CsvEntityExporter (molgenis-app-ngs 0.0.1 API)

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org.molgenis
Class CsvEntityExporter

java.lang.Object
  org.molgenis.CsvEntityExporter

public class CsvEntityExporter
extends Object
extends Object

Constructor Summary
`CsvEntityExporter()`

Method Summary
`void`	`exportAccession(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Accession to file.
`void`	`exportAccession(List<? extends Entity> entities, File file)`
`void`	`exportAll(File directory, Database db)` Default export all using a target directory and a database to export
`void`	`exportAll(File directory, Database db, boolean skipAutoId)` Export all where a boolean skip autoid fields forces an ignore of the auto id field ("id")
`void`	`exportAll(File directory, Database db, boolean skipAutoId, QueryRule... rules)` Export all with both a boolean skipAutoId and a set of QueryRules to specify both the skipping of auto id, and applying of a filter
`void`	`exportAll(File directory, Database db, QueryRule... rules)` Export all using a set of QueryRules used for all entities if applicable to that entity
`void`	`exportAll(File directory, List<? extends Entity>... entityLists)`
`void`	`exportBoolValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export BoolValue to file.
`void`	`exportBoolValue(List<? extends Entity> entities, File file)`
`void`	`exportCapturingKit(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export CapturingKit to file.
`void`	`exportCapturingKit(List<? extends Entity> entities, File file)`
`void`	`exportCategoricalValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export CategoricalValue to file.
`void`	`exportCategoricalValue(List<? extends Entity> entities, File file)`
`void`	`exportCategory(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Category to file.
`void`	`exportCategory(List<? extends Entity> entities, File file)`
`void`	`exportCharacteristic(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Characteristic to file.
`void`	`exportCharacteristic(List<? extends Entity> entities, File file)`
`void`	`exportDataSet(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export DataSet to file.
`void`	`exportDataSet(List<? extends Entity> entities, File file)`
`void`	`exportDateTimeValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export DateTimeValue to file.
`void`	`exportDateTimeValue(List<? extends Entity> entities, File file)`
`void`	`exportDateValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export DateValue to file.
`void`	`exportDateValue(List<? extends Entity> entities, File file)`
`void`	`exportDecimalValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export DecimalValue to file.
`void`	`exportDecimalValue(List<? extends Entity> entities, File file)`
`void`	`exportEmailValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export EmailValue to file.
`void`	`exportEmailValue(List<? extends Entity> entities, File file)`
`void`	`exportFlowcell(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Flowcell to file.
`void`	`exportFlowcell(List<? extends Entity> entities, File file)`
`void`	`exportFlowcellLane(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export FlowcellLane to file.
`void`	`exportFlowcellLane(List<? extends Entity> entities, File file)`
`void`	`exportHtmlValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export HtmlValue to file.
`void`	`exportHtmlValue(List<? extends Entity> entities, File file)`
`void`	`exportHyperlinkValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export HyperlinkValue to file.
`void`	`exportHyperlinkValue(List<? extends Entity> entities, File file)`
`void`	`exportIndividual(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Individual to file.
`void`	`exportIndividual(List<? extends Entity> entities, File file)`
`void`	`exportInstitute(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Institute to file.
`void`	`exportInstitute(List<? extends Entity> entities, File file)`
`void`	`exportIntValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export IntValue to file.
`void`	`exportIntValue(List<? extends Entity> entities, File file)`
`void`	`exportLongValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export LongValue to file.
`void`	`exportLongValue(List<? extends Entity> entities, File file)`
`void`	`exportMachine(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Machine to file.
`void`	`exportMachine(List<? extends Entity> entities, File file)`
`void`	`exportMolgenisEntity(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MolgenisEntity to file.
`void`	`exportMolgenisEntity(List<? extends Entity> entities, File file)`
`void`	`exportMolgenisFile(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MolgenisFile to file.
`void`	`exportMolgenisFile(List<? extends Entity> entities, File file)`
`void`	`exportMolgenisGroup(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MolgenisGroup to file.
`void`	`exportMolgenisGroup(List<? extends Entity> entities, File file)`
`void`	`exportMolgenisPermission(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MolgenisPermission to file.
`void`	`exportMolgenisPermission(List<? extends Entity> entities, File file)`
`void`	`exportMolgenisRole(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MolgenisRole to file.
