CITATION.cff

@@ -1,6 +1,9 @@
 cff-version: 1.1.0
 message: "Cite as"
-authors:
+author:
+  - family-names: Bauer
+    given-names: Daniel
+    orcid: https://orcid.org/0000-0001-9447-460X
   - family-names: Chadwick
     given-names: Eli
     orcid: https://orcid.org/0000-0002-0035-6475

README.md

@@ -451,6 +451,7 @@ Options:
 * Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
 * Copyright 2024 Data Centre, SciLifeLab, SE
 * Copyright 2024 National Institute of Informatics (NII), JP
+* Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
 
 Licensed under the
 Apache License, version 2.0 <https://www.apache.org/licenses/LICENSE-2.0>,

examples/fastapi/main.py

@@ -0,0 +1,64 @@
+# Copyright 2019-2024 The University of Manchester, UK
+# Copyright 2020-2024 Vlaams Instituut voor Biotechnologie (VIB), BE
+# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
+# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
+# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
+# Copyright 2024 Data Centre, SciLifeLab, SE
+# Copyright 2024 National Institute of Informatics (NII), JP
+# Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+Streaming RO-Crates from a web server
+
+This example demonstrates how to create an RO-Crate on-the-fly
+and stream the result to the client.
+By using `stream_zip`, the RO-Crate is not written to disk and remote
+data is only fetched on the fly.
+
+To run: `fastapi dev main.py`, then visit http://localhost:8000/crate
+"""
+
+from fastapi import FastAPI
+from fastapi.responses import StreamingResponse
+from rocrate.rocrate import ROCrate
+from io import StringIO
+
+app = FastAPI()
+
+
+@app.get("/crate")
+async def get():
+    crate = ROCrate()
+
+    # Add a remote file
+    crate.add_file(
+        "https://raw.githubusercontent.com/ResearchObject/ro-crate-py/refs/heads/master/test/test-data/sample_file.txt",
+        fetch_remote=True
+    )
+
+    # Add a file containing a string to the crate
+    crate.add_file(
+        source=StringIO("Hello, World!"),
+        dest_path="test-data/hello.txt"
+    )
+
+    # Stream crate to client as a zip file
+    return StreamingResponse(
+        crate.stream_zip(),
+        media_type="application/rocrate+zip",
+        headers={
+            "Content-Disposition": "attachment; filename=crate.zip",
+        }
+    )

examples/fastapi/requirements.txt

@@ -0,0 +1,3 @@
+../../
+fastapi
+fastapi-cli

examples/read_test_metadata.py

@@ -5,6 +5,7 @@
 # Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
 # Copyright 2024 Data Centre, SciLifeLab, SE
 # Copyright 2024 National Institute of Informatics (NII), JP
+# Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

rocrate/__init__.py

@@ -7,6 +7,7 @@
 # Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
 # Copyright 2024 Data Centre, SciLifeLab, SE
 # Copyright 2024 National Institute of Informatics (NII), JP
+# Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -30,6 +31,7 @@
 """
 
 __author__ = ", ".join((
+    'Daniel Bauer',
     'Eli Chadwick',
     'Paul De Geest',
     'Bert Droesbeke',
@@ -52,6 +54,7 @@
 Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
 Copyright 2024 Data Centre, SciLifeLab, SE
 Copyright 2024 National Institute of Informatics (NII), JP
+Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
 """
 __license__ = ("Apache License, version 2.0 "
                "<https://www.apache.org/licenses/LICENSE-2.0>")

rocrate/cli.py

@@ -5,6 +5,7 @@
 # Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
 # Copyright 2024 Data Centre, SciLifeLab, SE
 # Copyright 2024 National Institute of Informatics (NII), JP
+# Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

rocrate/memory_buffer.py

@@ -0,0 +1,52 @@
+# Copyright 2019-2024 The University of Manchester, UK
+# Copyright 2020-2024 Vlaams Instituut voor Biotechnologie (VIB), BE
+# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
+# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
+# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
+# Copyright 2024 Data Centre, SciLifeLab, SE
+# Copyright 2024 National Institute of Informatics (NII), JP
+# Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from io import RawIOBase
+
+
+class MemoryBuffer(RawIOBase):
+    """
+    A buffer class that supports reading and writing binary data.
+    The buffer automatically resets upon reading to make sure all data is read only once.
+    """
+
+    def __init__(self):
+        self._buffer = b''
+
+    def write(self, data):
+        if self.closed:
+            raise ValueError('write to closed file')
+        self._buffer += data
+        return len(data)
+
+    def read(self, size=-1):
+        if self.closed:
+            raise ValueError('read from closed file')
+        if size < 0:
+            data = self._buffer
+            self._buffer = b''
+        else:
+            data = self._buffer[:size]
+            self._buffer = self._buffer[size:]
+        return data
+
+    def __len__(self):
+        return len(self._buffer)

rocrate/metadata.py

@@ -5,6 +5,7 @@
 # Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
 # Copyright 2024 Data Centre, SciLifeLab, SE
 # Copyright 2024 National Institute of Informatics (NII), JP
+# Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

rocrate/model/__init__.py

@@ -5,6 +5,7 @@
 # Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
 # Copyright 2024 Data Centre, SciLifeLab, SE
 # Copyright 2024 National Institute of Informatics (NII), JP
+# Copyright 2025 Senckenberg Society for Nature Research (SGN), DE
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.