def read(self, xml, identifier):
"""
Load a JATS/NLM (PubMed) XML into a SciDoc.
:param xml: full xml string
:type xml: basestring
:param identifier: an identifier for this document, e.g. file name
If an actual full path, the path will be removed from it
when stored
:type identifier: basestring
:returns: :class:`SciDoc <SciDoc>` object
:rtype: SciDoc
"""
# this solves a "bug" in BeautifulStoneSoup with "sec" tags
BeautifulStoneSoup.NESTABLE_TAGS["sec"]=[]
#xml=fixNumberCitationsXML(xml)
soup=BeautifulStoneSoup(xml)
# Create a new SciDoc to store the paper
newDocument=SciDoc()
metadata=newDocument["metadata"]
metadata["filename"]=os.path.basename(identifier)
metadata["original_citation_style"]=detectCitationStyle(xml)
body=soup.find("body")
if not body:
# TODO: Make the error handling less terrible
debugAddMessage(newDocument,"error","NO <BODY> IN THIS PAPER! file: "+identifier)
newDocument["metadata"]["guid"]=cp.Corpus.generateGUID()
return newDocument
# Load metadata, either from corpus or from file
self.loadJATSMetadataFromPaper(newDocument, soup)
metadata["guid"]=cp.Corpus.generateGUID(metadata)
# Load all references from the XML
back=soup.find("back")
if back:
ref_list=back.find("ref-list")
# other things in <back> like appendices: ignore them for now
if ref_list:
for ref in ref_list.findAll("ref"):
self.loadJATSReference(ref, newDocument)
newDocument.updateReferences()
# Load Abstract
self.loadJATSAbstract(soup,newDocument)
for sec in body.findChildren("sec", recursive=False):
self.loadJATSSection(sec, newDocument, "root")
newDocument.updateAuthorsAffiliations()
return newDocument
def read(self, xml, identifier):
"""
Load a PaperXML into a SciDoc.
Args:
xml: full xml string
identifier: an identifier for this document, e.g. file name
Important: supply an actual path so that we can check
for the meatadata in bibtexml
If an actual full path, the path will be removed from it
when stored
Returns:
SciDoc instance
"""
## # this solves a "bug" in BeautifulStoneSoup with "sec" tags
## BeautifulStoneSoup.NESTABLE_TAGS["sec"]=[]
xml=self.cleanUpPaperXML(xml)
soup=BeautifulStoneSoup(xml, convertEntities=BeautifulStoneSoup.HTML_ENTITIES)
# Create a new SciDoc to store the paper
newDocument=SciDoc()
metadata=newDocument["metadata"]
metadata["filename"]=os.path.basename(identifier)
## if not citation_style:
## raise ValueError("Cannot determine citation style")
# default citation style if not otherwise detected
## citation_style="APA"
body=soup.find("body")
if not body:
# TODO: Make the error handling less terrible
debugAddMessage(newDocument,"error","NO <BODY> IN THIS PAPER! file: "+identifier)
## newDocument["metadata"]["guid"]=cp.Corpus.getFileUID(metadata["filename"])
return newDocument
# Load metadata, either from corpus or from file
self.loadPaperMetadata(newDocument, soup, identifier)
if metadata["surnames"] == []:
debugAddMessage(newDocument,"error","NO SURNAMES OF AUTHORS file: "+identifier)
return newDocument
if metadata["title"] == []:
debugAddMessage(newDocument,"error","NO TITLE file: "+identifier)
return newDocument
metadata["guid"]=cp.Corpus.generateGUID(metadata)
# Load all references from the XML
references=body.find("references")
if references:
self.loadPaperReferences(references, newDocument)
newDocument.updateReferences()
## print (newDocument.references)
## print("\n\n")
sections=body.findChildren("section", recursive=False)
detect_style_text="".join([sec.renderContents() for sec in sections[:3]])
## citation_style=detectCitationStyle(detect_style_text, default="APA")
# turns out I don't have a good detection algorithm for AFI
citation_style="APA"
metadata["original_citation_style"]=citation_style
# Load Abstract
self.loadPaperAbstract(soup,newDocument)
for sec in sections:
self.loadPaperSection(sec, newDocument, "root")
newDocument.updateReferences()
newDocument.updateAuthorsAffiliations()
return newDocument