`void`	`exportMolgenisRole(List<? extends Entity> entities, File file)`
`void`	`exportMolgenisRoleGroupLink(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MolgenisRoleGroupLink to file.
`void`	`exportMolgenisRoleGroupLink(List<? extends Entity> entities, File file)`
`void`	`exportMolgenisUser(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MolgenisUser to file.
`void`	`exportMolgenisUser(List<? extends Entity> entities, File file)`
`void`	`exportMrefValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export MrefValue to file.
`void`	`exportMrefValue(List<? extends Entity> entities, File file)`
`void`	`exportNgsUser(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export NgsUser to file.
`void`	`exportNgsUser(List<? extends Entity> entities, File file)`
`void`	`exportObservableFeature(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export ObservableFeature to file.
`void`	`exportObservableFeature(List<? extends Entity> entities, File file)`
`void`	`exportObservationSet(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export ObservationSet to file.
`void`	`exportObservationSet(List<? extends Entity> entities, File file)`
`void`	`exportObservationTarget(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export ObservationTarget to file.
`void`	`exportObservationTarget(List<? extends Entity> entities, File file)`
`void`	`exportObservedValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export ObservedValue to file.
`void`	`exportObservedValue(List<? extends Entity> entities, File file)`
`void`	`exportOntology(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Ontology to file.
`void`	`exportOntology(List<? extends Entity> entities, File file)`
`void`	`exportOntologyTerm(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export OntologyTerm to file.
`void`	`exportOntologyTerm(List<? extends Entity> entities, File file)`
`void`	`exportPanel(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Panel to file.
`void`	`exportPanel(List<? extends Entity> entities, File file)`
`void`	`exportPanelSource(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export PanelSource to file.
`void`	`exportPanelSource(List<? extends Entity> entities, File file)`
`void`	`exportPerson(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Person to file.
`void`	`exportPerson(List<? extends Entity> entities, File file)`
`void`	`exportPersonRole(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export PersonRole to file.
`void`	`exportPersonRole(List<? extends Entity> entities, File file)`
`void`	`exportPrepKit(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export PrepKit to file.
`void`	`exportPrepKit(List<? extends Entity> entities, File file)`
`void`	`exportProject(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Project to file.
`void`	`exportProject(List<? extends Entity> entities, File file)`
`void`	`exportProtocol(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Protocol to file.
`void`	`exportProtocol(List<? extends Entity> entities, File file)`
`void`	`exportRegular(File directory, Database db, boolean skipAutoId)` Export without system tables.
`void`	`exportRegular(File directory, Database db, boolean skipAutoId, QueryRule... rules)` Export without system tables.
`void`	`exportRuntimeProperty(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export RuntimeProperty to file.
`void`	`exportRuntimeProperty(List<? extends Entity> entities, File file)`
`void`	`exportSample(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Sample to file.
`void`	`exportSample(List<? extends Entity> entities, File file)`
`void`	`exportSampleBarcode(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export SampleBarcode to file.
`void`	`exportSampleBarcode(List<? extends Entity> entities, File file)`
`void`	`exportSampleBarcodeType(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export SampleBarcodeType to file.
`void`	`exportSampleBarcodeType(List<? extends Entity> entities, File file)`
`void`	`exportSpecial(File directory, Database db, boolean skipAutoId, List<Class<? extends Entity>> specialCases, boolean exclusion, QueryRule... rules)` Export while excluding or including certain entity types.
`void`	`exportSpecial(File directory, Database db, List<Class<? extends Entity>> specialCases, boolean exclusion)` Export while excluding or including certain entity types.
`void`	`exportSpecies(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Species to file.
`void`	`exportSpecies(List<? extends Entity> entities, File file)`
`void`	`exportStringValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export StringValue to file.
`void`	`exportStringValue(List<? extends Entity> entities, File file)`
`void`	`exportTextValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export TextValue to file.
`void`	`exportTextValue(List<? extends Entity> entities, File file)`
`void`	`exportValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export Value to file.
`void`	`exportValue(List<? extends Entity> entities, File file)`
`void`	`exportXrefValue(Database db, File f, List<String> fieldsToExport, QueryRule... rules)` export XrefValue to file.
`void`	`exportXrefValue(List<? extends Entity> entities, File file)`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

