1.31.0

• introduce statements in FactorValues by @arteymix
• improved parsing of GEO metadata for populating sample characteristics by @ppavlidis
• replace Compass with Hibernate Search
• new tool for finding obsolete terms by @ppavlidis
• remove Guava
• improve permission masking and jointures in AclQueryUtils
• migrated the CI to Jenkins Pipeline
• gradually getting rid of Apache Configuration 2 with built-in Spring support for property placeholders

FactorValue semantics

The main feature this release bring is the introduction of semantics in factor values. Previously, a factor value was annotated with a simple bag of ontology terms. In some cases, annotations were ambiguous and made it difficult to interpret the experimental design.

An example would be a treatment with two compounds and two doses. Which dose applies to which compound? This is resolved by creating two statements: "compound A delivered at dose B", "compound C delivered at dose D".

REST API-wise, we now display statements alongside old-style characteristics.

Our factor values are also made available in OWL/RDF. For example, the FactorValue #138393 from GSE10721 can be retrieved with:

curl -H Accept:application/rdf+xml https://gemma.msl.ubc.ca/ont/TGFVO/138393

Full Changelog: 1.30.6...1.31.0