Welcome to SciELO Site’s documentation!

SciELO Site is a product of SciELO Methodology.

Also read: SciELO local Website and SciELO PC Programs.

About

About SciELO Site

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

  9. 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.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

Processing

Generating the databases for SciELO website

Directories

_images/scieloweb-dir.png

The bases-work subdirectory hosts the sub-directories of each database during processing in addition to individual directories for each journal.

The serial subdirectory contains the directories of all journals which in turn have all the original numbers used in processing (this data may be discarded after processing is carried out and approved).

The bases subdirectory has the databases for the website.

_images/scieloweb-bases.png

The proc subdirectory has the processing scripts, and other files related to the processing.

GeraPadrao.bat

It is a script which generates the databases for the SciELO website.

  • INPUTS:
    • serial folder’s content:
      • databases generated by Converter from markup and body folders and were sent to the Linux server by EnviaBasesScieloPadrao.bat script of the local server.
      • scilista.lst which contains a list of journal issues to be add/replaced/deleted.
    • folders and files located in /var/www/scielo/bases-work/
    • log filename. e.g.: /var/www/scielo/proc/log/GeraPadrao.log
  • OUTPUTS:
    • folders and files located in /var/www/scielo/bases-work/
    • folders and files located in /var/www/scielo/bases/
    • log file. e.g.: /var/www/scielo/proc/log/GeraPadrao.log

Edit GeraPadrao.bat to set parameters to generate the website’s databases.

./GeraScielo.bat <serial_parent_path> <proc_parent_path> <log filename> <cria>

where

  • Parameter 1: serial_parent_path: e.g.: /var/www/scielo/
  • Parameter 2: proc_parent_path: e.g.: /var/www/scielo/
  • Parameter 3: log filename: e.g.: /var/www/scielo/proc/log/GeraPadrao.log
  • Parameter 4: optional parameter. Use the value cria, if you want to reset the log file, otherwise, the log file will be appended.

Warning

It is possible to use relative paths for parameters 1 to 3.

Examples:

./GeraScielo.bat .. .. log/GeraPadrao.log

./GeraScielo.bat .. .. log/GeraPadrao.log cria

Execute GeraPadrao.bat

Go to /var/www/scielo/proc

Edit/check scilista.lst which contains the list of journal issues of the website.

vi ../serial/scilista.lst

Execute

./GeraPadrao.bat

Exporting the databases for SciELO Network processing

This process is made through the utilitary Paperboy. Paperboy is a Python utilitary developed to replace the scripts:

  • Envia2MedlinePadrao.bat
  • static_files_catalog.sh

Installing Paperboy

Install guide: https://github.com/scieloorg/paperboy

Configuring Paperboy

After install the paperboy you must create a config.ini file to configure the source and destiny resources, and the ssh account that will be used to send data to the server.

Creating config.ini file

Access the directory /var/www/scielo/proc

cd /var/www/scielo/proc

Create a text file named paperboy_envia_to_scielo_config.ini in the proc directory, the file must follow the bellow format:

Note

You may also use a file name of your preference for the config file, having in mind you must to replace the name of the config file in the following guidances.

[app:main]
source_dir=c:/var/www/scielo
cisis_dir=c:/var/www/scielo/proc/cisis
server=localhost
port=21
user=anonymous
password=anonymous

source_dir: Absolute path to the directory where the SciELO website was installed.

cisis_dir: Absolute path to the directory where CISIS utilitary was installed

ssh_server: Domain of the server where the SciELO Site was installed

ssh_port: The FTP port (default 21)

ssh_user: A valid FTP username

ssh_password: A valid FTP password for the given username

Tip

Ask your FTP credentials to the SciELO team.

Creating envia.sh file

Create a text file named paperboy_envia_to_scielo.sh in the proc directory.

Note

You may also use a file name of your preference for the batch file, having in mind you must to replace the name of the config file in the following guidances.

The content of the .sh file must be:

export PAPERBOY_SETTINGS_FILE=/var/www/scielo/proc/paperboy_envia_to_scielo_config.ini
paperboy_delivery_to_scielo

Running

Run the script paperboy_envia_to_scielo_config.sh to send databases and reports to SciELO.

