org.molgenis
Class CsvEntityExporter

java.lang.Object
  org.molgenis.CsvEntityExporter

public class CsvEntityExporter
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	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	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	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	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	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	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	exportStudyDataRequest(Database db, File f, List<String> fieldsToExport, QueryRule... rules) export StudyDataRequest to file.
void	exportStudyDataRequest(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

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

exportStudyDataRequest

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

export StudyDataRequest to file.

Parameters:

db - the database to export from.

f - the file to export to.

Throws:

DatabaseException

IOException

ParseException

MolgenisModelException

exportStudyDataRequest

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

Throws:

IOException

MolgenisModelException