Package Bio :: Package Medline :: Module nlmmedline_010319_format
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Module nlmmedline_010319_format

source code

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.

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.Co...
  Abstract = <Martel.Expression.Group instance at 0x5ff2830>
  AbstractText = <Martel.Expression.Seq instance at 0x5ff25f0>
  Abstract_end = <Martel.Expression.Seq instance at 0x5ff27e8>
  Abstract_start = <Martel.Expression.Seq instance at 0x5ff2710>
  AccessionNumber = <Martel.Expression.Seq instance at 0x5ff9368>
  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 0x5ffa440>
  Affiliation = <Martel.Expression.Seq instance at 0x5ff3cf8>
  Agency = <Martel.Expression.Seq instance at 0x5ffa680>
  Article = <Martel.Expression.Group instance at 0x5ffb758>
  ArticleTitle = <Martel.Expression.Seq instance at 0x5ff6a28>
  Article_end = <Martel.Expression.Seq instance at 0x5ffb710>
  Article_start = <Martel.Expression.Seq instance at 0x5ffb638>
  Author = <Martel.Expression.Group instance at 0x5ff3f38>
  AuthorList = <Martel.Expression.Group instance at 0x5ff5638>
  AuthorList_end = <Martel.Expression.Seq instance at 0x5ff55f0>
  AuthorList_start = <Martel.Expression.Seq instance at 0x5ff5560>
  Author_end = <Martel.Expression.Seq instance at 0x5ff3ef0>
  Author_start = <Martel.Expression.Seq instance at 0x5ff3e18>
  Book = <Martel.Expression.Group instance at 0x5ff7200>
  Book_end = <Martel.Expression.Seq instance at 0x5ff71b8>
  Book_start = <Martel.Expression.Seq instance at 0x5ff70e0>
  CASRegistryNumber = <Martel.Expression.Seq instance at 0x5fff7e8>
  Chemical = <Martel.Expression.Group instance at 0x5fff9e0>
  ChemicalList = <Martel.Expression.Group instance at 0x5fffc68>
  ChemicalList_end = <Martel.Expression.Seq instance at 0x5fffc20>
  ChemicalList_start = <Martel.Expression.Seq instance at 0x5fff...
  Chemical_end = <Martel.Expression.Seq instance at 0x5fff998>
  Chemical_start = <Martel.Expression.Seq instance at 0x5fff8c0>
  CitationSubset = <Martel.Expression.Seq instance at 0x5ffff80>
  Coden = <Martel.Expression.Seq instance at 0x5ff8440>
  CollectionTitle = <Martel.Expression.Seq instance at 0x5ff67e8>
  CollectiveName = <Martel.Expression.Seq instance at 0x5ff0998>
  CommentIn = <Martel.Expression.Group instance at 0x5ffdc20>
  CommentIn_end = <Martel.Expression.Seq instance at 0x5ffdbd8>
  CommentIn_start = <Martel.Expression.Seq instance at 0x5ffdb00>
  CommentOn = <Martel.Expression.Group instance at 0x5ffd998>
  CommentOn_end = <Martel.Expression.Seq instance at 0x5ffd950>
  CommentOn_start = <Martel.Expression.Seq instance at 0x5ffd878>
  CommentsCorrections = <Martel.Expression.Group instance at 0x6...
  CommentsCorrections_end = <Martel.Expression.Seq instance at 0...
  CommentsCorrections_start = <Martel.Expression.Seq instance at...
  CopyrightInformation = <Martel.Expression.Seq instance at 0x5f...
  Country = <Martel.Expression.Seq instance at 0x5ff74d0>
