Package Bio :: Package Medline :: Module nlmmedline_011101_format
[hide private]
[frames] | no frames]

Module nlmmedline_011101_format

source code

nlmmedline_xml_format.py

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

http://www.nlm.nih.gov/databases/dtd/nlmmedline_011101.dtd http://www.nlm.nih.gov/databases/dtd/nlmmedlinecitation_011101.dtd http://www.nlm.nih.gov/databases/dtd/nlmcommon_011101.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(Alt(ForeName, FirstName+ Opt(Mid...
  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(Alt(PMID, 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 0x60205f0>
  AbstractText = <Martel.Expression.Seq instance at 0x60203b0>
  Abstract_end = <Martel.Expression.Seq instance at 0x60205a8>
  Abstract_start = <Martel.Expression.Seq instance at 0x60204d0>
  AccessionNumber = <Martel.Expression.Seq instance at 0x602aea8>
  AccessionNumberList = <Martel.Expression.Group instance at 0x6...
  AccessionNumberList_end = <Martel.Expression.Seq instance at 0...
  AccessionNumberList_start = <Martel.Expression.Seq instance at...
  Acronym = <Martel.Expression.Seq instance at 0x6029f80>
  Affiliation = <Martel.Expression.Seq instance at 0x60258c0>
  Agency = <Martel.Expression.Seq instance at 0x602a200>
  Article = <Martel.Expression.Group instance at 0x5854290>
  ArticleTitle = <Martel.Expression.Seq instance at 0x60265a8>
  Article_end = <Martel.Expression.Seq instance at 0x5854248>
  Article_start = <Martel.Expression.Seq instance at 0x5854170>
  Author = <Martel.Expression.Group instance at 0x6025b00>
  AuthorList = <Martel.Expression.Group instance at 0x6027200>
  AuthorList_end = <Martel.Expression.Seq instance at 0x60271b8>
  AuthorList_start = <Martel.Expression.Seq instance at 0x6027128>
  Author_end = <Martel.Expression.Seq instance at 0x6025ab8>
  Author_start = <Martel.Expression.Seq instance at 0x60259e0>
  Book = <Martel.Expression.Group instance at 0x6026d40>
  Book_end = <Martel.Expression.Seq instance at 0x6026cf8>
  Book_start = <Martel.Expression.Seq instance at 0x6026c20>
  CASRegistryNumber = <Martel.Expression.Seq instance at 0x5858200>
  Chemical = <Martel.Expression.Group instance at 0x5858680>
  ChemicalList = <Martel.Expression.Group instance at 0x5858908>
  ChemicalList_end = <Martel.Expression.Seq instance at 0x58588c0>
  ChemicalList_start = <Martel.Expression.Seq instance at 0x5858...
  Chemical_end = <Martel.Expression.Seq instance at 0x5858638>
  Chemical_start = <Martel.Expression.Seq instance at 0x5858560>
  CitationSubset = <Martel.Expression.Seq instance at 0x5858c20>
  Coden = <Martel.Expression.Seq instance at 0x6028f80>
  CollectionTitle = <Martel.Expression.Seq instance at 0x6026368>
  CollectiveName = <Martel.Expression.Seq instance at 0x601f710>
  CommentIn = <Martel.Expression.Group instance at 0x5855758>
  CommentIn_end = <Martel.Expression.Seq instance at 0x5855710>
  CommentIn_start = <Martel.Expression.Seq instance at 0x5855638>
  CommentOn = <Martel.Expression.Group instance at 0x58554d0>
  CommentOn_end = <Martel.Expression.Seq instance at 0x5855488>
