SciELO Web site for Windows Documentation

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1 SciELO Web site for Windows Documentation Release 5.x SciELO April 19, 2016

3 Contents 1 Installation of SciELO Website on Windows REQUIREMENTS SciELO Web Installation Guide Configuring Batch Scripts GeraPadrao.bat PaperBoy Delorean2Isis How to generate the content for the website Introduction Conventions Requirements GeraPadrao.bat Checking the result and log file Checking the local website How to transfer the data to the processing server Introduction Pre-requirements Conventions Preparing the data to the processing server Transfering files to the processing server Checking the transference Support How to solve common problems i

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5 The SciELO Web for Windows is basically used as a stage website where the producion team can check the articles produced before sending then to the official website. All the features within a SciELO Website will not be installed in this stage environment. The focus of this Guide is to guide the IT managers to intall the following tasks: 1. PC-Programs (Converter and Markup) 2. Delorean2Isis (Import databases from the Journal Manager to the markup process) 3. Staging SciELO Website on Windows (Just for articles check) 4. GeraPadrao (Processing of new data to publish the new data in the website) 5. Paperboy to send Translations, Databases, PDF s, Images and XML Files to the SciELO Site servers Contents 1

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7 CHAPTER 1 Installation of SciELO Website on Windows 1.1 REQUIREMENTS knowledge in Apache Httpd and PHP configuration Windows Apache or later Apache Configurations * Create an specific virtual host for the scielo site application PHP (required) PHP Modules * libpng * soap * zlib * XSL * XML PHP Configurations * short-open-tag = On * PHP must be working above de desired domain and directory. sugested domain: scielo.local sugested diretory: c:/var/www/scielo/htdocs Checking the info.php above the desired domain Save the following code into c:/var/www/scielo/htdocs/info.php file. <?php info_php();?> 3

8 Check if the code is working accessing: The page presented by the code above is like: Warning: Before start installing SciELO, the PHP must be configured and working with Apache server, above the selected domain. It is not part of this installation guide to help install all the requirements. 1.2 SciELO Web Installation Guide Configuring the Apache Virtual Host Warning: It was expected that a virtual host was already configured when preparing the requirements steps above. So, in most of the cases, will just be necessary to include the ALIAS and CGI-BIN configurations. The virtual host sample below is a general sample on how to configure the SciELO Virtual Host. This configuration could change according each hosting services and their security polices. Remember to fix all the paths if you are installing the SciELO Site in a different directory. <VirtualHost *:80> ServerAdmin scielo@scielo.local DocumentRoot "C:/var/www/scielo/htdocs/" ServerName scielo.local <Directory "C:/var/www/scielo/htdocs/"> Options FollowSymLinks +Indexes AllowOverride None Order allow,deny Allow from all DirectoryIndex index.html index.php Satisfy all </Directory> Alias /pdf/ "C:/var/www/scielo/bases/pdf/" Alias /translation/ "C:/var/www/scielo/bases/translation/" <Directory "C:/var/www/scielo/bases/pdf/"> Options FollowSymLinks +Indexes AllowOverride None Order allow,deny Allow from all Satisfy all </directory> ScriptAlias /cgi-bin/ "C:/var/www/scielo/cgi-bin/" <Directory "C:/var/www/scielo/cgi-bin/"> AllowOverride None Options None Order allow,deny Allow from all </directory> ErrorLog logs/scielo-local-error.log CustomLog logs/scielo-local-access.log common </VirtualHost> 4 Chapter 1. Installation of SciELO Website on Windows

9 1.2.2 Install SciELO Site 1. Creating the directories to receive the application c:\> md /var/www/scielo c:\> cd /var/www/scielo c:/var/www/scielo> 2. Downloading packages from GitHub Link of versions available for SciELO Site: Link of versions available for Windows Patch: Windows/tags 3. Firts, extract the SciELO Site package at c:/var/www/scielo> The created directory structure at c:/var/www/scielo> must be <package_name>/bases/ <package_name>/bases-work_modelo/ <package_name>/bases_modelo/ <package_name>/cgi-bin/ <package_name>/docs/ <package_name>/htdocs/ <package_name>/ignore.txt <package_name>/proc/ <package_name>/serial_modelo/ Move all the content from <package_name> to c:/var/www/scielo> Remove the empty directory <package_name> 4. Then, extract the SciELO Windows package at c:/var/www/scielo>. Warning: This extraction will overwrite some files from the SciELO Site package. You must accept all the files and dirctories replacements. 5. Some folders already exist. You must accept to overwrite them SciELO Web Installation Guide 5

