Installation and updating

REQUIREMENTS

  • CentOS release 6.7
  • Apache 2.2.15 or later
  • PHP 5.2.10 or 5.2.17 (required)
    • PHP Modules
      • libpng
      • soap
      • zlib
      • XSL
      • XML
  • vim
  • Git client
  • knowledge of Linux Administration
  • wget

Checking the version

The <SciELO website>/versionOverview.txt displays the current version of the website.

Check ScIELO Site: http://www.scielo.br/versionOverview.txt to see the most recent version.

Installation

  1. Preparing the environment and install

    1.1. Creating the directories to receive the application

    #>$ mkdir -f /var/www/scielo
    #>$ cd /var/www/scielo
    

    1.2. Installing by GitHub

    <branch_or_tag>

    <randomic_code>

    a code generated after unzip execution

    $ wget https://github.com/scieloorg/Web/zipball/<branch_or_tag>
    $ tar -xvf  <branch_or_tag> (when the package is a tar file but generally is zip)
    

    If it not works with tar command run as:

    $ unzip  <branch_or_tag>
    

    A folder named as scieloorg-<randomic_code> will be created.

    $ mv scieloorg-<randomic_code>/* .
    $ rm -Rf scieloorg-<randomic_code>
    $ rm <branch_or_tag>
    

    Warning

    Change <branch_or_tag> according to the latest version or the branch of the collection. If your SciELO site do not have an exclusive branch, you must use the branch name master.

    The created directory structure at /var/www/scielo must be

    bases/
    bases-work_modelo/
    bases_modelo/
    cgi-bin/
    docs/
    htdocs/
    ignore.txt
    proc/
    serial_modelo/
    
    _images/Metodologia-linux003.png

    1.3. Install the CISIS and WISIS tools at the SciELO Site diretories

    CISIS Package

    inside /var/www/scielo/proc/

    Download the CISIS package LindG4 version from the SciELO FTP products.

    Extrating cisis package using the follow command:

    #/var/www/scielo/proc/$>tar zxvf cisis-64bits-5.7c-lind.tar.gz
    

    The cisis directory will be created.

    To check the CISIS version, after extract the downloaded file at /var/www/scielo/proc/cisis, run:

    #/var/www/scielo/proc/cisis$>./mx what
    

    The result must be:

    CISIS Interface v5.7c/G/PC/512G/W/L4/M/32767/16/60/I/64bits - Utility MX
    CISIS Interface v5.7c/.iy0/Z/GIZ/DEC/ISI/UTL/INVX/B7/FAT/CIP/CGI/MX/W
    Copyright (c)BIREME/PAHO 2010. [http://reddes.bvsalud.org/projects/cisis]
    

    WWWISIS Package

    at /var/www/scielo/cgi-bin copy the wxis file from /var/www/scielo/proc/cisis rename it to wxis.exe

    To check the WWWISIS version, at /var/www/scielo/cgi-bin/, run:

    #/var/www/scielo/cgi-bin$>wxis.exe hello
    

    If you have already configured the virtual host, you can check WWWISIS version by accessing the url:

    http://vm.scielo.br/cgi-bin/wxis.exe?hello
    

    where vm.scielo.br is the website address

    The result must be:

    CISIS Interface v5.7c/G/PC/512G/W/L4/M/32767/16/60/I/64bits - XML IsisScript WWWISIS 7.1f
    CISIS Interface v5.7c/.iy0/Z/GIZ/DEC/ISI/UTL/INVX/B7/FAT/CIP/CGI/MX/W
    Copyright (c)BIREME/PAHO 2010. [http://reddes.bvsalud.org/projects/cisis]
    
    WXIS release date: Jun 26 2012
    
    WXIS|missing error|parameter|IsisScript|
    

Updating

  1. Create a temporary folder

  2. Identify your branch

    https://github.com/scieloorg/Web/tarball/<branch_name>

    cd /tmp
    wget https://github.com/scieloorg/Web/tarball/<branch_name> --no-check-certificate
    tar -xvf <branch_name>
    

    A file such as scieloorg-Web-<version-code>.tar.gz will be created. Where <version-code> changes according to the application version.

