Versions Compared

Old Version 8

changes.mady.by.user Armando Stellato

Saved on

compared with

New Version 9

changes.mady.by.user Armando Stellato

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Introduction

following recent updates in VocBench, these instructions will be completely rewritten for a quicker test drive, by using a small concept scheme and loading it with the triple store technology embedded with Sesame2. However, we leave the previous version until we update this section of the documentation

These instructions propose a quick installation method for having an AGROVOC installation of the VocBench Thesauri Management Web Application. Note that, by replacing “Agrovoc” with your specific dataset, and “Agrontology” with your own domain vocabulary, they should still be valid for handling your specific case.

VB offers a User Interface for many of the options that you will see represented through config files here but, as the package that comes with this guide is already pre-configured, you will find it easier to go through these specific configuration steps instead of using the UI.

For the same reason above, you just have to follow this guide up straightly, and all parameters have been already set for the AGROVOC installation. Whenever a parameter needs a value which is specific to your installation, we have put a placeholder for it. The list of placeholders is reported in the Legenda here below.

Please refer to the Installation, sections “Requirements” and “Installation Steps”, up to step 3: “Import the Administrator Database SQL Dump File”. For step 4, just drop the VB war in Tomcat, and then follow this guide for configuring the Config.properties file, then restart tomcat.

Legenda

{youradminemail.xxx} : these are placeholders for the configuration of a real email address which will be used to deliver email messages to the vocbench administrator

  • {youradminemail.address} : address of your {youradminemail} account
  • {youradminemail.user} : username of your {youradminemail} account
  • {youradminemail.pwd}: password of your {youradminemail} account
  • {youradminemail.host} : smtp server of URL of the service for sending emails through your {youradminemail} account
  • {youradminemail.port} : port for the outgoing mail service of your {youradminemail} account

{yourAdministratorDB.name}: this is a placeholder for admin DB of VB.
{yourDB.user} : this is a placeholder for the account you are using for storing the admin DB of VB
{yourDB.pwd}: a placeholder for the password of your {yourDB.user} account

{admin.emails}: a comma separated list of email addresses of administrators, which will be notified of any email, together with the main administrator

{owlim.license.path}: put here your full path to where you stored the OWLIM license file in your path, such as /path/fao1core.license, or C:/temp/fao1core.license

Configuration

  1. Import Administrator database.
  2. Copy your war file of VB inside tomcat.
  3. VB allows updating your configuration file at the time of first load after installation.
    • CFG.VERSION= 2.0
    • CFG.DISPLAYVERSION= 2.0
    • CFG.MODE= DEV
    • CFG.DB.CONNECTIONURL = jdbc:mysql://localhost:3306/{yourAdministratorDB.name}?requireSSL=false&useUnicode=true&characterEncoding=UTF-8
    • CFG.DB.USERNAME= {yourDB.user}
    • CFG.DB.PASSWORD= {yourDB.pwd}
    • CFG.MAIL.HOST={youradminemail.host}
    • CFG.MAIL.PORT={youradminemail.port}
    • CFG.MAIL.USER={youradminemail.user}
    • CFG.MAIL.PASSWORD={youradminemail.pwd}
    • CFG.MAIL.FROM={youradminemail.address}  
    • CFG.MAIL.FROM_ALIAS=VocBench Admin
    • CFG.MAIL.ADMIN={admin.emails}
    • CFG.MODELCLASS: Set org.fao.aoscs.model.semanticturkey.STManager to use Semantic Turkey
    • CFG.MANDATORY.DEFINITION.NAMESPACES = Add namespaces which requires mandatory definition's source and link (For multiple namespaces use semicolon ";" as a separator)
    • CFG.CODETYPE = set CODETYPE to “http://aims.fao.org/aos/agrovoc/AgrovocCode” if you want to set Agrovoc Code. Set it to empty if you are not installing VocBench for managing Agrovoc
    • CFG.CUSTOMDATATYPE= Add custom data types can be added via this parameter. To add multiple data types use semicolon ";" as a separator. For Agrovoc, add http://aims.fao.org/aos/agrovoc/AgrovocCode
  4. Optionally you can pre configure your war file with updated VB Configuration file. To preconfigure, after dropping the war file of VB inside tomcat, have it unzipped by tomcat, then and replace your specific installation information (see entries here below) on the Config.properties file located in vocbench2/WEB-INF/classes. Then, restart tomcat to have it re-loaded.
  5. From the Sesame Workbench for configuring OWLIM, create a new repository (and do not add any data!)
    1. Create new repository.
      • Type: OWLIM-SE
      • ID: AGROVOC_SKOS_VB_2013-07-12
      • Title: AGROVOC_SKOS_VB dated 2013-07-12
      • License file (leave blank for evaluation and use '/'): {owlim.license.path}
      • Repository type: file-repository
      • Ruleset: Empty
      • Base URL: http://aims.fao.org/aos/agrovoc/
      • Total cache memory (min 20m): 120m
      • Main index memory (min 20m): 80m
      • Use predicate indices: true
      • Predicate index memory (min 20m): 20m  
      • Full-text search memory (min 20m): 20m
      • Full-text search indexing policy: On commit
    2. Set custom OWLIM rule set to the path to the file builtin_owl2-rl-fixed.pie in this distribution (see instructions in “Appendix B: OWLIM specific notes” of the full instruction manual).
    3. Add RDF data
      • Base URI: http://aims.fao.org/aos/agrovoc/ (actually it may be left blank if importing an N-Triples or any other format for which the baseuri is already implicit in the file)
      • Context:  put nothing here. And beware, sometimes this can be filled up automatically while you fill other form fields! Give it a last glance before clicking ok at the end of this process, and if it has been filled up, clear it.
      • Data format: (autodetect)
      • RDF Data File: choose the file agrovoc_wb_20130507_VB.nt from its position in your filesystem

