"""
Add a datacite to your BIDS dataset.
details on the format of datacite for GIN: https://gin.g-node.org/G-Node/Info/wiki/DOIfile
"""
from __future__ import annotations
import argparse
import json
import logging
import sys
from pathlib import Path
from typing import Any
from typing import IO
import ruamel.yaml
from cffconvert.cli.create_citation import create_citation
from cffconvert.cli.validate_or_write_output import validate_or_write_output
from rich import print
from rich.prompt import Prompt
from . import _version
__version__ = _version.get_versions()["version"]
from bids2cite.authors import update_authors, authors_for_desc, authors_for_citation
from bids2cite.license import update_license, supported_licenses
from bids2cite.references import (
update_references,
references_for_datacite,
references_for_citation,
)
from bids2cite.utils import (
bids2cite_log,
print_ordered_list,
prompt_format,
log_levels,
default_log_level,
)
bids_dir = Path(__file__).parent.joinpath("tests", "bids")
log = logging.getLogger("bids2datacite")
[docs]def update_bidsignore(bids_dir: Path) -> None:
"""Update the .bidsignore file."""
log.info("updating .bidsignore")
bidsignore = bids_dir.joinpath(".bidsignore")
if not bidsignore.exists():
with bidsignore.open("w") as f:
f.write("datacite.yml")
else:
with bidsignore.open("r") as f:
content = f.read()
if "datacite.yml" not in content:
with bidsignore.open("a") as f:
f.write("datacite.yml")
[docs]def update_description(description: str | None = None, skip_prompt: bool = False) -> str:
"""Update the description of the dataset."""
log.info("update description")
if description not in [None, ""]:
description = description
elif not skip_prompt:
description = Prompt.ask(
prompt_format("\nPlease enter a description for the dataset")
)
print()
if description is None:
description = ""
return description
[docs]def update_keywords(
keywords: list[Any] | None = None, skip_prompt: bool = False
) -> list[str]:
"""Update the keywords of the dataset."""
log.info("updating keywords")
if keywords is None:
keywords = []
if not skip_prompt:
add_keyword = "yes"
while add_keyword == "yes":
print_ordered_list(msg="Current keywords:", items=keywords)
add_keyword = Prompt.ask(
prompt_format("Do you want to add more keywords?"),
default="yes",
choices=["yes", "no"],
)
if add_keyword != "yes":
break
new_keywords = Prompt.ask(
prompt_format(
"""Please enter keywords separated by comma
(for example: 'keyword1, keyword2')"""
)
)
tmp = new_keywords.strip().split(",")
for keyword in tmp:
keywords.append(keyword.strip())
return keywords
[docs]def update_funding(ds_desc: dict[str, Any], skip_prompt: bool = False) -> list[str]:
"""Update the funding of the dataset."""
log.info("update funding")
funding = []
if "Funding" in ds_desc and ds_desc["Funding"] not in [None, []]:
funding = ds_desc["Funding"]
if skip_prompt:
return funding
add_funding = "yes"
while add_funding == "yes":
print_ordered_list(msg="Current fundings:", items=funding)
add_funding = Prompt.ask(
prompt_format("Do you want to add more funding?"),
default="yes",
choices=["yes", "no"],
)
print()
if add_funding != "yes":
break
grant = Prompt.ask(
prompt_format("Please enter a funding (for example: 'EU, EU.12345')")
)
funding.append(grant)
return funding
[docs]def cli(argv: Any = sys.argv) -> None:
"""Execute the main script for CLI."""
log = bids2cite_log(name="bids2datacite")
parser = common_parser()
args = parser.parse_args(argv[1:])
# https://stackoverflow.com/a/53293042/14223310
log_level = log_levels().index(default_log_level())
# For each "-v" flag, adjust the logging verbosity accordingly
# making sure to clamp off the value from 0 to 4, inclusive of both
for adjustment in args.log_level or ():
log_level = min(len(log_levels()) - 1, max(log_level + adjustment, 0))
log_level_name = log_levels()[log_level]
log.setLevel(log_level_name)
tmp = args.keywords.split(",") if args.keywords else []
keywords = [x.strip() for x in tmp]
authors_file = None
if args.authors_file not in ["", None]:
authors_file = Path(args.authors_file)
if not authors_file.exists():
authors_file = None
licenses = supported_licenses()
licenses_choices = list(licenses.keys())
if args.license and args.license not in licenses_choices:
log.error(
f"""License '{args.license}' not supported.
Supported types are {licenses_choices}"""
)
sys.exit(1)
if args.output_format not in ["datacite", "citation"]:
log.error(
f"""Format '{args.output_format}' not supported.
