From ac99a685845666b22bc59ddad75580c32b92c77d Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 27 Mar 2024 16:42:55 +0000 Subject: [PATCH 1/4] add help text to CLI options --- rocrate/cli.py | 105 +++++++++++++++++++++++++++++++++++-------------- 1 file changed, 75 insertions(+), 30 deletions(-) diff --git a/rocrate/cli.py b/rocrate/cli.py index 035d2f9..a353893 100644 --- a/rocrate/cli.py +++ b/rocrate/cli.py @@ -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() @@ -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) @@ -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): @@ -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): @@ -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): @@ -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): @@ -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() From 4409f5ad3c1ab6ab2a5cb7ceec6a098d12466141 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 27 Mar 2024 16:45:01 +0000 Subject: [PATCH 2/4] update readme in line with CLI help --- README.md | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 895fc69..7dcd8d5 100644 --- a/README.md +++ b/README.md @@ -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. ``` @@ -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. ``` From 43ace225bc7df9ec4a592811ef05122240e46e98 Mon Sep 17 00:00:00 2001 From: simleo Date: Wed, 10 Apr 2024 12:13:29 +0200 Subject: [PATCH 3/4] exclude help text: more precise wording --- rocrate/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rocrate/cli.py b/rocrate/cli.py index a353893..486641b 100644 --- a/rocrate/cli.py +++ b/rocrate/cli.py @@ -88,7 +88,7 @@ def cli(): "--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.", + help="Exclude files or directories from the RO-Crate. NAME may be a single name or a comma-separated list of names.", ) @OPTION_CRATE_PATH def init(crate_dir, gen_preview, exclude): From d75e30ed46757487a3667a8889eb423be8d1cbc9 Mon Sep 17 00:00:00 2001 From: simleo Date: Wed, 10 Apr 2024 12:22:32 +0200 Subject: [PATCH 4/4] revert previous commit --- rocrate/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rocrate/cli.py b/rocrate/cli.py index 486641b..a353893 100644 --- a/rocrate/cli.py +++ b/rocrate/cli.py @@ -88,7 +88,7 @@ def cli(): "--exclude", type=CSV, metavar="NAME", - help="Exclude files or directories from the RO-Crate. NAME may be a single name or a comma-separated list of names.", + 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):