  CommentOn_start = <Martel.Expression.Seq instance at 0x58553b0>
  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 0x60...
  Country = <Martel.Expression.Seq instance at 0x6028050>
  DataBank = <Martel.Expression.Group instance at 0x602b638>
  DataBankList = <Martel.Expression.Group instance at 0x602bcf8>
  DataBankList_end = <Martel.Expression.Seq instance at 0x602bcb0>
  DataBankList_start = <Martel.Expression.Seq instance at 0x602b...
  DataBankName = <Martel.Expression.Seq instance at 0x602b3f8>
  DataBank_end = <Martel.Expression.Seq instance at 0x602b5f0>
  DataBank_start = <Martel.Expression.Seq instance at 0x602b518>
  DateCompleted = <Martel.Expression.Group instance at 0x585ba70>
  DateCompleted_end = <Martel.Expression.Seq instance at 0x585ba28>
  DateCompleted_start = <Martel.Expression.Seq instance at 0x585...
  DateCreated = <Martel.Expression.Group instance at 0x585bcf8>
  DateCreated_end = <Martel.Expression.Seq instance at 0x585bcb0>
  DateCreated_start = <Martel.Expression.Seq instance at 0x585bbd8>
  DateOfElectronicPublication = <Martel.Expression.Seq instance ...
  DateRevised = <Martel.Expression.Group instance at 0x585b7e8>
  DateRevised_end = <Martel.Expression.Seq instance at 0x585b7a0>
  DateRevised_start = <Martel.Expression.Seq instance at 0x585b6c8>
  Day = <Martel.Expression.Seq instance at 0x6021050>
  DeleteCitation = <Martel.Expression.Group instance at 0x585e0e0>
  Descriptor = <Martel.Expression.Seq instance at 0x6023ef0>
  DescriptorName = <Martel.Expression.Seq instance at 0x60245a8>
  EndPage = <Martel.Expression.Seq instance at 0x6025098>
  ErratumIn = <Martel.Expression.Group instance at 0x58559e0>
  ErratumIn_end = <Martel.Expression.Seq instance at 0x5855998>
  ErratumIn_start = <Martel.Expression.Seq instance at 0x58558c0>
  FirstName = <Martel.Expression.Seq instance at 0x601c950>
  ForeName = <Martel.Expression.Seq instance at 0x601cb90>
  GeneSymbol = <Martel.Expression.Seq instance at 0x5857a70>
  GeneSymbolList = <Martel.Expression.Group instance at 0x5857c68>
  GeneSymbolList_end = <Martel.Expression.Seq instance at 0x5857...
  GeneSymbolList_start = <Martel.Expression.Seq instance at 0x58...
  GeneralNote = <Martel.Expression.Seq instance at 0x5859320>
  Grant = <Martel.Expression.Group instance at 0x602a4d0>
  GrantID = <Martel.Expression.Seq instance at 0x6029d40>
  GrantList = <Martel.Expression.Group instance at 0x602ab90>
  GrantList_end = <Martel.Expression.Seq instance at 0x602ab48>
  GrantList_start = <Martel.Expression.Seq instance at 0x602aab8>
  Grant_end = <Martel.Expression.Seq instance at 0x602a488>
  Grant_start = <Martel.Expression.Seq instance at 0x602a3b0>
  Hour = <Martel.Expression.Seq instance at 0x6021710>
  ISOAbbreviation = <Martel.Expression.Seq instance at 0x6028d40>
  ISSN = <Martel.Expression.Seq instance at 0x6029758>
  Initials = <Martel.Expression.Seq instance at 0x601f290>
  Investigator = <Martel.Expression.Group instance at 0x5859518>
  InvestigatorList = <Martel.Expression.Group instance at 0x5859...
  InvestigatorList_end = <Martel.Expression.Seq instance at 0x58...
