Package Bio :: Package Medline :: Module nlmmedline_001211_format
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Module nlmmedline_001211_format

source code

A Martel format to parse the NLM's XML format for Medline.

http://www.nlm.nih.gov/databases/dtd/nlmmedline_001211.dtd http://www.nlm.nih.gov/databases/dtd/nlmmedlinecitation_001211.dtd http://www.nlm.nih.gov/databases/dtd/nlmcommon_001211.dtd

Formats: citation_format Format for one MedlineCitation. format Format for a whole file.

Functions [hide private]
 
_start_elem(element, *attrs) source code
 
_end_elem(element) source code
 
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>
source code
 
group_elem(element, expr, *attrs) source code
Variables [hide private]
  personal_name = LastName+ Opt(FirstName+ Opt(MiddleName))+ Opt...
  author_name = Alt(personal_name, CollectiveName)
  elements = ['Year', 'Month', 'Day', 'Season', 'MedlineDate', '...
  normal_date = Year+ Month+ Day+ Opt(Hour+ Opt(Minute+ Opt(Seco...
  pub_date = Alt((Year+ Opt(Alt((Month+ Opt(Day)), Season))), Me...
  Ref_template = RefSource+ Opt(MedlineID)+ Opt(Note)
  space = Any(" \t")
  DeleteCitation_start = Rep(space)+ Str("<DeleteCitation>")+ An...
  DeleteCitation_end = Rep(space)+ Str("</DeleteCitation>")+ Any...
  MedlineCitationSet_end = Str("</MedlineCitationSet>")+ Opt(Any...
  DOCTYPE = Str("<!DOCTYPE")+ Re(r"[^>]+")+ Str(">")+ AnyEol()
  citation_format = MedlineCitation
  header_format = Group("header", DOCTYPE+ MedlineCitationSet_st...
  footer_format = Opt(DeleteCitation)+ MedlineCitationSet_end
  format = HeaderFooter(None, {}, header_format, RecordReader.Un...
  Abstract = <Martel.Expression.Group instance at 0x587d1b8>
  AbstractAuthor = <Martel.Expression.Seq instance at 0x58899e0>
  AbstractText = <Martel.Expression.Seq instance at 0x587cf38>
  Abstract_end = <Martel.Expression.Seq instance at 0x587d170>
  Abstract_start = <Martel.Expression.Seq instance at 0x587d098>
  AccessionNumber = <Martel.Expression.Seq instance at 0x5884998>
  AccessionNumberList = <Martel.Expression.Group instance at 0x5...
  AccessionNumberList_end = <Martel.Expression.Seq instance at 0...
  AccessionNumberList_start = <Martel.Expression.Seq instance at...
  Acronym = <Martel.Expression.Seq instance at 0x5882ab8>
  AdditionalInformation = <Martel.Expression.Group instance at 0...
  AdditionalInformation_end = <Martel.Expression.Seq instance at...
  AdditionalInformation_start = <Martel.Expression.Seq instance ...
  Affiliation = <Martel.Expression.Seq instance at 0x587d488>
  Agency = <Martel.Expression.Seq instance at 0x5882cf8>
  Article = <Martel.Expression.Group instance at 0x5883d40>
  ArticleTitle = <Martel.Expression.Seq instance at 0x587f170>
  Article_end = <Martel.Expression.Seq instance at 0x5883cf8>
  Article_start = <Martel.Expression.Seq instance at 0x5883c20>
  Author = <Martel.Expression.Group instance at 0x587d6c8>
  AuthorList = <Martel.Expression.Group instance at 0x587dd88>
  AuthorList_end = <Martel.Expression.Seq instance at 0x587dd40>
  AuthorList_start = <Martel.Expression.Seq instance at 0x587dcb0>
  Author_end = <Martel.Expression.Seq instance at 0x587d680>
  Author_start = <Martel.Expression.Seq instance at 0x587d5a8>
  Book = <Martel.Expression.Group instance at 0x587f908>
  Book_end = <Martel.Expression.Seq instance at 0x587f8c0>
  Book_start = <Martel.Expression.Seq instance at 0x587f7e8>
  CASRegistryNumber = <Martel.Expression.Seq instance at 0x58886c8>
  Chemical = <Martel.Expression.Group instance at 0x58888c0>
  ChemicalList = <Martel.Expression.Group instance at 0x5888b48>
  ChemicalList_end = <Martel.Expression.Seq instance at 0x5888b00>
  ChemicalList_start = <Martel.Expression.Seq instance at 0x5888...
  Chemical_end = <Martel.Expression.Seq instance at 0x5888878>
  Chemical_start = <Martel.Expression.Seq instance at 0x58887a0>
  CitationSubset = <Martel.Expression.Seq instance at 0x5888e60>
  Coden = <Martel.Expression.Seq instance at 0x5880ab8>
  CollectionTitle = <Martel.Expression.Seq instance at 0x587eef0>
  CollectiveName = <Martel.Expression.Seq instance at 0x5878128>
  CommentIn = <Martel.Expression.Group instance at 0x5885cb0>
  CommentIn_end = <Martel.Expression.Seq instance at 0x5885c68>
  CommentIn_start = <Martel.Expression.Seq instance at 0x5885b90>
  CommentOn = <Martel.Expression.Group instance at 0x5885a28>
  CommentOn_end = <Martel.Expression.Seq instance at 0x58859e0>