Supported types are 'datacite' and 'citation'"""
)
sys.exit(1)
bids2cite(
bids_dir=Path(args.bids_dir).resolve(),
output_format=args.output_format,
description=args.description,
keywords=keywords,
license=args.license,
skip_prompt=args.skip_prompt,
authors_file=authors_file,
)
[docs]def bids2cite(
bids_dir: Path,
output_format: str,
description: str | None = None,
keywords: list[str] | None = None,
license: str | None = None,
skip_prompt: bool = False,
authors_file: Path | None = None,
) -> None: # sourcery skip: merge-dict-assign
"""Create a datacite.yml file for a BIDS dataset."""
log = bids2cite_log(name="bids2datacite")
log.info(f"bids_dir: {bids_dir}")
output_dir = bids_dir.joinpath("derivatives", "bids2cite")
output_dir.mkdir(exist_ok=True, parents=True)
ds_descr_file = bids_dir.joinpath("dataset_description.json")
yaml = ruamel.yaml.YAML()
yaml.indent(mapping=2, sequence=4, offset=2)
if not ds_descr_file.exists():
log.error(f"dataset_description.json not found in {bids_dir}")
sys.exit(1)
with open(ds_descr_file) as f:
ds_desc: dict[str, Any] = json.load(f)
description = update_description(description, skip_prompt)
authors = update_authors(ds_desc, skip_prompt, authors_file)
references = update_references(ds_desc, skip_prompt)
funding = update_funding(ds_desc, skip_prompt)
if license is not None:
ds_desc["License"] = license
(license_name, license_url) = update_license(
bids_dir, output_dir, ds_desc, skip_prompt
)
keywords = update_keywords(keywords, skip_prompt)
update_bidsignore(bids_dir)
"""dataset_description.json"""
ds_desc["Authors"] = authors_for_desc(authors)
ds_desc["ReferencesAndLinks"] = references_for_datacite(references)
ds_desc["Funding"] = funding
ds_desc["License"] = license_name
output_file = output_dir.joinpath("dataset_description.json")
log.info(f"updating {output_file}")
with open(output_file, "w", encoding="utf-8") as f:
json.dump(ds_desc, f, indent=4)
"""datacite.yml"""
if output_format == "datacite":
datacite: dict[str, Any] = {
"authors": [],
"title": ds_desc["Name"],
"description": "",
"keywords": [],
"license": {"name": "", "url": ""},
"resourcetype": "Dataset",
"references": [],
"templateversion": 1.2,
"funding": [],
}
datacite["description"] = description
datacite["authors"] = authors
datacite["references"] = references
datacite["funding"] = funding
datacite["license"]["name"] = license_name
datacite["license"]["url"] = license_url
datacite["keywords"] = keywords
datacite_file = output_dir.joinpath("datacite.yml")
log.info(f"creating {datacite_file}")
with open(datacite_file, "w", encoding="utf-8") as f:
yaml.dump(datacite, f)
"""CITATION.cff"""
if output_format == "citation":
citation: dict[str, Any] = {
"authors": [],
"title": ds_desc["Name"],
"message": "",
"license": "",
"type": "dataset",
"identifiers": [],
"cff-version": "1.2.0",
}
if keywords not in [None, []]:
citation["keywords"] = keywords
citation["license"] = license_name
citation["authors"] = authors_for_citation(authors)
citation["message"] = description
if description == "":
citation["message"] = "TODO"
citation["identifiers"] = references_for_citation(references)
citation_file = output_dir.joinpath("CITATION.cff")
log.info(f"creating {citation_file}")
with open(citation_file, "w", encoding="utf-8") as f:
yaml.dump(citation, f)
citation = create_citation(infile=citation_file, url=None)
validate_or_write_output(
outfile=None, outputformat=None, validate_only=True, citation=citation
)
[docs]class MuhParser(argparse.ArgumentParser):
"""Parser for the main script."""
def _print_message(self, message: str, file: IO[str] | None = None) -> None:
print(message, file=file)
[docs]def common_parser() -> MuhParser:
"""Execute the main script."""
parser = MuhParser(
description="BIDS app to create citation file for your BIDS dataset.",
epilog="""
For a more readable version of this help section,
see the online ".
""",
)
parser.add_argument(
"bids_dir",
help="""
The directory with the input dataset formatted according to the BIDS standard.
""",
)
parser.add_argument(
"-o",
"--output-format",
help="""Choose the output format between 'citation' for CITATION.cff
and 'datacite' for datacite.yml.""",
default="datacite",
)
parser.add_argument(
"-d", "--description", help="Description to add to the dataset.", default=""
)
parser.add_argument(
"-k",
"--keywords",
help="List of key words separated by commas to add to the citation file.",
default="",
)
licenses = supported_licenses()
licenses_choices = list(licenses.keys())
parser.add_argument(
"-l",
"--license",
help=f"License to add to choose from: {licenses_choices}",
default=None,
)
parser.add_argument(
"-s",
"--skip-prompt",
help="If you do not want to use the prompt interface.",
action="store_true",
)
parser.add_argument(
"--authors-file",
help=""".tsv file containing list of potential new authors with the columns:
first_name, last_name, ORCID (optional), affiliation (optional)""",
default="",
)
parser.add_argument(
"--verbose",
"-v",
dest="log_level",
action="append_const",
const=-1,
)
parser.add_argument(
"--version",
action="version",
help="show program's version number and exit",
version=f"{__version__}",
)
return parser