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Add help text for some CLI args #181

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merged 4 commits into from
Apr 10, 2024
Merged

Add help text for some CLI args #181

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ac99a68
add help text to CLI options
elichad Mar 27, 2024
4409f5a
update readme in line with CLI help
elichad Mar 27, 2024
43ace22
exclude help text: more precise wording
simleo Apr 10, 2024
d75e30e
revert previous commit
simleo Apr 10, 2024
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18 changes: 13 additions & 5 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -318,9 +318,12 @@ $ rocrate init --help
Usage: rocrate init [OPTIONS]

Options:
--gen-preview
-e, --exclude CSV
-c, --crate-dir PATH
--gen-preview Generate a HTML preview file for the crate.
-e, --exclude NAME Exclude files or directories from the metadata file.
NAME may be a single name or a comma-separated list of
names.
-c, --crate-dir PATH The path to the root data entity of the crate.
Defaults to the current working directory.
--help Show this message and exit.
```

Expand Down Expand Up @@ -409,8 +412,13 @@ Usage: rocrate add workflow [OPTIONS] PATH

Options:
-l, --language [cwl|galaxy|knime|nextflow|snakemake|compss|autosubmit]
-c, --crate-dir PATH
-P, --property KEY=VALUE
The workflow language.
-c, --crate-dir PATH The path to the root data entity of the
crate. Defaults to the current working
directory.
-P, --property KEY=VALUE Add an additional property to the metadata
for this entity. Can be used multiple times
to set multiple properties.
--help Show this message and exit.
```

Expand Down
105 changes: 75 additions & 30 deletions rocrate/cli.py
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Expand Up @@ -57,8 +57,21 @@ def convert(self, value, param, ctx):

CSV = CSVParamType()
KeyValue = KeyValueParamType()
OPTION_CRATE_PATH = click.option('-c', '--crate-dir', type=click.Path(), default=os.getcwd)
OPTION_PROPS = click.option('-P', '--property', type=KeyValue, multiple=True, metavar="KEY=VALUE")
OPTION_CRATE_PATH = click.option(
"-c",
"--crate-dir",
type=click.Path(),
default=os.getcwd,
help="The path to the root data entity of the crate. Defaults to the current working directory.",
)
OPTION_PROPS = click.option(
"-P",
"--property",
type=KeyValue,
multiple=True,
metavar="KEY=VALUE",
help="Add an additional property to the metadata for this entity. Can be used multiple times to set multiple properties.",
)


@click.group()
Expand All @@ -67,8 +80,16 @@ def cli():


@cli.command()
@click.option('--gen-preview', is_flag=True)
@click.option('-e', '--exclude', type=CSV)
@click.option(
"--gen-preview", is_flag=True, help="Generate a HTML preview file for the crate."
)
@click.option(
"-e",
"--exclude",
type=CSV,
metavar="NAME",
help="Exclude files or directories from the metadata file. NAME may be a single name or a comma-separated list of names.",
)
@OPTION_CRATE_PATH
def init(crate_dir, gen_preview, exclude):
crate = ROCrate(crate_dir, init=True, gen_preview=gen_preview, exclude=exclude)
Expand All @@ -83,7 +104,7 @@ def add():


@add.command()
@click.argument('path', type=click.Path(exists=True, dir_okay=False))
@click.argument("path", type=click.Path(exists=True, dir_okay=False))
@OPTION_CRATE_PATH
@OPTION_PROPS
def file(crate_dir, path, property):
Expand All @@ -99,7 +120,7 @@ def file(crate_dir, path, property):


@add.command()
@click.argument('path', type=click.Path(exists=True, file_okay=False))
@click.argument("path", type=click.Path(exists=True, file_okay=False))
@OPTION_CRATE_PATH
@OPTION_PROPS
def dataset(crate_dir, path, property):
Expand All @@ -115,8 +136,14 @@ def dataset(crate_dir, path, property):