Running the System

...

Expect improvements soon

Project Management

The following sections instruct the user on how to create a new project

  1. Project Creation/Deletion
  2. SKOS Concept scheme Management
  3. Ontology Import
  4. Namespace Prefix Mapping Management
  5. Loading pre-existing data
  6. Enabling Indexing

1.   Project creation/deletion

Create new project    

  • Login with the administrator privilege (Only administrator are allowed to delete the project)
  • Once logged in, list of currently available project will be displayed.
  • On the top right corner, click [+] button to add the project.
  • Add window will be prompted to input following parameters:
    • Project name
      • Name of the new project (e.g. {ST.PROJECT.NAME})
    • Project description
      • Description of the project
    • Project type
      • Type of the project (OWL, SKOS, SKOS-XL). Only SKOS-XL is available at the moment.
    • Base URI
    • Semantic Turkey Server URL
  • Click [Connect] button to test the connection to ST Server.
    • If failed, will prompt service failed message. Check if ST Server is running and connection URL is correct.
    • In case of successful connection, it will prompt list of triple Store: OntologyManagerFactorySesame2Impl
  • After triple store selection, it will prompt for available triple storage mode as follows
    • In memory/persistent
    • In memory/no persist
    • Native store/persistent
    • Remote access

  • Creating a plain Sesame2 project (no OWLIM)
    1. select “in memory/persistent”
    2. You can leave the other parameter values (1000, true, true) as they are
    3. Continue with the instructions as in “Running the system”

 

 Delete project

  • Login with the administrator privilege (Only administrator are allowed to delete the project)
  • Once logged in, list of currently available project will be displayed.
  • Select the project to be deleted.
  • On the top right corner, click [-] button to delete the project.
  • Delete window with project name will be prompted.
  • Click [Delete] button to confirm deletion.
  • Delete project will be removed from the list.

 

2.   SKOS Concept Scheme management

  • After login, you will be directed to concept module.
  • If no concept scheme is selected by default, you will be prompted to go to Scheme module to select concept scheme.
  • Click on the [Schemes] link on the main menu bar, to go to Schemes module.
  • List of available concept schemes will be displayed.
  • If none of them is available, click [+] button on top right corner of list box to add new scheme.
  • Add scheme window will be prompted to add following parameters:
    • Scheme URI
    • Scheme label
    • Scheme language
  • After clicking [Add] button, newly added scheme will be displayed in the list.
  • To select the scheme, click on the check box.
  • To delete the scheme, click [-] button on the right end of each scheme.
  • Delete scheme window with scheme URI will be displayed.
  • Click [Delete] button to remove the concept scheme.
  • NOTE: Add/delete scheme is available only to administrator but selection of concept scheme is available to all users.