  DataBank = <Martel.Expression.Group instance at 0x5ff9b00>
  DataBankList = <Martel.Expression.Group instance at 0x5ffb200>
  DataBankList_end = <Martel.Expression.Seq instance at 0x5ffb1b8>
  DataBankList_start = <Martel.Expression.Seq instance at 0x5ffb...
  DataBankName = <Martel.Expression.Seq instance at 0x5ff98c0>
  DataBank_end = <Martel.Expression.Seq instance at 0x5ff9ab8>
  DataBank_start = <Martel.Expression.Seq instance at 0x5ff99e0>
  DateCompleted = <Martel.Expression.Group instance at 0x6006dd0>
  DateCompleted_end = <Martel.Expression.Seq instance at 0x6006d88>
  DateCompleted_start = <Martel.Expression.Seq instance at 0x600...
  DateCreated = <Martel.Expression.Group instance at 0x6004098>
  DateCreated_end = <Martel.Expression.Seq instance at 0x6004050>
  DateCreated_start = <Martel.Expression.Seq instance at 0x6006f38>
  DateOfElectronicPublication = <Martel.Expression.Seq instance ...
  DateRevised = <Martel.Expression.Group instance at 0x6006b48>
  DateRevised_end = <Martel.Expression.Seq instance at 0x6006b00>
  DateRevised_start = <Martel.Expression.Seq instance at 0x6006a28>
  Day = <Martel.Expression.Seq instance at 0x5ff1290>
  DeleteCitation = <Martel.Expression.Group instance at 0x6005170>
  Descriptor = <Martel.Expression.Seq instance at 0x5ff4ab8>
  EndPage = <Martel.Expression.Seq instance at 0x5ff34d0>
  ErratumIn = <Martel.Expression.Group instance at 0x5ffdea8>
  ErratumIn_end = <Martel.Expression.Seq instance at 0x5ffde60>
  ErratumIn_start = <Martel.Expression.Seq instance at 0x5ffdd88>
  FirstName = <Martel.Expression.Seq instance at 0x6012e18>
  GeneSymbol = <Martel.Expression.Seq instance at 0x5fff098>
  GeneSymbolList = <Martel.Expression.Group instance at 0x5fff290>
  GeneSymbolList_end = <Martel.Expression.Seq instance at 0x5fff...
  GeneSymbolList_start = <Martel.Expression.Seq instance at 0x5f...
  GeneralNote = <Martel.Expression.Seq instance at 0x6002680>
  Grant = <Martel.Expression.Group instance at 0x5ffa950>
  GrantID = <Martel.Expression.Seq instance at 0x5ffa200>
  GrantList = <Martel.Expression.Group instance at 0x5ff9050>
  GrantList_end = <Martel.Expression.Seq instance at 0x5ffafc8>
  GrantList_start = <Martel.Expression.Seq instance at 0x5ffaf38>
  Grant_end = <Martel.Expression.Seq instance at 0x5ffa908>
  Grant_start = <Martel.Expression.Seq instance at 0x5ffa830>
  Hour = <Martel.Expression.Seq instance at 0x5ff1950>
  ISOAbbreviation = <Martel.Expression.Seq instance at 0x5ff8200>
  ISSN = <Martel.Expression.Seq instance at 0x5ff8bd8>
  Initials = <Martel.Expression.Seq instance at 0x5ff0518>
  Investigator = <Martel.Expression.Group instance at 0x6002878>
  InvestigatorList = <Martel.Expression.Group instance at 0x6002...
  InvestigatorList_end = <Martel.Expression.Seq instance at 0x60...
  InvestigatorList_start = <Martel.Expression.Seq instance at 0x...
  Investigator_end = <Martel.Expression.Seq instance at 0x6002830>
  Investigator_start = <Martel.Expression.Seq instance at 0x6002...