10 6. Some files already exist. You must accept to overwrite them. 6 Chapter 1. Installation of SciELO Website on Windows

11 1.2. SciELO Web Installation Guide 7

$The recommended version is CISIS 1660 To check the CISIS version, after unzip the donwloaded file at c:\var\www\scielo\proc\cisis>, run: c:\var\www\scielo\proc\cisis> mx what The result must be:$

12 7. Install the CISIS tool at the SciELO Site directories Download the CISIS package from the BIREME products website and extract it at c:/var/www/scielo/proc/cisis>. The recommended version is CISIS 1660 To check the CISIS version, after unzip the donwloaded file at c:\var\www\scielo\proc\cisis>, run: c:\var\www\scielo\proc\cisis> mx what The result must be: CISIS Interface v5.2b/gc/w/l/m/32767/16/60/i - Utility MX CISIS Interface v5.2b/.iy0/z/4gb/giz/dec/isi/utl/invx/b7/fat/cip/cgi/mx/w Copyright (c)bireme/paho [! 8. Install the WWWISIS tool at the SciELO Site directories Download the WWWISIS package from the BIREME products website and extract it at c:/var/www/scielo/cgi-bin>. The recommended version is WWWISIS 1660 To check the WWWISIS version, at c:varwwwscielocgi-bin, run: 8 Chapter 1. Installation of SciELO Website on Windows

$c:\var\www\scielo\cgi-bin$> wxis hello If you have already configured the virtual host, you can check WWWISIS version by accessing the url: http://scielo.local/cgi-bin/wxis.exe?hello where scielo.$

13 c:\var\www\scielo\cgi-bin$> wxis hello If you have already configured the virtual host, you can check WWWISIS version by accessing the url: where scielo.local is the website address The result must be: CISIS Interface v5.4.02_p5/gc/512g/w/l4/m/32767/16/60/i - XML!IsisScript WWWISIS 7.1d CISIS Interface v5.4.02_p5/.iy0/z/giz/dec/isi/utl/invx/b7/fat/cip/cgi/mx/w Copyright (c)bireme/paho [! Copyright (c)bireme/paho [! Copyright (c)bireme/paho [! WXIS release date: Sep Configuration of scielo.def.php 1. Creating scielo.def.php In C:/var/www/scielo/htdocs> there is a file named as scielo.def.php.template. Rename the file to scielo.def.php. Click on Yes button to accept the change SciELO Web Installation Guide 9

2. Edit scielo.def.php using your preferred text editor 3. Changing vm.scielo.br to scielo.local Search for vm.scielo.br and replace all the occurences by scielo.

14 2. Edit scielo.def.php using your preferred text editor 3. Changing vm.scielo.br to scielo.local Search for vm.scielo.br and replace all the occurences by scielo.local or for each other name previously configured at the virtualhost 4. Changing application path Search for /home/scielo/www/ and replace all the occurences by ** /var/www/scielo/** or for each other patch previously configured at the virtualhost 5. Save all the changes made 6. At this point, the website is probably working at: 7. Set the paramenters to 0 Zero once this website will be only available for articles tests in a stage environmnet. [CACHE] ENABLED_CACHE=0 [SOCKET] SOCK_PORT= ENABLE_ACCESS_LOG=0 [services] journal_manager=0 show_toolbox=0 show_datasus=0 show_reference=0 show_requests=0 show_login=0 show_send_by_ =0 show_cited_scielo=0 show_cited_google=0 show_similar_in_scielo=0 show_similar_in_google=0 show_article_references=0 show_scimago=0 show_article_wltranslation=0 show_fapesp_projects=0 show_press_releases=0 show_clinical_trials=0 show_ref_links=0 show_meta_citation_reference=0 show_ubio=0 8. Save all the changes made 9. The SciELO site is prepared to receive new production files for tests. 10 Chapter 1. Installation of SciELO Website on Windows

15 See the other guides about how to send data to the production server, and for processing in the root level of this documentation SciELO Web Installation Guide 11

