Merge branch 'master' into 1819-renku-config-endpoint

docs/commands.rst

@@ -27,6 +27,13 @@ Renku Command Line
 
 .. automodule:: renku.cli.init
 
+.. _cli-clone:
+
+``renku clone``
+---------------
+
+.. automodule:: renku.cli.clone
+
 .. _cli-config:
 
 ``renku config``

renku/cli/clone.py

@@ -20,14 +20,31 @@
 Cloning a Renku project
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-To clone a Renku project and set up required Git hooks and Git LFS use
-``renku clone`` command.
+To clone a Renku project use ``renku clone`` command. This command is preferred
+over using ``git clone`` because it sets up required Git hooks and enables
+Git-LFS automatically.
 
 .. code-block:: console
 
-    $ renku clone git+ssh://host.io/namespace/project.git
-        <destination-directory>
+    $ renku clone <repository-url> <destination-directory>
 
+It creates a new directory with the same name as the project. You can change
+the directory name by passing another name on the command line.
+
+By default, ``renku clone`` pulls data from Git-LFS after cloning. If you don't
+need the LFS data, pass ``--no-pull-data`` option to skip this step.
+
+.. Note:: To move a project to another Renku deployment you need to create a
+    new empty project in the target deployment and push both the
+    repository and Git-LFS objects to the new remote. Refer to Git documentation
+    for more details.
+
+    .. code-block:: console
+
+        $ git lfs fetch --all
+        $ git remote remove origin
+        $ git remote add origin <new-repository-url>
+        $ git push --mirror origin
 """
 
 import click
@@ -37,13 +54,11 @@
 
 
 @click.command()
-@click.option("--pull-data", is_flag=True, help="Pull data from Git-LFS.", default=False)
+@click.option("--no-pull-data", is_flag=True, help="Do not pull data from Git-LFS.", default=False)
 @click.argument("url")
 @click.argument("path", required=False, default=None)
-def clone(pull_data, url, path):
+def clone(no_pull_data, url, path):
     """Clone a Renku repository."""
-    click.echo("Cloning {} ...".format(url))
-
-    skip_smudge = not pull_data
-    project_clone(url=url, path=path, skip_smudge=skip_smudge, progress=GitProgress())
+    click.echo(f"Cloning {url} ...")
+    project_clone(url=url, path=path, skip_smudge=no_pull_data, progress=GitProgress())
     click.secho("OK", fg="green")

renku/cli/dataset.py

@@ -95,14 +95,13 @@
 . code-block:: console
 
     $ renku dataset show some-dataset
-    Some Dataset
-    ---------------
-    Just some dataset
-
     Name: some-dataset
     Created: 2020-12-09 13:52:06.640778+00:00
     Creator(s): John Doe<john.doe@example.com> [SDSC]
     Keywords: Dataset, Data
+    Title: Some Dataset
+    Description:
+    Just some dataset
 
 Deleting a dataset:
 
@@ -510,27 +509,28 @@ def show(name):
     """Handle datasets."""
     result = show_dataset().build().execute(name=name)
     ds = result.output
-    click.secho(ds["title"], bold=True)
-    click.echo("-" * min(len(ds["title"]), click.get_terminal_size()[0]))
 
-    Console().print(Markdown(ds["description"]))
-    click.echo()
     click.echo(click.style("Name: ", bold=True, fg="magenta") + click.style(ds["name"], bold=True))
-    click.echo(click.style("Created: ", bold=True, fg="magenta") + ds["created_at"])
+    click.echo(click.style("Created: ", bold=True, fg="magenta") + (ds.get("created_at", "") or ""))
 
     creators = []
-    for creator in ds["creators"]:
+    for creator in ds.get("creators", []):
         if creator["affiliation"]:
             creators.append(f"{creator['name']} <{creator['email']}> [{creator['affiliation']}]")
         else:
             creators.append(f"{creator['name']} <{creator['email']}>")
 
     click.echo(click.style("Creator(s): ", bold=True, fg="magenta") + ", ".join(creators))
     if ds["keywords"]:
-        click.echo(click.style("Keywords: ", bold=True, fg="magenta") + ", ".join(ds["keywords"]))
+        click.echo(click.style("Keywords: ", bold=True, fg="magenta") + ", ".join(ds.get("keywords", "")))
 
     if ds["version"]:
-        click.echo(click.style("Version: ", bold=True, fg="magenta") + ds["version"])
+        click.echo(click.style("Version: ", bold=True, fg="magenta") + ds.get("version", ""))
+
+    click.echo(click.style("Title: ", bold=True, fg="magenta") + click.style(ds.get("title", ""), bold=True))
+
+    click.echo(click.style("Description: ", bold=True, fg="magenta"))
+    Console().print(Markdown(ds.get("description", "") or ""))
 
 
 @dataset.command()

renku/core/management/migrations/m_0005__2_cwl.py

@@ -193,6 +193,9 @@ def _migrate_single_step(client, cmd_line_tool, path, commit=None, parent_commit
             if listing.entry == '$({"listing": [], "class": "Directory"})':
                 created_outputs.append(listing.entryname)
 
+    # NOTE: multiple outputs might bind to the same input; we use this copy to find output bindings
+    all_inputs = inputs.copy()
+
     for o in outputs:
         prefix = None
         position = None
@@ -203,8 +206,11 @@ def _migrate_single_step(client, cmd_line_tool, path, commit=None, parent_commit
             if name.endswith(")"):
                 name = name[:-1]
 
-            matched_input = next(i for i in inputs if i.id == name)
-            inputs.remove(matched_input)
+            matched_input = next(i for i in all_inputs if i.id == name)
+            try:
+                inputs.remove(matched_input)
+            except ValueError:
+                pass
 
             if isinstance(matched_input.default, dict):
                 path = client.workflow_path / Path(matched_input.default["path"])

tests/cli/test_migrate.py

@@ -48,6 +48,15 @@ def test_migrate_project(isolated_runner, old_project):
     assert client.project.name
 
 
+@pytest.mark.migration
+@pytest.mark.parametrize("old_project", ["old-workflows-v0.10.0.git"], indirect=["old_project"])
+def test_migrate_duplicated_input_binding(isolated_runner, old_project):
+    """Check migrating CWLs with multiple outputs binding to the same input."""
+    result = isolated_runner.invoke(cli, ["migrate", "--no-commit"])
+
+    assert 0 == result.exit_code, result.output
+
+
 @pytest.mark.migration
 def test_migration_check(isolated_runner, project):
     """Test migrate on old repository."""