owlcollab / owlcollab/owltools

Add or confirm support for GAF 2.2 to owltools

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bug
Dominant language
Java
Stars
115
Forks
34
PR merge metrics
No merged PRs in 30d

Description

I believe that currently owltools would not support the upcoming GAF 2.2 spec particularly well. While the only material difference for the new spec is that many more qualifiers are allowed, eyeballing a few sections in owltools, it seems that often what is there for the qualifiers is hard-coded in.

For example, I've found possibly problematic sections in:

./OWLTools-Annotation/src/main/java/owltools/gaf/godb/GoMySQLDatabaseDumper.java:520:								this.getTermInternalId("contributes_to"),
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/GpadGpiObjectsBuilder.java:304:			relation = "contributes_to";
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/BuilderTools.java:146:	contributesTo("contributes_to", "(contributes[_ ]to)"),
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/BuilderTools.java:371:	sb.append("contributes_to");
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/BuilderTools.java:404:	qualifiers.add("contributes_to");
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/GafObjectsBuilder.java:257:			relation = "contributes_to";
./OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:391:	comb_aqual = comb_aqual + "contributes_to";
./OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:392:	annotation_doc.addField("qualifier", "contributes_to");
./Golr-Client/src/main/java/org/bbop/golr/java/RetrieveGolrAnnotations.java:97:else if ("contributes_to".equalsIgnoreCase(qualifier)) {

(obviously not exhaustive)

For our purposes, owltools can assume that the incoming files are "good" 2.2/2.1--we just want to make sure that the additional qualifiers can pass through where hard-coded lists now exist.

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Research direction

Start by tracing the hard-coded qualifier handling in OWLTools-Annotation/src/main/java/owltools/gaf/parser/BuilderTools.java, GafObjectsBuilder.java, and GpadGpiObjectsBuilder.java. Then inspect the listed GoMySQLDatabaseDumper, GafSolrDocumentLoader, and RetrieveGolrAnnotations paths for additional restrictions. Done means valid GAF 2.2 qualifiers pass through the parser and downstream loaders without relying on an exhaustive hard-coded list.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
tooling
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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