owlcollab / owlcollab/owltools
Add or confirm support for GAF 2.2 to owltools
Nobody has claimed this yet.
- 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.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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