16 12 Chapter 1. Installation of SciELO Website on Windows

17 CHAPTER 2 Configuring Batch Scripts 2.1 GeraPadrao.bat Edit c:\var\www\scielo\proc\gerapadrao.bat Fix the path according to the SciELO Site directory, for the lines below: call notepad \scielo\serial\scilista.lst *** rmdir /S /Q \scielo\web\bases-work rmdir /S /Q \scielo\web\bases\artigo rmdir /S /Q \scielo\web\bases\iah rmdir /S /Q \scielo\web\bases\issue rmdir /S /Q \scielo\web\bases\newissue *** md \scielo\web\bases-work *** call GeraScielo.bat \scielo \scielo\web log\gerapadrao.log adiciona call GeraScielo <path_data> <path_web_site> <log_file> adiciona where <path_data>: path which contains serial folder. e. g.: \scielo <path_website>: path which contains the website application. e. g.: \scielo\web <log_file>: path/name for the log file. e. g.: log\ log [cria] is an optional parameter. Writing cria, the current log file is deleted and a new one is created. considering the path \var\www\scielo the changes must be: GeraScielo \var\www\scielo \var\www\scielo log\gerapadrao.log adiciona 2.2 PaperBoy Paperboy is a Python utilitary developed to replace the scripts: EnviaImgPdfScieloPadrao.bat 13

18 EnviaTranslationSciELOPadrao.bat EnviaBasesScieloPadrao.bat EnviaXmlScieloPadrao.bat This utilitary was developed to address ftp incompatibilities with windows and Linux servers Installing Install guide: Configuring 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. Access the directory \var\www\scielo\proc Creating config.ini file Create a text file named paperboy_config.ini in the proc directory, the file must follow the bellow format: [app:main] source_dir=c:/var/www/scielo cisis_dir=c:/var/www/scielo/proc/cisis scilista=c:/var/www/scielo/serial/scilista.lst destiny_dir=/var/www/scielo ssh_server=localhost ssh_port=22 ssh_user=anonymous ssh_password=anonymous source_dir: Absolute path to the directory where the SciELO Local website was installed. cisis_dir: Absolute path to the directory where CISIS utilitary was installed scilista: Absolute path to the scilista file with the list of issues that should be add, updated or deleted from the website destiny_dir: Absolute path to the directory where the SciELO Site was installed in the server. ssh_server: Domain of the SFTP or FTP server, where the SciELO Site was installed ssh_port: 22 to use SFTP or 21 to use FTP. ssh_user: A valid SFTP or FTP username ssh_password: A valid SFTP or FTP password for the given username Creating envia.bat file Create a text file named paperboy_envia.bat in the proc directory. set PAPERBOY_SETTINGS_FILE=/var/www/scielo/proc/paperboy_config.ini paperboy -m -o /var/www/scielo/proc/log/paperboy_envia.log 14 Chapter 2. Configuring Batch Scripts

19 2.2.3 Running Run the script paperboy_envia.bat to update the SciELO Site server. paperboy_envia.bat 2.3 Delorean2Isis This script is used to download the SciELO databases managed in the SciELO Manager to the local website for covertion pourpose. It is necessary when your Collection is using the new catalog manager SciELO Manager Installing Downloading and unzipping Download the package (delorean2isis-master.zip) and unzip it at c:. Unzip the package in c:/: cd / unzip delorean2isis-master.zip rename delorean2isis-master delorean2isis Installing requirements Python 2.7 must be previously installed cd c:/delorean2isis pip install -r requirements.txt Creating config.py file Create a text file named config.py in the c:/delorean2isis directory, the file must follow the bellow format: #coding:utf-8 #!/usr/bin/python API_URL = ' API_USER = '' API_KEY = '' DELOREAN_URL = ' ISIS_PATH = "" DATABASES = ["title", "issue"] DATABASE_FST = {'title': 'tit_issn', 'issue': 'issue'} 2.3. Delorean2Isis 15