  3. Extract the downloaded file.

    #tmp$> tar xvfzp scieloorg-Web-v5.14-12-gd37aad4.tar.gz
    

    The created file structure will be like:

    scieloorg-Web-XXXXXXXX-XXXXXXXX/
    bases/
    bases_modelo/
    bases-work/
    bases-work_modelo/
    cgi-bin/
    htdocs/
    logs/
    proc/
    serial/
    serial_modelo/
    
  4. Compress only the necessary folders to update.

    #tmp$> cd scieloorg-Web-XXXXXXXX-XXXXXXXX
    #tmp/scieloorg-Web-XXXXXXXX-XXXXXXXX$> tar cvfzp scielo_tmp.tgz htdocs/ cgi-bin/ proc/
    

    scielo_tmp.tgz will only have htdocs, cgi-bin, proc folders.

  5. Move the tgz temporary file to the SciELO Website folder.

    #tmp/scieloorg-Web-XXXXXXXX-XXXXXXXX$> mv scielo_tmp.tgz /var/www/scielo
    
  6. Go to the application SciELO website folder.

    #tmp/scieloorg-Web-XXXXXXXX-XXXXXXXX$> cd /var/www/scielo
    
  7. Extract scielo_tmp.tgz

    #var/www/scielo$> tar xvfzp scielo_tmp.tgz
    
  8. Remove the tgz file

    #var/www/scielo$> rm scielo_tmp.tgz
    

Configurations

Mandatory configurations

Configuring scielo.def.php

Edit the file: /var/www/scielo/htdocs/scielo.def.php

Warning

Some parameters must be configured.

Copying the file scielo.def.php.template to scielo.def.php

#var/www/scielo$>cp htdocs/scielo.def.php.template htdocs/scielo.def.php
#var/www/scielo$>vi htdocs/scielo.def.php

This file is organized by blocks name using [BLOCK_NAME]. Each section have a set of parameters to be edited.

At this moment, you will configure only the mandatory parameters to run the website with basic features.

To configure other features, such as Bibliometrics, Access Statistics, SCIMAGO, etc, read Special configurations.

Configuring the SciELO Site Identification

[SITE_INFO]
SITE_NAME=SciELO - Scientific Electronic Library Online
SHORT_NAME=Scielo Brazil
SITE_AUTHOR=FAPESP – BIREME
ADDRESS_1=Rua Botucatu, 862 - Vila Clementino
ADDRESS_2=04023-901 São Paulo SP
COUNTRY=Brasil
PHONE_NUMBER="+55 11 5576-9863"
FAX_NUMBER="+55 11 5575-8868"
E_MAIL=scielo@bireme.br
STANDARD_LANG=en
APP_NAME=scielo
ANALYTICS_CODE=scl

The APP_NAME and ANALYTICS_CODE parameter value are provided by the SciELO Team.

[SCIELO]
SERVER_SCIELO=vm.scielo.br

[FULLTEXT_SERVICES]
access="http://vm.scielo.br/applications/scielo-org/pages/services/articleRequestGraphicPage.php?pid=PARAM_PID&caller=PARAM_SERVER"
cited_SciELO="http://vm.scielo.br/scieloOrg/php/citedScielo.php?pid=PARAM_PID"
send_mail="http://vm.scielo.br/applications/scielo-org/pages/services/sendMail.php?pid=PARAM_PID&caller=PARAM_SERVER"

Set SERVER_SCIELO to domain of your SciELO Site installation.

[PATH]
PATH_XSL=/var/www/scielo/htdocs/xsl/
PATH_DATABASE=/var/www/scielo/bases/
PATH_PDF=/var/www/scielo/bases/pdf
PATH_TRANSLATION=/var/www/scielo/bases/translation/
PATH_HTDOCS=/var/www/scielo/htdocs/
PATH_OAI=/var/www/scielo/htdocs/oai/
PATH_PROC=/var/www/scielo/proc/

[XML_ERROR]
LOG_XML_ERROR_FILENAME=/var/www/scielo/logs/xml_error_log.txt

Configuring iah.def

Edit the file: /var/www/scielo/htdocs/iah/iah.def

some parameters must be configured.

