def loadJATSReference(self, ref, doc):
"""
Load a reference from the bibliography section.
:param ref: xml node for reference element
:param doc: :class `SciDoc <SciDoc>` instance we're loading this for
:returns: dict with the new loaded reference
:rtype: dict
"""
xmltext=ref.__repr__()
authorlist=[]
surnames=[]
original_id=ref["id"]
citation_type_key="publication-type"
element=ref.find("element-citation")
if not element:
element=ref.find("mixed-citation")
if not element:
element=ref.find("citation")
if element:
citation_type_key="citation-type"
author_group=ref.find("person-group",{"person-group-type":"author"})
if not author_group:
collab=ref.find("collab")
if collab:
authorlist.append(guessNamesOfPlainTextAuthor(collab.text))
else:
author_group=ref
if author_group:
authors=author_group.findAll("name")
else:
authors=None
collab=ref.find("collab")
if collab:
authorlist.append({"family":collab.text, "given":""})
surnames.append(collab.text)
if authors:
for a in authors:
astring=a.__repr__()
surname=a.find("surname")
if surname:
surnames.append(surname.text)
given_names=a.find("given-names")
if given_names and surname:
authorlist.append({"given": given_names.text, "family": surname.text})
else:
astring=cleanxml(astring)
authorlist.append(guessNamesOfPlainTextAuthor(astring))
else:
srnms=ref.findAll("surname")
for s in srnms:
surnames.append(s.text)
newref=doc.addReference()
## newref["xml"]=xmltext
## newref["text"]=cleanxml(xmltext)
newref["authors"]=authorlist
newref["surnames"]=surnames
newref["external_links"]=[]
newref["title"]="<NO TITLE>"
if not element:
newref["xml"]=xmltext
return newref
article_title=ref.find("article-title")
source=element.find("source")
if source:
newref["publication-name"]=source.text
else:
newref["publication-name"]=""
try:
newref["publication-type"]=element[citation_type_key]
except:
newref["publication-type"]="unknown"
if newref["publication-type"]=="book":
if source:
newref["title"]=source.text
else:
if article_title:
newref["title"]=article_title.text
elif newref["publication-type"]=="journal":
if article_title:
newref["title"]=article_title.text
elif newref["publication-type"]=="other":
if article_title:
newref["title"]=article_title.text
elif source:
newref["title"]=source.text
self.extractInfoFromPatentText(ref.__repr__(), newref)
self.loadJATSmetadataIfExists(element,["volume","issue","fpage","lpage","year"],newref)
id=element.find("pub-id",{"pub-id-type":"doi"})
if id:
newref["doi"]=id.text
id=element.find("pub-id",{"pub-id-type":"pmid"})
if id:
newref["pmid"]=id.text
id=element.find("pub-id",{"pub-id-type":"pmc"})
if id:
newref["pmcid"]=id.text
if newref["title"] == "":
newref["title"]="<NO TITLE FOUND>"
## comment=element.find("comment")
## if comment:
## extlink=comment.find("ext-link",{"ext-link-type":"uri"})
extlinks=element.findAll("ext-link",{"ext-link-type":"uri"})
for extlink in extlinks:
newref["external_links"].append(extlink["xlink:href"])
if original_id and self.USE_ORIGINAL_REF_ID:
newref["id"]=original_id
return newref
def loadParsCitReference(self, reference):
"""
Given an XML <citation> node, loads all the relevant values from it.
Args:
reference: XML node
Returns:
metadata of reference
"""
metadata={
"title":"title", # key: the key in the final dict. Value: the XML tag to look for
"year":"date",
"volume":"volume",
"pages":"pages",
"journal":"journal",
"publisher":"publisher",
"location":"location",
"raw_string":"rawstring",
"institution":"institution",
}
for key in metadata:
# substitute each value string by its value in the XML, if found
node=reference.find(metadata[key])
if node:
text=node.text.strip(".") # just to be annoying. get the actual text of the node
else:
text=""
metadata[key]=text
# often the title will end up as anything else: location, journal
if len(metadata["title"]) < 2:
if len(metadata.get("journal","")) > 2:
metadata["title"]=metadata["journal"]
metadata["journal"]=""
elif len(metadata.get("location","")) > 2:
metadata["title"]=metadata["location"]
metadata["location"]=""
if metadata["title"].startswith("Building and Using"):
pass
# All parsers get the "In Proceedings of..." wrong and put it in the title.
# this is a manual hack fix
rx_fix_title_in=re.compile(r"([,.] ?In[\:]? (\w.*))")
match=rx_fix_title_in.search(metadata["title"])
if match:
metadata["journal"]=match.group(2) + metadata.get("journal","")
metadata["title"]=rx_fix_title_in.sub("", metadata["title"]).strip(" ,")
rx_fix_title_thesis=re.compile(r", ((?:(?:Doctoral|MSc)? ?[Tt]hesis|(?:\w+|([A-Z]\. ?)+)[Dd]issertation).*)",flags=re.IGNORECASE)
match=rx_fix_title_thesis.search(metadata["title"])
if match:
metadata["journal"]=match.group(1) + metadata.get("journal","")
metadata["title"]=rx_fix_title_thesis.sub("", metadata["title"]).strip(" ,")
# remove hanging ". In" at the end of the title
metadata["title"]=re.sub(r"[.,;] ?In ?$","",metadata["title"])
for atype in ["journal", "booktitle"]:
node=reference.find(atype)
if node:
metadata["publication"]=node.text.strip(".,: ")
#TODO: expand this to inproceedings, etc.
metadata["type"] = atype
metadata["authors"]=[]
author_nodes=reference.findAll("author")
for author_string in [author.text for author in author_nodes]:
metadata["authors"].append(guessNamesOfPlainTextAuthor(author_string))
metadata["surnames"]=[author["family"] for author in metadata["authors"]]
return metadata