  CommentOn_start = <Martel.Expression.Seq instance at 0x5885908>
  CommentsCorrections = <Martel.Expression.Group instance at 0x5...
  CommentsCorrections_end = <Martel.Expression.Seq instance at 0...
  CommentsCorrections_start = <Martel.Expression.Seq instance at...
  CopyrightInformation = <Martel.Expression.Seq instance at 0x58...
  Country = <Martel.Expression.Seq instance at 0x587fbd8>
  DataBank = <Martel.Expression.Group instance at 0x5883128>
  DataBankList = <Martel.Expression.Group instance at 0x58837e8>
  DataBankList_end = <Martel.Expression.Seq instance at 0x58837a0>
  DataBankList_start = <Martel.Expression.Seq instance at 0x5883...
  DataBankName = <Martel.Expression.Seq instance at 0x5884ea8>
  DataBank_end = <Martel.Expression.Seq instance at 0x58830e0>
  DataBank_start = <Martel.Expression.Seq instance at 0x5884fc8>
  DateCompleted = <Martel.Expression.Group instance at 0x588a560>
  DateCompleted_end = <Martel.Expression.Seq instance at 0x588a518>
  DateCompleted_start = <Martel.Expression.Seq instance at 0x588...
  DateCreated = <Martel.Expression.Group instance at 0x588a7e8>
  DateCreated_end = <Martel.Expression.Seq instance at 0x588a7a0>
  DateCreated_start = <Martel.Expression.Seq instance at 0x588a6c8>
  DateOfElectronicPublication = <Martel.Expression.Seq instance ...
  DateRevised = <Martel.Expression.Group instance at 0x588a2d8>
  DateRevised_end = <Martel.Expression.Seq instance at 0x588a290>
  DateRevised_start = <Martel.Expression.Seq instance at 0x588a1b8>
  Day = <Martel.Expression.Seq instance at 0x58789e0>
  DeleteCitation = <Martel.Expression.Group instance at 0x588b758>
  Descriptor = <Martel.Expression.Seq instance at 0x587bab8>
  EndPage = <Martel.Expression.Seq instance at 0x587c4d0>
  ErratumIn = <Martel.Expression.Group instance at 0x5885f38>
  ErratumIn_end = <Martel.Expression.Seq instance at 0x5885ef0>
  ErratumIn_start = <Martel.Expression.Seq instance at 0x5885e18>
  FirstName = <Martel.Expression.Seq instance at 0x58735a8>
  GeneSymbol = <Martel.Expression.Seq instance at 0x5887f38>
  GeneSymbolList = <Martel.Expression.Group instance at 0x5888170>
  GeneSymbolList_end = <Martel.Expression.Seq instance at 0x5888...
  GeneSymbolList_start = <Martel.Expression.Seq instance at 0x58...
  Grant = <Martel.Expression.Group instance at 0x5882f80>
  GrantID = <Martel.Expression.Seq instance at 0x5882878>
  GrantList = <Martel.Expression.Group instance at 0x5884680>
  GrantList_end = <Martel.Expression.Seq instance at 0x5884638>
  GrantList_start = <Martel.Expression.Seq instance at 0x58845a8>
  Grant_end = <Martel.Expression.Seq instance at 0x5882f38>
  Grant_start = <Martel.Expression.Seq instance at 0x5882e60>
  Hour = <Martel.Expression.Seq instance at 0x58790e0>
  ISOAbbreviation = <Martel.Expression.Seq instance at 0x5880878>
  ISSN = <Martel.Expression.Seq instance at 0x5882290>
  Initials = <Martel.Expression.Seq instance at 0x5873c68>
  Issue = <Martel.Expression.Seq instance at 0x5880cf8>
  Journal = <Martel.Expression.Group instance at 0x58825a8>
  JournalIssue = <Martel.Expression.Group instance at 0x5880f80>
  JournalIssue_end = <Martel.Expression.Seq instance at 0x5880f38>
  JournalIssue_start = <Martel.Expression.Seq instance at 0x5880...
  Journal_end = <Martel.Expression.Seq instance at 0x5882560>
  Journal_start = <Martel.Expression.Seq instance at 0x5882488>
  Keyword = <Martel.Expression.Seq instance at 0x58897a0>
  Language = <Martel.Expression.Seq instance at 0x587e0e0>
  LastName = <Martel.Expression.Seq instance at 0x5873a28>
  MedlineCitation = MedlineCitation
  MedlineCitationSet = <Martel.Expression.Group instance at 0x58...
  MedlineCitationSet_start = <Martel.Expression.Seq instance at ...
  MedlineCitation_end = <Martel.Expression.Seq instance at 0x588...
  MedlineCitation_start = <Martel.Expression.Seq instance at 0x5...
  MedlineCode = <Martel.Expression.Seq instance at 0x5880098>
  MedlineDate = <Martel.Expression.Seq instance at 0x5878e60>
  MedlineID = <Martel.Expression.Seq instance at 0x5885320>
  MedlineJournalInfo = <Martel.Expression.Group instance at 0x58...
  MedlineJournalInfo_end = <Martel.Expression.Seq instance at 0x...
  MedlineJournalInfo_start = <Martel.Expression.Seq instance at ...
  MedlinePgn = <Martel.Expression.Seq instance at 0x587c290>
  MedlineTA = <Martel.Expression.Seq instance at 0x587fe18>
  MeshHeading = <Martel.Expression.Group instance at 0x587bcb0>
