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

Installation Instructions

Installation on a local machine

Install composer on Ubuntu 16.04

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 composer on Mac

• 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

• Notes for Installation on Ubuntu: [https://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VOSUbuntuNotes]
• install virtuoso open source
• Install Virtuoso ** sudo apt-get install virtuoso-opensource
• SPARQL interface: [http://localhost:8890/sparql](Link URL)
• To create backups (dump data): [https://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VirtRDFDatasetDump]
• The correct statement procedure: [https://bitbucket.org/lucasaugustomcc/phd-prototype/wiki/CREATE%20PROCEDURE%20dump_one_graph]
• Set permissions on SPARQL: [http://localhost:8890/conductor](Link URL) dba:dba
• • Open Interactive SQL (iSQL):

###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

• sudo apt-get install ruby ruby-dev gcc make libxml2-dev
• sudo gem install taverna-t2flow
• • [https://github.com/myExperiment/workflow_parser-t2flow](Link URL)

YesWorkflow

Install Graphviz

$ sudo apt-get install graphviz

Install Java JRE

$ sudo apt-get install default-jre

Remote Server - Virtual Machine

• sudo apt-get install haveged
• sudo update-rc.d haveged defaults
• [https://www.digitalocean.com/community/tutorials/how-to-setup-additional-entropy-for-cloud-servers-using-haveged](Link URL)