./paperboy_envia_to_scielo_config.sh > /var/www/scielo/proc/log/paperboy_envia_to_scielo_config.log
Notes
  • Ask the SciELO team for you SSH credentials.
  • You must configure a CRON to run periodically the processing. (Preferable Weekly or after all the database updates)
  • The log files are:
    • /var/www/scielo/proc/log/paperboy_envia_to_scielo_config.log

CrossRef: Deposit with budget control

This processing selects the articles and generate the XML files to deposit on CrossRef, according to some conditions:

  • budget
  • current articles price
  • backfiles price
  • articles publication date
  • priority order: most recent to older, or older to most recent

Check deposit fees http://www.crossref.org/02publishers/20pub_fees.html

Configuration

Configure proc/scielo_crs/shs/crossRef_config.sh
# CrossRef connection
crossrefUserName=
crossrefPassword=
depositor_institution=
depositor_prefix=
depositor_email=
depositor_url=

# BUDGET
# current articles fee
RECENT_FEE=

# Firs year of articles considered current
# All Current records (2007-2009). So, 2007
FIRST_YEAR_OF_RECENT_FEE=

# backfiles fee
BACKFILES_FEE=
crossrefUserName username given by CrossRef
crossrefPassword password given by CrossRef
depositor_institution depositor institution name
depositor_prefix depositor prefix given by CrossRef
depositor_email e-mail to receive processing results from CrossRef
depositor_url SciELO Website URL
RECENT_FEE check at http://www.crossref.org/02publishers/20pub_fees.html E.g.: 1.0, for $1.00
FIRST_YEAR_OF_RECENT_FEE check at http://www.crossref.org/02publishers/20pub_fees.html E.g.: 2014 for (2014-2016)
BACKFILES_FEE check at http://www.crossref.org/02publishers/20pub_fees.html E.g.: 0.25, for $0.25
Configure proc/scielo_crs/shs/xref.cip

Use the template proc/scielo_crs/shs/xref.cip.template to create xref.cip or edit it.

Replace all /home/scielo/www/proc by the proc path. E.g.: /var/www/scielo/proc

BIREME_TABS_GCHARENT.*=/home/scielo/www/proc/scielo_crs/databases/tabs/gcharent.*
Y.*=/home/scielo/www/bases/title/title.*
ARTICLE_DB.*=/home/scielo/www/bases/artigo/artigo.*
ARTIGO_DB.*=/home/scielo/www/bases/artigo/artigo.*
DB_BILL.*=/home/scielo/www/proc/scielo_crs/databases/budget/bill.*

DB_BILL_BKP.*=/home/scielo/www/proc/scielo_crs/databases/budget/bill_BKP.*

DB_BG.*=/home/scielo/www/proc/scielo_crs/databases/crossref/budget.*
XREF_DOI_REPORT.*=/home/scielo/www/proc/scielo_crs/databases/crossref/crossref_DOIReport.*
DB_PRESUPUESTOS.*=/home/scielo/www/proc/scielo_crs/databases/budget/presupuestos.*

DB_BATCH_RUN_BUDGET.*=/home/scielo/www/proc/scielo_crs/databases/budget/batch_run_budget.*
DB_BATCH_RUN.*=/home/scielo/www/proc/scielo_crs/databases/budget/batch_run.*
DB_CTRL_BG.*=/home/scielo/www/proc/scielo_crs/databases/budget/budgetctrl.*
Configure proc/scielo_crs/shs/db_presupuestos.txt

It is a table in which each line is a budget.

Keep the first line which is a commentary.

Use SPACE character to separate each column.

This file must be edited whenever there is new budget.

