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ROBOT is licensed under the
BSD 3-Clause License.
Theme by orderedlist
--labels
)--fail-on
)--profile
)--tdb
)--limit
, --base-iri
)The report
command runs a series of quality control SPARQL queries over the input ontology and generates a TSV or YAML report file based on the results. Each query has a logging level to define the severity of the issue: ERROR, WARN, or INFO.
ERROR
: Must be fixed before releasing the ontology. These issues will cause problems for users, such as classes with multiple labels.WARN
: Should be fixed as soon as possible. These will not cause problems for all users, but may not be what they expect. For example, a class that is inferred to be equivalent to another named class.INFO
: Should be fixed if possible. These are for consistency and cleanliness, such as definitions that do not start with an uppercase character.
robot report --input edit.owl --output report.tsv
A summary of the report is also printed to the console:
Violations: 710
-----------------
ERROR: 109
WARN: 572
INFO: 29
The following formats are supported by report
:
The format will be determined by the extension of the --output
(e.g., if the output is report.csv
, the format will be CSV). If you’d like to override this, you can include the --format
option. For example, to force YAML format, include --format YAML
.
HTML format will either be a “standalone” HTML page, or, if you plan to include this table in an existing HTML page, just the HTML table by including --standalone false
. All HTML content is based on Bootstrap.
If you do not provide an --output
and your format is CSV or TSV, all violations will be printed to the console in that format. An --output
must be provided for HTML, JSON, and YAML formats. You can also choose to print the details of the first n
number of violations using --print <n>
. If the format is CSV, it will be printed as comma-separated values, otherwise it will be printed as tab-separated values.
robot report --input edit.owl \
--print 5 \
--output report.tsv
This will print the first five violations and also write the report to report.tsv
. If you do not provide an --output
while using --print <n>
, only the first n
violations will be printed to the terminal.
The report output contains a series of CURIEs and/or IRIs. If you wish to include the entity labels, simply add --labels true
. For large ontologies, this may take a bit longer to complete.
By default, report
will fail if any ERROR
-level violations are found. This can be changed by setting the --fail-on
level to a different logging level. For example, if you want your report to fail if there are any WARN
-level violations:
robot report --input edit.owl \
--fail-on WARN \
--output report.tsv
If the report fails, the command will exit with a status of 1
, but a report will still be generated and written to the output file. To always pass (even with errors), you can set the fail-on level to “none”:
robot report --input uberon_fragment.owl \
--fail-on none \
--output results/report.tsv
report
runs a number of queries, each with a default logging level. See the full list.
Each query retrieves a triple in the form of ?entity ?property ?value
. The ?entity
is the violating entity, the ?property
is the property that is being violated, and ?value
is what is causing the violation (which could be empty).
For example, the query to retrieve references to deprecated classes:
SELECT DISTINCT ?entity ?property ?value WHERE
{?value owl:deprecated true .
?entity a owl:Class .
?entity ?property ?value }
Here, the ?value
is any deprecated class that is referenced in another entity’s axioms.
You can provide your own queries to use in the report (which can be included in the profile, described below). Please make sure to follow this ?entity ?property ?value
pattern when writing these queries.
Each QC query is given the corresponding logging level shown above in the default profile. The profile is a simple text file with a logging level followed by the query name (separated by a tab). Each line represents one query configuration:
ERROR definition_cardinality
INFO deprecated_class
report
allows the user to define their own profile to configure different logging levels and include their own QC queries with the --profile
option:
robot report --input edit.owl \
--profile my-profile.txt \
--output results/my-report.tsv
For all default queries, include the query name shown above. If you do not wish to include a default query in your report, simply omit it from your profile. Any queries not named in the profile will not be run. Furthermore, your own queries can be included by providing the desired logging level followed by the absolute or relative path.
Note that in order for the queries to be included in the report, they must return exactly three variables: ?entity ?property ?value
.
As an example, consider the query we have already mentioned:
SELECT DISTINCT ?entity ?property ?value WHERE
{?value owl:deprecated true .
?entity a owl:Class .
?entity ?property ?value }
For other examples, you can refer to the full list of default checks.
This example would create a report with references to deprecated classes as ERROR and the user query violations as INFO:
ERROR deprecated_class
INFO file:///absolute/path/to/other_query.rq
INFO file:./relative/path/to/other_query.rq
report
may fail on some very large ontologies when ROBOT cannot fit the entire ontology into memory. You can either increase the available memory (see Java Options), or use the --tdb true
option to load the ontology as an Apache Jena TDB Dataset instead of with OWL API:
robot report --input edit.owl \
--tdb true \
--output my-report.tsv
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>
.
Once the report is complete, ROBOT will remove the TDB directory. You can include --keep-tdb-mappings true
to prevent ROBOT from removing the TDB directory (which may be beneficial if you want to reuse it with query). This will greatly reduce the execution time of subsequent TDB-based operations on the ontology.
Large numbers of results from the report queries may cause an OutOfMemoryError
. To prevent this, you can limit the number of results with --limit <INTEGER>
:
robot report --input edit.owl \
--limit 10000 \
--output my-report.tsv
This example will only include the first 10,000 results for each report query, meaning that some violation counts may be incomplete. Typically, you should not need to include a limit, but when working with large ontologies (using TDB), there may be hundreds of thousands of results.
The results can also be restricted to entities following one or more URI prefixes.
robot report --input edit.owl \
--base-iri "http://purl.obolibrary.org/obo/UBERON_" \
--base-iri "https://github.com/ontodev/robot/examples/edit" \
--base-iri "http://purl.obolibrary.org/obo/UBPROP_" \
--output my-base-report.tsv
Note that if you want annotations on your ontology itself be checked, be sure to
include a suitable URI prefix. For example, in the snippet above, we have
included https://github.com/ontodev/robot/examples/edit
, which ensures that
ontology annotations on https://github.com/ontodev/robot/examples/edit.owl
are
included in the test results.
By default the report command will operate over the specified ontology, ignoring the import chain. This means if your ontology uses a class, and the class label is asserted in an import, you will receive a missing label error.
To change this behavior, you can merge the imports closure using the merge command. This can be done by chaining commands together, for example:
robot merge --collapse-import-closure true -i my-ont.owl report -o my-ont-report.tsv
Only info
, warn
, and error
are valid inputs for --fail-on
.
The argument for the --limit
option must be a number.
All queries must bind ?entity ?property ?value
for correct formatting. If ?entity
is ever null
, the query cannot be reported on.
The argument for the --print
option must be a number.
The logging level defined in a profile must be ERROR
, WARN
, or INFO
.
When not using the file:
prefix in your --profile
, make sure you are only using rule names from the list of default report queries).