Updated functions to produce neuroglancer links for tracing workflows…

… from seatable * added hidden function crantr:::crant_table_update_tracing to add ngl_link to rows with 'TRACING_ISSUE' as a status * fixed crant_scene by pointing it to the right layer for CRANT root IDs * helper function crant_ngl_segments to get CRANT root IDs from CRANT scenes
flyconnectome · Oct 27, 2024 · 1f5b590 · 1f5b590
1 parent dc96eb2
commit 1f5b590
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Showing 5 changed files with 262 additions and 256 deletions.
diff --git a/R/ant-table.R b/R/ant-table.R
@@ -300,4 +300,54 @@ crant_table_annotate <- function(root_ids,
   invisible()
 }
 
+# crant table update tracing
+# hidden
+crant_table_update_tracing <- function(table = "CRANTb_meta",
+                                       base = "CRANTb"){
+
+  # Get current table
+  cat('reading CRANT meta seatable...\n')
+  ac <- crant_table_query(sql = sprintf('select _id, root_id, status, ngl_link from %s',table),
+                          base = base) %>%
+    dplyr::select(!!rlang::sym("root_id"),
+                  !!rlang::sym("status"),
+                  !!rlang::sym("ngl_link"),
+                  !!rlang::sym("_id"))
+  ac[ac=="0"] <- NA
+  ac[ac==""] <- NA
+
+  # Only add ngl_link for a certain set of statuses
+  cat('generating neuroglancer links ...\n')
+  n_rows <- nrow(ac %>% dplyr::filter(grepl("TRACING_ISSUE$|PROOFREADING_ISSUE$|PARTIALLY_PROOFREAD$", status)))
+  p <- dplyr::progress_estimated(n_rows)
+  ac.new <- ac %>%
+    dplyr::filter(grepl("TRACING_ISSUE$|PROOFREADING_ISSUE$|PARTIALLY_PROOFREAD$", !!rlang::sym("status"))) %>%
+    dplyr::rowwise() %>%
+    dplyr::mutate(
+      ngl_id = {
+        p$tick()$print() # Update progress bar
+        tryCatch(paste(crant_ngl_segments(!!rlang::sym("ngl_link")),collapse="_"), error = function(e) NA)
+      }
+    ) %>%
+    dplyr::mutate(ngl_link = dplyr::case_when(
+      is.na(!!rlang::sym("ngl_link")) ~ crant_scene(!!rlang::sym("root_id"), shorten_url = TRUE),
+      !is.na(!!rlang::sym("ngl_id")) & !grepl(!!rlang::sym("root_id"),!!rlang::sym("ngl_id")) ~ crant_scene(!!rlang::sym("root_id"), shorten_url = TRUE),
+      TRUE ~ ngl_link
+    )) %>%
+    dplyr::ungroup() %>%
+    dplyr::select(-!!rlang::sym("ngl_id")) %>%
+    as.data.frame()
 
+  # Update
+  cat('updating CRANTb_meta seatable...\n')
+  ac.new[is.na(ac.new)] <- ''
+  crant_table_update_rows(df = ac.new,
+                          base = "CRANTb",
+                          table = "CRANTb_meta",
+                          append_allowed = FALSE,
+                          chunksize = 1000)
+  cat('done.')
+
+  # Return
+  invisible()
+}
diff --git a/R/crant.R b/R/crant.R
@@ -6,6 +6,7 @@
 #' but could point to another dataset layer.
 #' @param open Whether to open the URL in your browser (see
 #'   \code{\link{browseURL}})
+#' @param shorten_url logical, whether or not to produce a shortened URL.
 #' @return A character vector containing a single Neuroglancer URL (invisibly
 #'   when \code{open=TRUE}).
 #' @export
@@ -18,16 +19,17 @@
 #' }
 crant_scene <- function(ids=NULL,
                         open=FALSE,
-                        layer = NULL,
+                        shorten_url = FALSE,
+                        layer = "proofreadable seg",
                         url=paste0("https://spelunker.cave-explorer.org/#!middleauth+",
                                    "https://global.daf-apis.com/nglstate/api/v1/",
                                    "5733498854834176")) {
-  url=sub("#!middleauth+", "?", url, fixed = T)
-  parts=unlist(strsplit(url, "?", fixed = T))
-  json=try(fafbseg::flywire_fetch(parts[2], token=fafbseg::chunkedgraph_token(), return = 'text', cache = TRUE)) # token = crant_token()
+  url <- sub("#!middleauth+", "?", url, fixed = T)
+  parts <- unlist(strsplit(url, "?", fixed = T))
+  json <- try(fafbseg::flywire_fetch(parts[2], token=fafbseg::chunkedgraph_token(), return = 'text', cache = TRUE)) # NOT token = crant_token()
   if(inherits(json, 'try-error')) {
     badtoken=paste0("You have a token but it doesn't seem to be authorised for CAVE or global.daf-apis.com.\n",
-                    "Have you definitely used `crant_set_token()` to make a token for the CAVE datasets?")
+                    "Have you definitely used `flywire_set_token()` to make a token for the CAVE datasets?")
     if(grepl(500, json))
       stop("There seems to be a (temporary?) problem with the zetta server!")
     else if(grepl(401, json))
@@ -39,14 +41,18 @@ crant_scene <- function(ids=NULL,
     else
       stop(badtoken)
   }
-  u=fafbseg::ngl_encode_url(json, baseurl = parts[1])
+  u <- fafbseg::ngl_encode_url(json, baseurl = parts[1])
   if(!is.null(ids)){
-    banc_ngl_segments(u, layer=layer) <- crant_ids(ids)
+    crant_ngl_segments(u, layer=layer) <- crant_ids(ids)
   }
   if(open) {
     browseURL(u)
     invisible(u)
-  } else (u)
+  } else if(shorten_url){
+    crant_shorturl(u)
+  }else{
+    u
+  }
 }
 
 #' Set the token to be used to authenticate to CRANT autosegmentation resources