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W2Share Website: http://w2share.lis.ic.unicamp.br

Installation Instructions

Installation on a local machine

  1. Run: $ sudo apt-get update
  2. If this was not done before: Install wget for file download in ubuntu $ sudo apt-get install wget
  3. Download the composer.phar from https://getcomposer.org/download via wget or built-in curl $ wget https://getcomposer.org/composer.phar or $ curl -O https://getcomposer.org/composer.phar **-O is capital O not Zero(0)
  4. Rename composer.phar to composer $ mv composer.phar composer
  5. Make composer executable $ chmod +x composer
  6. Now composer can be run locally through $ ./composer However, composer is available where you are, i.e., current directory where the composer file is.
  7. Make composer available globally move it to /user/local/bin by running $ sudo mv composer /usr/local/bin
  8. Now composer will be available anywhere by simply $ composer
  • Install git

  • Install netbeans PHP

  • Install php-curl and dependencies (This depends of the version of php that you are using)

    • sudo apt-get update
    • sudo apt-get install php-curl
    • sudo apt-get install php-xml
  • If you are using php7.0 you can use:

    • sudo apt-get install php7.0-curl php7.0-mbstring php7.0-zip php7.0-xml

Installation on a Web Server

  • PHP

  • Apache2

  • MySQL

  • Module PHP for Apache

  • $ sudo apt-get install apache2 php libapache2-mod-php php-mysql

  • If you are working on Ubuntu, it may be necessary to set the file 000-default.conf. Run this: $ sudo nano /etc/apache2/sites-enabled/000-default.conf

  • And search for:

    • ServerAdmin webmaster@localhost
    • DocumentRoot /var/www/html
    • Change the last line to: DocumentRoot /var/www/
  • save your changes.

  • To run the server, you can use: sudo systemctl restart apache2

Install Virtuoso

###For Load ttl files into virtuoso###

GRANT execute ON DB.DBA.SPARUL_LOAD TO "SPARQL"

###To insert triples into virtuoso###

  • GRANT execute ON SPARQL_INSERT_DICT_CONTENT TO "SPARQL"
  • GRANT execute ON SPARQL_INSERT_DICT_CONTENT TO SPARQL_UPDATE

###For update (delete and insert) run this:###

  • GRANT execute ON DB.DBA.SPARQL_MODIFY_BY_DICT_CONTENTS TO "SPARQL"
  • GRANT execute ON DB.DBA.SPARQL_MODIFY_BY_DICT_CONTENTS TO SPARQL_UPDATE
  • GRANT SPARQL_UPDATE to "SPARQL"

###For delete run this###

  • GRANT execute ON DB.DBA.SPARQL_DELETE_DICT_CONTENT TO "SPARQL"
  • GRANT execute ON DB.DBA.SPARQL_DELETE_DICT_CONTENT TO SPARQL_UPDATE

###To allow SPARUL statements to be run, add this:###

  • GRANT execute ON DB.DBA.SPARUL_RUN TO "SPARQL"
  • GRANT execute ON DB.DBA.SPARUL_RUN TO SPARQL_UPDATE

###EDIT : To allow graph deletion, run the following:###

  • GRANT execute on DB.DBA.SPARUL_CLEAR TO "SPARQL"
  • GRANT execute on DB.DBA.RDF_QUAD TO "SPARQL"
  • GRANT delete on DB.DBA.RDF_QUAD TO "SPARQL"
  • GRANT execute ON SPARUL_CLEAR TO "SPARQL"
  • GRANT execute ON SPARUL_CLEAR TO SPARQL_UPDATE
  • GRANT DELETE ON RDF_QUAD TO "SPARQL"
  • GRANT DELETE ON RDF_QUAD TO SPARQL_UPDATE

###Yet another grant (Virtuoso 7.0) NEED TO DO THIS for inserts to work!!!!###

  • GRANT execute ON DB.DBA.RDF_OBJ_ADD_KEYWORD_FOR_GRAPH TO "SPARQL"

  • GRANT execute ON DB.DBA.RDF_OBJ_ADD_KEYWORD_FOR_GRAPH TO SPARQL_UPDATE

  • GRANT execute ON DB.DBA.L_O_LOOK TO "SPARQL"

  • GRANT execute ON DDB.DBA.L_O_LOOK TO SPARQL_UPDATE

###After run the commands, the output sould be: The statement execution did not return a result set

Install Database

  • install phpmyadmin
  • configure parameters.yml with database name, user and password
  • create database "prototype" in mysql
  • create table using symfony command:
    • sudo rm -R app/cache/* && sudo rm -R app/logs/* (if you have problems with permission on directories cache and logs)
    • php app/console doctrine:schema:update --force

Install Project

  • cd /var/www (The project will be installed/cloned into /var/www)
  • clone repository phd-prototype from bitbucket: https://github.com/lis-unicamp/w2share.git
  • Inside /var/www/w2share/, to create the following directories:
    • mkdir web/uploads
    • mkdir web/uploads/documents
    • mkdir app/cache
    • mkdir app/sessions
    • mkdir vendor

After install the project

  • In the file parameters.yml (app/config/parameters.yml) assign a value to the attribute secret

    • secret: "This is a secret key"
  • Execute composer:

  • execute in menu (from your IDE - e.x., Netbeans, Eclipse): Select phd-prototype -> Composer -> Install (no-dev) or using a terminal (It's necessary to be in the path where the project is located. In our case, var/www/php-prototype):

  • "/usr/bin/php" "/usr/local/bin/composer" "--ansi" "--no-interaction" "install" "--no-dev"

  • Execute Symfony to create the assets

    • execute in menu (from your IDE - e.x., Netbeans, Eclipse): Select phd-prototype -> Symfony -> Run Command:
    • In the field Filter write install. Then, in Matching Task, select assesst:install, and click button Run.
    • In Parameters write --symlink web. click button Run.

Script Ruby : Taverna t2flow to Image

YesWorkflow

Install Graphviz

$ sudo apt-get install graphviz

Install Java JRE

$ sudo apt-get install default-jre

Remote Server - Virtual Machine

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