Copy the file iah.def.template to iah.def and open it to edit.

#var/www/scielo$>cp htdocs/iah/iah.def.template htdocs/iah/iah.def
#var/www/scielo$>vi htdocs/iah/iah.def

The value for PATH_CGI-BIN must be changed to the application path previously configured for the virtual host on the APACHE Server.

The value for PATH_DATABASE must be changed to the application path previously configured for the virtual host on the APACHE Server.

[PATH]
PATH_CGI-BIN=/var/www/scielo/cgi-bin/iah/
PATH_DATABASE=/var/www/scielo/bases/

[IAH]
LOG_DATABASE=/var/www/scielo/bases/logdia/iahlog

The value for LOGO URL must be changed to the application path previously configured for the virtual host on the APACHE Server.

The value for HEADER URL must be changed to the application path previously configured for the virtual host on the APACHE Server.

[HEADER]
LOGO URL=www.scielo.br
HEADER URL=www.scielo.br

The value for MANAGER E-MAIL must be changed to the application path previously configured for the virtual host on the APACHE Server.

The directory configured for LOG_DATABASE must have write permission for the user apache

[IAH]
MANAGER E-MAIL=scielo@bireme.br
LOG_DATABASE=/var/www/scielo/bases/logdia/iahlog

Configuring article.def

Edit the file /var/www/scielo/htdocs/iah/article.def

Warning

some parameters must be configured.

Copy the file article.def.template to article.def

#var/www/scielo$>mv htdocs/iah/article.def.template htdocs/iah/article.def
#var/www/scielo$>vi htdocs/iah/article.def

Changing the applications path

[FILE_LOCATION]
FILE HEADER.IAH=/var/www/scielo/cgi-bin/iah-styles/header.pff
FILE QUERY.IAH=/var/www/scielo/cgi-bin/iah-styles/query.pft
FILE LIST6003.PFT=/var/www/scielo/cgi-bin/iah-styles/list6003.pft
FILE PROC.PFT=/var/www/scielo/htdocs/pfts/proc_split_mst.pft
FILE iso.pft=/var/www/scielo/cgi-bin/iah-styles/fbiso.pft
FILE abn.pft=/var/www/scielo/cgi-bin/iah-styles/fbabn.pft
FILE van.pft=/var/www/scielo/cgi-bin/iah-styles/fbvan.pft
FILE places.pft=/var/www/scielo/cgi-bin/iah-styles/place-generico.pft
FILE month1.pft=/var/www/scielo/cgi-bin/iah-styles/month1.pft
FILE month2.pft=/var/www/scielo/cgi-bin/iah-styles/month2.pft
FILE scistyle.pft=/var/www/scielo/cgi-bin/iah-styles/scistyle.pft
FILE AHBTOP.HTM=/var/www/scielo/cgi-bin/iah-styles/%lang%/ahbtop.htm
FILE AHLIST.PFT=/var/www/scielo/cgi-bin/iah-styles/%lang%/ahlist.pft
FILE ahlist.pft=/var/www/scielo/cgi-bin/iah-styles/%lang%/ahlist.pft
FILE citation.xml=/var/www/scielo/cgi-bin/iah-styles/fbisoXML.pft

Changing the application path

[VARIABLES]
VARIABLE APP_PATH=/var/www/scielo
VARIABLE APP_REVISTAS_PATH=/var/www/scielo/htdocs/revistas/

Configuring title.def

Edit the file /var/www/scielo/htdocs/iah/title.def

Warning

some parameters must be configured.

