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Sesame Repository Management

Contents

Loading OpenRDF Workbench

The following are the Sesame workbench locations.

Production Sesame workbench - http://auscope-services.arrc.csiro.au/openrdf-workbench/

Test Sesame workbench - http://auscope-services-test.arrc.csiro.au/openrdf-workbench/

Please contact a member of the Project Team if unsure where to load any data:

SESAME Repository Management via Openrdf-Workbench

Step-by-step method for adding the vocabulary to the repository using the OpenRDF Workbench
  • Change Server - Sesame Server on test and production server only accept GET operations, in order to load a new vocabulary you need workbench to point to localhost:8080

  • change_server_workbench.png

  • Load the OpenRDF Workbench
  • addrepo-1.JPG

  • Select "New repository" in navigation bar on the left

  • Enter id and title details in the form that appears. In this case, id is "new-vocab" and Title is "Demo Vocabulary. Click the "Next" button. addrepo-2.2.JPG

  • Configure the repository type : the following information act as a guide for user to decide which store to use :
    • In Memory Store" - an RDF repository that stores its data in main memory. It is designed for datasets with fewer than 100,000 triples. The memory store uses hash tables, and when these hash tables fill up it copies the values to larger hash tables. This can cause strain on the garbage collection due to lots of memory being allocated and freed.
    • Native Java Store - stores and retrieves its data directly to/from disk. It is designed for datasets between one hundred thousand and one hundred million triples. On most operating systems, if there is sufficient physical memory, the native store will act like an in-memory store, because the read/write commands will be cached in memory by the OS. This technique allows the native store to operate quite well for hundreds of millions of triples.
    • Refer to Sesame User Guide for more information.
  • In most of our use cases, where the dataset has less than 100,000 triples, "In Memory Store" will be chosen. It's important to set the "Persist" option as "Yes". Click on "Create" button to create the repository. If the Persist option is "No", then anything stored in the repository will not appear the next time the server is rebooted.
  • addrepo-3.JPG

  • If successful, you should see the Summary info page with the repository details. addrepo-4.JPG

Adding a 'vocabulary' to the repository

  • Select a Repository to work from. This can be done by clicking on the "change" hyperlink near the top navigation section for "Current Selections" and then clicking on the repository to work from in the list shown. In this case, we will select "new-vocab".

  • addVocab.JPG

  • Click on the "Add" hyperlink under the "Modify" section of the Left navigation bar. The "Add RDF" page should appear.

  • addrepo-5.JPG

  • For SISSvoc we recommend first publishing the vocabulary as an RDF document at a public web address. The vocabulary is then loaded into the repository from the web resource rather than a local file
    1. To add an RDF vocabulary from a web resource, enter the URL in the RDF Data URL: field
    2. Select the Data Format:for the document
      • usually either RDF/XML or Turtle
    3. Accept the default value for the Context:(i.e. the URL for the web resource)
      • The Sesame context field, effectively annotates the repository with provenance information of the vocabulary.
      • In this field a URI must be enclosed in angle brackets
    4. Set the Base URI: to the value specified in the document.
      • This may be the same as the URL for the document, but would normally not include a format extension (e.g. .rdf, .ttl).
      • It will usually be the same as the 'Ontology URI' in the document if one is present.
      • In this field it is not enclosed in angle brackets.
    5. Click upload, if successful, the Summary info page will be displayed.
    6. addrepo-7.JPG

Modifying a 'vocabulary' in the vocabulary service

The following allows for adding items to a vocabulary and adding properties to existing items and vocabularies.

For this section, we will use the following example of updating a skos concept - Carat. In the example we add a mapping to the equivalent URN.

Before:
       <skos:Concept rdf:about="http://www.csiro.au/units-posc2.2/Carat">
                 <skos:broader rdf:resource="http://www.csiro.au/units-posc2.2/MassUoM"/>  
       </skos:Concept>

After:
       <skos:Concept rdf:about="http://www.csiro.au/units-posc2.2/Carat">
           <skos:broader rdf:resource="http://www.csiro.au/units-posc2.2/MassUoM"/>
           <skos:exactMatch rdf:resource="urn:ogc:def:uom:UCUM::%5Bcar_m%5D"/>
       </skos:Concept>

  • Ensure that the updated statements are saved in a file with well-formed and valid RDF. For example, poscUnits22-simulate-update.skos. Below is a screenshot of the posc:Carat triples before the update:

  • update-data1a.JPG

  • Click on the "Add" link on the left navigation bar. Select the file to upload - this is the file with the added or modified statements. Click on the "Upload" button. The workbench then submits the file and the Sesame server processes the additions / updates.

