From d4257162faceb4e2c33c0a354208d55b29a05b53 Mon Sep 17 00:00:00 2001 From: Rucknium Date: Tue, 9 Aug 2022 22:53:08 +0000 Subject: [PATCH] Revert prior optimization commit due to troubleshooting failure --- construct-edgelist.R | 29 +++++++++-------------------- 1 file changed, 9 insertions(+), 20 deletions(-) diff --git a/construct-edgelist.R b/construct-edgelist.R index 9cf9e05..51daba7 100644 --- a/construct-edgelist.R +++ b/construct-edgelist.R @@ -9,6 +9,10 @@ library(DBI) data.dir <- "" # Input data directory here, with trailing "/" +source("https://gist.githubusercontent.com/jeffwong/5925000/raw/bf02ed0dd2963169a91664be02fb18e45c4d1e20/sqlitewritetable.R") +# From https://gist.github.com/jeffwong/5925000 +# Modifies RSQLite's sqliteWriteTable function so as to reject duplicates + con <- DBI::dbConnect(RSQLite::SQLite(), paste0(data.dir, "tx-graph-node-indices.db")) DBI::dbExecute(con, "PRAGMA max_page_count = 4294967292;") @@ -21,7 +25,8 @@ DBI::dbExecute(con, "PRAGMA max_page_count = 4294967292;") DBI::dbExecute(con, "CREATE TABLE nodes ( node TEXT, -node_index INTEGER PRIMARY KEY +node_index INTEGER PRIMARY KEY AUTOINCREMENT, +unique(node) )") @@ -63,31 +68,15 @@ for (file.iter in tx.graph.files) { new.nodes <- unique(c(tx.graph.chunk$origin, tx.graph.chunk$destination)) - nodes.to.insert <- data.frame(node = new.nodes, stringsAsFactors = FALSE) - - DBI::dbWriteTable(con, "nodes", - nodes.to.insert, append = TRUE) + nodes.to.insert <- data.frame(node = new.nodes, node_index = NA, stringsAsFactors = FALSE) + mysqliteWriteTable(con, "nodes", + nodes.to.insert, append = TRUE, row.names = FALSE, ignore = TRUE) cat(nrow(nodes.to.insert), "Nodes written\n") - - } -base::date() -DBI::dbExecute(con, "DELETE FROM nodes - WHERE rowid NOT IN ( - SELECT MIN(rowid) - FROM nodes - GROUP BY node - )") -base::date() -# 1 hour - -# Suggested by https://stackoverflow.com/questions/25884095/how-can-i-delete-duplicates-in-sqlite -# Must do this at the end to make sure did not leave any out -# from the tail end of the last 1000 iters DBI::dbWriteTable(con, "edgelist_intermediate_1", data.frame(origin = character(0), destination = character(0),