First column:
ID - unique identified
Second column:
budget amount
Third column:
budget ISO date (YYYYMMDD, that is, 4 digits year, 2 digits month, 2 digits day)

E.g.:

In Jan 4, 2015, there is $150.00 (one hundred fifty dollars) and in Feb 4, 2015, there is $250.00 (two hundred fifty dollars):

1 150.00 20150104
2 250.00 20150204

In March 10, 2015, new budget: $100.00

3 100.00 20150310

db_presupuestos.txt contents:

1 150.00 20150104
2 250.00 20150204
3 100.00 20150310

When to execute

Execute it ONLY after finishing GeraPadrao.bat.

How to execute

Go to the corresponding path. E.g.:

cd /var/www/scielo/proc/scielo_crs/shs/

Execute:

./xref_run_budget.sh <budget ID> <Order> <processing mode> <Count> <ISSNYEAR>

Parameters description:

<budget ID>
budget ID will be spent
<Order>
Descending for most recent to older articles Ascending for older articles to most recent
<processing mode>
  • ALL = select all the articles, including the articles previously processed.
  • ONLY_NEVER_PROCESSED = select the articles never processed before.
  • ONLY_NEVER_SUBMITTED = select the articles which failed to submit the XML or failed to register the DOI.
<Count>
Limit the amount of articles to be process Use a number to the amount of articles or use ALL to process all
<ISSNYEAR>
Optional. Select the articles by ISSN and year. Use ALL for all the articles Use ISSN and year to a specific selection: E.g.: 1020-30402008

Examples:

./xref_run_budget.sh 2 Descending ONLY_NEVER_PROCESSED 100

./xref_run_budget.sh 2 Descending ONLY_NEVER_PROCESSED ALL 1020-30402008

Results

In proc/scielo_crs/databases/budget, there are:

  • presupuestos – database generated from db_presupuestos.txt (budget registration)
  • budgetctrl – database which registers the budget consumption
  • bill – database which registers the expenses of each article
  • batch_run_budget – database which registers the data of each execution
bill database
../../cisis/mx ../databases/budget/bill

Contents:

mfn=     2
880  "S0717-73562009000100008"
 65  "20090600"
  4  "requested"
  2  "1.0"
  3  "20090714 110457 2 194"
  1  "1"
121  "000001"
100  "20090714_110450_2_194"
30  "new^xcrossRef_sent_200907141104S0717-73562009000100008.log"

Description:

880 article PID
65 article publication date
4 status: requested (success) or dont (not registered, failure)
2 DOI price
3 processing date/time
1 budget ID
4 processing order number
100 execution ID
30 status; same as v30 and v930 of CrossRef_DOIReport database
batch_run_budget database

Add one register for each execution.

../../cisis/mx ../databases/budget/batch_run_budget

Contents:

mfn=     1
  1  "1"
100  "20090714_110450_2_194"
190  "20090714 110450 2 194"
102  "0"
200  "2007"
201  "1.0"
202  "0.15"
121  "000001"
  2  "1.00"
 90  "20090714 110457 2 194"

Description:

1 budget ID
100 execution ID
190 Start Date and time
190 Finish Date and time
102 initial budget, before the ejecution
200 initial year of current articles
201 DOI price for current articles
202 DOI price for backfiles
121 quantity of selected articles in this execution
2 expenses in this execution
XML for DOI deposit

The XML files are generated in proc/scielo_crs/output/crossref/. The structure below is:

– <ISSN>/ANO/NUMERO/ARTIGO/xml.
`– <YEAR>
`– <ISSUE>
`– <ARTICLE>
`– <filename>.xml
LOG

proc/scielo_crs/output/crossref/report_error.txt contains the processing errors.

Example:

PID=S0717-73562009000100001
log file: ../output/crossref/log/validationErrors_200907151502S0717-73562009000100001.log
data de processamento: 2009000100001
crossref_DOIReport

proc/scielo_crs/databases/crossref/crossref_DOIReport contains the result of the processing of each article / DOI.

../../cisis/mx ../databases/crossref/crossref_DOIReport

Contents:

mfn=     2
 30  "new"
930  "crossref_sent_200907141104S0717-73562009000100008.log"
880  "S0717-73562009000100008"
 10  "20090714 110457 2 194"

Description:

30 Status of the registration
930 DTD validation result
880 article PID
10 date and time of the registration

CrossRef: Deposit without budget control

This processing generates CrossRef Deposit XML files and submit them to register articles DOI.

