A lot of the past week has been focused on some catching up and tidying up in my active projects in metadata manipulation and publishing tools, EML, RNeXML, and rfigshare. The full story of the week and half unfolds on github, but summarizing progress here.
rfigshare
Changes to httr interface orginally broke rfigshare, though working with @hadley the original mechanism was restored through sign_oauth1.0(). The changes provided a much nicer mechanism for handling oauth authentication without having to specify tokens directly, and resulted in a relatively straightforward overhaul of the authentication mechanism in the package, while still preserving the package API. During this process I also tackled a bunch of outstanding issues, such as: pretty-printing results, fixing behavior of search and adding authors, getting embeddable image URLs and flushing out the test suite and activiting full travis integration of the tests. See package NEWS for a more complete list (v0.2-9 and v0.3). This version is now on CRAN.
In the process I learned a bit more about httr’s oauth handling.
RNeXML
Main focus has been moving manuscript text foward, flushing out a more complete description of package functions, organization, and use cases. In particular this has focused on:
Outlining the tiered levels of metadata manipulation (from the elementrary
get_metadata()to the XPath and SPARQL queries) and metadata generation (fromtitleandcreatorto automatic taxonomic reference links using taxize to building on existing and custom ontologies; and the related example of extending the schema itself using metadata (simmap).Finalizing and writing out this simmap example was the other goal, illustrating extending the package.
Lost too much time on some of the fine points of travis integration with package dependencies on specific users and branches of Github, on omegahat, and cases where apt-get cannot get background dependencies automatically.
EML
Still need to continue mansucript writing and extending functionality; meanwhile minor changes to reflect updates to rfigshare and to travis integration.
rfishbase
Some momentum on rfishbase2.0 thanks to involvement from @tpoi