CsvEntityExporter

public CsvEntityExporter()

Method Detail

exportAll

public void exportAll(File directory,
                      Database db)
               throws Exception

Default export all using a target directory and a database to export

Parameters:: directory -; db -
Throws:: Exception

exportAll

public void exportAll(File directory,
                      Database db,
                      QueryRule... rules)
               throws Exception

Export all using a set of QueryRules used for all entities if applicable to that entity

Parameters:: directory -; db -; rules -
Throws:: Exception

exportAll

public void exportAll(File directory,
                      Database db,
                      boolean skipAutoId)
               throws Exception

Export all where a boolean skip autoid fields forces an ignore of the auto id field ("id")

Parameters:: directory -; db -; skipAutoId -
Throws:: Exception

exportAll

public void exportAll(File directory,
                      Database db,
                      boolean skipAutoId,
                      QueryRule... rules)
               throws Exception

Export all with both a boolean skipAutoId and a set of QueryRules to specify both the skipping of auto id, and applying of a filter

Parameters:: directory -; db -; skipAutoId -; rules -
Throws:: Exception

exportRegular

public void exportRegular(File directory,
                          Database db,
                          boolean skipAutoId)
                   throws Exception

Export without system tables.

Throws:: Exception

exportRegular

public void exportRegular(File directory,
                          Database db,
                          boolean skipAutoId,
                          QueryRule... rules)
                   throws Exception

Export without system tables.

Throws:: Exception

exportAll

public void exportAll(File directory,
                      List<? extends Entity>... entityLists)
               throws Exception

Throws:: Exception

exportSpecial

public void exportSpecial(File directory,
                          Database db,
                          List<Class<? extends Entity>> specialCases,
                          boolean exclusion)
                   throws Exception

Export while excluding or including certain entity types. Defaults set: skip autoId, no QueryRules. If exclusion is set to true, the specialCases are used to exlude those entities from the export (entities not in list are exported). If exclusion is set to false, the specialCases are used to include those entities in the export (only entities in list are exported).

Throws:: Exception

exportSpecial

public void exportSpecial(File directory,
                          Database db,
                          boolean skipAutoId,
                          List<Class<? extends Entity>> specialCases,
                          boolean exclusion,
                          QueryRule... rules)
                   throws Exception

Export while excluding or including certain entity types. If exclusion is set to true, the specialCases are used to exlude those entities from the export (entities not in list are exported). If exclusion is set to false, the specialCases are used to include those entities in the export (only entities in list are exported). TODO: Could maybe replace exportAll(File directory, List ... entityLists) ?

Throws:: Exception

exportNgsUser

public void exportNgsUser(Database db,
                          File f,
                          List<String> fieldsToExport,
                          QueryRule... rules)
                   throws DatabaseException,
                          IOException,
                          ParseException,
                          MolgenisModelException

export NgsUser to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportNgsUser

public void exportNgsUser(List<? extends Entity> entities,
                          File file)
                   throws IOException,
                          MolgenisModelException

Throws:: IOException; MolgenisModelException

exportSampleBarcodeType

public void exportSampleBarcodeType(Database db,
                                    File f,
                                    List<String> fieldsToExport,
                                    QueryRule... rules)
                             throws DatabaseException,
                                    IOException,
                                    ParseException,
                                    MolgenisModelException

export SampleBarcodeType to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportSampleBarcodeType

public void exportSampleBarcodeType(List<? extends Entity> entities,
                                    File file)
                             throws IOException,
                                    MolgenisModelException

Throws:: IOException; MolgenisModelException

exportSampleBarcode

public void exportSampleBarcode(Database db,
                                File f,
                                List<String> fieldsToExport,
                                QueryRule... rules)
                         throws DatabaseException,
                                IOException,
                                ParseException,
                                MolgenisModelException

export SampleBarcode to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportSampleBarcode

public void exportSampleBarcode(List<? extends Entity> entities,
                                File file)
                         throws IOException,
                                MolgenisModelException

