And create the indexes for all those node + property
And for operations like this:
MERGE (uniprotid:Uniprotid{uniprotid: csvimport.ID, Name:csvimport.Name,
Uniprot_title: csvimport.Uniprot_Title}
please use a constraint:
create constraint on (uniprotid:Uniprotid) assert uniprotid.uniprotid is unique;
and the merge operation like this, so it can actually leverage the
index/constraint.
> MERGE (uniprotid:Uniprotid{uniprotid: csvimport.ID}) ON CREATE SET
> uniprotid.Name=csvimport.Name,uniprotid.Uniprot_title=csvimport.Uniprot_Title
...
Am 18.06.2014 um 09:18 schrieb Pavan Kumar <[email protected]>:
> My query looks like following
> USING PERIODIC COMMIT 1000
> LOAD CSV WITH HEADERS FROM
> "file:D:/Graph_Database/DrugBank_database/DrugbankFull_Database.csv"
> AS csvimport
> merge (uniprotid:Uniprotid{uniprotid: csvimport.ID, Name:csvimport.Name,
> Uniprot_title: csvimport.Uniprot_Title})
> merge (genename:Gene_Name{genename: csvimport.Gene_Name})
> merge (Genbank_prtn:GenBank_Protein{GenBank_protein_id:
> csvimport.GenBank_Protein_ID})
> merge (Genbank_gene:GenBank_Gene{GenBank_gene_id: csvimport.GenBank_Gene_ID})
> merge (pdbid:PDBID{PDBid: csvimport.PDB_ID})
> merge (geneatlas:Geneatlasid{Geneatlas: csvimport.GenAtlas_ID})
> merge (HGNC:HGNCid{hgnc: csvimport.HGNC_ID})
> merge (species:Species{Species: csvimport.Species})
> merge (genecard:Genecardid{Genecard: csvimport.GeneCard_ID})
> merge (drugid:DrugID{DrugID: csvimport.Drug_IDs})
> merge (uniprotid)-[:Genename]->(genename)
> merge (uniprotid)-[:GenBank_ProteinID]->(Genbank_prtn)
> merge (uniprotid)-[:GenBank_GeneID]->(Genbank_gene)
> merge (uniprotid)-[:PDBID]->(pdbid)
> merge (uniprotid)-[:GeneatlasID]->(geneatlas)
> merge (uniprotid)-[:HGNCID]->(HGNC)
> merge (uniprotid)-[:Species]->(species)
> merge (uniprotid)-[:GenecardID]->(genecard)
> merge (uniprotid)-[:DrugID]->(drugid)
>
> I am attaching sample csv file also. Please find it.
> As suggested, I will try with new version of neo4j
>
>
> On Wed, Jun 18, 2014 at 12:41 PM, Michael Hunger
> <[email protected]> wrote:
> What does your query look like?
> Please switch to Neo4j 2.1.2
>
> And create indexes / constraints for the nodes you're inserting with MERGE or
> looking up via MATCH.
>
> Michael
>
> Am 18.06.2014 um 08:46 schrieb Pavan Kumar <[email protected]>:
>
>> Hi,
>> I have deployed neo4j 2.1.0-M01 on windows which has 8GB RAM. I am trying to
>> import CSV file which has 30000 records. I am using USING PERIODIC COMMIT
>> 1000 LOAD CSV command for importing, but it gives unknown error. I have
>> modified neo4j.properties file as adviced in the blogs. My neo4j.properties
>> now looks like
>> # Default values for the low-level graph engine
>>
>> neostore.nodestore.db.mapped_memory=200M
>> neostore.relationshipstore.db.mapped_memory=4G
>> neostore.propertystore.db.mapped_memory=500M
>> neostore.propertystore.db.strings.mapped_memory=500M
>> neostore.propertystore.db.arrays.mapped_memory=500M
>>
>> # Enable this to be able to upgrade a store from an older version
>> allow_store_upgrade=true
>>
>> # Enable this to specify a parser other than the default one.
