Add --clean-obo option to convert.
#1236
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This commit adds a `--clean-obo` option to the `convert` command.
The option accepts a space-separated list of options that dictate how
OBO output should be tweaked:
* `drop-extra-labels` (if an entity has more than one rdfs:label
annotation, keep the first label only);
* `drop-extra-definitions` (likewise, but for IAO:0000115 definitions);
* `drop-extra-comments` (likewise, but for rdfs:comment annotations);
* `merge-comments` (merge rdfs:comment annotations into a single
annotation);
* `drop-untranslatable-axioms` (drop axioms that cannot be represented in
the OBO format instead of putting them in a owl-axioms header tag);
* `drop-gci-axioms` (drop general concept inclusion axioms).
In addition, the option accepts the following keywords:
* `strict`: equivalent to `drop-extra-{labels,definitions,comments}`;
* `simple`: equivalent to `strict drop-untranslatable-axioms
drop-gci-axioms`;
* `true`: equivalent to `simple`.
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Not sure what caused the Java 11 test to take more than 10 minutes (thereby triggering a failure)… Can’t reproduce here, on my machine the test suite runs fine with Java 11, Java 17, and Java 21 in about 2.5 minutes. |
Whatever it was it was temporary |
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This is really excellent! I'm very happy with the design, and the code looks good too. Please add some tests, the I'll kick the tired, and we'll get this merged. |
I've also seen intermittent timeouts from one of the three Java versions, but haven't noticed a pattern, and it will be hell to debug. So I just re-run the failing one and it usually passes the second time. Not ideal. |
Add two unit tests for the new methods dropExtraAnnotations and mergeExtraAnnotations in the OntologyHelper class.
Test the overall --clean-obo feature with three new integration tests in
convert.md.
The tests use a new sample file (cl_module.ofn) which is a small CL
module built around CL:0000583 ("alveolar macrophage"). That module
contains instances of all the things that --clean-obo is suppose to deal
with:
* supernumerary annotations (two comments on CL:0000583)
* axioms that are not translatable into pure OBO:
'has characteristic' some 'cell morphology' SubClassOf cell
* (translatable) GCI axioms:
cell and ('has characteristic' some mononucleate)
SubClassOf 'has part' some nucleus`
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@jamesaoverton Tests added. :) |
robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java
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Add an optional argument to OntologyHelper.mergeExtraAnnotations to allow the caller to specify the separator string to insert between annotation values, when merging annotations together. The default separator is a single space character. This is a code-level feature only. The separator string is _not_ customizable from the command-line, when comment annotations are merged as part of `--clean-obo merge-comments`.
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Sorry for taking so long to get back to this. Much appreciated! |
Resolves [#995]
docs/have been added/updatedmvn verifysays all tests passmvn sitesays all JavaDocs correctCHANGELOG.mdhas been updatedThis PR adds a
--clean-obooption to theconvertcommand, as discussed in #995.The option accepts a space-separated list of keywords that dictate how OBO output should be tweaked:
drop-extra-labels: if an entity has more than onerdfs:labelannotation, keep the first label only;drop-extra-definitions: likewise, but forIAO:0000115definitions;drop-extra-comments: likewise, but forrdfs:commentannotations;merge-comments: alternative todrop-extra-comments: mergerdfs:commentannotations into a single annotation, instead of keeping only the first one;drop-untranslatable-axioms: drop axioms that cannot be represented in the OBO format instead of putting them in aowl-axiomsheader tag;drop-gci-axioms: drop general concept inclusion axioms.In addition, the option accepts the following shortcut keywords:
strict: equivalent todrop-extra-labels drop-extra-definitions drop-extra-comments;simple: equivalent tostrict drop-untranslatable-axioms drop-gci-axioms;true: equivalent tosimple.