  MeshHeadingList = <Martel.Expression.Group instance at 0x587bf38>
  MeshHeadingList_end = <Martel.Expression.Seq instance at 0x587...
  MeshHeadingList_start = <Martel.Expression.Seq instance at 0x5...
  MeshHeading_end = <Martel.Expression.Seq instance at 0x587bc68>
  MeshHeading_start = <Martel.Expression.Seq instance at 0x587bb90>
  MiddleName = <Martel.Expression.Seq instance at 0x58737e8>
  Minute = <Martel.Expression.Seq instance at 0x5879320>
  Month = <Martel.Expression.Seq instance at 0x58787a0>
  NCBIArticle = <Martel.Expression.Group instance at 0x5885050>
  NCBIArticle_end = <Martel.Expression.Seq instance at 0x5883fc8>
  NCBIArticle_start = <Martel.Expression.Seq instance at 0x5883ef0>
  NameOfSubstance = <Martel.Expression.Seq instance at 0x5888488>
  NlmUniqueID = <Martel.Expression.Seq instance at 0x5879b00>
  Note = <Martel.Expression.Seq instance at 0x5885560>
  NumberOfReferences = <Martel.Expression.Seq instance at 0x5887...
  OtherAbstract = <Martel.Expression.Group instance at 0x5889bd8>
  OtherAbstract_end = <Martel.Expression.Seq instance at 0x5889b90>
  OtherAbstract_start = <Martel.Expression.Seq instance at 0x588...
  PMID = <Martel.Expression.Seq instance at 0x5879d40>
  Pagination = <Martel.Expression.Group instance at 0x587c9e0>
  Pagination_end = <Martel.Expression.Seq instance at 0x587c998>
  Pagination_start = <Martel.Expression.Seq instance at 0x587c8c0>
  PersonalNameSubject = <Martel.Expression.Group instance at 0x5...
  PersonalNameSubjectList = <Martel.Expression.Group instance at...
  PersonalNameSubjectList_end = <Martel.Expression.Seq instance ...
  PersonalNameSubjectList_start = <Martel.Expression.Seq instanc...
  PersonalNameSubject_end = <Martel.Expression.Seq instance at 0...
  PersonalNameSubject_start = <Martel.Expression.Seq instance at...
  ProcurementSource = <Martel.Expression.Seq instance at 0x5889560>
  PubDate = <Martel.Expression.Group instance at 0x587f560>
  PubDate_end = <Martel.Expression.Seq instance at 0x587f518>
  PubDate_start = <Martel.Expression.Seq instance at 0x587f440>
  PublicationType = <Martel.Expression.Seq instance at 0x587e320>
  PublicationTypeList = <Martel.Expression.Group instance at 0x5...
  PublicationTypeList_end = <Martel.Expression.Seq instance at 0...
  PublicationTypeList_start = <Martel.Expression.Seq instance at...
  Publisher = <Martel.Expression.Seq instance at 0x587f3b0>
  RefSource = <Martel.Expression.Seq instance at 0x58857a0>
  RepublishedFrom = <Martel.Expression.Group instance at 0x5886200>
  RepublishedFrom_end = <Martel.Expression.Seq instance at 0x588...
  RepublishedFrom_start = <Martel.Expression.Seq instance at 0x5...
  RepublishedIn = <Martel.Expression.Group instance at 0x5886488>
  RepublishedIn_end = <Martel.Expression.Seq instance at 0x5886440>
  RepublishedIn_start = <Martel.Expression.Seq instance at 0x588...
  RetractionIn = <Martel.Expression.Group instance at 0x5886998>
  RetractionIn_end = <Martel.Expression.Seq instance at 0x5886950>
  RetractionIn_start = <Martel.Expression.Seq instance at 0x5886...
  RetractionOf = <Martel.Expression.Group instance at 0x5886710>
  RetractionOf_end = <Martel.Expression.Seq instance at 0x58866c8>
  RetractionOf_start = <Martel.Expression.Seq instance at 0x5886...
  Season = <Martel.Expression.Seq instance at 0x5878c20>
  Second = <Martel.Expression.Seq instance at 0x5879560>
  SpaceFlightMission = <Martel.Expression.Seq instance at 0x5889...
  SponsoringAgency = <Martel.Expression.Seq instance at 0x5889320>
  StartPage = <Martel.Expression.Seq instance at 0x587c710>
  SubHeading = <Martel.Expression.Seq instance at 0x587b440>
  Suffix = <Martel.Expression.Seq instance at 0x5873ea8>
  Title = <Martel.Expression.Seq instance at 0x587e830>
  UpdateIn = <Martel.Expression.Group instance at 0x5886c20>
  UpdateIn_end = <Martel.Expression.Seq instance at 0x5886bd8>
  UpdateIn_start = <Martel.Expression.Seq instance at 0x5886b00>
  UpdateOf = <Martel.Expression.Group instance at 0x5886ea8>
  UpdateOf_end = <Martel.Expression.Seq instance at 0x5886e60>
  UpdateOf_start = <Martel.Expression.Seq instance at 0x5886d88>
  VernacularTitle = <Martel.Expression.Seq instance at 0x587ecb0>
  Volume = <Martel.Expression.Seq instance at 0x587ea70>
  Year = <Martel.Expression.Seq instance at 0x5878560>
  __warningregistry__ = {('Bio.Medline.NLMMedlineXML was depreca...
  e = 'Second'
Function Details [hide private]