  • update-data1.JPG

  • Below is a screenshot of the same query to posc:Carat showing the added statement.

  • update-data2.JPG

Deleting / Clearing a repository

This section covers deleting elements in a repository, clearing the entire repository and deleting a repository handle.

Deleting elements in a repository

  • Click on the "Remove" link on the left navigation bar.
  • awb-delete1.JPG

  • Enter parts of a triple or an entire triple. If fields are left blank, the system will treat those as wildcard fields. Click the "Remove" button to delete those statements. The screenshot below shows an example that deletes all triples involving posc:Carat.

  • awb-delete2.JPG

Clearing a repository

  • To clear all statements in the repository, click on the "Clear" link on the left navigation bar. The screen will then show the form to clear the repository. To clear all statements in the current repository, leave the "Context" field blank, and click the "Clear Context(s)" button. If there are contexts defined, enter that in the "Context" field instead and click the "Clear Context(s)" button.

  • awb-clear1.JPG

Deleting a repository handle

  • To delete a repository handle, click on the "Delete repository" link on the left navigation bar. This will bring up the form to perform this operation.

  • Select the repository to delete. In this example, we will be deleting the "new-vocab" repository.

  • Click the delete button.

  • The repository handle will be deleted
NOTE: This operation only deletes the handle to the repository, not its data. They will still remain in the repository, so if you really want to delete the repository and its data, you must clear the repository before deleting the handle. Otherwise, if a new repository is defined with the name of a previously deleted repository (e.g. new-vocab), the undeleted data associated with the repository handle will appear and may produce erroneous data. The only definitive way to remove a repository and its content is to log on the repository server and manually remove the folder/files (SESAMERepositoryMigration#Whipping_a_repository).

awb-del-repo1.JPG
Topic attachments
I Attachment Action Size Date Who Comment
addVocab.JPGJPG addVocab.JPG manage 46.2 K 08 Jul 2009 - 14:37 JacquelineGithaiga  
addrepo-1.JPGJPG addrepo-1.JPG manage 51.2 K 08 Jul 2009 - 13:10 JacquelineGithaiga  
addrepo-2.2.JPGJPG addrepo-2.2.JPG manage 38.9 K 08 Jul 2009 - 14:36 JacquelineGithaiga  
addrepo-3.JPGJPG addrepo-3.JPG manage 38.2 K 08 Jul 2009 - 14:36 JacquelineGithaiga  
addrepo-4.JPGJPG addrepo-4.JPG manage 35.7 K 08 Jul 2009 - 14:36 JacquelineGithaiga  
addrepo-5.JPGJPG addrepo-5.JPG manage 58.2 K 08 Jul 2009 - 14:36 JacquelineGithaiga  
addrepo-6.JPGJPG addrepo-6.JPG manage 62.5 K 15 Jul 2009 - 11:11 JacquelineGithaiga  
addrepo-7.JPGJPG addrepo-7.JPG manage 36.5 K 08 Jul 2009 - 14:37 JacquelineGithaiga  
addrepo1.JPGJPG addrepo1.JPG manage 49.2 K 08 Jul 2009 - 14:20 JacquelineGithaiga  
addvocab-1.JPGJPG addvocab-1.JPG manage 53.8 K 08 Jul 2009 - 14:37 JacquelineGithaiga  
awb-clear1.JPGJPG awb-clear1.JPG manage 42.2 K 08 Jul 2009 - 14:38 JacquelineGithaiga  
awb-del-repo1.JPGJPG awb-del-repo1.JPG manage 32.6 K 08 Jul 2009 - 14:44 JacquelineGithaiga  
awb-delete1.JPGJPG awb-delete1.JPG manage 57.6 K 08 Jul 2009 - 14:38 JacquelineGithaiga  
awb-delete2.JPGJPG awb-delete2.JPG manage 62.9 K 08 Jul 2009 - 14:46 JacquelineGithaiga  
change_server_workbench.pngpng change_server_workbench.png manage 133.6 K 17 Jan 2012 - 11:46 JacquelineGithaiga  
update-data1.JPGJPG update-data1.JPG manage 48.7 K 08 Jul 2009 - 14:40 JacquelineGithaiga  
update-data1a.JPGJPG update-data1a.JPG manage 58.2 K 08 Jul 2009 - 14:40 JacquelineGithaiga  
update-data2.JPGJPG update-data2.JPG manage 67.3 K 08 Jul 2009 - 14:40 JacquelineGithaiga  
Topic revision: r28 - 15 Aug 2012, FlorenceTan
 

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