[Bioperl-guts-l] bioperl-live/scripts/biblio biblio.PLS,1.1,1.2

Martin Senger senger at pub.open-bio.org
Sat Jul 23 08:41:57 EDT 2005


Update of /home/repository/bioperl/bioperl-live/scripts/biblio
In directory pub.open-bio.org:/tmp/cvs-serv4247/scripts/biblio

Modified Files:
	biblio.PLS 
Log Message:
Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI


Index: biblio.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/biblio/biblio.PLS,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** biblio.PLS	3 Mar 2003 13:31:00 -0000	1.1
--- biblio.PLS	23 Jul 2005 12:41:55 -0000	1.2
***************
*** 12,18 ****
  #   retrieving citations from it.
  #
! #   Usage: biblio -h
  #
! #   senger at ebi.ac.uk
  #   February 2002
  #
--- 12,18 ----
  #   retrieving citations from it.
  #
! #   Usage: biblio.PLS -h
  #
! #   martin.senger at gmail.com
  #   February 2002
  #
***************
*** 283,287 ****
  =head1 NAME
  
! biblio - bioperl client for accessing and querying a bibliographic
  repository.
  
--- 283,287 ----
  =head1 NAME
  
! biblio.PLS - bioperl client for accessing and querying a bibliographic
  repository.
  
***************
*** 290,300 ****
  Usage:
  
!   biblio [vh]
!   biblio [bcFgOpq]         [-l <URL>]
!   biblio [abcdDeFknmOpqrs] [-l <URL>] -i <collection-ID>
!   biblio [abcdDeFknmOpqrs] [-l <URL>] - -find <keywords> \
           [-attrs <attrs>]...
!   biblio [Vq]              [-l <URL>]
!   biblio [FOq]             [-f <filename>]
  
  =head1 DESCRIPTION
--- 290,300 ----
  Usage:
  
!   biblio.PLS [vh]
!   biblio.PLS [bcFgOpq]         [-l <URL>]
!   biblio.PLS [abcdDeFknmOpqrs] [-l <URL>] -i <collection-ID>
!   biblio.PLS [abcdDeFknmOpqrs] [-l <URL>] - -find <keywords> \
           [-attrs <attrs>]...
!   biblio.PLS [Vq]              [-l <URL>]
!   biblio.PLS [FOq]             [-f <filename>]
  
  =head1 DESCRIPTION
***************
*** 317,321 ****
    -l <URL> ... a location where a Bibliographic Query service is
                 provided as a WebService
!                (default: http://industry.ebi.ac.uk/soap/openBQS)
  
  =head2 What query collection to use:
--- 317,321 ----
    -l <URL> ... a location where a Bibliographic Query service is
                 provided as a WebService
!                (default: http://www.ebi.ac.uk/openbqs/services/MedlineSRS)
  
  =head2 What query collection to use:
***************
*** 403,441 ****
  =head1 EXAMPLES
  
!   biblio -l http://localhost:8080/soap/servlet/rpcrouter -c
!   biblio - -find Java -attrs abstract -find perl
  
  Several separate invocations sharing the same query collection:
  
!   biblio -p -q - -find Brazma,Robinson > b.tmp
!   biblio -i `cat b.tmp` -d
!   MEDLINENEW/21583752
!   MEDLINE2002/20155445
!   MEDLINE2002/20431611
! 
!   biblio -i `cat b.tmp` -g MEDLINENEW/21583752
    <MedlineCitation Status="Completed">
-   <MedlineID>21583752</MedlineID>
     ...
    </MedlineCitation>
  
!   biblio -i `cat b.tmp` -e
    Exists: 1       Has next: 1
  
!   biblio -i `cat b.tmp` -D
    Destroyed OK.
  
!   biblio -i `cat b.tmp` -e
    Exists: 0       Has next: 0
  
  Access to controlled vocabularies:
  
!   biblio -Vn
!   MEDLINE2002/JournalArticle/properties
!   MEDLINE2002/Person/properties
!   MEDLINE2002/*/publication_type
!   ...
  
!   biblio -Vv::MEDLINE2002/JournalArticle/properties
    AllText
    ID
--- 403,444 ----
  =head1 EXAMPLES
  
!   biblio.PLS - -find Java -attrs abstract -find perl
  
  Several separate invocations sharing the same query collection:
  
!   biblio.PLS -p -q - -find Brazma,Robinson > b.tmp
!   biblio.PLS -i `cat b.tmp` -d
!   MEDLINE2005/10693778
!   MEDLINE2005/10977099
!   MEDLINE2005/11726920
!   MEDLINE2005/12225585
!   MEDLINE2005/12227734
!   biblio.PLS -i `cat b.tmp` -g 10693778
    <MedlineCitation Status="Completed">
     ...
    </MedlineCitation>
  
!   biblio.PLS -i `cat b.tmp` -e
    Exists: 1       Has next: 1
  
!   biblio.PLS -i `cat b.tmp` -D
    Destroyed OK.
  
!   biblio.PLS -i `cat b.tmp` -e
    Exists: 0       Has next: 0
  
  Access to controlled vocabularies:
  
!   biblio.PLS -Vn
!   MEDLINE2005/JournalArticle/properties
!   MEDLINENEW/resource_types
!   MEDLINE2005/resource_types
!   MEDLINE2005/Person/properties
!   MEDLINE2005/*/publication_type
!   MEDLINENEW/JournalArticle/properties
!   repository_subsets
!   MEDLINE2005/*/citation_subset
  
!   biblio.PLS -Vv::MEDLINE2005/JournalArticle/properties
    AllText
    ID
***************
*** 446,451 ****
  Converting local XML MEDLINE file:
  
!   biblio -f a_file.xml -Oo   ... to Perl objects
!   biblio -f a_file.xml -Or   ... as a raw hash
  
  =head1 ENVIRONMENT VARIABLES
--- 449,455 ----
  Converting local XML MEDLINE file:
  
!   biblio.PLS -g 10693778 > a_file.xml
!   biblio.PLS -f a_file.xml -Oo   ... to Perl objects
!   biblio.PLS -f a_file.xml -Or   ... as a raw hash
  
  =head1 ENVIRONMENT VARIABLES
***************
*** 457,461 ****
  
    export HTTPPROXY=http://128.243.220.41:3128
!   biblio -c
  
  =head1 FEEDBACK
--- 461,465 ----
  
    export HTTPPROXY=http://128.243.220.41:3128
!   biblio.PLS -c
  
  =head1 FEEDBACK
***************
*** 481,489 ****
  =head1 AUTHOR - Martin Senger
  
! Email senger at ebi.ac.uk
  
  =head1 HISTORY
  
  Written February 2002
  
  =cut
--- 485,494 ----
  =head1 AUTHOR - Martin Senger
  
! Email martin.senger at gmail.com
  
  =head1 HISTORY
  
  Written February 2002
+ Updated July 2005
  
  =cut



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