Feature: use fanc meta from neck connective repo

DESCRIPTION

@@ -31,6 +31,7 @@ Imports:
     magrittr,
     bit64,
     usethis,
+    data.table,
     methods
 Suggests: 
     malevnc (> 0.3.1),

R/meta.R

@@ -172,7 +172,39 @@
 
 fanc_meta <- function(ids=NULL, ...) {
   ids=fanc_ids(ids)
-  fancr::with_fanc(fancorbanc_meta(table='neuron_information', ids=ids, ...))
+  df=fancr::with_fanc(fancorbanc_meta(table='neuron_information', ids=ids, ...))
+  metaf=getOption('coconatfly.fanc_meta')
+  if(!is.null(metaf)) {
+    # we can use an unevaluated call as an option
+    # by evaluating we can trigger function
+    if(is.call(metaf))
+      metaf=eval(metaf)
+    else if(is.function(metaf))
+      metaf=metaf()
+
+    df2 <- if(is.data.frame(metaf))
+      metaf
+    else if(is.character(metaf)) {
+      ext=tools::file_ext(metaf)
+      if(ext=='tsv') {
+          data.table::fread(metaf, integer64 = 'character')
+      } else if(ext=='feather') {
+        arrow::read_feather(metaf)
+      } else stop("Unsupported extension:", ext, " for FANC metadata file!")
+    } else stop("options('coconatfly.fancmeta') must be path to a file, a function or an unevaluated R `call`.")
+    df2$root_id=fancr::with_fanc(fafbseg::flywire_updateids(df2$root_id, df2$supervoxel_id, version = fanc_version()))
+    df2 <- df2 |>
+      rename(id=root_id) |>
+      select(-supervoxel_id, -cell_id)
+    df=dplyr::bind_rows(df2, df)
+    df <- df |>
+      filter(!duplicated(id))
+    if(length(ids)>0) {
+      df <- left_join(data.frame(id=ids), df, by='id')
+    }
+  }
+  df$side=sub("HS|idline$", "", df$side)
+  df
 }
 
 banc_meta <- function(ids=NULL, ...) {

R/zzz.R

@@ -0,0 +1,10 @@
+.onLoad <- function(libname, pkgname) {
+  # set up experimental extra
+  coconatfly.fanc_meta=getOption('coconatfly.fanc_meta')
+  if(is.null(coconatfly.fanc_meta)) {
+    options(coconatfly.fanc_meta=function() {
+      fafbseg::flywire_sirepo_file_memo('https://github.com/flyconnectome/2023neckconnective/blob/dev/data/fanc-neckconnective-anns.tsv', read=TRUE)
+    })
+  }
+  invisible()
+}