  Issue = <Martel.Expression.Seq instance at 0x5ff8680>
  Journal = <Martel.Expression.Group instance at 0x5ff8ef0>
  JournalIssue = <Martel.Expression.Group instance at 0x5ff8908>
  JournalIssue_end = <Martel.Expression.Seq instance at 0x5ff88c0>
  JournalIssue_start = <Martel.Expression.Seq instance at 0x5ff8...
  Journal_end = <Martel.Expression.Seq instance at 0x5ff8ea8>
  Journal_start = <Martel.Expression.Seq instance at 0x5ff8dd0>
  Keyword = <Martel.Expression.Seq instance at 0x6003b90>
  KeywordList = <Martel.Expression.Group instance at 0x60061b8>
  KeywordList_end = <Martel.Expression.Seq instance at 0x6006170>
  KeywordList_start = <Martel.Expression.Seq instance at 0x60060e0>
  Language = <Martel.Expression.Seq instance at 0x5ff5950>
  LastName = <Martel.Expression.Seq instance at 0x5ff02d8>
  MedlineCitation = MedlineCitation
  MedlineCitationSet = <Martel.Expression.Group instance at 0x60...
  MedlineCitationSet_start = <Martel.Expression.Seq instance at ...
  MedlineCitation_end = <Martel.Expression.Seq instance at 0x600...
  MedlineCitation_start = <Martel.Expression.Seq instance at 0x6...
  MedlineCode = <Martel.Expression.Seq instance at 0x5ff7950>
  MedlineDate = <Martel.Expression.Seq instance at 0x5ff1710>
  MedlineID = <Martel.Expression.Seq instance at 0x5ffbcf8>
  MedlineJournalInfo = <Martel.Expression.Group instance at 0x5f...
  MedlineJournalInfo_end = <Martel.Expression.Seq instance at 0x...
  MedlineJournalInfo_start = <Martel.Expression.Seq instance at ...
  MedlinePgn = <Martel.Expression.Seq instance at 0x5ff3290>
  MedlineTA = <Martel.Expression.Seq instance at 0x5ff7710>
  MeshHeading = <Martel.Expression.Group instance at 0x5ff4cb0>
  MeshHeadingList = <Martel.Expression.Group instance at 0x5ff4f38>
  MeshHeadingList_end = <Martel.Expression.Seq instance at 0x5ff...
  MeshHeadingList_start = <Martel.Expression.Seq instance at 0x5...
  MeshHeading_end = <Martel.Expression.Seq instance at 0x5ff4c68>
  MeshHeading_start = <Martel.Expression.Seq instance at 0x5ff4b90>
  MiddleName = <Martel.Expression.Seq instance at 0x5ff0098>
  Minute = <Martel.Expression.Seq instance at 0x5ff1b90>
  Month = <Martel.Expression.Seq instance at 0x5ff1050>
  NCBIArticle = <Martel.Expression.Group instance at 0x5ffba28>
  NCBIArticle_end = <Martel.Expression.Seq instance at 0x5ffb9e0>
  NCBIArticle_start = <Martel.Expression.Seq instance at 0x5ffb908>
  NameOfSubstance = <Martel.Expression.Seq instance at 0x5fff5a8>
  NlmUniqueID = <Martel.Expression.Seq instance at 0x5ff2b00>
  Note = <Martel.Expression.Seq instance at 0x5ffbf38>
  NumberOfReferences = <Martel.Expression.Seq instance at 0x6000...
  OriginalReportIn = <Martel.Expression.Group instance at 0x5ffd...
  OriginalReportIn_end = <Martel.Expression.Seq instance at 0x5f...
  OriginalReportIn_start = <Martel.Expression.Seq instance at 0x...
  OtherAbstract = <Martel.Expression.Group instance at 0x6006908>
  OtherAbstract_end = <Martel.Expression.Seq instance at 0x60068c0>
  OtherAbstract_start = <Martel.Expression.Seq instance at 0x600...
