Fix handling of unique bodyids

R/connectivity.R

@@ -15,7 +15,7 @@ neuprint_get_adjacency_matrix <- function(bodyids, dataset = NULL, all_segments
       "WHERE n.bodyId IN input AND m.bodyId IN input",
       "RETURN n.bodyId AS upstream, m.bodyId AS downstream, c.weight AS weight, n.%s AS upName, m.%s AS downName"
     ),
-    id2json(bodyids),
+    id2json(bodyids, uniqueids = TRUE),
     all_segments.json,
     namefield,
     namefield
@@ -50,17 +50,21 @@ neuprint_connection_table <- function(bodyids, prepost = c("PRE","POST"), roi =
   prepost = match.arg(prepost)
   conn=neuprint_login(conn)
   all_segments.json = ifelse(all_segments,"Segment","Neuron")
+  bodyids=unique(id2bit64(bodyids))
   if(!is.null(roi)){
     roicheck = neuprint_check_roi(rois=roi, dataset = dataset, conn = conn, ...)
   }
   if(progress){
-    d  = do.call(rbind, pbapply::pblapply(bodyids, function(bi) tryCatch(neuprint_connection_table(
+    # sadly you can't lapply a set of int64 ...
+    d  = do.call(rbind, pbapply::pblapply(as.character(bodyids), function(bi) tryCatch(neuprint_connection_table(
       bodyids = bi,
       prepost = prepost,
       roi = roi,
       progress = FALSE,
       dataset = dataset, conn = conn, ...),
       error = function(e) NULL)))
+    d <-  d[order(d$weight,decreasing=TRUE),]
+    rownames(d) <- NULL
     return(d)
   }
   cypher = sprintf(paste("WITH %s AS bodyIds UNWIND bodyIds AS bodyId",
@@ -85,6 +89,7 @@ neuprint_connection_table <- function(bodyids, prepost = c("PRE","POST"), roi =
   d$weight <- as.integer(d$weight)
   d$prepost <-  ifelse(prepost=="PRE",0,1)
   d <-  d[order(d$weight,decreasing=TRUE),]
+  rownames(d) <- NULL
   d[,c("bodyid", "partner", "roi","weight", "prepost")]
 }
 
@@ -119,7 +124,7 @@ neuprint_common_connectivity <- function(bodyids, statuses = NULL,
   all_segments = ifelse(all_segments,"true","false")
   Payload = noquote(sprintf('{"dataset":"%s","neuron_ids":%s,"statuses":%s,"find_inputs":%s,"all_segments":%s}',
                             dataset,
-                            id2json(bodyids),
+                            id2json(bodyids, uniqueids = TRUE),
                             ifelse(is.null(statuses),jsonlite::toJSON(list()),jsonlite::toJSON(statuses)),
                             find_inputs,
                             all_segments))
@@ -169,6 +174,8 @@ neuprint_simple_connectivity <- function(bodyids,
                                          ...){
   prepost = match.arg(prepost)
   find_inputs = ifelse(prepost=="PRE", "false","true")
+  # nb looks odd, but convert back to character to allow pblapply ...
+  bodyids=as.character(unique(id2bit64(bodyids)))
   if(length(bodyids)>10){
     m  = Reduce(function(x,y,...) dplyr::full_join(x,y,by=c("name",ifelse(prepost=="PRE","output","input"),"type")),(pbapply::pblapply(bodyids, function(bi) tryCatch(neuprint_simple_connectivity(
                                 bodyids = bi,
@@ -254,8 +261,8 @@ neuprint_get_paths <- function(body_pre, body_post, n, weightT=5, roi=NULL,
                            "ALL (x in relationships(p) WHERE x.weight >= %s %s)",
                            "RETURN length(p) AS `length(path)`,[n in nodes(p) | [n.bodyId, n.instance, n.type]] AS path,[x in relationships(p) | x.weight] AS weights"
   ),
-  id2json(body_pre),
-  id2json(body_post),
+  id2json(body_pre, uniqueids = TRUE),
+  id2json(body_post, uniqueids = TRUE),
   all_segments.json,
   n[1]-1,
   n[2],
@@ -320,8 +327,8 @@ neuprint_get_shortest_paths <- function(body_pre,body_post,weightT=5,roi=NULL,da
                            "ALL (x in relationships(p) WHERE x.weight >= %s %s)",
                            "RETURN length(p) AS `length(path)`,[n in nodes(p) | [n.bodyId, n.instance, n.type]] AS path,[x in relationships(p) | x.weight] AS weights"
   ),
-  id2json(body_pre),
-  id2json(body_post),
+  id2json(body_pre, uniqueids = TRUE),
+  id2json(body_post, uniqueids = TRUE),
   all_segments.json,
   all_segments.json,
   weightT,

R/ids.R

@@ -1,5 +1,5 @@
 # private function to convert 1 or more 64 bit ids (e.g. body ids) to JSON
-id2json <- function(x, uniqueids=TRUE, ...) {
+id2json <- function(x, uniqueids=FALSE, ...) {
   bx=id2bit64(x)
   if(isTRUE(uniqueids)) bx=unique(bx)
   jsonlite::toJSON(bx, ...)

R/name.R

@@ -10,6 +10,15 @@
 #' }
 neuprint_get_neuron_names <- function(bodyids, dataset = NULL, all_segments = FALSE, conn = NULL, ...) {
   all_segments.json = ifelse(all_segments,"Segment","Neuron")
+  bodyids <- id2bit64(bodyids)
+  if(any(duplicated(bodyids))) {
+    ubodyids=unique(bodyids)
+    unames=neuprint_get_neuron_names(bodyids=ubodyids, dataset=dataset,
+                                     conn=conn, all_segments=all_segments, ...)
+    res=unames[match(bodyids, ubodyids)]
+    return(res)
+  }
+
   cypher = sprintf("WITH %s AS bodyIds UNWIND bodyIds AS bodyId MATCH (n:`%s`) WHERE n.bodyId=bodyId RETURN n.instance AS name",
                    id2json(bodyids),
                    all_segments.json)

tests/testthat/test-connectivity.R

@@ -0,0 +1,10 @@
+skip_if(as.logical(Sys.getenv("SKIP_NP_SERVER_TESTS")))
+
+test_that("neuprint_connection_table works", {
+  expect_is(t1 <- neuprint_connection_table(c(818983130, 1796818119)),
+            'data.frame')
+  # ensure we get the same answer with progress=TRUE
+  expect_equal(neuprint_connection_table(c(818983130, 1796818119),
+                                         progress = TRUE),
+               t1)
+})

tests/testthat/test-ids.R

@@ -20,11 +20,11 @@ test_that("id conversion works", {
                med.json)
 
   expect_equal(as.character(id2json(c(bigid, bigid))),
-               big.json)
-  expect_equal(as.character(id2json(c(bigid, bigid), uniqueids=FALSE)),
                big.json2)
-  expect_equal(as.character(id2json(list(bigid, bigid))),
+  expect_equal(as.character(id2json(c(bigid, bigid), uniqueids=TRUE)),
                big.json)
+  expect_equal(as.character(id2json(list(bigid, bigid))),
+               big.json2)
 
   df=data.frame(bodyId=bigid)
   expect_equal(as.character(id2json(df)),