Hi,
Is there a way to create edges from consecutive vertices in the same class ?
I've been trying to do is by loading a csv file with vertices and edges
information. The vertices are created without a problem but the edges are
either not created and no error is give or i get an error mentioning
duplicate records even if there are no duplicate records in the file.
The Orientdb version i'm using is 2.0.12
here is a sample of the file i want to load :
reference_nt_L1,previous_nt,coordinate,assembly_L2,chromosome_L3,position_L3
T,chr13:20187463,chr13:20187464,hg19,chr13,20187464
T,chr13:20187464,chr13:20187465,hg19,chr13,20187465
T,chr13:20187465,chr13:20187466,hg19,chr13,20187466
A,chr13:20187466,chr13:20187467,hg19,chr13,20187467
the json file
{
"source": { "file": { "path": "/home/jenica/data/chrfrags/gjb2_frag.csv"
} },
"extractor": { "row": {} },
"transformers": [
{ "csv": {} },
{ "vertex": { "class": "position_L1" } },
{ "edge": { "class": "previous_nt",
"joinFieldName": "coordinate",
"lookup": "position_L1.previous_nt",
"direction": "in"
}
}
],
"loader": {
"orientdb": {
"dbURL":
"plocal:/home/jenica/programs/orientdb-community-2.0.12/databases/blog10",
"dbType": "graph",
"classes": [
{"name": "position_L1", "extends": "V"},
{"name": "previous_nt", "extends": "E"}
], "indexes": [
{"class":"position_L1", "fields":["nt:string"], "type":"UNIQUE" }
]
}
}
}
and the error i get
OrientDB etl v.2.0.12 (build @BUILD@) www.orientechnologies.com
BEGIN ETL PROCESSOR
Error in Pipeline execution:
com.orientechnologies.orient.core.storage.ORecordDuplicatedException:
Cannot index record
position_L1{reference_nt_L1:T,previous_nt:chr13:20187462,coordinate:chr13:20187463,assembly_L2:hg19,chromosome_L3:chr13,position_L3:20187463}:
found duplicated key 'chr13:20187463' in index 'position_L1.coordinate'
previously assigned to the record #11:0 RID=#11:0
com.orientechnologies.orient.core.storage.ORecordDuplicatedException:
Cannot index record
position_L1{reference_nt_L1:T,previous_nt:chr13:20187462,coordinate:chr13:20187463,assembly_L2:hg19,chromosome_L3:chr13,position_L3:20187463}:
found duplicated key 'chr13:20187463' in index 'position_L1.coordinate'
previously assigned to the record #11:0 RID=#11:0
at
com.orientechnologies.orient.core.index.OIndexTxAwareOneValue.checkEntry(OIndexTxAwareOneValue.java:225)
at
com.orientechnologies.orient.core.index.OClassIndexManager.checkIndexedPropertiesOnCreation(OClassIndexManager.java:326)
at
com.orientechnologies.orient.core.index.OClassIndexManager.checkIndexes(OClassIndexManager.java:570)
at
com.orientechnologies.orient.core.index.OClassIndexManager.onRecordBeforeCreate(OClassIndexManager.java:395)
at
com.orientechnologies.orient.core.hook.ODocumentHookAbstract.onTrigger(ODocumentHookAbstract.java:218)
at
com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.callbackHooks(ODatabaseDocumentTx.java:986)
at
com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.executeSaveRecord(ODatabaseDocumentTx.java:1721)
at
com.orientechnologies.orient.core.tx.OTransactionNoTx.saveRecord(OTransactionNoTx.java:102)
at
com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.save(ODatabaseDocumentTx.java:2312)
at
com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.save(ODatabaseDocumentTx.java:118)
at
com.orientechnologies.orient.core.record.impl.ODocument.save(ODocument.java:1727)
at
com.orientechnologies.orient.core.record.impl.ODocument.save(ODocument.java:1718)
at
com.tinkerpop.blueprints.impls.orient.OrientElement.save(OrientElement.java:311)
at
com.tinkerpop.blueprints.impls.orient.OrientElement.save(OrientElement.java:291)
at
com.tinkerpop.blueprints.impls.orient.OrientElement.setProperty(OrientElement.java:186)
at
com.orientechnologies.orient.etl.transformer.OVertexTransformer.executeTransform(OVertexTransformer.java:69)
at
com.orientechnologies.orient.etl.transformer.OAbstractTransformer.transform(OAbstractTransformer.java:37)
at
com.orientechnologies.orient.etl.OETLPipeline.execute(OETLPipeline.java:110)
at
com.orientechnologies.orient.etl.OETLProcessor.executeSequentially(OETLProcessor.java:487)
at
com.orientechnologies.orient.etl.OETLProcessor.execute(OETLProcessor.java:291)
at
com.orientechnologies.orient.etl.OETLProcessor.main(OETLProcessor.java:161)
ETL process halted:
com.orientechnologies.orient.etl.OETLProcessHaltedException:
com.orientechnologies.orient.core.storage.ORecordDuplicatedException:
Cannot index record
position_L1{reference_nt_L1:T,previous_nt:chr13:20187462,coordinate:chr13:20187463,assembly_L2:hg19,chromosome_L3:chr13,position_L3:20187463}:
found duplicated key 'chr13:20187463' in index 'position_L1.coordinate'
previously assigned to the record #11:0 RID=#11:0
thank you
Jenica
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