/**
* Imports OntologyTerm from tab/comma delimited File.
*
* @param OntologyTermFile a tab delimited file with OntologyTerm data.
*/
private static void importOntologyTerm(Database db, File OntologyTermFile)
throws DatabaseException, IOException, Exception {
logger.debug("trying to import " + OntologyTermFile);
if (!OntologyTermFile.exists()) {
logger.warn("OntologyTerm.txt file is missing, skipped import");
} else {
// read OntologyTerm from file
CsvReader reader = new CsvFileReader(OntologyTermFile);
List<OntologyTerm> ontologyTermList =
db.toList(OntologyTerm.class, reader, Integer.MAX_VALUE); // should have no limit
logger.debug("loaded " + ontologyTermList.size() + " OntologyTerm objects");
// redirect incoming and outgoing fkeys
List<Integer> ontologyTermIds = new ArrayList<Integer>(); // also doesn't scale
for (int i = 0;
i < ontologyTermList.size();
i++) // sorry, not a real list so need to put back!!
{
OntologyTerm object = ontologyTermList.get(i);
// remember index of this id for incoming fkeys
ontologyTermIds.add(object.getId());
// redirect outgoing fkeys
if (object.getOntology() != null)
object.setOntology_Id(ontologyIdMap.get(object.getOntology_Id()));
// add assay back to list
ontologyTermList.set(i, object);
}
// add to database
db.add(ontologyTermList);
for (int i = 0; i < ontologyTermList.size(); i++) {
ontologyTermIdMap.put(ontologyTermIds.get(i), ontologyTermList.get(i).getId());
}
}
}
@Override
public List<HtmlInput<?>> getInputs() {
List<HtmlInput<?>> inputs = new ArrayList<HtmlInput<?>>();
// Autoid: Field(entity=ProtocolApplication_ontol11768, name=autoid, type=int, auto=true,
// nillable=false, readonly=false, default=null)
{
IntInput input =
new IntInput("ProtocolApplication_ontol11768_autoid", getEntity().getAutoid());
input.setLabel("autoid");
input.setDescription("automatic id field to ensure ordering of mrefs");
input.setNillable(false);
input.setReadonly(isReadonly() || getEntity().isReadonly());
input.setHidden(!isNewRecord());
if (this.getCompactView().size() > 0 && !this.getCompactView().contains(input.getName())) {
input.setCollapse(true);
}
inputs.add(input);
}
// OntologyReference: Field(entity=ProtocolApplication_ontol11768, name=ontologyReference,
// type=xref[OntologyTerm.id], xref_label='name', auto=false, nillable=false, readonly=false,
// default=null)
{
// TODO: when we have JPA this should become:
// XrefInput input = new XrefInput("ProtocolApplication_ontol11768_ontologyReference",
// getEntity().getOntologyReference());
// create xref dummy object
OntologyTerm dummy = null;
if (getEntity().getOntologyReference_Id() != null) {
dummy = new OntologyTerm();
dummy.setId(getEntity().getOntologyReference_Id());
dummy.setName(getEntity().getOntologyReference_Name());
}
XrefInput input =
new XrefInput(
"ProtocolApplication_ontol11768_ontologyReference",
org.molgenis.core.OntologyTerm.class,
dummy);
input.setLabel("ontologyReference");
input.setDescription("");
input.setNillable(false);
input.setReadonly(isReadonly() || getEntity().isReadonly());
if (this.getHiddenColumns().contains(input.getName())) {
input.setHidden(!isNewRecord());
}
if (this.getCompactView().size() > 0 && !this.getCompactView().contains(input.getName())) {
input.setCollapse(true);
}
inputs.add(input);
}
// InvestigationElement: Field(entity=ProtocolApplication_ontol11768, name=InvestigationElement,
// type=xref[ProtocolApplication.id], xref_label=, auto=false, nillable=false, readonly=false,
// default=null)
{
// TODO: when we have JPA this should become:
// XrefInput input = new XrefInput("ProtocolApplication_ontol11768_InvestigationElement",
// getEntity().getInvestigationElement());
// create xref dummy object
ProtocolApplication dummy = null;
if (getEntity().getInvestigationElement_Id() != null) {
dummy = new ProtocolApplication();
dummy.setId(getEntity().getInvestigationElement_Id());
dummy.setName(getEntity().getInvestigationElement_Name());
}
XrefInput input =
new XrefInput(
"ProtocolApplication_ontol11768_InvestigationElement",
org.molgenis.protocol.ProtocolApplication.class,
dummy);
input.setLabel("InvestigationElement");
input.setDescription("");
input.setNillable(false);
input.setReadonly(isReadonly() || getEntity().isReadonly());
if (this.getHiddenColumns().contains(input.getName())) {
input.setHidden(!isNewRecord());
}
if (this.getCompactView().size() > 0 && !this.getCompactView().contains(input.getName())) {
input.setCollapse(true);
}
inputs.add(input);
}
return inputs;
}
public ImportWizardExcelPrognosis(File excelFile) throws Exception {
Workbook workbook = Workbook.getWorkbook(excelFile);
ArrayList<String> lowercasedSheetNames = new ArrayList<String>();
Map<String, String> lowerToOriginalName = new HashMap<String, String>();
try {
for (String sheetName : workbook.getSheetNames()) {
lowercasedSheetNames.add(sheetName.toLowerCase());
lowerToOriginalName.put(sheetName.toLowerCase(), sheetName);
}
if (lowercasedSheetNames.contains("molgenisrole")) {
String originalSheetname = lowerToOriginalName.get("molgenisrole");