Configuration

Configure proc/scielo_crs/shs/crossRef_config.sh
# CrossRef connection
crossrefUserName=
crossrefPassword=
depositor_institution=
depositor_prefix=
depositor_email=
depositor_url=
crossrefUserName username given by CrossRef
crossrefPassword password given by CrossRef
depositor_institution depositor institution name
depositor_prefix depositor prefix given by CrossRef
depositor_email e-mail to receive processing results from CrossRef
depositor_url SciELO Website URL
Configure proc/scielo_crs/shs/xref.cip

Use the template proc/scielo_crs/shs/xref.cip.template to create xref.cip or edit it.

Replace all /home/scielo/www/proc by the proc path. E.g.: /var/www/scielo/proc

BIREME_TABS_GCHARENT.*=/home/scielo/www/proc/scielo_crs/databases/tabs/gcharent.*
Y.*=/home/scielo/www/bases/title/title.*
ARTICLE_DB.*=/home/scielo/www/bases/artigo/artigo.*
ARTIGO_DB.*=/home/scielo/www/bases/artigo/artigo.*
XREF_DOI_REPORT.*=/home/scielo/www/proc/scielo_crs/databases/crossref/crossref_DOIReport.*

When to execute

Execute it ONLY after finishing GeraPadrao.bat.

How to execute

Go to the corresponding path. E.g.:

cd /var/www/scielo/proc/scielo_crs/shs/

Execute:

./xref_run.sh <ISSN_OR_PID>

Parameters description:

<ISSN_OR_PID>
optional Use no value to process all the articles which have not be processed before. Use PID of an issue or an article Use ISSN of a journal

Examples:

./xref_run.sh

./xref_run.sh 1020-30402008

Results

XML for DOI deposit

The XML files are generated in proc/scielo_crs/output/crossref/. The structure below is:

– <ISSN>/ANO/NUMERO/ARTIGO/xml.
`– <YEAR>
`– <ISSUE>
`– <ARTICLE>
`– <filename>.xml
LOG

proc/scielo_crs/output/crossref/report_error.txt contains the processing errors.

Example:

PID=S0717-73562009000100001
log file: ../output/crossref/log/validationErrors_200907151502S0717-73562009000100001.log
data de processamento: 2009000100001
crossref_DOIReport

proc/scielo_crs/databases/crossref/crossref_DOIReport contains the result of the processing of each article / DOI.

../../cisis/mx ../databases/crossref/crossref_DOIReport

Contents:

mfn=     2
 30  "new"
930  "crossref_sent_200907141104S0717-73562009000100008.log"
880  "S0717-73562009000100008"
 10  "20090714 110457 2 194"

Description:

30 Status of the registration
930 DTD validation result
880 article PID
10 date and time of the registration

CrossRef - Display DOI on SciELO Website

This processing generates, for each journals issue, one database which is used by SciELO Website to display the articles DOI.

Input: crossref_DOIReport database

When to execute

Execute after DOI deposit processing.

How to execute

1. scilista creation

This pre processing identifies the records which status in crossref_DOIReport database is not “error” and generates the scilista file according to the format:

Example:

neuro v19n6 S1130-147320080006
neuro v20n1 S1130-147320090001

Attention

Last line must be empty

  1. Go to proc directory
  2. Execute the command:

Example:

./doi/scilista/scilista4art.bat scilista_doi.txt
2. doi database creation
  1. Go to proc directory
  2. Execute the command:
./doi/create/doi4art.bat <scilista>

Example:

./doi/create/doi4art.bat scilista_doi.txt

Results

This processing generates the databases in bases-work/doi/<acron>/<issue_id>/<issue_id>.*

Example:

bases-work/doi/neuro/v20n1/v20n1
bases-work/doi/neuro/v19n1/v19n1
3. Updating the Website

Copy the bases-work/doi to bases/doi of the production server (Website).

