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¶
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>
- tag is corresponding to the versions.
E.g.: v5.21. Link to the versions at SciELO’s GitHub
- branch is the current version plus customizations for the country/collection.
E.g.: scielo_esp Check the branch name of each collection.
<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/
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$>wxis.exe hello
If you have already configured the virtual host, you can check WWWISIS version by accessing the url:
http://vm.scielo.br/cgi-bin/wxis.exe?hello
where vm.scielo.br is the website address
The result must be:
CISIS Interface v5.7c/G/PC/512G/W/L4/M/32767/16/60/I/64bits - XML IsisScript WWWISIS 7.1f CISIS Interface v5.7c/.iy0/Z/GIZ/DEC/ISI/UTL/INVX/B7/FAT/CIP/CGI/MX/W Copyright (c)BIREME/PAHO 2010. [http://reddes.bvsalud.org/projects/cisis] WXIS release date: Jun 26 2012 WXIS|missing error|parameter|IsisScript|
Updating¶
Create a temporary folder
-
https://github.com/scieloorg/Web/tarball/<branch_name>
cd /tmp wget https://github.com/scieloorg/Web/tarball/<branch_name> --no-check-certificate tar -xvf <branch_name>
A file such as scieloorg-Web-<version-code>.tar.gz will be created. Where <version-code> changes according to the application version.
Extract the downloaded file.
#tmp$> 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/
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.
Move the tgz temporary file to the SciELO Website folder.
#tmp/scieloorg-Web-XXXXXXXX-XXXXXXXX$> mv scielo_tmp.tgz /var/www/scielo
Go to the application SciELO website folder.
#tmp/scieloorg-Web-XXXXXXXX-XXXXXXXX$> cd /var/www/scielo
Extract scielo_tmp.tgz
#var/www/scielo$> tar xvfzp scielo_tmp.tgz
Remove the tgz file
#var/www/scielo$> rm scielo_tmp.tgz
Ensure script permissions on the proc directory
# sudo find proc/ -name “*.sh” -type f -exec chmod -R 755 "{}" \; # sudo find proc/ -name “*.bat” -type f -exec chmod -R 755 "{}" \; # chmod 755 proc/call # chmod 755 proc/rem
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.phpThis 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=sclThe 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.defThe 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/iahlogThe 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.brThe 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.defChanging 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.pftChanging 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.defChange 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.pftChange 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