[Bioc-devel] TypeInfo
Dear Robert and Martin, thanks for your answers! That is really encouraging and interesting. I had read the R News article / vignette (but then was surprised at seeing so little use in madman/Rpacks and in the svn log of the package directory.)
Martin wrote:
If you'd like an example, point to a suitable function and I'll generate something
The function "justvsn" would be appropriate.
The input arguments to S4 methods are already strongly typed, so for these methods the benefit of TypeInfo is restricted to specifying return values.
Question: I have a function
setGeneric("vsn2",
function(x, reference, strata, ...)
standardGeneric("vsn2"))
and methods like:
setMethod("vsn2", "ExpressionSet",
function(x, reference, strata, ...)
vsnMatrix(exprs(x), reference, strata, ...))
for which not _all_ arguments are typed in the signature (vsnMatrix is a
'normal' R function). As far as I understand (and it may be wrong),
these arguments can also not be typed with TypeInfo. So is this style of
programming discouraged?
Best wishes
Wolfgang
Martin Morgan wrote:
Hi Wolfgang -- Yes, you should do it! There's a vignette in TypeInfo written in the form of an R News article (though not published as such) that outlines the basic steps & benefits. It's used in our RWebServices packages, which should make it to Rpacks real soon now. We've exposed functionality of DNAcopy, PROcess and affy as web services (http://cabig.bioconductor.org/axis/services; affy is not there yet, these are not meant to be 'production' services). There's a powerpoint presentation at http://tinyurl.com/34u4lq discussing some issues; slides 7-15 illustrate some of the functionality, slides 27-28 sketch TypeInfo approaches. TypeInfo provides functionality that is useful for ensuring that incoming and return arguments match specified type. This means that the code in the functions can focus on the operations they perform, rather than checking that the arguments are valid. TypeInfo also provides the language 'reflection' that's necessary when moving from a weakly typed language like R to strongly typed languages like Java or xsd-based web representations of data and methods. It also makes creation of, e.g., graphical widgets easier. There are costs to TypeInfo, in that the argument and return types are actually checked (could be computationally expensive, but probably not in terms of the overall functionality of vsn). Also, TypeInfo offers advanced features that are beyond what the ArrayExpress people want -- basically, you'll want to stick to SimulataneousTypeSpecification with TypedSignature matching arguments to specific classes (TypeInfo could, in principle, do things like make sure that the lengths of different input vectors were the same, or that there were no NA values, or...) Which also points to an important issue, that to be useful in the web services environment TypeInfo has to identify either primitive types (e.g., "numeric") or S4 classes; S3 classes are not structured enough to be useful. The input arguments to S4 methods are already strongly typed, so for these methods the benefit of TypeInfo is restricted to specifying return values. In terms of the ArrayExpress request, my experience has been that the web environment probably wants to 'see' only selected functions or functions that integrate a series of steps into a convenient work flow. The basic issues are: big data transfer (which will make repeated 'interactive' calls impossibly slow); restricted functionality (side effects like image creation are hard to deal / need to be made into main effects with in the web context); and maybe a need to expose only methods and parameters that are suitable for consumption by the general populace rather than the full gamut of options relevant to exploratory analyses or research statisticians. For these reasons, we ended up writing 'wrapper' packages that contain a small number of 'work flow' functions that take and return S4 classes, and that have TypeInfo applied. We did some initial investigation with vsn and it seemed quite possible to add the necessary information. If you'd like an example, point to a suitable function and I'll generate something for you. Martin Wolfgang Huber <huber at ebi.ac.uk> writes:
Hi Martin, Robert, Seth
what's up with "TypeInfo"? Seems that nobody has been using it so far in
Bioconductor:
huber at lobito:~/madman/Rpacks$ find . -name DESCRIPTION \
-exec grep -H TypeInfo {} \;
./TypeInfo/DESCRIPTION:Package: TypeInfo
......and nothing else......
and the last substantial svn commits are from 2005.
Misha's person at ArrayExpress who wants to put Web-GUIs on
bioc-packages has asked me to provide the functions in vsn with
TypeInfo, is that something worthwhile?
Best wishes
Wolfgang
------------------------------------------------------------------
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber