Version: 5.0.0

TSV, CSV files

Generic data loader for TSV or CSV files. It can load more than one class (in the example below Gene, Organism and Protein) and create one to many, many to many relations between the entities loaded. Available from 5.0.7 release.

Types of data loaded#

TSV (Tab-Separated Values) or CSV (Comma-Separated Values) files

How to load the data into your mine#

N/A - will parse any file in TSV/CSV format

Add delimited to the list of datasources to be integrated#

Project XML example

<source name="my-data-source" type="delimited">
<property name="delimited.dataSourceName" value="TSV Source Name"/>
<property name="delimited.dataSetTitle" value="TSV Data Set"/>
<property name="delimited.licence" value="http//"/>
<property name="delimited.hasHeader" value="true"/>
<property name="delimited.columns" value="Gene.primaryIdentifier, Organism.taxonId, null,Protein.primaryIdentifier,Protein.primaryAccession"/>
<property name="delimited.includes" value="test.tsv"/>
<property name="" location="{directory containing delimited files}"/>
delimited.dataSourceNamename of datasetdetermines name of dataset objectyes
delimited.dataSetTitlename of datasourcedetermines name of datasource objectyes
delimited.columnsname of fieldsdetermines the fields to load, use null to skip a valueyes of the TSV/CSV data filethese data will be loaded into the databaseyes
includesname of data filethis data file will be loaded into the databaseno
delimited.separatorDefault value is: tab. Possible values: tab/TAB/comma/COMMAtype of separator file to be loadedno
delimited.hasHeaderDefault value is: true. Possible values: true/falsedetemines if the file has a headerno
licenceURL pointing to standard data licence for dataupdates DataSet.licence with valueno