@add.command()
@click.argument('path', type=click.Path(exists=True))
@click.option('-l', '--language', type=click.Choice(LANG_CHOICES), default="cwl")
@click.argument("path", type=click.Path(exists=True))
@click.option(
"-l",
"--language",
type=click.Choice(LANG_CHOICES),
default="cwl",
help="The workflow language.",
)
@OPTION_CRATE_PATH
@OPTION_PROPS
def workflow(crate_dir, path, language, property):
Expand All @@ -128,50 +155,64 @@ def workflow(crate_dir, path, language, property):
# For now, only support marking an existing file as a workflow
raise ValueError(f"{source} is not in the crate dir {crate_dir}")
# TODO: add command options for main and gen_cwl
crate.add_workflow(source, dest_path, main=True, lang=language, gen_cwl=False, properties=dict(property))
crate.add_workflow(
source,
dest_path,
main=True,
lang=language,
gen_cwl=False,
properties=dict(property),
)
crate.metadata.write(crate_dir)


@add.command(name="test-suite")
@click.option('-i', '--identifier')
@click.option('-n', '--name')
@click.option('-m', '--main-entity')
@click.option("-i", "--identifier")
@click.option("-n", "--name")
@click.option("-m", "--main-entity")
@OPTION_CRATE_PATH
@OPTION_PROPS
def suite(crate_dir, identifier, name, main_entity, property):
crate = ROCrate(crate_dir, init=False, gen_preview=False)
suite = crate.add_test_suite(
identifier=add_hash(identifier), name=name, main_entity=main_entity,
properties=dict(property)
identifier=add_hash(identifier),
name=name,
main_entity=main_entity,
properties=dict(property),
)
crate.metadata.write(crate_dir)
print(suite.id)


@add.command(name="test-instance")
@click.argument('suite')
@click.argument('url')
@click.option('-r', '--resource', default="")
@click.option('-s', '--service', type=click.Choice(SERVICE_CHOICES), default="jenkins")
@click.option('-i', '--identifier')
@click.option('-n', '--name')
@click.argument("suite")
@click.argument("url")
@click.option("-r", "--resource", default="")
@click.option("-s", "--service", type=click.Choice(SERVICE_CHOICES), default="jenkins")
@click.option("-i", "--identifier")
@click.option("-n", "--name")
@OPTION_CRATE_PATH
@OPTION_PROPS
def instance(crate_dir, suite, url, resource, service, identifier, name, property):
crate = ROCrate(crate_dir, init=False, gen_preview=False)
instance_ = crate.add_test_instance(
add_hash(suite), url, resource=resource, service=service,
identifier=add_hash(identifier), name=name, properties=dict(property)
add_hash(suite),
url,
resource=resource,
service=service,
identifier=add_hash(identifier),
name=name,
properties=dict(property),
)
crate.metadata.write(crate_dir)
print(instance_.id)


@add.command(name="test-definition")
@click.argument('suite')
@click.argument('path', type=click.Path(exists=True))
@click.option('-e', '--engine', type=click.Choice(ENGINE_CHOICES), default="planemo")
@click.option('-v', '--engine-version')
@click.argument("suite")
@click.argument("path", type=click.Path(exists=True))
@click.option("-e", "--engine", type=click.Choice(ENGINE_CHOICES), default="planemo")
@click.option("-v", "--engine-version")
@OPTION_CRATE_PATH
@OPTION_PROPS
def definition(crate_dir, suite, path, engine, engine_version, property):
Expand All @@ -183,19 +224,23 @@ def definition(crate_dir, suite, path, engine, engine_version, property):
# For now, only support marking an existing file as a test definition
raise ValueError(f"{source} is not in the crate dir {crate_dir}")
crate.add_test_definition(
add_hash(suite), source=source, dest_path=dest_path, engine=engine,
engine_version=engine_version, properties=dict(property)
add_hash(suite),
source=source,
dest_path=dest_path,
engine=engine,
engine_version=engine_version,
properties=dict(property),
)
crate.metadata.write(crate_dir)


@cli.command()
@click.argument('dst', type=click.Path(writable=True))
@click.argument("dst", type=click.Path(writable=True))
@OPTION_CRATE_PATH
def write_zip(crate_dir, dst):
crate = ROCrate(crate_dir, init=False, gen_preview=False)
crate.write_zip(dst)


if __name__ == '__main__':
if __name__ == "__main__":
cli()
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