dbnsfp variant: replaced annotate with annotateEntity. Closed resource leak for buffered readers. Edited determineFeatures. The file and features are no longer class constants.
CADD: removed unused imports. Runtime properties now set. replaced annotate with annotateEntity. tabix and cadd file are no longer class constants. fixed resource leak for buffered reader.
removed unused imports.
CGD: Fixed resource leak for buffered reader. removed unused imports. cgd file now runtime property
dbnsfp gene: removed unused imports. gene file now runtime property. replaced annotate with annotateEntity. fixed resource leak for buffered readers. features and gene file are no longer class constants.
dbNSFP annotators: Header is no longer parsed for features, all features are not hardcoded inside the annotator class. This allows for setting the type per feature, instead of only strings. Removed determineFeature method from both annotators.
removed js from template that was not using it. prevents javaScript errors
Added a new method to the RepositoryAnnotator super class. annotationDataExists checks if the location that was set with runtime properties actually contains a file. If not, the annotator is disabled.
All annotators: Added annotationDataExists method. Annotators now check whether the runtime property that was set actually leads to an existing file. If the file does not exist, the annotator is simply disabled.
Runtime properties for every annotator are set using the molgenis.home directory as a base. Every annotator checks individually whether a RTP actually leads to a file.
Removed annotationDataExists from the interface
annotationDataExists now an abstract method, usable by canAnnotate. Instead of setting canAnnotate to false, return false directly.
Annotators: Instead of setting a boolean based on the file.exists method, return the outcome of .exists() right away.