Hi, I have tried creating constraints and index before attempting LOAD CSV command Commands are executing for long time and it it showing me "Unknown error" Any idea why it is giving me such error, I am running it on windows machine which has 8GB RAM. Do i have to change properties in neo4j.properties file Kindly help me
On Wed, Jun 18, 2014 at 8:20 PM, david fauth <[email protected]> wrote: > Run the Create Constraint commands then attempt your LOAD CSV command. > > > On Wednesday, June 18, 2014 5:13:42 AM UTC-4, Pavan Kumar wrote: > >> Hi, >> So My cypher will be like >> ---------------------------------------------------------- >> USING PERIODIC COMMIT 1000 >> LOAD CSV WITH HEADERS FROM >> "file:D:/Graph_Database/DrugBank_database/DrugbankFull_Database.csv" >> AS csvimport >> create constraint on (uniprotid:Uniprotid) assert uniprotid.uniprotid is >> unique; >> MERGE (uniprotid:Uniprotid{uniprotid: csvimport.ID}) ON CREATE SET >> uniprotid.Name=csvimport.Name,uniprotid.Uniprot_title= >> csvimport.Uniprot_Title >> create constraint on (genename:Gene_Name) assert genename:Gene_Name is >> unique; >> merge (genename:Gene_Name{genename: csvimport.Gene_Name}) >> and so on... >> merge (uniprotid)-[:Genename]->(genename) >> merge (uniprotid)-[:GenBank_ProteinID]->(Genbank_prtn) >> and so on... >> --------------------------------------------------------- >> Is that right...? i tried the same statements in 2.1.2 and i am getting >> the following errors. >> >> 1. Invalid input 'n': expected 'p/P' (line 5, column 20) >> >> >> "create constraint on (uniprotid:Uniprotid) assert uniprotid.uniprotid is >> unique;" >> >> >> 2. Cannot merge node using null property value for uniprotid >> >> >> Kindly help >> >> >> >> >> On Wed, Jun 18, 2014 at 1:44 PM, Michael Hunger < >> [email protected]> wrote: >> >>> I don't understand. >>> >>> Michael >>> >>> Am 18.06.2014 um 10:11 schrieb Pavan Kumar <[email protected]>: >>> >>> When i use create statements, it is not considering the empty fileds >>> from the CSV file. So used Merge command >>> >>> >>> On Wed, Jun 18, 2014 at 1:09 PM, Michael Hunger < >>> [email protected]> wrote: >>> >>>> 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 >>>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "Neo4j" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "Neo4j" group. >>>>> To unsubscribe from this topic, visit https://groups.google.com/d/ >>>>> topic/neo4j/a2DdoKkbyYo/unsubscribe. >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> [email protected]. >>>>> >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> >>>> >>>> -- >>>> Thanks & Regards, >>>> Pavan Kumar >>>> Project Engineer >>>> CDAC -KP >>>> Ph +91-7676367646 >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "Neo4j" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> >>>> For more options, visit https://groups.google.com/d/optout. >>>> <SAmple_Drugbank.xls> >>>> >>>> >>>> >>>> -- >>>> You received this message because you are subscribed to a topic in the >>>> Google Groups "Neo4j" group. >>>> To unsubscribe from this topic, visit https://groups.google.com/d/ >>>> topic/neo4j/a2DdoKkbyYo/unsubscribe. >>>> To unsubscribe from this group and all its topics, send an email to >>>> [email protected]. >>>> >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >>> >>> -- >>> Thanks & Regards, >>> Pavan Kumar >>> Project Engineer >>> CDAC -KP >>> Ph +91-7676367646 >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "Neo4j" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> >>> For more options, visit https://groups.google.com/d/optout. >>> >>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "Neo4j" group. >>> To unsubscribe from this topic, visit https://groups.google.com/d/ >>> topic/neo4j/a2DdoKkbyYo/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> [email protected]. >>> >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> >> -- >> Thanks & Regards, >> Pavan Kumar >> Project Engineer >> CDAC -KP >> Ph +91-7676367646 >> > -- > You received this message because you are subscribed to a topic in the > Google Groups "Neo4j" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/neo4j/a2DdoKkbyYo/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > For more options, visit https://groups.google.com/d/optout. > -- Thanks & Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- You received this message because you are subscribed to the Google Groups "Neo4j" group. 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