  InvestigatorList_start = <Martel.Expression.Seq instance at 0x...
  Investigator_end = <Martel.Expression.Seq instance at 0x58594d0>
  Investigator_start = <Martel.Expression.Seq instance at 0x5859...
  Issue = <Martel.Expression.Seq instance at 0x6029200>
  Journal = <Martel.Expression.Group instance at 0x6029a70>
  JournalIssue = <Martel.Expression.Group instance at 0x6029488>
  JournalIssue_end = <Martel.Expression.Seq instance at 0x6029440>
  JournalIssue_start = <Martel.Expression.Seq instance at 0x6029...
  Journal_end = <Martel.Expression.Seq instance at 0x6029a28>
  Journal_start = <Martel.Expression.Seq instance at 0x6029950>
  Keyword = <Martel.Expression.Seq instance at 0x585c830>
  KeywordList = <Martel.Expression.Group instance at 0x585ce18>
  KeywordList_end = <Martel.Expression.Seq instance at 0x585cdd0>
  KeywordList_start = <Martel.Expression.Seq instance at 0x585cd40>
  Language = <Martel.Expression.Seq instance at 0x6027518>
  LastName = <Martel.Expression.Seq instance at 0x601f050>
  MedlineCitation = MedlineCitation
  MedlineCitationSet = <Martel.Expression.Group instance at 0x58...
  MedlineCitationSet_start = <Martel.Expression.Seq instance at ...
  MedlineCitation_end = <Martel.Expression.Seq instance at 0x585...
  MedlineCitation_start = <Martel.Expression.Seq instance at 0x5...
  MedlineCode = <Martel.Expression.Seq instance at 0x60284d0>
  MedlineDate = <Martel.Expression.Seq instance at 0x60214d0>
  MedlineID = <Martel.Expression.Seq instance at 0x5854830>
  MedlineJournalInfo = <Martel.Expression.Group instance at 0x60...
  MedlineJournalInfo_end = <Martel.Expression.Seq instance at 0x...
  MedlineJournalInfo_start = <Martel.Expression.Seq instance at ...
  MedlinePgn = <Martel.Expression.Seq instance at 0x6024e18>
  MedlineTA = <Martel.Expression.Seq instance at 0x6028290>
  MeshHeading = <Martel.Expression.Group instance at 0x6024878>
  MeshHeadingList = <Martel.Expression.Group instance at 0x6024b00>
  MeshHeadingList_end = <Martel.Expression.Seq instance at 0x602...
  MeshHeadingList_start = <Martel.Expression.Seq instance at 0x6...
  MeshHeading_end = <Martel.Expression.Seq instance at 0x6024830>
  MeshHeading_start = <Martel.Expression.Seq instance at 0x6024758>
  MiddleName = <Martel.Expression.Seq instance at 0x601cdd0>
  Minute = <Martel.Expression.Seq instance at 0x6021950>
  Month = <Martel.Expression.Seq instance at 0x601fdd0>
  NCBIArticle = <Martel.Expression.Group instance at 0x5854560>
  NCBIArticle_end = <Martel.Expression.Seq instance at 0x5854518>
  NCBIArticle_start = <Martel.Expression.Seq instance at 0x5854440>
  NameOfSubstance = <Martel.Expression.Seq instance at 0x5857f80>
  NlmUniqueID = <Martel.Expression.Seq instance at 0x60208c0>
  Note = <Martel.Expression.Seq instance at 0x5854a70>
  NumberOfReferences = <Martel.Expression.Seq instance at 0x5857...
  OriginalReportIn = <Martel.Expression.Group instance at 0x5854...
  OriginalReportIn_end = <Martel.Expression.Seq instance at 0x58...
  OriginalReportIn_start = <Martel.Expression.Seq instance at 0x...
  OtherAbstract = <Martel.Expression.Group instance at 0x585b5a8>
