[Bioc-devel] Significant User Interface Change to AnnotationHub and ExperimentHub

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Fri Mar 29 20:30:52 CET 2019

It has been a concern for awhile to have file level checks for when a remote
data resource has been updated.  While we implemented the option to be able to
force download (hub[[force=TRUE]]) we still felt like this should be improved
upon.  With the creation of BiocFileCache, we decided it was time for the Hubs
to switch to use BiocFileCache in the backend to utilize this functionality.

We have pushed these changes to devel Bioc 3.9.

Another big change that came along with this upgraded backend is the default
caching location. BiocFileCache utilized rappdirs::user_cache_dir to determine
the default location of the directory where files would be stored. This has also
been updated in the Hubs. The strategy for naming downloaded files
is also updated to be consistent with BiocFileCache.  So when you update to the
latest versions of AnnotationHub or ExperimentHub , all previously downloaded
resources will have to be redownloaded as the old cache will no longer be valid
and will not recognize the files.

For convenience we provide the helper function
convertHub() / convertHub(hubType="ExperimentHub") that will transition
between the old hub default and new hub default locations, attempting to
redownload any previously downloaded resources. It does not
destroy the old cache location so you will still be able to reference old files,
just not through the Hub interface. If any resources cannot be redownloaded,
please refer to `?AnnotationHub::getInfoOnIds` that is a new helper functinon to
get details on resources.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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