20 You can copy the c:/delorean2isis/config.py.template to c:/delorean2isis/config.py to have a fresh and new config.py file. API_URL: URL for the SciELO Manager API (ask it to the SciELO Team). API_USER: Your SciELO Manager username. API_KEY: Your SciELO Manager Token. Login to the SciELO Manager and access the user informations to have your API_KEY. It will be available in the label API Token. DELOREAN_URL: URL for the Delorean utilitary (ask it to the SciELO Team). ISIS_PATH: Full path to the ISIS utilitary DATABASES: Databases that will be downloaded. (Do not change this item) DATABASES_FST: Databases that will be downloaded. (Do not change this item) Creating a bash file to run deloreans2isis Create a bash file named sincroniza.bat in the c:/delorean2isis directory. This file must contain the following content. cd c:/delorean2isis python delorean2isis.py -c <collection_slug> -o c:/var/www/scielo/proc/serial -c Collection slug in the SciELO Manager. -o Full path to the SciELO serial folder. If you used the SciELO patterns while installing the SciELO Site and SciELO utilitaries, the serial folder should be in c:/var/www/scielo/proc/serial. Hint: Ask the collection_slug for the SciELO Team Running Run the script sincroniza.bat to update the SciELO Site server. cd c:/delorean2isis sincroniza.bat Notes Maybe you want to include a link for the sincroniza.bat file in a appropriate place, avoiding the uses to know it is available in c:/deloreans2isis. For exemple: Include a link in the desktop. 16 Chapter 2. Configuring Batch Scripts

21 CHAPTER 3 How to generate the content for the website 3.1 Introduction The next step after converting the articles is to generate the local website ( which will present and search information inserted in the database. 3.2 Conventions All the examples in this topic show the directory structure for the standard installation of the SciELO website: /var/www/scielo/serial (*) /var/www/scielo/bases /var/www/scielo/bases-work /var/www/scielo/cgi-bin /var/www/scielo/htdocs /var/www/scielo/proc (*) data structure required for SciELO PC Programs. 3.3 Requirements 1. images of the articles must be in: /var/www/scielo/htdocs/img/revistas/<acronym>/v*n* 2. pdf files of the articles must be in: /var/www/scielo/bases/pdf/<acronym>/v*n* 3. translations files of the articles must be in: /var/www/scielo/bases/translations/<acronym>/v*n* 4. database of the articles, created by Converter, must be in: /var/www/scielo/serial/<acronym>/v*n*base 5. title and issue database must be in: /scielo/serial/title and /var/www/scielo/serial/issue, respectively. 3.4 GeraPadrao.bat 1. Open a DOS session 17

22 2. Go to proc directory 3. Execute: (a) To update the website content 18 Chapter 3. How to generate the content for the website

23 GeraPadrao (b) To create a new content to the website GeraPadrao novo 4. Answer: continue or cancel 5. If continue, edit /var/www/scielo/serial/scilista.txt with the following format: Example: <journal_acronym> v*n* <journal_acronym> v*n* bjmbr v31n1pr bjmbr v31n1 jbc 2011naheadpr jbc 2011nahead jbc v115n1 jbca n100 rv v10s1 ra v10n10s1 rs v11n1s0 jed vseriin10 1. Save and close this file 2. Enter to continue 3. End 4. Open Checking the result and log file Processing output is displayed on the screen (standard output) and is stored in the log file: /var/www/scielo/log/gerapadrao.log or the file informed in GeraPadrao. In case of error, processing stops, and wait for an user s intervention. Example: Cancel or Continue After processing is completed, it is recommendable to check the log file Checking the result and log file 19

24 3.6 Checking the local website In this phase, the local website is checked to make sure it is working correctly. Execute the next steps, only if the local website is working properly. Check if the errors are about content, which must be fixed, using SciELO PC Programs. Check if the errors are about processing. 20 Chapter 3. How to generate the content for the website

25 CHAPTER 4 How to transfer the data to the processing server 4.1 Introduction The next step after checking the local website is to transfer the databases and files to the processing server. 4.2 Pre-requirements PaperBoy 4.3 Conventions In the local server, all the examples in this topic show the directory structure for the standard installation of the SciELO website: /var/www/scielo/serial (*) /var/www/scielo/bases /var/www/scielo/bases-work /var/www/scielo/cgi-bin /var/www/scielo/htdocs /var/www/scielo/proc /var/www/scielo/serial (*) data structure required for SciELO PC Programs. In the processing server, all the examples in this topic show the directory structure for the standard /var/www/scielo/ /var/www/scielo/bases/ /var/www/scielo/htdocs/ /var/www/scielo/proc/ /var/www/scielo/serial/ 21

