import functools
import logging
import requests
from beaker.cache import CacheManager
from beaker.util import parse_cache_config_options
from galaxy.structured_app import BasicSharedApp
from galaxy.util import DEFAULT_SOCKET_TIMEOUT
log = logging.getLogger(__name__)
[docs]class CitationsManager:
[docs] def __init__(self, app: BasicSharedApp) -> None:
self.app = app
self.doi_cache = DoiCache(app.config)
[docs] def parse_citation(self, citation_elem):
return parse_citation(citation_elem, self)
def _get_tool(self, tool_id):
tool = self.app.toolbox.get_tool(tool_id)
return tool
[docs]class DoiCache:
[docs] def __init__(self, config):
cache_opts = {
"cache.type": config.citation_cache_type,
"cache.data_dir": config.citation_cache_data_dir,
"cache.lock_dir": config.citation_cache_lock_dir,
"cache.url": config.citation_cache_url,
"cache.table_name": config.citation_cache_table_name,
"cache.schema_name": config.citation_cache_schema_name,
}
self._cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache("doi")
def _raw_get_bibtex(self, doi):
doi_url = f"https://doi.org/{doi}"
headers = {"Accept": "application/x-bibtex"}
res = requests.get(doi_url, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT)
# To decode the response content, res.text tries to determine the
# content encoding from the Content-Type header (res.encoding), and if
# that fails, falls back to guessing from the content itself (res.apparent_encoding).
# The guessed encoding is sometimes wrong, better to default to utf-8.
if res.encoding is None:
res.encoding = "utf-8"
return res.text
[docs] def get_bibtex(self, doi):
createfunc = functools.partial(self._raw_get_bibtex, doi)
return self._cache.get(key=doi, createfunc=createfunc)
[docs]def parse_citation(elem, citation_manager):
"""
Parse an abstract citation entry from the specified XML element.
"""
citation_type = elem.attrib.get("type", None)
citation_class = CITATION_CLASSES.get(citation_type, None)
if not citation_class:
log.warning(f"Unknown or unspecified citation type: {citation_type}")
return None
try:
citation = citation_class(elem, citation_manager)
except Exception as e:
raise Exception(f"Invalid citation of type '{citation_type}' with content '{elem.text}': {e}")
return citation
[docs]class CitationCollection:
[docs] def __init__(self):
self.citations = []
def __iter__(self):
return self.citations.__iter__()
def __len__(self):
return len(self.citations)
[docs] def add(self, new_citation):
for citation in self.citations:
if citation.equals(new_citation):
# TODO: We have two equivalent citations, pick the more
# informative/complete/correct.
return False
self.citations.append(new_citation)
return True
[docs]class BaseCitation:
[docs] def to_dict(self, citation_format):
if citation_format == "bibtex":
return dict(
format="bibtex",
content=self.to_bibtex(),
)
else:
raise Exception(f"Unknown citation format {citation_format}")
[docs] def equals(self, other_citation):
if self.has_doi() and other_citation.has_doi():
return self.doi() == other_citation.doi()
else:
# TODO: Do a better job figuring out if this is the same citation.
return self.to_bibtex() == other_citation.to_bibtex()
[docs] def has_doi(self):
return False
[docs]class BibtexCitation(BaseCitation):
[docs] def __init__(self, elem, citation_manager):
self.raw_bibtex = elem.text.strip()
[docs] def to_bibtex(self):
return self.raw_bibtex
[docs]class DoiCitation(BaseCitation):
BIBTEX_UNSET = object()
[docs] def __init__(self, elem, citation_manager):
self.__doi = elem.text.strip()
self.doi_cache = citation_manager.doi_cache
self.raw_bibtex = DoiCitation.BIBTEX_UNSET
[docs] def has_doi(self):
return True
[docs] def doi(self):
return self.__doi
[docs] def to_bibtex(self):
if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
try:
self.raw_bibtex = self.doi_cache.get_bibtex(self.__doi)
except Exception:
log.exception("Failed to fetch bibtex for DOI %s", self.__doi)
if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
return f"""@MISC{{{self.__doi},
DOI = {{{self.__doi}}},
note = {{Failed to fetch BibTeX for DOI.}}
}}"""
else:
return self.raw_bibtex
CITATION_CLASSES = dict(
bibtex=BibtexCitation,
doi=DoiCitation,
)