def inputs(ctx, client, revision, paths):
r"""Show inputs files in the repository.
<PATHS> Files to show. If no files are given all input files are shown.
"""
from renku.core.models.provenance.activities import ProcessRun
graph = Graph(client)
paths = set(paths)
nodes = graph.build(revision=revision)
commits = {node.commit for node in nodes}
candidates = {(node.commit, node.path)
for node in nodes if not paths or node.path in paths}
input_paths = set()
for commit in commits:
activity = graph.activities[commit]
if isinstance(activity, ProcessRun):
for usage in activity.qualified_usage:
for entity in usage.entity.entities:
path = str((usage.client.path / entity.path).relative_to(
client.path
))
usage_key = (entity.commit, entity.path)
if path not in input_paths and usage_key in candidates:
input_paths.add(path)
click.echo('\n'.join(graph._format_path(path) for path in input_paths))
ctx.exit(0 if not paths or len(input_paths) == len(paths) else 1)
def siblings(client, revision, paths):
"""Show siblings for given paths."""
graph = Graph(client)
nodes = graph.build(paths=paths, revision=revision)
siblings_ = set(nodes)
for node in nodes:
siblings_ |= graph.siblings(node)
paths = {node.path for node in siblings_}
for path in paths:
click.echo(graph._format_path(path))
def outputs(ctx, client, revision, paths):
r"""Show output files in the repository.
<PATHS> Files to show. If no files are given all output files are shown.
"""
graph = Graph(client)
filter = graph.build(paths=paths, revision=revision)
output_paths = graph.output_paths
click.echo('\n'.join(graph._format_path(path) for path in output_paths))
if paths:
if not output_paths:
ctx.exit(1)
from renku.core.models.datastructures import DirectoryTree
tree = DirectoryTree.from_list(item.path for item in filter)
for output in output_paths:
if tree.get(output) is None:
ctx.exit(1)
return
def outputs(ctx, client, revision, verbose, paths):
r"""Show output files in the repository.
<PATHS> Files to show. If no files are given all output files are shown.
"""
graph = Graph(client)
filter_ = graph.build(paths=paths, revision=revision)
output_paths = {}
for activity in graph.activities.values():
if isinstance(activity, ProcessRun):
for entity in activity.generated:
if entity.path not in graph.output_paths:
continue
output_paths[entity.path] = Result(
path=entity.path, commit=entity.commit, time=activity.ended_at_time, workflow=activity.path
)
if not verbose:
click.echo("\n".join(graph._format_path(path) for path in output_paths.keys()))
else:
records = list(output_paths.values())
records.sort(key=lambda v: v[0])
HEADERS["time"] = "generation time"
click.echo(tabulate(collection=records, headers=HEADERS))
if paths:
if not output_paths:
ctx.exit(1)
from renku.core.models.datastructures import DirectoryTree
tree = DirectoryTree.from_list(item.path for item in filter_)
for output in output_paths:
if tree.get(output) is None:
ctx.exit(1)
return
def inputs(ctx, client, revision, verbose, paths):
r"""Show inputs files in the repository.
<PATHS> Files to show. If no files are given all input files are shown.
"""
graph = Graph(client)
paths = set(paths)
nodes = graph.build(revision=revision)
commits = {node.activity.commit if hasattr(node, "activity") else node.commit for node in nodes}
commits |= {node.activity.commit for node in nodes if hasattr(node, "activity")}
candidates = {(node.commit, node.path) for node in nodes if not paths or node.path in paths}
input_paths = {}
for commit in commits:
activity = graph.activities.get(commit)
if not activity:
continue
if isinstance(activity, ProcessRun):
for usage in activity.qualified_usage:
for entity in usage.entity.entities:
path = str((usage.client.path / entity.path).relative_to(client.path))
usage_key = (entity.commit, entity.path)
if path not in input_paths and usage_key in candidates:
input_paths[path] = Result(
path=path, commit=entity.commit, time=activity.started_at_time, workflow=activity.path
)
if not verbose:
click.echo("\n".join(graph._format_path(path) for path in input_paths))
else:
records = list(input_paths.values())
records.sort(key=lambda v: v[0])
HEADERS["time"] = "usage time"
click.echo(tabulate(collection=records, headers=HEADERS))
ctx.exit(0 if not paths or len(input_paths) == len(paths) else 1)
def status(ctx, client, revision, no_output, path):
"""Show a status of the repository."""
graph = Graph(client)
# TODO filter only paths = {graph.normalize_path(p) for p in path}
status = graph.build_status(revision=revision, can_be_cwl=no_output)
if client.has_external_files():
click.echo(
'Changes in external files are not detected automatically. To '
'update external files run "renku dataset update -e".')
try:
click.echo('On branch {0}'.format(client.repo.active_branch))
except TypeError:
click.echo('Git HEAD is detached!\n'
' Please move back to your working branch to use renku\n')
if status['outdated']:
click.echo('Files generated from newer inputs:\n'
' (use "renku log [<file>...]" to see the full lineage)\n'
' (use "renku update [<file>...]" to '
'generate the file from its latest inputs)\n')
for filepath, stts in sorted(status['outdated'].items()):
outdated = (', '.join('{0}#{1}'.format(
click.style(graph._format_path(n.path), fg='blue', bold=True),
_format_sha1(graph, n),
) for n in stts if n.path and n.path not in status['outdated']))
click.echo('\t{0}: {1}'.format(
click.style(graph._format_path(filepath), fg='red', bold=True),
outdated))
click.echo()
else:
click.secho('All files were generated from the latest inputs.',
fg='green')
if status['multiple-versions']:
click.echo(
'Input files used in different versions:\n'
' (use "renku log --revision <sha1> <file>" to see a lineage '
'for the given revision)\n')
for filepath, files in sorted(status['multiple-versions'].items()):
# Do not show duplicated commits! (see #387)
commits = {_format_sha1(graph, key) for key in files}
click.echo('\t{0}: {1}'.format(
click.style(graph._format_path(filepath), fg='blue',
bold=True),
', '.join(
# Sort the commit hashes alphanumerically to have a
# predictable output.
sorted(commits))))
click.echo()
if status['deleted']:
click.echo('Deleted files used to generate outputs:\n'
' (use "git show <sha1>:<file>" to see the file content '
'for the given revision)\n')
for filepath, node in status['deleted'].items():
click.echo('\t{0}: {1}'.format(
click.style(graph._format_path(filepath), fg='blue',
bold=True), _format_sha1(graph, node)))
click.echo()
ctx.exit(1 if status['outdated'] else 0)