Throws:: IOException; MolgenisModelException

exportCapturingKit

public void exportCapturingKit(Database db,
                               File f,
                               List<String> fieldsToExport,
                               QueryRule... rules)
                        throws DatabaseException,
                               IOException,
                               ParseException,
                               MolgenisModelException

export CapturingKit to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportCapturingKit

public void exportCapturingKit(List<? extends Entity> entities,
                               File file)
                        throws IOException,
                               MolgenisModelException

Throws:: IOException; MolgenisModelException

exportPrepKit

public void exportPrepKit(Database db,
                          File f,
                          List<String> fieldsToExport,
                          QueryRule... rules)
                   throws DatabaseException,
                          IOException,
                          ParseException,
                          MolgenisModelException

export PrepKit to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportPrepKit

public void exportPrepKit(List<? extends Entity> entities,
                          File file)
                   throws IOException,
                          MolgenisModelException

Throws:: IOException; MolgenisModelException

exportProject

public void exportProject(Database db,
                          File f,
                          List<String> fieldsToExport,
                          QueryRule... rules)
                   throws DatabaseException,
                          IOException,
                          ParseException,
                          MolgenisModelException

export Project to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportProject

public void exportProject(List<? extends Entity> entities,
                          File file)
                   throws IOException,
                          MolgenisModelException

Throws:: IOException; MolgenisModelException

exportSample

public void exportSample(Database db,
                         File f,
                         List<String> fieldsToExport,
                         QueryRule... rules)
                  throws DatabaseException,
                         IOException,
                         ParseException,
                         MolgenisModelException

export Sample to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportSample

public void exportSample(List<? extends Entity> entities,
                         File file)
                  throws IOException,
                         MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMachine

public void exportMachine(Database db,
                          File f,
                          List<String> fieldsToExport,
                          QueryRule... rules)
                   throws DatabaseException,
                          IOException,
                          ParseException,
                          MolgenisModelException

export Machine to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMachine

public void exportMachine(List<? extends Entity> entities,
                          File file)
                   throws IOException,
                          MolgenisModelException

Throws:: IOException; MolgenisModelException

exportFlowcell

public void exportFlowcell(Database db,
                           File f,
                           List<String> fieldsToExport,
                           QueryRule... rules)
                    throws DatabaseException,
                           IOException,
                           ParseException,
                           MolgenisModelException

export Flowcell to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportFlowcell

public void exportFlowcell(List<? extends Entity> entities,
                           File file)
                    throws IOException,
                           MolgenisModelException

Throws:: IOException; MolgenisModelException

exportFlowcellLane

public void exportFlowcellLane(Database db,
                               File f,
                               List<String> fieldsToExport,
                               QueryRule... rules)
                        throws DatabaseException,
                               IOException,
                               ParseException,
                               MolgenisModelException

export FlowcellLane to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportFlowcellLane

public void exportFlowcellLane(List<? extends Entity> entities,
                               File file)
                        throws IOException,
                               MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMolgenisEntity

public void exportMolgenisEntity(Database db,
                                 File f,
                                 List<String> fieldsToExport,
                                 QueryRule... rules)
                          throws DatabaseException,
                                 IOException,
                                 ParseException,
                                 MolgenisModelException

export MolgenisEntity to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMolgenisEntity

public void exportMolgenisEntity(List<? extends Entity> entities,
                                 File file)
                          throws IOException,
                                 MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMolgenisFile

public void exportMolgenisFile(Database db,
                               File f,
                               List<String> fieldsToExport,
                               QueryRule... rules)
                        throws DatabaseException,
                               IOException,
                               ParseException,
                               MolgenisModelException

export MolgenisFile to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMolgenisFile

public void exportMolgenisFile(List<? extends Entity> entities,
                               File file)
                        throws IOException,
                               MolgenisModelException

