Could path,DelayedArray-method just defer to the path() of its @seed?

[LTLA]

Curently path(<DelayedArray>) just calls path(<DelayedOp>), which effectively tries to call path(seed(object)). Could a dedicated path,DelayedArray-method be added that calls path(object@seed)?

As per the conclusion of #119, my ReloadedArraySeed class now inherits from DelayedUnaryIsoOp, but its path() method is not respected when calling path(<ReloadedArray>). This is because the seed() call follows the new inheritance path for the DelayedUnaryIsoOp, retrieving the ReloadedArraySeed's seed instead of the ReloadedArraySeed itself. Subsequently, the path() call uses the seed's method instead of my custom ReloadedArraySeed method, which is not intended.

The proposed change to path(object@seed) should not affect any existing behavior. If @seed is a DelayedOp, path() will still call seed() to get the underlying seed; and if @seed is something else, directly using its path() method is arguably less surprising than whatever we might get from following seed() (if it even runs at all, e.g., error from multiple seeds).

[hpages]

Hmm.. even with the dedicated path,DelayedArray-method, my current path,DelayedOp-method method is still in the way:

library(DelayedArray)
y <- DelayedArray(rsparsematrix(1000, 100, 0.05))
y <- log1p(abs(y) / 1:100)

library(alabaster.matrix)
z <- ReloadedArray(path=tempdir(), y)

path(z)
# [1] "/tmp/RtmpXXEFKs"

path(z * 10)
# Error: unable to find an inherited method for function ‘path’ for signature ‘object = "dgCMatrix"’

Adding the dedicated path,DelayedArray-method:

setMethod(path, "DelayedArray", function(object, ...) path(object@seed, ...))

path(z * 10)
# Error: unable to find an inherited method for function ‘path’ for signature ‘object = "dgCMatrix"’

Need to implement path() in a recursive manner, like I did for seed(). Then no need for dedicated methods for DelayedArray or ReloadedArray objects. You'll only need the path,ReloadedArraySeed-method.

Working on that change now...

sessionInfo()

R Under development (unstable) (2024-10-22 r87265)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 23.10

Matrix products: default
BLAS:   /home/hpages/R/R-4.5.r87265/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] alabaster.matrix_1.7.3 alabaster.base_1.7.2   DelayedArray_0.33.2   
 [4] SparseArray_1.7.2      S4Arrays_1.7.1         abind_1.4-8           
 [7] IRanges_2.41.1         S4Vectors_0.45.2       MatrixGenerics_1.19.0 
[10] matrixStats_1.4.1      BiocGenerics_0.53.3    generics_0.1.3        
[13] Matrix_1.7-1          

loaded via a namespace (and not attached):
 [1] zlibbioc_1.53.0         lattice_0.22-6          rhdf5filters_1.19.0    
 [4] XVector_0.47.0          Rhdf5lib_1.29.0         HDF5Array_1.35.1       
 [7] grid_4.5.0              rhdf5_2.51.0            compiler_4.5.0         
[10] tools_4.5.0             alabaster.schemas_1.7.0 Rcpp_1.0.13-1          
[13] jsonlite_1.8.9          crayon_1.5.3           

[hpages]

Done in DelayedArray 0.33.3 (see commit a782607).

With this version:

library(DelayedArray)
y <- DelayedArray(rsparsematrix(1000, 100, 0.05))
y <- log1p(abs(y) / 1:100)

library(alabaster.matrix)
z <- ReloadedArray(path=tempdir(), y)

path(z)
# [1] "/tmp/RtmpoVqLhJ"

path(z * 10)
# [1] "/tmp/RtmpoVqLhJ"

You should no longer need the path() method for ReloadedArray objects.

[LTLA]

Thanks, looks good on my end.