  OtherAbstract_end = <Martel.Expression.Seq instance at 0x585b560>
  OtherAbstract_start = <Martel.Expression.Seq instance at 0x585...
  OtherID = <Martel.Expression.Seq instance at 0x5859f38>
  PMID = <Martel.Expression.Seq instance at 0x6020b00>
  Pagination = <Martel.Expression.Group instance at 0x60255a8>
  Pagination_end = <Martel.Expression.Seq instance at 0x6025560>
  Pagination_start = <Martel.Expression.Seq instance at 0x6025488>
  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...
  PubDate = <Martel.Expression.Group instance at 0x6026998>
  PubDate_end = <Martel.Expression.Seq instance at 0x6026950>
  PubDate_start = <Martel.Expression.Seq instance at 0x6026878>
  PublicationType = <Martel.Expression.Seq instance at 0x6027758>
  PublicationTypeList = <Martel.Expression.Group instance at 0x6...
  PublicationTypeList_end = <Martel.Expression.Seq instance at 0...
  PublicationTypeList_start = <Martel.Expression.Seq instance at...
  Publisher = <Martel.Expression.Seq instance at 0x60267e8>
  QualifierName = <Martel.Expression.Seq instance at 0x6023878>
  RefSource = <Martel.Expression.Seq instance at 0x5854cb0>
  RegistryNumber = <Martel.Expression.Seq instance at 0x5858440>
  RepublishedFrom = <Martel.Expression.Group instance at 0x5855c68>
  RepublishedFrom_end = <Martel.Expression.Seq instance at 0x585...
  RepublishedFrom_start = <Martel.Expression.Seq instance at 0x5...
  RepublishedIn = <Martel.Expression.Group instance at 0x5855ef0>
  RepublishedIn_end = <Martel.Expression.Seq instance at 0x5855ea8>
  RepublishedIn_start = <Martel.Expression.Seq instance at 0x585...
  RetractionIn = <Martel.Expression.Group instance at 0x5856440>
  RetractionIn_end = <Martel.Expression.Seq instance at 0x58563f8>
  RetractionIn_start = <Martel.Expression.Seq instance at 0x5856...
  RetractionOf = <Martel.Expression.Group instance at 0x58561b8>
  RetractionOf_end = <Martel.Expression.Seq instance at 0x5856170>
  RetractionOf_start = <Martel.Expression.Seq instance at 0x5856...
  Season = <Martel.Expression.Seq instance at 0x6021290>
  Second = <Martel.Expression.Seq instance at 0x6021b90>
  SpaceFlightMission = <Martel.Expression.Seq instance at 0x585c...
  StartPage = <Martel.Expression.Seq instance at 0x60252d8>
  SubHeading = <Martel.Expression.Seq instance at 0x6023200>
  Suffix = <Martel.Expression.Seq instance at 0x601f4d0>
  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 0x6027c68>
  UpdateIn = <Martel.Expression.Group instance at 0x58566c8>
  UpdateIn_end = <Martel.Expression.Seq instance at 0x5856680>
  UpdateIn_start = <Martel.Expression.Seq instance at 0x58565a8>
  UpdateOf = <Martel.Expression.Group instance at 0x5856950>
  UpdateOf_end = <Martel.Expression.Seq instance at 0x5856908>
  UpdateOf_start = <Martel.Expression.Seq instance at 0x5856830>
  VernacularTitle = <Martel.Expression.Seq instance at 0x6026128>
  Volume = <Martel.Expression.Seq instance at 0x6027ea8>
  Year = <Martel.Expression.Seq instance at 0x601fb90>
  __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(Alt(ForeName, 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 0x602b128>