Throws:: IOException; MolgenisModelException

exportRuntimeProperty

public void exportRuntimeProperty(Database db,
                                  File f,
                                  List<String> fieldsToExport,
                                  QueryRule... rules)
                           throws DatabaseException,
                                  IOException,
                                  ParseException,
                                  MolgenisModelException

export RuntimeProperty to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportRuntimeProperty

public void exportRuntimeProperty(List<? extends Entity> entities,
                                  File file)
                           throws IOException,
                                  MolgenisModelException

Throws:: IOException; MolgenisModelException

exportCharacteristic

public void exportCharacteristic(Database db,
                                 File f,
                                 List<String> fieldsToExport,
                                 QueryRule... rules)
                          throws DatabaseException,
                                 IOException,
                                 ParseException,
                                 MolgenisModelException

export Characteristic to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportCharacteristic

public void exportCharacteristic(List<? extends Entity> entities,
                                 File file)
                          throws IOException,
                                 MolgenisModelException

Throws:: IOException; MolgenisModelException

exportObservationTarget

public void exportObservationTarget(Database db,
                                    File f,
                                    List<String> fieldsToExport,
                                    QueryRule... rules)
                             throws DatabaseException,
                                    IOException,
                                    ParseException,
                                    MolgenisModelException

export ObservationTarget to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportObservationTarget

public void exportObservationTarget(List<? extends Entity> entities,
                                    File file)
                             throws IOException,
                                    MolgenisModelException

Throws:: IOException; MolgenisModelException

exportIndividual

public void exportIndividual(Database db,
                             File f,
                             List<String> fieldsToExport,
                             QueryRule... rules)
                      throws DatabaseException,
                             IOException,
                             ParseException,
                             MolgenisModelException

export Individual to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportIndividual

public void exportIndividual(List<? extends Entity> entities,
                             File file)
                      throws IOException,
                             MolgenisModelException

Throws:: IOException; MolgenisModelException

exportOntology

public void exportOntology(Database db,
                           File f,
                           List<String> fieldsToExport,
                           QueryRule... rules)
                    throws DatabaseException,
                           IOException,
                           ParseException,
                           MolgenisModelException

export Ontology to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportOntology

public void exportOntology(List<? extends Entity> entities,
                           File file)
                    throws IOException,
                           MolgenisModelException

Throws:: IOException; MolgenisModelException

exportSpecies

public void exportSpecies(Database db,
                          File f,
                          List<String> fieldsToExport,
                          QueryRule... rules)
                   throws DatabaseException,
                          IOException,
                          ParseException,
                          MolgenisModelException

export Species to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportSpecies

public void exportSpecies(List<? extends Entity> entities,
                          File file)
                   throws IOException,
                          MolgenisModelException

Throws:: IOException; MolgenisModelException

exportOntologyTerm

public void exportOntologyTerm(Database db,
                               File f,
                               List<String> fieldsToExport,
                               QueryRule... rules)
                        throws DatabaseException,
                               IOException,
                               ParseException,
                               MolgenisModelException

export OntologyTerm to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportOntologyTerm

public void exportOntologyTerm(List<? extends Entity> entities,
                               File file)
                        throws IOException,
                               MolgenisModelException

Throws:: IOException; MolgenisModelException

exportAccession

public void exportAccession(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export Accession to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportAccession

public void exportAccession(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportValue

public void exportValue(Database db,
                        File f,
                        List<String> fieldsToExport,
                        QueryRule... rules)
                 throws DatabaseException,
                        IOException,
                        ParseException,
                        MolgenisModelException

export Value to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportValue

public void exportValue(List<? extends Entity> entities,
                        File file)
                 throws IOException,
                        MolgenisModelException

Throws:: IOException; MolgenisModelException

exportBoolValue

public void exportBoolValue(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export BoolValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportBoolValue

public void exportBoolValue(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportDateValue

public void exportDateValue(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export DateValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportDateValue

public void exportDateValue(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportDateTimeValue

public void exportDateTimeValue(Database db,
                                File f,
                                List<String> fieldsToExport,
                                QueryRule... rules)
                         throws DatabaseException,
                                IOException,
                                ParseException,
                                MolgenisModelException

export DateTimeValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportDateTimeValue

public void exportDateTimeValue(List<? extends Entity> entities,
                                File file)
                         throws IOException,
                                MolgenisModelException