simple_elem(element, *attrs)

source code 

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.


Variables Details [hide private]

personal_name

Value:
LastName+ Opt(FirstName+ Opt(MiddleName))+ Opt(Initials)+ Opt(Suffix)

elements

Value:
['Year',
 'Month',
 'Day',
 'Season',
 'MedlineDate',
 'Hour',
 'Minute',
 'Second']

normal_date

Value:
Year+ Month+ Day+ Opt(Hour+ Opt(Minute+ Opt(Second)))

pub_date

Value:
Alt((Year+ Opt(Alt((Month+ Opt(Day)), Season))), MedlineDate)

DeleteCitation_start

Value:
Rep(space)+ Str("<DeleteCitation>")+ AnyEol()

DeleteCitation_end

Value:
Rep(space)+ Str("</DeleteCitation>")+ AnyEol()

MedlineCitationSet_end

Value:
Str("</MedlineCitationSet>")+ Opt(AnyEol())

header_format

Value:
Group("header", DOCTYPE+ MedlineCitationSet_start)

format

Value:
HeaderFooter(None, {}, header_format, RecordReader.Until, ("<MedlineCi\
tation>",), citation_format, RecordReader.EndsWith, ("</MedlineCitatio\
n>",), footer_format, RecordReader.Everything, (),)

