feat(dataset): external storage backend

.github/workflows/test_deploy.yml

@@ -710,7 +710,8 @@ jobs:
       - name: Install system packages
         run: |
           sudo apt-get update -y
-          sudo apt-get install -y libyaml-0-2 libyaml-dev rclone fuse
+          sudo apt-get install -y libyaml-0-2 libyaml-dev unzip fuse
+          sudo -v ; curl https://rclone.org/install.sh | sudo bash
       - uses: actions/cache@master
         id: dependency-cache
         with:
@@ -807,7 +808,8 @@ jobs:
       - name: Install system packages
         run: |
           sudo apt-get update -y
-          sudo apt-get install -y libyaml-0-2 libyaml-dev rclone fuse
+          sudo apt-get install -y libyaml-0-2 libyaml-dev unzip fuse
+          sudo -v ; curl https://rclone.org/install.sh | sudo bash
       - uses: actions/cache@master
         id: dependency-cache
         with:

renku/__init__.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2017-2023- Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/checks/__init__.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,10 +19,10 @@
 from .datasets import (
     check_dataset_files_outside_datadir,
     check_dataset_old_metadata_location,
+    check_external_files,
     check_invalid_datasets_derivation,
     check_missing_files,
 )
-from .external import check_missing_external_files
 from .githooks import check_git_hooks_installed
 from .migration import check_migration
 from .project import check_project_id_group
@@ -43,7 +42,7 @@
     "check_lfs_info",
     "check_migrated_activity_ids",
     "check_migration",
-    "check_missing_external_files",
+    "check_external_files",
     "check_missing_files",
     "check_project_id_group",
     "check_project_structure",

renku/command/checks/activities.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/checks/datasets.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -70,6 +69,9 @@ def check_missing_files(dataset_gateway: IDatasetGateway, **_):
     missing = defaultdict(list)
 
     for dataset in dataset_gateway.get_all_active_datasets():
+        # NOTE: Datasets with storage backend don't have local copies of files
+        if dataset.storage:
+            continue
         for file_ in dataset.files:
             path = project_context.path / file_.entity.path
             file_exists = path.exists() or (file_.is_external and os.path.lexists(path))
@@ -163,7 +165,7 @@ def check_dataset_files_outside_datadir(fix, dataset_gateway: IDatasetGateway, *
         detected_files = []
 
         for file in dataset.files:
-            if file.is_external:
+            if file.is_external or file.linked:
                 continue
             try:
                 get_safe_relative_path(project_context.path / file.entity.path, project_context.path / data_dir)
@@ -194,3 +196,50 @@ def check_dataset_files_outside_datadir(fix, dataset_gateway: IDatasetGateway, *
         return False, problems
 
     return True, None
+
+
+@inject.autoparams("dataset_gateway")
+def check_external_files(fix, dataset_gateway: IDatasetGateway, **_):
+    """Find external files.
+
+    Args:
+        fix: Whether to fix found issues.
+        dataset_gateway(IDatasetGateway): The injected dataset gateway.
+        _: keyword arguments.
+
+    Returns:
+        Tuple of whether no external files are found and string of found problems.
+    """
+    from renku.core.dataset.dataset import file_unlink
+
+    external_files = []
+    datasets = defaultdict(list)
+
+    for dataset in dataset_gateway.get_all_active_datasets():
+        for file in dataset.files:
+            if file.is_external:
+                external_files.append(file.entity.path)
+                datasets[dataset.name].append(file)
+
+    if not external_files:
+        return True, None
+
+    external_files_str = "\n\t".join(sorted(external_files))
+
+    if not fix:
+        problems = (
+            f"\n{WARNING}: External files are deprecated in favor of an external dataset backend.\n"
+            "Use 'renku dataset rm' or rerun 'renku doctor' with '--fix' flag to remove them:\n\t"
+            f"{external_files_str}\n"
+        )
+        return False, problems
+
+    communication.info(
+        "The following external files were deleted from the project. You need to add them later manually using a "
+        f"dataset with an external storage backend:\n\t{external_files_str}"
+    )
+
+    for name, files in datasets.items():
+        file_unlink(name=name, yes=True, dataset_files=files)
+
+    return True, None

renku/command/checks/githooks.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/checks/migration.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/checks/project.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/checks/storage.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/checks/validate_shacl.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/checks/workflow.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/command_builder/__init__.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/command_builder/command.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2018-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/command_builder/communication.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2018-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/command_builder/database.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2018-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/command_builder/lock.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2018-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/command_builder/migration.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2018-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/command_builder/repo.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2018-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/dataset.py

@@ -26,12 +26,12 @@
     import_dataset,
     list_dataset_files,
     list_datasets,
-    mount_external_storage,
-    pull_external_data,
+    mount_cloud_storage,
+    pull_cloud_storage,
     remove_dataset,
     search_datasets,
     show_dataset,
-    unmount_external_storage,
+    unmount_cloud_storage,
     update_datasets,
 )
 from renku.core.dataset.dataset_add import add_to_dataset
@@ -127,18 +127,18 @@ def list_tags_command():
     return Command().command(list_dataset_tags).with_database().require_migration()
 
 
-def pull_external_data_command():
-    """Command for pulling/copying data from an external storage."""
-    command = Command().command(pull_external_data).lock_dataset().with_database(write=True)
+def pull_cloud_storage_command():
+    """Command for pulling/copying data from a cloud storage."""
+    command = Command().command(pull_cloud_storage).lock_dataset().with_database(write=True)
     return command.require_migration().with_commit(commit_only=DATASET_METADATA_PATHS + [CONFIG_LOCAL_PATH])
 
 
-def mount_external_storage_command(unmount: bool):
-    """Command for mounting an external storage."""
-    command = unmount_external_storage if unmount else mount_external_storage
+def mount_cloud_storage_command(unmount: bool):
+    """Command for mounting a cloud storage."""
+    command = unmount_cloud_storage if unmount else mount_cloud_storage
     return Command().command(command).lock_dataset().with_database(write=False).require_migration()
 
 
-def unmount_external_storage_command():
-    """Command for unmounting an external storage."""
-    return Command().command(unmount_external_storage).lock_dataset().with_database(write=False).require_migration()
+def unmount_cloud_storage_command():
+    """Command for unmounting a cloud storage."""
+    return Command().command(unmount_cloud_storage).lock_dataset().with_database(write=False).require_migration()

renku/command/format/__init__.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

renku/command/format/activity.py

@@ -1,6 +1,5 @@
-#
-# Copyright 2021 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");