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"""
A Martel format to parse the NLM's XML format for Medline.
http://www.nlm.nih.gov/databases/dtd/nlmmedline_010319.dtd
http://www.nlm.nih.gov/databases/dtd/nlmmedlinecitation_010319.dtd
http://www.nlm.nih.gov/databases/dtd/nlmcommon_010319.dtd
Formats:
citation_format Format for one MedlineCitation.
format Format for a whole file.
"""
import sys
from Martel import *
from Martel import RecordReader
self = sys.modules[__name__]
def _start_elem(element, *attrs):
if attrs:
attr_groups = []
for attr in attrs:
group = Str(attr) + Str("=") + \
Str('"') + Group(attr, Re(r'[^<&"]+')) + Str('"')
attr_groups.append(group)
start = Str("<") + Str(element) + \
Rep(Str(" ") + Alt(*attr_groups)) + \
Str(">")
else:
start = Str("<%s>" % element)
return start
def _end_elem(element):
return Str("</%s>" % element)
def simple_elem(element, *attrs):
"""simple_elem(element, *attrs)
Create a Martel Expression in this module's namespace that will
recognize an XML element in the form of:
<element>data</element>
The whole element must be on a single line. The Expression will
be created in the module's namespace with the same name as the
element.
"""
start, end = _start_elem(element, *attrs), _end_elem(element)
group_name = element
group_expression = Re(r"[^<]+")
expr = start + \
Group(group_name, group_expression) + \
end + \
AnyEol()
setattr(self, element, expr)
# Group expressions. A group consists of the start and end elements
# with an expression in-between. The Expression for the group will be
# called "NAME".
def group_elem(element, expr, *attrs):
start_name, end_name = "%s_start" % element, "%s_end" % element
start_expr = getattr(self, start_name, None)
if start_expr is None:
start_expr = _start_elem(element, *attrs) + AnyEol()
setattr(self, start_name, start_expr)
end_expr = getattr(self, end_name, None)
if end_expr is None:
end_expr = _end_elem(element) + AnyEol()
setattr(self, end_name, end_expr)
group_expr = start_expr + expr + end_expr
group_expr = Group(element, group_expr)
setattr(self, element, group_expr)
######################################################################
# Implement Martel expressions that recognize: #
# http://www.nlm.nih.gov/databases/dtd/nlmcommon_010319.dtd #
######################################################################
########################################
# Personal and Author names
elements = [
"FirstName", "MiddleName", "LastName",
"Initials", "Suffix",
"CollectiveName"
]
[simple_elem(e) for e in elements]
personal_name = LastName + \
Opt(FirstName + Opt(MiddleName)) + \
Opt(Initials) + \
Opt(Suffix)
author_name = Alt(personal_name, CollectiveName)
########################################
# Dates
elements = [
"Year", "Month", "Day",
"Season", "MedlineDate",
"Hour", "Minute", "Second"
]
[simple_elem(e) for e in elements]
normal_date = Year + Month + Day + \
Opt(Hour + Opt(Minute + Opt(Second)))
pub_date = Alt((Year + Opt(Alt((Month + Opt(Day)), Season))), MedlineDate)
simple_elem("CopyrightInformation")
simple_elem("AbstractText")
group_elem("Abstract", AbstractText + Opt(CopyrightInformation))
########################################
# NCBIArticle
simple_elem("NlmUniqueID")
simple_elem("PMID")
simple_elem("SubHeading", "MajorTopicYN")
simple_elem("Descriptor", "MajorTopicYN")
group_elem("MeshHeading", Descriptor + Rep(SubHeading))
group_elem("MeshHeadingList", Rep1(MeshHeading))
simple_elem("MedlinePgn")
simple_elem("EndPage")
simple_elem("StartPage")
group_elem("Pagination",
Alt(StartPage + Opt(EndPage) + Opt(MedlinePgn), MedlinePgn))
simple_elem("Affiliation")
group_elem("Author", author_name + Opt(Affiliation))
group_elem("AuthorList", Rep1(Author), "CompleteYN")
simple_elem("Language")
simple_elem("PublicationType")
group_elem("PublicationTypeList", Rep1(PublicationType))
simple_elem("Title") # These were moved up, so that the definitions
simple_elem("Volume") # will be before Book.