AccessionNumberList_end

Value:
<Martel.Expression.Seq instance at 0x602b0e0>

AccessionNumberList_start

Value:
<Martel.Expression.Seq instance at 0x602afc8>

ChemicalList_start

Value:
<Martel.Expression.Seq instance at 0x58587e8>

CommentsCorrections

Value:
<Martel.Expression.Group instance at 0x5856f80>

CommentsCorrections_end

Value:
<Martel.Expression.Seq instance at 0x5856f38>

CommentsCorrections_start

Value:
<Martel.Expression.Seq instance at 0x5856e60>

CopyrightInformation

Value:
<Martel.Expression.Seq instance at 0x6020170>

DataBankList_start

Value:
<Martel.Expression.Seq instance at 0x602bc20>

DateCompleted_start

Value:
<Martel.Expression.Seq instance at 0x585b950>

DateOfElectronicPublication

Value:
<Martel.Expression.Seq instance at 0x6028b00>

GeneSymbolList_end

Value:
<Martel.Expression.Seq instance at 0x5857c20>

GeneSymbolList_start

Value:
<Martel.Expression.Seq instance at 0x5857b48>

InvestigatorList

Value:
<Martel.Expression.Group instance at 0x58597a0>

InvestigatorList_end

Value:
<Martel.Expression.Seq instance at 0x5859758>

InvestigatorList_start

Value:
<Martel.Expression.Seq instance at 0x5859680>

Investigator_start

Value:
<Martel.Expression.Seq instance at 0x58593f8>

JournalIssue_start

Value:
<Martel.Expression.Seq instance at 0x6029368>

MedlineCitationSet

Value:
<Martel.Expression.Group instance at 0x585e368>

MedlineCitationSet_start

Value:
<Martel.Expression.Seq instance at 0x585e320>

MedlineCitation_end

Value:
<Martel.Expression.Seq instance at 0x585db48>

MedlineCitation_start

Value:
<Martel.Expression.Seq instance at 0x585dab8>

MedlineJournalInfo

Value:
<Martel.Expression.Group instance at 0x60287a0>

MedlineJournalInfo_end

Value:
<Martel.Expression.Seq instance at 0x6028758>

MedlineJournalInfo_start

Value:
<Martel.Expression.Seq instance at 0x6028680>

MeshHeadingList_end

Value:
<Martel.Expression.Seq instance at 0x6024ab8>

MeshHeadingList_start

Value:
<Martel.Expression.Seq instance at 0x60249e0>

NumberOfReferences

Value:
<Martel.Expression.Seq instance at 0x5857248>

OriginalReportIn

Value:
<Martel.Expression.Group instance at 0x5854f80>

OriginalReportIn_end

Value:
<Martel.Expression.Seq instance at 0x5854f38>

OriginalReportIn_start

Value:
<Martel.Expression.Seq instance at 0x5854e60>

OtherAbstract_start

Value:
<Martel.Expression.Seq instance at 0x585b4d0>

PersonalNameSubject

Value:
<Martel.Expression.Group instance at 0x5857440>

PersonalNameSubjectList

Value:
<Martel.Expression.Group instance at 0x58577e8>

PersonalNameSubjectList_end

Value:
<Martel.Expression.Seq instance at 0x58577a0>

PersonalNameSubjectList_start

Value:
<Martel.Expression.Seq instance at 0x5857680>

PersonalNameSubject_end

Value:
<Martel.Expression.Seq instance at 0x58573f8>

PersonalNameSubject_start

Value:
<Martel.Expression.Seq instance at 0x5857320>

PublicationTypeList

Value:
<Martel.Expression.Group instance at 0x6027998>

PublicationTypeList_end

Value:
<Martel.Expression.Seq instance at 0x6027950>

PublicationTypeList_start

Value:
<Martel.Expression.Seq instance at 0x6027878>

RepublishedFrom_end

Value:
<Martel.Expression.Seq instance at 0x5855c20>

RepublishedFrom_start

Value:
<Martel.Expression.Seq instance at 0x5855b48>

RepublishedIn_start

Value:
<Martel.Expression.Seq instance at 0x5855dd0>

RetractionIn_start

Value:
<Martel.Expression.Seq instance at 0x5856320>

RetractionOf_start

Value:
<Martel.Expression.Seq instance at 0x5856098>

SpaceFlightMission

Value:
<Martel.Expression.Seq instance at 0x585c170>

SummaryForPatientsIn

Value:
<Martel.Expression.Group instance at 0x5855290>

SummaryForPatientsIn_end

Value:
<Martel.Expression.Seq instance at 0x5855248>

SummaryForPatientsIn_start

Value:
<Martel.Expression.Seq instance at 0x5855170>

__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'>,
  16): 1}