>> #cypher_parser_version=2.0
>>
>> # Keep logical logs, helps debugging but uses more disk space, enabled for
>> # legacy reasons To limit space needed to store historical logs use values
>> such
>> # as: "7 days" or "100M size" instead of "true"
>> keep_logical_logs=true
>>
>> # Autoindexing
>>
>> # Enable auto-indexing for nodes, default is false
>> node_auto_indexing=true
>>
>> # The node property keys to be auto-indexed, if enabled
>> #node_keys_indexable=name,age
>>
>> # Enable auto-indexing for relationships, default is false
>> relationship_auto_indexing=true
>>
>> # The relationship property keys to be auto-indexed, if enabled
>> #relationship_keys_indexable=name,age
>>
>> # Setting for Community Edition:
>> cache_type=weak
>>
>> Still i am facing the same problem. Is there any other file to change
>> properties. Kindly help me in this issue.
>> Thanks in advance
>>
>> On Tuesday, 4 March 2014 21:24:03 UTC+5:30, Aram Chung wrote:
>> Hi,
>>
>> I was asked to post this here by Mark Needham (@markhneedham) who thought my
>> query took longer than it should.
>>
>> I'm trying to see how graph databases could be used in investigative
>> journalism: I was loading in New York State's Active Corporations: Beginning
>> 1800 data from
>> https://data.ny.gov/Economic-Development/Active-Corporations-Beginning-1800/n9v6-gdp6
>> as a 1964486-row csv (and deleted all U+F8FF characters, because I was
>> getting "[null] is not a supported property value"). The Cypher query I used
>> was
>>
>> USING PERIODIC COMMIT 500
>> LOAD CSV
>> FROM
>> "file://path/to/csv/Active_Corporations___Beginning_1800__without_header__wonky_characters_fixed.csv"
>> AS company
>> CREATE (:DataActiveCorporations
>> {
>> DOS_ID:company[0],
>> Current_Entity_Name:company[1],
>> Initial_DOS_Filing_Date:company[2],
>> County:company[3],
>> Jurisdiction:company[4],
>> Entity_Type:company[5],
>>
>> DOS_Process_Name:company[6],
>> DOS_Process_Address_1:company[7],
>> DOS_Process_Address_2:company[8],
>> DOS_Process_City:company[9],
>> DOS_Process_State:company[10],
>> DOS_Process_Zip:company[11],
>>
>> CEO_Name:company[12],
>> CEO_Address_1:company[13],
>> CEO_Address_2:company[14],
>> CEO_City:company[15],
>> CEO_State:company[16],
>> CEO_Zip:company[17],
>>
>> Registered_Agent_Name:company[18],
>> Registered_Agent_Address_1:company[19],
>> Registered_Agent_Address_2:company[20],
>> Registered_Agent_City:company[21],
>> Registered_Agent_State:company[22],
>> Registered_Agent_Zip:company[23],
>>
>> Location_Name:company[24],
>> Location_Address_1:company[25],
>> Location_Address_2:company[26],
>> Location_City:company[27],
>> Location_State:company[28],
>> Location_Zip:company[29]
>> }
>> );
>>
>> Each row is one node so it's as close to the raw data as possible. The idea
>> is loosely that these nodes will be linked with new nodes representing
>> people and addresses verified by reporters.
>>
>> This is what I got:
>>
>> +-------------------+
>> | No data returned. |
>> +-------------------+
>> Nodes created: 1964486
>> Properties set: 58934580
>> Labels added: 1964486
>> 4550855 ms
>>
>> Some context information:
>> Neo4j Milestone Release 2.1.0-M01
>> Windows 7
>> java version "1.7.0_03"
>>
>> Best,
>> Aram
>>
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>
>
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>
> --
> Thanks & Regards,
> Pavan Kumar
> Project Engineer
> CDAC -KP
> Ph +91-7676367646
>
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> <SAmple_Drugbank.xls>
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