Michael,
As discussed on the Slack channel, the problem does seem to go away with a
brand new clean instance of neo4j.
Commands are as follows…
load csv with headers from "file:///chromosomes.txt" AS line
create (:Chromosome { name: line.`Chromosome/scaffold name`});
create index on :Chromosome(name);
using periodic commit 1000
LOAD CSV with headers FROM "file:///genes.txt" AS line
create ( :Gene { id: line.`Gene stable ID`, name: line.`Gene name`,
description: line.`Gene description`, type: line.`Gene type`});
create index on :Gene(id);
using periodic commit 1000
load csv with headers from "file:///genes-to-chromosomes.txt" as line
match (chromosome:Chromosome {name: line.`Chromosome/scaffold name`})
match (gene:Gene {id: line.`Gene stable ID`})
merge (gene)-[:MAPS_TO {start: toInteger(line.`Gene start (bp)`), end:
toInteger(line.`Gene end (bp)`), strand: toInteger(line.Strand)}]->(chromosome);
It’s the last one that takes the time,
File parameters are:
chromosomes.txt - 33 lines, 112bytes
genes.txt - 17718 lines, 1.4Mbytes
genes-to-chromosomes.txt - 17718 lines, 720Kbytes
So not a significant data set.
Output of :schema is…
Indexes
ON :Chromosome(name) ONLINE
ON :Gene(id) ONLINE
ON :Transcript(id) ONLINE
No constraints
Later,
Andy
On 5 Jul 2017, at 09:28, 'Michael Hunger' via Neo4j
<[email protected]<mailto:[email protected]>> wrote:
Can you share your commands and their count? And the size of the csv.
Also the output of :schema
Von meinem iPhone gesendet
Am 04.07.2017 um 18:17 schrieb Andy Law
<[email protected]<mailto:[email protected]>>:
Trying to load data representing 2 node types and one set of relationships
between the two.
Loading from CSV files with headers
Working in the browser interface, loading the two node data sets (32 and 17717
nodes respectively) and the relationships between them takes less than 6 seconds
Working in the cypher-shell pasting individual commands in one after the other
(same as using the browser interface) the data load takes about the same length
of time.
Putting the commands into a text script file and piping it into cypher-shell
takes 9 minutes and 55 seconds (10 minutes).
What is going on here? Anyone else seen this?
For the record, I'm on a Late 2012 27-inch iMac with 24GB RAM. Running OSX
10.11.6 and with Java 1.8.0_131-b11. Neo4J is 3.2.1 Community Edition.
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