3.   Ontology Import

  • To import ontology, follow these link on the top menu bar
    • Administration > Ontology
  • Under Imports box, list of imported ontology will be displayed.
  • To import ontology, click [+] button on the top right corner
  • Four options are available
    • Add import from local file
      • This option will import ontology from the locally by providing following parameter
        • Base URI: base uri of the ontology (e.g. http://www.w3.org/2008/05/skos-xl#)
        • Local file : browse locally available ontology file (e.g. c:\skos-xl.rdf)
        • Mirror file: Name of the ontology file to be stored in server as mirror file (e.g. skos-xl.rdf)
    • Add import from ontology mirror
      • This option will import ontology from the mirror file available in the server by selecting from the list
  • To delete the imported ontology, click [-] button on the right end of each ontology.

4.   Namespace Prefix Mapping Management

  • To manage namespace, follow these link on the top menu bar
    • Administration > Ontology
  • Under namespace management box, list of available namespace with their prefix will be displayed.
  • To add new namespace, click [+] button on the top right corner
  • Provide namespace (http://aims.fao.org/aos/

...

  • agrontology#) and prefix (agro) and click [Add] button.
  • To edit namespace, click [pen] button on the right end of the namespace in the list.
  • Change namespace prefix and click [Edit] button.
  • To delete namespace, click [-] button on the right end of the namespace in the list.
  • Delete namespace window will be prompted with namespace and prefix.
  • Click [Delete] button to delete the namespace.

5.   Loading pre-existing data

Creating a new blank project by using Sesame2

  1. Very important: do not use the same Semantic Turkey installation. Just unzip again the server and data folders into another directory (do not even copy the same directories you already unzipped and used for Agrovoc, but take fresh copies from the installation zips). Before running it, however, you have to perform the following actions
    1. Enter inside the ST-Server\configurations\services and open file: “org.ops4j.pax.web.properties” inside a text editor
    2. Change the port number to another free port of your choice (e.g. 1975)
    3. Run as usual through the batches
  2. Now follow the same steps as in “Running the system” for creating a new project. The difference is:
    1. Choose whatever: Project name, project description, base uri you like
    2. As Semantic Turkey Server URL, adopt the previous one, but with the port number modified (no more 1979) to reflect your new port number
    3. As TripleStore, again OntologyManagerFactorySesame2Impl, and again click connect
    4. Now instead of remote access, select “in memory/persistent”
    5. You can leave the other parameter values (1000, true, true) as they are
  3. Continue with the instructions as in “Running the system”

...

  • To load RDF data, click on the [Load data] link in the main menu bar.
  • Input following parameter

...

  • Add import from ontology mirror
  • Namespace: http://aims.fao.org/aos/agrontology. Note that In general, when using VocBench with your own dataset, you need the ontology vocabulary which is being used to model your data, as in each tab of the concept details panel, VocBench looks for subproperties of given standard properties, and so it needs to know where the properties being used are hooked up.

...

...

    • RDF file: browser data file to be imported. (e.g. agrovoc_wb_20130507_VB.nt)
  • Click [Import button] to import data.
  • This process may take some time depending on the size of the data.

6.   Enabling indexing

  • To enable indexing, click on [Advanced search] link below top menu bar at the top right end.
  • Click on the [index] button at the right end.
  • It will prompt to confirm if you want to index. Click the [Ok] button to enable indexing.
  • This process may take some time.
  • This action is only available to administrator users.

 

Creating a new User

We suppose here that you are both the user and administrator of vocbench (see section 4 on VOCBENCH setup).

To add a new user in VocBench follow these steps:

  • Go to http://localhost:8080/vocbench-2.0/index.html and click on "Create an account" under the login form on the right of the page
  • Input all the required information. It is better, even if it is not mandatory, to specify the "Languages you wish to manage" and the "Ontology you wish to manage"
  • At this point the account is not yet allowed to log on.
    • As a user, you can wait for the confirmation email that a request has been sent to the administrator
    • As administrator, you can wait for the email and follow its instructions

If you do not receive any email (maybe a misplaced configuration) you need to manually enable the account by modifying the admin DB (see FAQ 1)