Throws:: IOException; MolgenisModelException

exportDecimalValue

public void exportDecimalValue(Database db,
                               File f,
                               List<String> fieldsToExport,
                               QueryRule... rules)
                        throws DatabaseException,
                               IOException,
                               ParseException,
                               MolgenisModelException

export DecimalValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportDecimalValue

public void exportDecimalValue(List<? extends Entity> entities,
                               File file)
                        throws IOException,
                               MolgenisModelException

Throws:: IOException; MolgenisModelException

exportEmailValue

public void exportEmailValue(Database db,
                             File f,
                             List<String> fieldsToExport,
                             QueryRule... rules)
                      throws DatabaseException,
                             IOException,
                             ParseException,
                             MolgenisModelException

export EmailValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportEmailValue

public void exportEmailValue(List<? extends Entity> entities,
                             File file)
                      throws IOException,
                             MolgenisModelException

Throws:: IOException; MolgenisModelException

exportHtmlValue

public void exportHtmlValue(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export HtmlValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportHtmlValue

public void exportHtmlValue(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportHyperlinkValue

public void exportHyperlinkValue(Database db,
                                 File f,
                                 List<String> fieldsToExport,
                                 QueryRule... rules)
                          throws DatabaseException,
                                 IOException,
                                 ParseException,
                                 MolgenisModelException

export HyperlinkValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportHyperlinkValue

public void exportHyperlinkValue(List<? extends Entity> entities,
                                 File file)
                          throws IOException,
                                 MolgenisModelException

Throws:: IOException; MolgenisModelException

exportIntValue

public void exportIntValue(Database db,
                           File f,
                           List<String> fieldsToExport,
                           QueryRule... rules)
                    throws DatabaseException,
                           IOException,
                           ParseException,
                           MolgenisModelException

export IntValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportIntValue

public void exportIntValue(List<? extends Entity> entities,
                           File file)
                    throws IOException,
                           MolgenisModelException

Throws:: IOException; MolgenisModelException

exportLongValue

public void exportLongValue(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export LongValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportLongValue

public void exportLongValue(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMrefValue

public void exportMrefValue(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export MrefValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMrefValue

public void exportMrefValue(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportStringValue

public void exportStringValue(Database db,
                              File f,
                              List<String> fieldsToExport,
                              QueryRule... rules)
                       throws DatabaseException,
                              IOException,
                              ParseException,
                              MolgenisModelException

export StringValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportStringValue

public void exportStringValue(List<? extends Entity> entities,
                              File file)
                       throws IOException,
                              MolgenisModelException

Throws:: IOException; MolgenisModelException

exportTextValue

public void exportTextValue(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export TextValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportTextValue

public void exportTextValue(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMolgenisRole

public void exportMolgenisRole(Database db,
                               File f,
                               List<String> fieldsToExport,
                               QueryRule... rules)
                        throws DatabaseException,
                               IOException,
                               ParseException,
                               MolgenisModelException

export MolgenisRole to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMolgenisRole

public void exportMolgenisRole(List<? extends Entity> entities,
                               File file)
                        throws IOException,
                               MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMolgenisGroup

public void exportMolgenisGroup(Database db,
                                File f,
                                List<String> fieldsToExport,
                                QueryRule... rules)
                         throws DatabaseException,
                                IOException,
                                ParseException,
                                MolgenisModelException

export MolgenisGroup to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMolgenisGroup

public void exportMolgenisGroup(List<? extends Entity> entities,
                                File file)
                         throws IOException,
                                MolgenisModelException

Throws:: IOException; MolgenisModelException

exportPersonRole

public void exportPersonRole(Database db,
                             File f,
                             List<String> fieldsToExport,
                             QueryRule... rules)
                      throws DatabaseException,
                             IOException,
                             ParseException,
                             MolgenisModelException

export PersonRole to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportPersonRole

public void exportPersonRole(List<? extends Entity> entities,
                             File file)
                      throws IOException,
                             MolgenisModelException