Copy the file title.def.template to title.def

#var/www/scielo$>cp htdocs/iah/title.def.template htdocs/iah/title.def
#var/www/scielo$>vi htdocs/iah/title.def

Change the application path

[FILE_LOCATION]
FILE HEADER.IAH=/var/www/scielo/cgi-bin/iah-styles/header.pft
FILE scistyle.pft=/var/www/scielo/cgi-bin/iah-styles/scistyle.pft
FILE places.pft=/var/www/scielo/cgi-bin/iah-styles/place-generico.pft
FILE iso.pft=/var/www/scielo/cgi-bin/iah-styles/fbsrc1.pft
FILE van.pft=/var/www/scielo/cgi-bin/iah-styles/fbsrc1.pft
FILE abn.pft=/var/www/scielo/cgi-bin/iah-styles/fbsrc1.pft

Change the application path

[VARIABLES]
VARIABLE APP_PATH=/var/www/scielo
VARIABLE APP_REVISTAS_PATH=/var/www/scielo/htdocs/revistas/

1.8. Permissions

755 apache:apache htdocs

755 apache:apache bases

Special Configurations

To configure other features, such as Bibliometrics, Access Statistics, SCIMAGO, etc.

Google Analytics

Warning

Run each step from the htdocs directory.

Edit the configuration file.

#var/www/scielo/htdocs$> vi scielo.def.php

Ask SciELO team for your APP_NAME.

ACTIVATE_GOOGLE=1
GOOGLE_CODE=<google_code>

e.g.:

ACTIVATE_GOOGLE=1
GOOGLE_CODE=UA-01010101010-1
Note:
To have this code, you must have an account in Google Analytics.

Bibliometric reports website

Warning

Run each step from the htdocs directory.

Edit the configuration file.

#var/www/scielo/htdocs$> vi scielo.def.php

Ask SciELO team for your APP_NAME and ANALYTICS_CODE.

[SITE_INFO]
APP_NAME=scielo
ANALYTICS_CODE=scl

Indicate the domain for Bibliometric reports website editing STAT_SERVER_CITATION and STAT_SERVER_COAUTH.

  • Change the parameter app=scielo to app=<same as APP_NAME>

  • Change the parameter according to the following example.

    Note: Bibliometric reports website is other website which is also part of SciELO.

    [SCIELO]
    STAT_SERVER_CITATION=http://statbiblio.scielo.org/
    STAT_SERVER_COAUTH=http://statbiblio.scielo.org/
    
    [LOG]
    ENABLE_STATISTICS_LINK=1
    ENABLE_CITATION_REPORTS_LINK=1
    

Access Statistics

Warning

Run each step from the htdocs directory.

Edit the configuration file.

#var/www/scielo/htdocs$> vi scielo.def.php

Ask SciELO team for your APP_NAME and ANALYTICS_CODE.

[SITE_INFO]
APP_NAME=scielo
ANALYTICS_CODE=scl

[LOG]
ACTIVATE_LOG=1
ENABLE_STATISTICS_LINK=1

Set show_requests to 1, to enable the Access Statistics link.

[services]
...
show_requests=1
...

SCIMAGO

The root directory for this processing is /var/www/scielo/proc/scielo_sjr

The following steps run at the directory proc/scielo_sjr.

Copying the config file.

#var/www/scielo/proc/scielo_sjr$> cp shs/config.sh.template shs/config.sh

Editing the config file and changing the paths if necessary.

#var/www/scielo/proc/scielo_sjr$> vi shs/config.sh

Config file sample. If you are already using /var/www/scielo as the application path, so no changes are need.

#!/bin/bash
# ------------------------------------------------------------------------- #
# variaveis com caminho para bases de dados utilizadas no processmento.
# ------------------------------------------------------------------------- #
export scielo_dir="/var/www/scielo"
export scielo_proc="/var/www/scielo/proc"
export database_dir="$scielo_dir/bases"
export cisis_dir="$scielo_dir/proc/cisis"
# ------------------------------------------------------------------------- #

Run the script to harvest the SCIMAGO charts.

#var/www/scielo/proc/scielo_sjr$> cd shs/
#var/www/scielo/proc/scielo_sjr$> ./sjr_run.sh