Sheet sheet = workbook.getSheet(originalSheetname);
MolgenisRoleExcelReader excelReader = new MolgenisRoleExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
MolgenisRole entity = new MolgenisRole();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("molgenisgroup")) {
String originalSheetname = lowerToOriginalName.get("molgenisgroup");
Sheet sheet = workbook.getSheet(originalSheetname);
MolgenisGroupExcelReader excelReader = new MolgenisGroupExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
MolgenisGroup entity = new MolgenisGroup();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("institute")) {
String originalSheetname = lowerToOriginalName.get("institute");
Sheet sheet = workbook.getSheet(originalSheetname);
InstituteExcelReader excelReader = new InstituteExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
Institute entity = new Institute();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("ontology")) {
String originalSheetname = lowerToOriginalName.get("ontology");
Sheet sheet = workbook.getSheet(originalSheetname);
OntologyExcelReader excelReader = new OntologyExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
Ontology entity = new Ontology();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("ontologyterm")) {
String originalSheetname = lowerToOriginalName.get("ontologyterm");
Sheet sheet = workbook.getSheet(originalSheetname);
OntologyTermExcelReader excelReader = new OntologyTermExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
OntologyTerm entity = new OntologyTerm();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("person")) {
String originalSheetname = lowerToOriginalName.get("person");
Sheet sheet = workbook.getSheet(originalSheetname);
PersonExcelReader excelReader = new PersonExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
Person entity = new Person();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("molgenisuser")) {
String originalSheetname = lowerToOriginalName.get("molgenisuser");
Sheet sheet = workbook.getSheet(originalSheetname);
MolgenisUserExcelReader excelReader = new MolgenisUserExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
MolgenisUser entity = new MolgenisUser();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("molgenisrolegrouplink")) {
String originalSheetname = lowerToOriginalName.get("molgenisrolegrouplink");
Sheet sheet = workbook.getSheet(originalSheetname);
MolgenisRoleGroupLinkExcelReader excelReader = new MolgenisRoleGroupLinkExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
MolgenisRoleGroupLink entity = new MolgenisRoleGroupLink();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("molgenisfile")) {
String originalSheetname = lowerToOriginalName.get("molgenisfile");
Sheet sheet = workbook.getSheet(originalSheetname);
MolgenisFileExcelReader excelReader = new MolgenisFileExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
MolgenisFile entity = new MolgenisFile();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("runtimeproperty")) {
String originalSheetname = lowerToOriginalName.get("runtimeproperty");
Sheet sheet = workbook.getSheet(originalSheetname);
RuntimePropertyExcelReader excelReader = new RuntimePropertyExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
RuntimeProperty entity = new RuntimeProperty();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("publication")) {
String originalSheetname = lowerToOriginalName.get("publication");
Sheet sheet = workbook.getSheet(originalSheetname);
PublicationExcelReader excelReader = new PublicationExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
Publication entity = new Publication();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("usecase")) {
String originalSheetname = lowerToOriginalName.get("usecase");
Sheet sheet = workbook.getSheet(originalSheetname);
UseCaseExcelReader excelReader = new UseCaseExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
UseCase entity = new UseCase();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("molgenisentity")) {
String originalSheetname = lowerToOriginalName.get("molgenisentity");
Sheet sheet = workbook.getSheet(originalSheetname);
MolgenisEntityExcelReader excelReader = new MolgenisEntityExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
MolgenisEntity entity = new MolgenisEntity();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
if (lowercasedSheetNames.contains("molgenispermission")) {
String originalSheetname = lowerToOriginalName.get("molgenispermission");
Sheet sheet = workbook.getSheet(originalSheetname);
MolgenisPermissionExcelReader excelReader = new MolgenisPermissionExcelReader();
List<String> allHeaders = excelReader.getNonEmptyHeaders(sheet);
MolgenisPermission entity = new MolgenisPermission();
headersToMaps(originalSheetname, allHeaders, entity.getFields());
}
for (String sheetName : lowerToOriginalName.values()) {
if (importOrder.contains(sheetName)) {
sheetsImportable.put(sheetName, true);
} else {
sheetsImportable.put(sheetName, false);
}
}
} catch (Exception e) {
throw e;
} finally {
workbook.close();
}
}
