• Created by Unknown User (jrpence), last modified on Jul 19, 2011

Qualify

The purpose of this tools is to allow batch changes to be applied to data within a jena model.

Reason for Use

When there are sections of data that need to be removed or changed then the qualify tool is a way of performing
those changes without the need to know how to form the sparql update queries.

Parameters

wordiness - (optional) sets the lowest level of log messages to be displayed to the console. The lower the log level, the more detailed the messages.

  • Possible Values:
    • OFF - Results in no messages being displayed.
    • ERROR - Results in only messages from the ERROR level to be displayed. Error messages detail when the tool has experienced an error preventing it from completing its task
    • WARN - Results in only messages above and including WARN level messages to be displayed. Match does not produce any WARN level messages.
    • INFO - (Default) Results in all messages above and including INFO level messages to be displayed. INFO level messages detail when the tool has started and ended and when it begins/ends a phase ('Finding matches' and 'Beginning Rename of matches') and how many matches have been found.
    • DEBUG - Results in all messages above and including DEBUG level messages to be displayed. DEBUG level messages detail each matching input URI to its VIVO URI as they are processed. Additionally, it will display stacktrace information if an error occurs.
    • ALL or TRACE - Results in all messages above and including TRACE level messages to be displayed, since trace is the lowest level it is the same as ALL in practice. TRACE level messages details every matching set as it is processed in each phase along with SPARQL queries and start and stop for their execution.
      modelsource - Provides the information needed for the connection to the source data model, which is the model that will be searched and modified.
  • model.conf.xml
    predicate - When making changing the data related to a predicate this is the value which will be used as that predicate.
  • predicate
    regexMatch - When using regular expressions from a matching string, this is the field which will hold that string with regex characters.
  • Regex string
    textMatch - When matching a text string, this is the field which will hold that string.
  • match string
    value - This field gives the value that is used to replace the selected strings.
  • replacevalue
    remove-namespace - This namespace is to be removed during the run of quality when paired with predicate-clean or clean-resources. Any resources within this namespace are removed from the model. It is used when there is a namespace used for part of the harvest but is not part of the data that is due for harvest.
  • namespace
    predicate-clean - A flag to signify that the triples which have a predicate within the given remove-namespace are removed from the source. This is useful when removing the data can be specified by a predicate namespace.
  • true
    clean-resources - This flag signifies that triples which have either a subject or object within the given remove-namespace is to be removed.
  • true

Qualification will execute specific user defined sparql queries against a model in order to clean and qualify the data contained inside the model before storing inside of VIVO. Qualification queries will be site specific. As such the default configuration for the harvester doesn't currently invoke Qualification.

Overview

Short Option

Long Option

Parameter Value Map

Description

Required

d

datatype

RDF_PREDICATE

data type (rdf predicate)

false

i

jenaConfig

CONFIG_FILE

config file for jena model

false

I

jenaOverride

JENA_PARAM = VALUE

override the JENA_PARAM of jena model config using VALUE

false

r

regexMatch

REGEX

Match this regex expression

false

t

textMatch

MATCH_STRING

Match this exact text string

false

v

value

REPLACE_VALUE

Replace matching record data with this value

false

n

remove-namespace

RDF_NAMESPACE

Specify namespace for p/predicate clean and -c/-clean-resources flag

false

p

predicate-clean

 

remove all statements where the predicate is from the given n/-remove-namespace

false

c

clean-resources

 

remove all statements where the subject or object is from the given n/-remove-namespace

false

Usage

preparation:
Qualify="java $OPTS -Dprocess-task=Qualify org.vivoweb.harvester.qualify.Qualify"
MATCHEDINPUT="-i $H2MODEL -ImodelName=$MATCHEDNAME -IdbUrl=$MATCHEDDBURL -IcheckEmpty=$CHECKEMPTY"

Call:
$Qualify $MATCHEDINPUT -n http://vivoweb.org/ontology/score -p

Methods

strReplace

  1. Get statements of the specified dataType with the oldValue
  2. iterate through those statements
    1. replace oldValue with newValue

regexReplace

  1. get statements with the given predicate and who's object matches the regexMatch filter
  2. assemble insert and delete sparql statements to delete the old and insert the new.

cleanResources

  1. construct and call the query to remove subjects and objects in the given namespace

cleanPredicates

  1. construct and call the query to remove predicates in the given namespace

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