def main():
parser = argparse.ArgumentParser()
parser.add_argument('type', help='What type to generate')
parser.add_argument('target',
type=dir_path,
help='Directory to write output to')
args = parser.parse_args()
schema_versions = dict_schema_versions()
versions = sorted(schema_versions[args.type])
assert versions, f'No versions for {args.type}'
max_version = max(versions)
is_assay = get_is_assay(args.type)
if is_assay:
table_schemas = {v: get_table_schema(args.type, v) for v in versions}
directory_schema = get_directory_schema(args.type)
else:
table_schemas = {v: get_other_schema(args.type, v) for v in versions}
directory_schema = {}
# README.md:
with open(Path(args.target) / 'README.md', 'w') as f:
url = f'https://hubmapconsortium.github.io/ingest-validation-tools/{args.type}/'
f.write(f'Moved to [github pages]({url}).')
# index.md:
with open(Path(args.target) / 'index.md', 'w') as f:
f.write(
generate_readme_md(table_schemas,
directory_schema,
args.type,
is_assay=is_assay))
# YAML:
for v in versions:
schema = table_schemas[v]
first_field = schema['fields'][0]
if first_field['name'] == 'version':
assert first_field['constraints']['enum'] == [v], \
f'Wrong version constraint in {args.type}-v{v}.yaml'
assert schema['fields'][0]
with open(Path(args.target) / f'v{v}.yaml', 'w') as f:
f.write('# Generated YAML: PRs should not start here!\n' +
dump_yaml(schema))
# Data entry templates:
with open(
Path(args.target) / get_tsv_name(args.type, is_assay=is_assay),
'w') as f:
max_schema = table_schemas[max_version]
f.write(generate_template_tsv(max_schema))
create_xlsx(max_schema,
Path(args.target) /
get_xlsx_name(args.type, is_assay=is_assay),
idempotent=True,
sheet_name='Export as TSV')
def main():
parser = argparse.ArgumentParser()
parser.add_argument('target',
type=dir_path,
help='Directory to write output to')
args = parser.parse_args()
metadata_type = 'sample'
table_schema = get_sample_schema()
(Path(args.target) / get_tsv_name(metadata_type)).write_text(
generate_template_tsv(table_schema))
(Path(args.target) / 'README.md').write_text(
generate_readme_md(table_schema, {}, metadata_type, is_top_level=True))
def main():
parser = argparse.ArgumentParser()
parser.add_argument('type', help='What type to generate')
parser.add_argument('target',
type=dir_path,
help='Directory to write output to')
args = parser.parse_args()
schema_versions = dict_schema_versions()
versions = sorted(schema_versions[args.type])
max_version = max(versions)
is_assay = get_is_assay(args.type)
if is_assay:
table_schemas = {v: get_table_schema(args.type, v) for v in versions}
directory_schema = get_directory_schema(args.type)
else:
table_schemas = {v: get_other_schema(args.type, v) for v in versions}
directory_schema = {}
# README:
with open(Path(args.target) / 'README.md', 'w') as f:
f.write(
generate_readme_md(table_schemas,
directory_schema,
args.type,
is_assay=is_assay))
# YAML:
for v in versions:
with open(Path(args.target) / f'v{v}.yaml', 'w') as f:
f.write('# Generated YAML: PRs should not start here!\n' +
dump_yaml(table_schemas[v]))
# Data entry templates:
with open(
Path(args.target) / get_tsv_name(args.type, is_assay=is_assay),
'w') as f:
max_schema = table_schemas[max_version]
f.write(generate_template_tsv(max_schema))
create_xlsx(max_schema,
Path(args.target) /
get_xlsx_name(args.type, is_assay=is_assay),
idempotent=True,
sheet_name='Export as TSV')
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
'type',
choices=list_types(),
help='What type to generate')
parser.add_argument(
'target',
type=dir_path,
help='Directory to write output to')
args = parser.parse_args()
table_schema = get_table_schema(args.type)
directory_schemas = get_directory_schemas(args.type)
with open(Path(args.target) / get_tsv_name(args.type), 'w') as f:
f.write(generate_template_tsv(table_schema))
with open(Path(args.target) / 'README.md', 'w') as f:
f.write(generate_readme_md(table_schema, directory_schemas, args.type))
with open(Path(args.target) / 'unified.yaml', 'w') as f:
f.write(
f'# NOTE: Do not edit this; It is generated by {__file__}.\n\n'
+ dump_yaml(table_schema))