Verify

Contents

1. Overview
2. Fail on Violation (--fail-on-violation)
3. Executing on Disk (--tdb)

Overview

The verify command is used to check an ontology for violations of rules. Each rule is expressed as a SPARQL SELECT query that matches violations of the rule. If the query produces any results, verify will exit with an error message that reports the violations. If the ontology conforms to the rule, the query should find no violations, and the verify command will succeed.

In the verify command, you specify a set of queries using the --queries parameter and specify an output directory for the result using the --output-dir parameter, e.g. --queries query-file-1 query-file-2 … --output-dir some-directory

For example:

robot verify --input asserted-equiv.owl --queries equivalent.sparql --output-dir results/

Should output as a response:

Rule /ontodev/robot/examples/equivalent.sparql: 1 violation(s)
first,second,firstLabel,secondLabel
http://purl.obolibrary.org/obo/TEST_A,http://purl.obolibrary.org/obo/TEST_B,,

And the CSV file results/equivalent.csv should have:

first,second,firstLabel,secondLabel
http://purl.obolibrary.org/obo/TEST_A,http://purl.obolibrary.org/obo/TEST_B,,

Fail on Violation

By default, this command will fail with a non-zero exit code when any violations are found. If you wish the command to succeed (e.g., for use for warnings in workflows), you can include --fail-on-violation false. Note that it will still log FAIL Rule [rule name] on the command line.

robot verify --input asserted-equiv.owl \
  --queries equivalent.sparql \
  --fail-on-violation false \
  --output-dir results/

Executing on Disk

For very large ontologies, it may be beneficial to load the ontology to a mapping file on disk rather than loading it into memory. This is supported by an Apache Jena TDB Dataset. To execute verify with TDB, use --tdb true:

robot verify --input asserted-equiv.ttl \
  --tdb true \
  --queries equivalent.sparql \
  --fail-on-violation false \
  --output-dir results/

Please note that this will only work with ontologies in RDF/XML or Turtle syntax, and not with Manchester Syntax. Attempting to load an ontology in a different syntax will result in a Syntax Error. ROBOT will create a directory to store the ontology as a dataset, which defaults to .tdb. You can change the location of the TDB directory by using --tdb-directory <directory>. If a --tdb-directory is specified, you do not need to include --tdb true. If you’ve already created a TDB directory, you can verify from the TDB dataset without needing to specify an --input - just include the --tdb-directory.

Once the verify operation is complete, ROBOT will remove the TDB directory. If you are performing many verify commands on one ontology, you can include --keep-tdb-mappings true to prevent ROBOT from removing the TDB directory. This will greatly reduce the execution time of subsequent TDB-based operations on the ontology.

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Error Messages

Verification Failed

At least one of the query you specifies returned results. The number of failures for each rule will be printed. A CSV file will be generated with the results that matched the rule.

Missing Query Error

You must specify at least one query to execute with --queries.