Questions about cisis and wxis versions

The commands must display the “same version”:

cisis/what

wxis hello

Migration from Lind to LindG4

If the cisis and wxis versions were migrated from Lind to LindG4, the files which extension is *.iy0 must be delete, otherwise the indexes will be generated, but they will not be properly read.

The files extensions that must be kept are:

  • indexes files: * .cnt * .iyp * .ly1 * .ly2 * .n01 * .n02
  • database files: * .mst * .xrf

Attention

The *.iy0 files must be remove from the public server too.

Find the files to delete

find . -name "*.iy0"

Content of the website

The website’s content are:
  • informative pages
  • images
  • PDF files
  • versions of the articles in other language (translations)
  • databases

How to update the content

Considering the location of the files and databases, the website’s contents are considered updated if all these files are updated on their corresponding location.

It means:

  • bases/*
  • bases/pdf
  • bases/translation
  • htdocs/img/revistas
  • htdocs/revistas

Location of the webpages about the journal

The webpages of the journal (also known as secondary or informative pages) are in a folder structure like htdocs/revistas/<acronym>/.

E.g.: htdocs/revistas/bjmbr/

Location of the images of the journal

The images of the articles are in a folder structure like htdocs/img/revistas/<acronym>/.

E.g.: htdocs/img/revistas/bjmbr/

Location of the images of the articles

The images of the articles are in a folder structure like htdocs/img/revistas/<acronym>/<issue_id>/.

E.g.: htdocs/img/revistas/bjmbr/v45n4/

Location of the PDF files of the journal

The PDF files of the articles are in a folder structure like bases/pdf/<acronym>/<issue_id>.

E.g.: bases/pdf/bjmbr/v45n4/

Location of the Translation files of the journal

The translation files of the articles are in a folder structure like bases/translation/<acronym>/<issue_id>.

E.g.: bases/translation/bjmbr/v45n4/

Location of the databases

All the databases are in bases/*

Network Info

Network Websites

Consultar: http://www.scielo.org/

Change Log

v5.22

web

Including uBio at toolbox. To enable the uBio link, configure show_ubio=1

v5.21

web

How to cite using APA standard At article tool box, add link to other text version Display DOI found at bases/doi/doi, which was generated by xref_check FIXED Issue navegation: at the oldest issue, it is presenting erroneously a previous issue which does not exist

proc

xref_check (check if DOI is registered at CrossRef) proc_xref (query for references, including h records, and for all the collections)

v5.20

web

FIXED a bug at issues navegation button (ticket 292) FIXED link to related article in press release, when this page is opened by a web page out of the scielo website (ticket 293)

proc

scielo_crs: do not generate doi for press release texts and the link has to go to the full text in the English version (294,295)

v5.19

bases

Bases Cited Related Areasgeo Lattes para Bases Modelo Including LINDG4 model databases

web

  1. sci_serial. enhancement. present links to the other SciELO collections in which the journal is registered.
  2. sci_issuetoc. bug. Issuetoc page of a review issue, the previous button tried to show the ahead issue, that does not exist, so the previous button should show the last issue.
  3. sci_arttext. bug. Provisional texts: Link to PDF was presented twice.

proc

  1. New GeraPadrao. check migration before deleting records in original db.
  2. GeraNewcodeAux. new. generate standard subjects list
  3. proc_doi. bug. fix a message, fix (v880 => v880^*), fix entities, generation of reports
  4. GeraIssue.bat. bug. press release problem
  5. jEval: different treatment for journal which publish one article per issue.

v5.18.r3

proc

  1. paragraphs.xis: Fix loading of paragraphs for translated texts, which has no references.
  2. CreateBaseP.bat: Fix mx calling
  3. CriaDiretorio.bat: create more than one level of folders
  4. GeraIssue.bat: include instructions to separate issues databases (v31n1) for CouchDB.

v5.18 (time out problem)

web

#275 DOI for references (proc and web) #281 presentation of doi as url http://dx.doi.org/ as recommed by CrossRef.