26 4.4 Preparing the data to the processing server Checking scilista.lst 1. Check the existence of scilista.lst and its content, it means, list of the journal issues to add/remove/update Checking databases in serial 1. database of the articles, created by Converter, must be in: /scielo/serial/<acronym>/v*n*base 2. title and issue databases must be in: /scielo/serial/title and /scielo/serial/issue, respectively Checking images, translations and PDF files 1. Check the existence of images of the journals: plogo.gif and glogo.gif in /scielo/web/htdocs/img/revistas/<acronym>/ 2. Check the existence of secondary pages: *.htm in /scielo/web/htdocs/revistas/<acronym>/ 3. Check the existence of images of the articles in /scielo/web/htdocs/img/revistas/<acronym>/<vol-num>/ 4. Check the existence of PDF files of the articles in /scielo/web/bases/pdf/<acronym>/<vol-num>/ 5. Check the existence of the translation files of the articles in /scielo/web/bases/translation/<acronym>/<volnum>/ 4.5 Transfering files to the processing server Transfering databases This procedure sends the databases from local server to the processing server by FTP. From /scielo/web/proc, run EnviaBasesScieloPadrao.bat, which must be previously configured. EnviaBasesSciELOPadrao.bat Transfering files This procedure transfers by SSH or FTP, from the local server to the homologation server, the images, pdfs, translations, xml s of the articles of the journal issues listed in scilista.txt file. paperboy_envia.bat Processing output is displayed on the screen (standard output) and is stored in the log file: /scielo/web/log/paperboy_enviao.log. After processing is completed, it is recommendable to check the log file. 22 Chapter 4. How to transfer the data to the processing server

27 4.6 Checking the transference In the processing server, check the folders: Databases: /var/www/scielo/serial and its subdirectories. There must be a structure like: <acronym>/<issue_id>/base/<issue_id>.mst and <acronym>/<issue_id>/base/<issue_id>.xrf /var/www/scielo/serial/scilista.lst - contains the journals issues to be processed Images, HTML and PDF files: Translation files: /var/www/scielo/htdocs/img/revistas/<acronym>/<issue_id>/<img_files> /var/www/scielo/htdocs/revistas/<acronym>/*.htm /var/www/scielo/bases/pdf/<acronym>/<issue_id>/<pdf_files> /var/www/scielo/bases/translation/<acronym>/<issue_id>/<html_files> 4.6. Checking the transference 23

28 24 Chapter 4. How to transfer the data to the processing server

CHAPTER 5 Support 5.1 How to solve common problems 5.1.1 Website home page As accessing http://teste.scielo.

29 CHAPTER 5 Support 5.1 How to solve common problems Website home page As accessing the website present unexpected presentation. Edit the php.ini file. This file is located on PHP standard directory. 25

30 Open this file, using WordPad or Notepad, then search for short_open_tag 26 Chapter 5. Support

31 Change short_open_tag = Off to short_open_tag = On Save the file Restart Apache. Open How to solve common problems 27

$loadxml]: Premature end of data in tag LIST line 39 in Entity, line: 42 in C:\SciELO\www\htdocs \class.xsltransformerphp5.php on line 29 This error is related to missing databases.$ They must be generated using GeraPadrao. 5.1.

They must be generated using GeraPadrao. 5.1.

32 5.1.2 Alphabetic list Access Click on Alphabetic list link If the website look like the image below: or if the message Warning: DOMDocument::loadXML() [domdocument.loadxml]: Premature end of data in tag LIST line 39 in Entity, line: 42 in C:\SciELO\www\htdocs \class.xsltransformerphp5.php on line 29 This error is related to missing databases. They must be generated using GeraPadrao Table of contents page does not load This error is related to author identification in the markup file. Check the authors Article or abstract page does not load This error can be related to: missing databases (related, cited, etc) authors were not correctly identified or have special characters in their names. How to get support. 28 Chapter 5. Support

[UNIT 1 <Continued>]: <Understanding Apache>

[UNIT 1 <Continued>]: <Understanding Apache> [UNIT 1 ]: Directives DocumentRoot This directive specifies the root directory of the server s content hierarchy, Syntax DocumentRoot dir Where dir is the directory s