Source code for galaxy.managers.citations

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: = app self.doi_cache = DoiCache(app.config)
[docs] def citations_for_tool(self, tool): return tool.citations
[docs] def citations_for_tool_ids(self, tool_ids): citation_collection = CitationCollection() for tool_id in tool_ids: tool = self._get_tool(tool_id) for citation in self.citations_for_tool(tool): citation_collection.add(citation) return citation_collection.citations
[docs] def parse_citation(self, citation_elem): return parse_citation(citation_elem, self)
def _get_tool(self, tool_id): tool = 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"{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, )