  OtherID = <Martel.Expression.Seq instance at 0x60032d8>
  PMID = <Martel.Expression.Seq instance at 0x5ff2d40>
  Pagination = <Martel.Expression.Group instance at 0x5ff39e0>
  Pagination_end = <Martel.Expression.Seq instance at 0x5ff3998>
  Pagination_start = <Martel.Expression.Seq instance at 0x5ff38c0>
  PersonalNameSubject = <Martel.Expression.Group instance at 0x6...
  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...
  PubDate = <Martel.Expression.Group instance at 0x5ff6e18>
  PubDate_end = <Martel.Expression.Seq instance at 0x5ff6dd0>
  PubDate_start = <Martel.Expression.Seq instance at 0x5ff6cf8>
  PublicationType = <Martel.Expression.Seq instance at 0x5ff5b90>
  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 0x5ff6c68>
  RefSource = <Martel.Expression.Seq instance at 0x5ffd1b8>
  RepublishedFrom = <Martel.Expression.Group instance at 0x5ffe170>
  RepublishedFrom_end = <Martel.Expression.Seq instance at 0x5ff...
  RepublishedFrom_start = <Martel.Expression.Seq instance at 0x5...
  RepublishedIn = <Martel.Expression.Group instance at 0x5ffe3f8>
  RepublishedIn_end = <Martel.Expression.Seq instance at 0x5ffe3b0>
  RepublishedIn_start = <Martel.Expression.Seq instance at 0x5ff...
  RetractionIn = <Martel.Expression.Group instance at 0x5ffe908>
  RetractionIn_end = <Martel.Expression.Seq instance at 0x5ffe8c0>
  RetractionIn_start = <Martel.Expression.Seq instance at 0x5ffe...
  RetractionOf = <Martel.Expression.Group instance at 0x5ffe680>
  RetractionOf_end = <Martel.Expression.Seq instance at 0x5ffe638>
  RetractionOf_start = <Martel.Expression.Seq instance at 0x5ffe...
  Season = <Martel.Expression.Seq instance at 0x5ff14d0>
  Second = <Martel.Expression.Seq instance at 0x5ff1dd0>
  SpaceFlightMission = <Martel.Expression.Seq instance at 0x6003...
  StartPage = <Martel.Expression.Seq instance at 0x5ff3710>
  SubHeading = <Martel.Expression.Seq instance at 0x5ff4440>
  Suffix = <Martel.Expression.Seq instance at 0x5ff0758>
  SummaryForPatientsIn = <Martel.Expression.Group instance at 0x...
  SummaryForPatientsIn_end = <Martel.Expression.Seq instance at ...
  SummaryForPatientsIn_start = <Martel.Expression.Seq instance a...
  Title = <Martel.Expression.Seq instance at 0x5ff6128>
  UpdateIn = <Martel.Expression.Group instance at 0x5ffeb90>
  UpdateIn_end = <Martel.Expression.Seq instance at 0x5ffeb48>
  UpdateIn_start = <Martel.Expression.Seq instance at 0x5ffea70>
  UpdateOf = <Martel.Expression.Group instance at 0x5ffee18>
  UpdateOf_end = <Martel.Expression.Seq instance at 0x5ffedd0>
  UpdateOf_start = <Martel.Expression.Seq instance at 0x5ffecf8>
  VernacularTitle = <Martel.Expression.Seq instance at 0x5ff65a8>
  Volume = <Martel.Expression.Seq instance at 0x5ff6368>
  Year = <Martel.Expression.Seq instance at 0x5ff0dd0>
  __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.CountLines, (4,), c\
itation_format, RecordReader.EndsWith, ("</MedlineCitation>",), footer\
_format, RecordReader.Everything, (),)