AccessionNumberList

Value:
<Martel.Expression.Group instance at 0x5884bd8>

AccessionNumberList_end

Value:
<Martel.Expression.Seq instance at 0x5884b90>

AccessionNumberList_start

Value:
<Martel.Expression.Seq instance at 0x5884ab8>

AdditionalInformation

Value:
<Martel.Expression.Group instance at 0x588a098>

AdditionalInformation_end

Value:
<Martel.Expression.Seq instance at 0x588a050>

AdditionalInformation_start

Value:
<Martel.Expression.Seq instance at 0x5889f38>

ChemicalList_start

Value:
<Martel.Expression.Seq instance at 0x5888a28>

CommentsCorrections

Value:
<Martel.Expression.Group instance at 0x5887488>

CommentsCorrections_end

Value:
<Martel.Expression.Seq instance at 0x5887440>

CommentsCorrections_start

Value:
<Martel.Expression.Seq instance at 0x5887368>

CopyrightInformation

Value:
<Martel.Expression.Seq instance at 0x587ccf8>

DataBankList_start

Value:
<Martel.Expression.Seq instance at 0x5883710>

DateCompleted_start

Value:
<Martel.Expression.Seq instance at 0x588a440>

DateOfElectronicPublication

Value:
<Martel.Expression.Seq instance at 0x5880638>

GeneSymbolList_end

Value:
<Martel.Expression.Seq instance at 0x5888128>

GeneSymbolList_start

Value:
<Martel.Expression.Seq instance at 0x5888050>

JournalIssue_start

Value:
<Martel.Expression.Seq instance at 0x5880e60>

MedlineCitationSet

Value:
<Martel.Expression.Group instance at 0x588b9e0>

MedlineCitationSet_start

Value:
<Martel.Expression.Seq instance at 0x588b998>

MedlineCitation_end

Value:
<Martel.Expression.Seq instance at 0x588b200>

MedlineCitation_start

Value:
<Martel.Expression.Seq instance at 0x588b170>

MedlineJournalInfo

Value:
<Martel.Expression.Group instance at 0x58802d8>

MedlineJournalInfo_end

Value:
<Martel.Expression.Seq instance at 0x5880290>

MedlineJournalInfo_start

Value:
<Martel.Expression.Seq instance at 0x58801b8>

MeshHeadingList_end

Value:
<Martel.Expression.Seq instance at 0x587bef0>

MeshHeadingList_start

Value:
<Martel.Expression.Seq instance at 0x587be18>

NumberOfReferences

Value:
<Martel.Expression.Seq instance at 0x5887710>

OtherAbstract_start

Value:
<Martel.Expression.Seq instance at 0x5889ab8>

PersonalNameSubject

Value:
<Martel.Expression.Group instance at 0x5887908>

PersonalNameSubjectList

Value:
<Martel.Expression.Group instance at 0x5887cb0>

PersonalNameSubjectList_end

Value:
<Martel.Expression.Seq instance at 0x5887c68>

PersonalNameSubjectList_start

Value:
<Martel.Expression.Seq instance at 0x5887b48>

PersonalNameSubject_end

Value:
<Martel.Expression.Seq instance at 0x58878c0>

PersonalNameSubject_start

Value:
<Martel.Expression.Seq instance at 0x58877e8>

PublicationTypeList

Value:
<Martel.Expression.Group instance at 0x587e560>

PublicationTypeList_end

Value:
<Martel.Expression.Seq instance at 0x587e518>

PublicationTypeList_start

Value:
<Martel.Expression.Seq instance at 0x587e440>

RepublishedFrom_end

Value:
<Martel.Expression.Seq instance at 0x58861b8>

RepublishedFrom_start

Value:
<Martel.Expression.Seq instance at 0x58860e0>

RepublishedIn_start

Value:
<Martel.Expression.Seq instance at 0x5886368>

RetractionIn_start

Value:
<Martel.Expression.Seq instance at 0x5886878>

RetractionOf_start

Value:
<Martel.Expression.Seq instance at 0x58865f0>

SpaceFlightMission

Value:
<Martel.Expression.Seq instance at 0x58890e0>

__warningregistry__

Value:
{('Bio.Medline.NLMMedlineXML was deprecated, as it does not seem to be\
 able to parse recent Medline XML files. If you want to continue to us\
e this module, please get in contact with the Biopython developers at \
biopython-dev@biopython.org to avoid permanent removal of this module \
from Biopython',
  <type 'exceptions.DeprecationWarning'>,
  15): 1}