Throws:: IOException; MolgenisModelException

exportObservableFeature

public void exportObservableFeature(Database db,
                                    File f,
                                    List<String> fieldsToExport,
                                    QueryRule... rules)
                             throws DatabaseException,
                                    IOException,
                                    ParseException,
                                    MolgenisModelException

export ObservableFeature to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportObservableFeature

public void exportObservableFeature(List<? extends Entity> entities,
                                    File file)
                             throws IOException,
                                    MolgenisModelException

Throws:: IOException; MolgenisModelException

exportCategory

public void exportCategory(Database db,
                           File f,
                           List<String> fieldsToExport,
                           QueryRule... rules)
                    throws DatabaseException,
                           IOException,
                           ParseException,
                           MolgenisModelException

export Category to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportCategory

public void exportCategory(List<? extends Entity> entities,
                           File file)
                    throws IOException,
                           MolgenisModelException

Throws:: IOException; MolgenisModelException

exportProtocol

public void exportProtocol(Database db,
                           File f,
                           List<String> fieldsToExport,
                           QueryRule... rules)
                    throws DatabaseException,
                           IOException,
                           ParseException,
                           MolgenisModelException

export Protocol to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportProtocol

public void exportProtocol(List<? extends Entity> entities,
                           File file)
                    throws IOException,
                           MolgenisModelException

Throws:: IOException; MolgenisModelException

exportDataSet

public void exportDataSet(Database db,
                          File f,
                          List<String> fieldsToExport,
                          QueryRule... rules)
                   throws DatabaseException,
                          IOException,
                          ParseException,
                          MolgenisModelException

export DataSet to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportDataSet

public void exportDataSet(List<? extends Entity> entities,
                          File file)
                   throws IOException,
                          MolgenisModelException

Throws:: IOException; MolgenisModelException

exportObservationSet

public void exportObservationSet(Database db,
                                 File f,
                                 List<String> fieldsToExport,
                                 QueryRule... rules)
                          throws DatabaseException,
                                 IOException,
                                 ParseException,
                                 MolgenisModelException

export ObservationSet to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportObservationSet

public void exportObservationSet(List<? extends Entity> entities,
                                 File file)
                          throws IOException,
                                 MolgenisModelException

Throws:: IOException; MolgenisModelException

exportPanel

public void exportPanel(Database db,
                        File f,
                        List<String> fieldsToExport,
                        QueryRule... rules)
                 throws DatabaseException,
                        IOException,
                        ParseException,
                        MolgenisModelException

export Panel to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportPanel

public void exportPanel(List<? extends Entity> entities,
                        File file)
                 throws IOException,
                        MolgenisModelException

Throws:: IOException; MolgenisModelException

exportPanelSource

public void exportPanelSource(Database db,
                              File f,
                              List<String> fieldsToExport,
                              QueryRule... rules)
                       throws DatabaseException,
                              IOException,
                              ParseException,
                              MolgenisModelException

export PanelSource to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportPanelSource

public void exportPanelSource(List<? extends Entity> entities,
                              File file)
                       throws IOException,
                              MolgenisModelException

Throws:: IOException; MolgenisModelException

exportCategoricalValue

public void exportCategoricalValue(Database db,
                                   File f,
                                   List<String> fieldsToExport,
                                   QueryRule... rules)
                            throws DatabaseException,
                                   IOException,
                                   ParseException,
                                   MolgenisModelException

export CategoricalValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportCategoricalValue

public void exportCategoricalValue(List<? extends Entity> entities,
                                   File file)
                            throws IOException,
                                   MolgenisModelException

Throws:: IOException; MolgenisModelException

exportInstitute

public void exportInstitute(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export Institute to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportInstitute

public void exportInstitute(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportPerson

public void exportPerson(Database db,
                         File f,
                         List<String> fieldsToExport,
                         QueryRule... rules)
                  throws DatabaseException,
                         IOException,
                         ParseException,
                         MolgenisModelException

export Person to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportPerson

public void exportPerson(List<? extends Entity> entities,
                         File file)
                  throws IOException,
                         MolgenisModelException