proc

#275 DOI for references (proc and web) #276 jEval (journal evaluation to continue in collection) proc_lang fixed #282 GeraPadrao geração de bases p

v5.17

web

To enable this feature include the parameter show_meta_citation_reference=1 in the group [services] on scielo.def.php file

proc

Included the HTML META citation reference for Google Scholar.

v5.16.r

web

Removed the citation reference

v5.16

web

Fix the URI of OAI full text Add templates files to send e-mail Add citation reference on SciELO sci_arttext.xis and sci_arttext.xsl #269 Na página do artigo no título do periódico colocar um link para sua home #270 Na home do periódico juntamente com os links das páginas secundarias, acrescentar um link para página externa do periódico, quando houver.

v5.15

web

Alter the return of caracter set from UTF-8 to ISO-8859-1 on webservice. Since Jan-27,2011, 4.1.0 is discontinued. Removing root element from XML output

proc

fix OAI problem when record is a press release article

v5.14

web

Presentation of DOI which is provided by the journal editor

v5.13

web

Ajustes nos webservices de problemas gerados após mudanças realizadas na versão v5.12

v5.12

web

Ajustes nos webservices para entregar XML sem camada de WSDL.

v5.11

web

#252 Na home, o link para o portal (seja www.scielo.org, ou www.portal.revenf.bvsalud.org) tem que ser obtido do scielo.def.php

v5.10

web

Removido include para o arquivo cipar.xis no pressrelease.xis

v5.9

web

r4263 Removendo arquivo WXIS.EXE. Os arquivos deverão ser copiados do site de produtos da BIREME #115 Correções aplicadas somente em SciELObr, interface em inglês. r4270 Faltante utf-8 enconding no webservices serviço de new_titles r4271 Atualizado conforme solicitado no ticket #220 (closes #220) #220 Atualizado conforme solicitado. #r4275 Adicionado pastas wxis e gizmo no webservices faltantes na versão php5 #251 Trocando a codificação do arquivo sci_isoref.xis de UTF-8 para ISO-8859-1. Problemas na exibição de caracteres acentuados.

proc

r4262 Removendo arquivos do MX. Os arquivos deverão ser copiados do site de produtos da BIREME

v5.8

web

#240, corrigindo o título do artigo na tag meta/citation_title da página sci_abstract

v5.7-pr

web

#237, tratando & na url de clinical trial

v5.6-pr

web

#231, corrigindo link de tradução automática causado por mudança na caixa de serviços #8

v5.5-pr

web

#219, havia uma aspas a mais, prejudicando a apresentação apenas no IE

v5.4-pr

web

#221 Adiconado tags meta para busca no Google Scholar #223 Error do clinical trials

v5.3-pr

web

#8 Melhorias na interface da caixa de serviçoes #35 Adicionado Social Bookmarks na caixa de serviçoes #51 Ajustado utf-8 como saida padrão PHP 5 e Java

v5.2-pr

web

#219, tradução para africaner e outros #217 scielo_crs se o documento já tiver doi, verifica o prefixo do provedor local, se sim, fazer o registro no CrossRef, caso contrario ignorar

v5.1-pr

web

Ajustado o link na caixa de serviços do artigo.

v5.0-pr

web

Realizado alteração nas classes de transformação para php5(Notificações do php para essa versão deve ser suprimidos) #215 correção de apresentação da licença CC

v4.48

web

Última versão para php 4.3.11

v4.47

web

#212 apresentação de DOI em alguns artigos ex-provisional

v4.46

web

Melhorias nos Web Services, a fim de contemplar coleta seletiva de novos issues de revistas específicas. #208 task: Alterado, no sumário eletrônico de Provisional Article, o link “text in english” por “abstract in english”.

v4.45

web

Anulado a melhoria #191 botões de navegação para publicação adiantada, pois desajustou o desenho de varias páginas dependendo do Browser utilizado

v4.44

web

#191 enhancement - botões de navegação para publicação adiantada #182 bug :reopen, corrigindo um bug no processamento de crossref com controle de verba; geração da lista de PID.

v4.43

web

#201 bug: a lista de press releases não estava aparecendo completa na página do título

Support

How to get support.

Indices and tables