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Source code for galaxy.managers.citations

import functools
import os
import requests

from beaker.cache import CacheManager
from beaker.util import parse_cache_config_options

import logging
log = logging.getLogger( __name__ )


[docs]class CitationsManager( object ):
[docs] def __init__( self, app ): self.app = 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, tool_directory ): return parse_citation( citation_elem, tool_directory, self )
def _get_tool( self, tool_id ): tool = self.app.toolbox.get_tool( tool_id ) return tool
[docs]class DoiCache( object ):
[docs] def __init__( self, config ): cache_opts = { 'cache.type': getattr( config, 'citation_cache_type', 'file'), 'cache.data_dir': getattr( config, 'citation_cache_data_dir', None), 'cache.lock_dir': getattr( config, 'citation_cache_lock_dir', None), } self._cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('doi')
def _raw_get_bibtex( self, doi ): dx_url = "http://dx.doi.org/" + doi headers = {'Accept': 'text/bibliography; style=bibtex, application/x-bibtex'} req = requests.get(dx_url, headers=headers) return req.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, directory, citation_manager ): """ Parse an abstract citation entry from the specified XML element. The directory parameter should be used to find external files for this citation. """ citation_type = elem.attrib.get( 'type', None ) citation_class = CITATION_CLASSES.get( citation_type, None ) if not citation_class: log.warning("Unknown or unspecified citation type: %s" % citation_type) return None return citation_class( elem, directory, citation_manager )
[docs]class CitationCollection( object ):
[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( object ):
[docs] def to_dict( self, citation_format ): if citation_format == "bibtex": return dict( format="bibtex", content=self.to_bibtex(), ) else: raise Exception("Unknown citation format %s" % 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, directory, citation_manager ): bibtex_file = elem.attrib.get("file", None) if bibtex_file: raw_bibtex = open(os.path.join(directory, bibtex_file), "r").read() else: raw_bibtex = elem.text.strip() self._set_raw_bibtex( raw_bibtex )
def _set_raw_bibtex( self, raw_bibtex ): self.raw_bibtex = raw_bibtex
[docs] def to_bibtex( self ): return self.raw_bibtex
[docs]class DoiCitation( BaseCitation ): BIBTEX_UNSET = object()
[docs] def __init__( self, elem, directory, 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 """@MISC{%s, DOI = {%s}, note = {Failed to fetch BibTeX for DOI.} }""" % (self.__doi, self.__doi) else: return self.raw_bibtex
CITATION_CLASSES = dict( bibtex=BibtexCitation, doi=DoiCitation, )