Throws:: IOException; MolgenisModelException

exportXrefValue

public void exportXrefValue(Database db,
                            File f,
                            List<String> fieldsToExport,
                            QueryRule... rules)
                     throws DatabaseException,
                            IOException,
                            ParseException,
                            MolgenisModelException

export XrefValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportXrefValue

public void exportXrefValue(List<? extends Entity> entities,
                            File file)
                     throws IOException,
                            MolgenisModelException

Throws:: IOException; MolgenisModelException

exportObservedValue

public void exportObservedValue(Database db,
                                File f,
                                List<String> fieldsToExport,
                                QueryRule... rules)
                         throws DatabaseException,
                                IOException,
                                ParseException,
                                MolgenisModelException

export ObservedValue to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportObservedValue

public void exportObservedValue(List<? extends Entity> entities,
                                File file)
                         throws IOException,
                                MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMolgenisUser

public void exportMolgenisUser(Database db,
                               File f,
                               List<String> fieldsToExport,
                               QueryRule... rules)
                        throws DatabaseException,
                               IOException,
                               ParseException,
                               MolgenisModelException

export MolgenisUser to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMolgenisUser

public void exportMolgenisUser(List<? extends Entity> entities,
                               File file)
                        throws IOException,
                               MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMolgenisRoleGroupLink

public void exportMolgenisRoleGroupLink(Database db,
                                        File f,
                                        List<String> fieldsToExport,
                                        QueryRule... rules)
                                 throws DatabaseException,
                                        IOException,
                                        ParseException,
                                        MolgenisModelException

export MolgenisRoleGroupLink to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMolgenisRoleGroupLink

public void exportMolgenisRoleGroupLink(List<? extends Entity> entities,
                                        File file)
                                 throws IOException,
                                        MolgenisModelException

Throws:: IOException; MolgenisModelException

exportMolgenisPermission

public void exportMolgenisPermission(Database db,
                                     File f,
                                     List<String> fieldsToExport,
                                     QueryRule... rules)
                              throws DatabaseException,
                                     IOException,
                                     ParseException,
                                     MolgenisModelException

export MolgenisPermission to file.

Parameters:: db - the database to export from.; f - the file to export to.
Throws:: DatabaseException; IOException; ParseException; MolgenisModelException

exportMolgenisPermission

public void exportMolgenisPermission(List<? extends Entity> entities,
                                     File file)
                              throws IOException,
                                     MolgenisModelException

Throws:: IOException; MolgenisModelException

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org.molgenis Class CsvEntityExporter

CsvEntityExporter

exportAll

exportAll

exportAll

exportAll

exportRegular

exportRegular

exportAll

exportSpecial

exportSpecial

exportNgsUser

exportNgsUser

exportSampleBarcodeType

exportSampleBarcodeType

exportSampleBarcode

exportSampleBarcode

exportCapturingKit

exportCapturingKit

exportPrepKit

exportPrepKit

exportProject

exportProject

exportSample

exportSample

exportMachine

exportMachine

exportFlowcell

exportFlowcell

exportFlowcellLane

exportFlowcellLane

exportMolgenisEntity

exportMolgenisEntity

exportMolgenisFile

exportMolgenisFile

exportRuntimeProperty

exportRuntimeProperty

exportCharacteristic

exportCharacteristic

exportObservationTarget

exportObservationTarget

exportIndividual

exportIndividual

exportOntology

exportOntology

exportSpecies

exportSpecies

exportOntologyTerm

exportOntologyTerm

exportAccession

exportAccession

exportValue

exportValue

exportBoolValue

exportBoolValue

exportDateValue

exportDateValue

exportDateTimeValue

exportDateTimeValue

exportDecimalValue

exportDecimalValue

exportEmailValue

exportEmailValue

exportHtmlValue

exportHtmlValue

exportHyperlinkValue

exportHyperlinkValue

exportIntValue

exportIntValue

exportLongValue

exportLongValue

exportMrefValue

exportMrefValue

exportStringValue

exportStringValue

exportTextValue

exportTextValue

exportMolgenisRole

exportMolgenisRole

exportMolgenisGroup

org.molgenis
Class CsvEntityExporter