BiocProject 0.2.1 - unreleased

Added

  • pipeline interface support, including functions: getPipelineInterfaces, outputsByPipeline, outputsByProtocol, getPipelines,getProtocolMappings and samplesByProtocol

Changed

  • the bioconductor section can be provided in either in the pipeline interface or in the project config. The project config location is given the priority

BiocProject 0.2 - 2019-04-19

Added

  • the native show methods are redefined for the objects returned by BiocProject::BiocProject function, so that they display the PEP component of the object metadata
  • BiocProject function now handles the case when multiple data processing functions are defined in the config file. The last one is used if there’s no match in readFunName and any of the functions sourced from the file specified in readFunPath

Changed

  • updates in the vignettes related to changes of metadata keys in the Project config
  • when the data processing function function is read from file, it is used within a newly created environment so that it is not left in the .GlobalEnv after the BiocProject function execution

BiocProject 0.1.1 - 2019-02-15

Added

  • passes BiocCheck
  • added option to specify additional arguments in the config file using a funcArgs subsection within the bioconductor section of the PEP config yaml file.

Changed

  • now, any object can be returned by the data processing function, rather than requiring objects to inherit from Annotated
  • when errors are encountered, BiocProject now returns a PEP (pepr::Project) along with the error message in a S4Vectors::List object
  • the bioconductor section of the config file now follows the Bioconductor coding style (camelCaps)

BiocProject 0.1 - 2019-01-28

Added

  • methods: is (overwrites this method behavior just for the class Annotated), .is.project, samples, config for signature Annotated
  • functions: .insertPEP and BiocProject (the workhorse of the package)

Changed

  • complete concept redesign: no BiocProject class. The objects returned by the custom data reading function have to be of class Annotated and the PEP is inserted as the first element of its metadata() list

BiocProject 0.0.4 - 2019-01-25

Changed

  • better custom data loading function error/warning communication
  • all exceptions are caught with BiocProject constructor
  • fix .updateSubconfig(.Object@config, sp) : Subproject not found: warning in toProject method

BiocProject 0.0.3 - 2018-12-21

Changed

  • the default values for all optional arguments are NULL
  • change lambda function to anonymous function

BiocProject 0.0.2 - 2018-12-01

Changed

  • the object constructor does not fail if the pepr::Project object is provided in the funcArgs arguments list
  • if the user-supplied function errors or throws a warning, appropriate messages are nicely displayed
  • errors and warnings (if any) are returned instead of the data
  • if the object constructor can’t find the function file, the message is more informative

BiocProject 0.0.1 - 2018-11-20

Added

  • add BiocProject::BiocProject constructor function
  • add BiocProject::getData method to extract the data from the object
  • allow for passing additional arguments for user-provided functions in BiocProject::BiocProject
  • allow to use lambda functions with func parameter

Changed

  • make BiocProject class inherit from pepr::Project and base::list
  • the initialize method can read in the data with the provided func
  • the object constructor does not fail if the pepr::Project object is provided in the funcArgs arguments list