simple_elem("VernacularTitle")
simple_elem("CollectionTitle")
simple_elem("ArticleTitle")
simple_elem("Publisher")
group_elem("PubDate", pub_date)
group_elem("Book", PubDate + Publisher + Title +
Opt(AuthorList) + Opt(CollectionTitle) + Opt(Volume))
simple_elem("Country")
simple_elem("MedlineTA")
simple_elem("MedlineCode")
group_elem("MedlineJournalInfo",
Opt(Country) + MedlineTA + Opt(MedlineCode) + Opt(NlmUniqueID))
simple_elem("DateOfElectronicPublication")
simple_elem("ISOAbbreviation")
simple_elem("Coden")
simple_elem("Issue")
group_elem("JournalIssue", Opt(Volume) + Opt(Issue) + PubDate)
simple_elem("ISSN")
group_elem("Journal",
Opt(ISSN) + \
JournalIssue + \
Opt(Coden) + \
Opt(Title) + \
Opt(ISOAbbreviation)
)
simple_elem("GrantID")
simple_elem("Acronym")
simple_elem("Agency")
group_elem("Grant", Opt(GrantID) + Opt(Acronym) + Opt(Agency))
group_elem("GrantList", Rep1(Grant), "CompleteYN")
simple_elem("AccessionNumber")
group_elem("AccessionNumberList", Rep1(AccessionNumber))
simple_elem("DataBankName")
group_elem("DataBank", DataBankName + Opt(AccessionNumberList))
group_elem("DataBankList", Rep1(DataBank), "CompleteYN")
group_elem("Article",
Alt(Journal, Book) + \
ArticleTitle + \
Pagination + \
Opt(Abstract) + \
Opt(Affiliation) + \
Opt(AuthorList) + \
Rep1(Language) + \
Opt(DataBankList) + \
Opt(GrantList) + \
PublicationTypeList + \
Opt(VernacularTitle) + \
Opt(DateOfElectronicPublication)
)
group_elem("NCBIArticle", PMID + Article + Opt(MedlineJournalInfo))
######################################################################
# Implement Martel expressions that recognize: #
# http://www.nlm.nih.gov/databases/dtd/nlmmedlinecitation_010319.dtd #
######################################################################
simple_elem("MedlineID")
simple_elem("Note")
simple_elem("RefSource")
Ref_template = RefSource + Opt(MedlineID) + Opt(Note)
########################################
# MedlineCitation
group_elem("OriginalReportIn", Ref_template)
group_elem("SummaryForPatientsIn", Ref_template)
group_elem("CommentOn", Ref_template)
group_elem("CommentIn", Ref_template)
group_elem("ErratumIn", Ref_template)
group_elem("RepublishedFrom", Ref_template)
group_elem("RepublishedIn", Ref_template)
group_elem("RetractionOf", Ref_template)
group_elem("RetractionIn", Ref_template)
group_elem("UpdateIn", Ref_template)
group_elem("UpdateOf", Ref_template)
group_elem("CommentsCorrections",
Rep(CommentOn) + Rep(CommentIn) + \
Rep(ErratumIn) + \
Rep(RepublishedFrom) + Rep(RepublishedIn) + \
Rep(RetractionOf) + Rep(RetractionIn) + \
Rep(UpdateIn) + Rep(UpdateOf) + \
Rep(SummaryForPatientsIn) + Rep(OriginalReportIn)
)
simple_elem("NumberOfReferences")
group_elem("PersonalNameSubject", personal_name)
group_elem("PersonalNameSubjectList", Rep1(PersonalNameSubject))
simple_elem("GeneSymbol")
group_elem("GeneSymbolList", Rep1(GeneSymbol))
simple_elem("NameOfSubstance")
simple_elem("CASRegistryNumber")
group_elem("Chemical", CASRegistryNumber + NameOfSubstance)
group_elem("ChemicalList", Rep1(Chemical))
simple_elem("CitationSubset")
simple_elem("GeneralNote", "Owner")