AccessionNumberList

Value:
<Martel.Expression.Group instance at 0x5ff95a8>

AccessionNumberList_end

Value:
<Martel.Expression.Seq instance at 0x5ff9560>

AccessionNumberList_start

Value:
<Martel.Expression.Seq instance at 0x5ff9488>

ChemicalList_start

Value:
<Martel.Expression.Seq instance at 0x5fffb48>

CommentsCorrections

Value:
<Martel.Expression.Group instance at 0x6000488>

CommentsCorrections_end

Value:
<Martel.Expression.Seq instance at 0x6000440>

CommentsCorrections_start

Value:
<Martel.Expression.Seq instance at 0x6000368>

CopyrightInformation

Value:
<Martel.Expression.Seq instance at 0x5ff23b0>

DataBankList_start

Value:
<Martel.Expression.Seq instance at 0x5ffb128>

DateCompleted_start

Value:
<Martel.Expression.Seq instance at 0x6006cb0>

DateOfElectronicPublication

Value:
<Martel.Expression.Seq instance at 0x5ff7f80>

GeneSymbolList_end

Value:
<Martel.Expression.Seq instance at 0x5fff248>

GeneSymbolList_start

Value:
<Martel.Expression.Seq instance at 0x5fff170>

InvestigatorList

Value:
<Martel.Expression.Group instance at 0x6002b00>

InvestigatorList_end

Value:
<Martel.Expression.Seq instance at 0x6002ab8>

InvestigatorList_start

Value:
<Martel.Expression.Seq instance at 0x60029e0>

Investigator_start

Value:
<Martel.Expression.Seq instance at 0x6002758>

JournalIssue_start

Value:
<Martel.Expression.Seq instance at 0x5ff87e8>

MedlineCitationSet

Value:
<Martel.Expression.Group instance at 0x60053f8>

MedlineCitationSet_start

Value:
<Martel.Expression.Seq instance at 0x60053b0>

MedlineCitation_end

Value:
<Martel.Expression.Seq instance at 0x6004bd8>

MedlineCitation_start

Value:
<Martel.Expression.Seq instance at 0x6004b48>

MedlineJournalInfo

Value:
<Martel.Expression.Group instance at 0x5ff7c20>

MedlineJournalInfo_end

Value:
<Martel.Expression.Seq instance at 0x5ff7bd8>

MedlineJournalInfo_start

Value:
<Martel.Expression.Seq instance at 0x5ff7b00>

MeshHeadingList_end

Value:
<Martel.Expression.Seq instance at 0x5ff4ef0>

MeshHeadingList_start

Value:
<Martel.Expression.Seq instance at 0x5ff4e18>

NumberOfReferences

Value:
<Martel.Expression.Seq instance at 0x6000758>

OriginalReportIn

Value:
<Martel.Expression.Group instance at 0x5ffd440>

OriginalReportIn_end

Value:
<Martel.Expression.Seq instance at 0x5ffd3f8>

OriginalReportIn_start

Value:
<Martel.Expression.Seq instance at 0x5ffd320>

OtherAbstract_start

Value:
<Martel.Expression.Seq instance at 0x6006830>

PersonalNameSubject

Value:
<Martel.Expression.Group instance at 0x6000950>

PersonalNameSubjectList

Value:
<Martel.Expression.Group instance at 0x6000d40>

PersonalNameSubjectList_end

Value:
<Martel.Expression.Seq instance at 0x6000cf8>

PersonalNameSubjectList_start

Value:
<Martel.Expression.Seq instance at 0x6000bd8>

PersonalNameSubject_end

Value:
<Martel.Expression.Seq instance at 0x6000908>

PersonalNameSubject_start

Value:
<Martel.Expression.Seq instance at 0x6000830>

PublicationTypeList

Value:
<Martel.Expression.Group instance at 0x5ff5dd0>

PublicationTypeList_end

Value:
<Martel.Expression.Seq instance at 0x5ff5d88>

PublicationTypeList_start

Value:
<Martel.Expression.Seq instance at 0x5ff5cb0>

RepublishedFrom_end

Value:
<Martel.Expression.Seq instance at 0x5ffe128>

RepublishedFrom_start

Value:
<Martel.Expression.Seq instance at 0x5ffe050>

RepublishedIn_start

Value:
<Martel.Expression.Seq instance at 0x5ffe2d8>

RetractionIn_start

Value:
<Martel.Expression.Seq instance at 0x5ffe7e8>

RetractionOf_start

Value:
<Martel.Expression.Seq instance at 0x5ffe560>

SpaceFlightMission

Value:
<Martel.Expression.Seq instance at 0x60034d0>

SummaryForPatientsIn

Value:
<Martel.Expression.Group instance at 0x5ffd710>

SummaryForPatientsIn_end

Value:
<Martel.Expression.Seq instance at 0x5ffd6c8>

SummaryForPatientsIn_start

Value:
<Martel.Expression.Seq instance at 0x5ffd5f0>

__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}