Gerstein Lab Publications
Main By Subject By Grant Pre-1997 Medline Scripts & XML Search Other Links

Papers Page Documentation

Main Directories, Scripts and Content

Papers Template

Password-protected directory on the server containing scripts for generating the papers site.

Important Files

Update Grid and Forms

Other Files

downloadMEDLINE.cgi

See also: downloadXML.cgi.

downloadXML.cgi

edit.cgi

Update Grid and Forms

Contains:

The Update Grid and Forms are made to update the papers page from the papers website.

See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

editform.html

  • Form to Create a new E-print.
  • Calls formupdate.cgi

    • See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

    formupdate.cgi

    See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

    grid.html

    See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

    grid.pl

    See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

    Individual Directory

    See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

    indvupdate.cgi

    - Called from /web/papers/individual/[labid].html.
    - Updates existing e-print citation.xml files with information from individual forms in "individual" directory.

    See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

    update.cgi

    See also: editform.html, formupdate.cgi, grid.html, Individual Directory, indvupdate.cgi, and update.cgi.

    importEprint.sh

    See also: papers.cgi and skel

    papers.cgi

    Most important papers people will use, simply invokes other scripts.

    See also: papers.pl and importEprint.sh

    papers.pl

    NOTE: DownloadXML.cgi : /web/papers_template/DownloadXML.cgi must be run at least once before running this script

    See also: papers-tags.htm, papers-ids.htm, papers.xml, Grants, Subjects and papers-simple.html

    rollback.cgi

    Papers

    Contains:

    See also: Grant Directory, Subject Directory, skel Directory, papers-simple.htm, papers-tags.htm, and update.cgi.

    Grant Directory

    See also: Subject Directory

    index.html

    index-all.html

    Lab Papers

  • Individual directories [labid] that contain an index.html file and an index-all.html file.
  • The index.html file is short version of the index-all.html file, displaying the Title, Authors, and links to the website, pre-print, and medline.
  • The index-all.html file displays the contents of the paper's citation file as well the information from the index.html file.

    • links.html

    NCBIData.xml

    Papers before 1997

    - The html, xml, and simple html file for papers before 1997.

    papers-ids.htm

    papers-simple.html

    papers-tags.htm

     

  • A compilation of all citation files.

    • papers.xml

    Skel Directory

  • A directory containing folders [labid] each with a citation.xml file. This is used to generate papers.xml in papers.pl as well as the update grid.

    • Subject Directory

    E-print

    Details of the Updating papers process

    Root directory: /web/papers

    In order performed:
    -------------------------------------------------------------------------------------------------------------
    Update Papers Calls : Papers.cgi: /web/papers_template/papers.cgi
    -------------------------------------------------------------------------------------------------------------
    Creates copies of help folders, citation examples, copy of scripts in /web/papers
    -------------------------------------------------------------------------------------------------------------

    - Copies 1) /web/papers_template/html 2) .xml files in papers_template to /web/papers

    - Copies 1) /web/papers_template/scripts 2) /web/papers_template/helpto /web/papers/xml

    -------------------------------------------------------------------------------------------------------------
    Calls ImportEprint.sh : /web/papers_template/ImportEprint.sh
    -------------------------------------------------------------------------------------------------------------
    ImportEprint.sh backs up the old skel directory containing the citation.xml files, and copies the updated files from the e-print directory to the skel directory

    -Deletes old skel directory
    - Creates new skel directory and Copies over all citation files from e-print directory

    -------------------------------------------------------------------------------------------------------------
    Calls papers.pl : /web/papers_template/papers.pl
    -------------------------------------------------------------------------------------------------------------

    NOTE: DownloadXML.cgi : /web/papers_template/DownloadXML.cgi must be run at least once before running this script

    In order performed:

    - Function generateDOM: Creates papers.xml from NCBIData.xml (Papers.xml is basically in the format of the citation files.)

    ##################################
    #---------- MAIN INDEX ----------#
    ##################################
    Creates index.html : /web/index.html

    - Print header
    - Print Paper Total, each year total
    - For each paper:
    -Print paper using &printPaper()
    - Make subdirectory : /web/papers/"labid
    - Create Index.html : /web/papers/"labid"/index.html
    - Create index-all.html : /web/papers/"labid"/index-all.html

    ########################################
    #---------- SIMPLIFIED INDEX ----------#
    ########################################
    Creates papers-simple.html : /web/papers/papers-simple.html a text version of papers page

    Creates before97-simple.html : /web/papers/before97-simple.html a text version of he before97 papers page

    - Print Paper Total, each year total
    - For each Paper:
    - print paper using &printNARCitation()
    - Creates before97-simple.html and prints text version of papers before 1997

    ###########################################
    #---------- INDEX WITH XML TAGS ----------#
    ###########################################
    Creates papers-tags.htm : /web/papers/papers-tags.htm a tag version of the papers page

    Creates papers-ids.htm : /web/papers/papers-ids.htm a table displaying all papers linked to from "other"

    - Print tags of each Paper manually to papers-tags.htm
    - Creates table and adds each paper manually to papers-ids.htm

    ###################################
    #---------- GRANT PAGES ----------#
    ###################################
    Note: Grants are created by creating a new directory in /web/papers/grant with an info.xml file and a description.html file.

    Creates index.html for Grants page : /web/papers/grant/ from info.xml

    - Calls function &createGrantPage()
    - Creates grant index page using info.xml and variable in program that holds the content of papers.xml
    - Includes description.html
    - Prints papers associated with grant using &printPaper()

    ###################################
    #--------- SUBJECT PAGES ---------#
    ###################################
    Note: Subjects are created by creating a new directory in /web/papers/subject with an info.xml file and a description.html file.

    Creates index.html for Subjects page : /web/papers/subject/ from info.xml

    - Calls function &createSubjectPage()
    - Creates subject index page using info.xml and variable in program that holds the content of papers.xml
    - Includes description.html
    - Prints papers associated with subject using &printPaper()