group_elem("Investigator", personal_name + Opt(Affiliation))
group_elem("InvestigatorList", Rep1(Investigator))
simple_elem("OtherID", "Source")
simple_elem("SpaceFlightMission")
simple_elem("Keyword", "MajorTopicYN")
group_elem("KeywordList", Rep1(Keyword), "Owner")
group_elem("OtherAbstract",
AbstractText + Opt(CopyrightInformation),
"Type")
group_elem("DateRevised", normal_date)
group_elem("DateCompleted", normal_date)
group_elem("DateCreated", normal_date)
group_elem("MedlineCitation",
MedlineID + \
Opt(PMID) + \
DateCreated + \
Opt(DateCompleted) + \
Opt(DateRevised) + \
Article + \
MedlineJournalInfo + \
Opt(ChemicalList) + \
Rep(CitationSubset) + \
Opt(CommentsCorrections) + \
Opt(GeneSymbolList) + \
Opt(MeshHeadingList) + \
Opt(NumberOfReferences) + \
Opt(PersonalNameSubjectList) + \
Rep(OtherID) + \
Rep(OtherAbstract) + \
Rep(KeywordList) + \
Rep(SpaceFlightMission) + \
Opt(InvestigatorList) + \
Rep(GeneralNote),
"Owner"
)
######################################################################
# Implement Martel expressions that recognize: #
# http://www.nlm.nih.gov/databases/dtd/nlmmedline_010319.dtd #
######################################################################
# The DeleteCitation tags start with spaces, so I have to make a
# special case for it.
space = Any(" \t")
DeleteCitation_start = Rep(space) + Str("<DeleteCitation>") + AnyEol()
DeleteCitation_end = Rep(space) + Str("</DeleteCitation>") + AnyEol()
# The file doesn't always end in a newline, so make MedlineCitationSet
# end in an optional Eol.
MedlineCitationSet_end = Str("</MedlineCitationSet>") + Opt(AnyEol())
group_elem("DeleteCitation", Alt(Rep1(MedlineID), Rep1(PMID)))
group_elem("MedlineCitationSet", Rep(MedlineCitation) + Opt(DeleteCitation))
######################################################################
# Other stuff #
# #
######################################################################
# Should match the proper dtd in here...
DOCTYPE = Str("<!DOCTYPE") + Re(r"[^>]+") + Str(">") + AnyEol()
citation_format = MedlineCitation
# I'm going to use a RecordReader so that I can parse one record at a
# time, instead of sucking the whole XML file into memory. Each
# citation is going to be a record. Thus, the header is everything
# before the first citation and the footer is everything after the
# last citation.
header_format = Group("header", DOCTYPE + MedlineCitationSet_start)
footer_format = Opt(DeleteCitation) + MedlineCitationSet_end
format = HeaderFooter(
None, {},
# Unfortunately, RecordReader.Until doesn't work because some
# MedlineCitations have attributes are in the form
# <MedlineCitation Owner="NLM">. "<MedlineCitation" by itself
# won't differentiate between the beginning of a
# MedlineCitationSet or the beginning of a MedlineCitation. Thus,
# I'm just going to read the first 4 lines and hope that's the
# whole header.
#header_format, RecordReader.Until, ("<MedlineCitation>",),
header_format, RecordReader.CountLines, (4,),
citation_format, RecordReader.EndsWith, ("</MedlineCitation>",),
footer_format, RecordReader.Everything, (),
)
|
