@Override
public void handleEvent(Event event) {
// TODO Auto-generated method stub
Vector<String> values = this.setPlatformsUI.getValues();
Vector<String> samples = this.setPlatformsUI.getSamples();
File file =
new File(
this.dataType.getPath().toString()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping.tmp");
File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
if (stsmf == null) {
this.setPlatformsUI.displayMessage("Error: no subject to sample mapping file");
}
try {
FileWriter fw = new FileWriter(file);
BufferedWriter out = new BufferedWriter(fw);
out.write(
"study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n");
try {
BufferedReader br = new BufferedReader(new FileReader(stsmf));
String line = br.readLine();
while ((line = br.readLine()) != null) {
String[] fields = line.split("\t", -1);
String sample = fields[3];
String platform;
if (samples.contains(sample)) {
platform = values.get(samples.indexOf(sample));
} else {
br.close();
return;
}
out.write(
fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + platform
+ "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8]
+ "\n");
}
br.close();
} catch (Exception e) {
this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage());
out.close();
e.printStackTrace();
}
out.close();
try {
File fileDest;
if (stsmf != null) {
String fileName = stsmf.getName();
stsmf.delete();
fileDest = new File(this.dataType.getPath() + File.separator + fileName);
} else {
fileDest =
new File(
this.dataType.getPath()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping");
}
FileUtils.moveFile(file, fileDest);
((GeneExpressionData) this.dataType).setSTSMF(fileDest);
} catch (IOException ioe) {
this.setPlatformsUI.displayMessage("File error: " + ioe.getLocalizedMessage());
return;
}
} catch (Exception e) {
this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage());
e.printStackTrace();
}
this.setPlatformsUI.displayMessage("Subject to sample mapping file updated");
WorkPart.updateSteps();
WorkPart.updateFiles();
}
@Override
public void handleEvent(Event event) {
// TODO Auto-generated method stub
File file =
new File(
this.dataType.getPath().toString()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping.tmp");
File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
if (stsmf == null) {
this.setStudyTreeUI.displayMessage("Error: no subject to sample mapping file");
}
String category = "";
TreeNode node = this.setStudyTreeUI.getRoot();
if (!node.hasChildren()) {
this.setStudyTreeUI.displayMessage("You have to set a category code");
return;
}
node = node.getChildren().get(0);
while (node != null) {
if (category.compareTo("") == 0) {
category += node.toString().replace(' ', '_');
} else {
category += "+" + node.toString().replace(' ', '_');
}
if (node.hasChildren()) {
node = node.getChildren().get(0);
} else {
node = null;
}
}
try {
FileWriter fw = new FileWriter(file);
BufferedWriter out = new BufferedWriter(fw);
out.write(
"study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n");
try {
BufferedReader br = new BufferedReader(new FileReader(stsmf));
String line = br.readLine();
while ((line = br.readLine()) != null) {
String[] fields = line.split("\t", -1);
out.write(
fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + fields[3] + "\t" + fields[4]
+ "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + category
+ "\n");
}
br.close();
} catch (Exception e) {
this.setStudyTreeUI.displayMessage("File error: " + e.getLocalizedMessage());
out.close();
e.printStackTrace();
}
out.close();
try {
File fileDest;
if (stsmf != null) {
String fileName = stsmf.getName();
stsmf.delete();
fileDest = new File(this.dataType.getPath() + File.separator + fileName);
} else {
fileDest =
new File(
this.dataType.getPath()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping");
}
FileUtils.moveFile(file, fileDest);
((GeneExpressionData) this.dataType).setSTSMF(fileDest);
} catch (IOException ioe) {
this.setStudyTreeUI.displayMessage("File error: " + ioe.getLocalizedMessage());
return;
}
} catch (Exception e) {
this.setStudyTreeUI.displayMessage("Eerror: " + e.getLocalizedMessage());
e.printStackTrace();
}
this.setStudyTreeUI.displayMessage("Subject to sample mapping file updated");
WorkPart.updateSteps();
WorkPart.updateFiles();
}
/**
* Loads the gene expression data: -initiate Kettle environment -Find Kettle files -Set Kettle
* parameters -Calls the Kettle job -Save the log file
*/
@Override
public void handleEvent(Event event) {
this.topNode = this.loadDataUI.getTopNode();
this.path = this.dataType.getPath().getAbsolutePath();
this.sortName =
this.dataType.getStudy().getPath().getParentFile().getAbsolutePath()
+ File.separator
+ ".sort";
loadDataUI.openLoadingShell();
new Thread() {
public void run() {
try {
String[] splited = topNode.split("\\\\", -1);
if (splited[0].compareTo("") != 0) {
loadDataUI.setMessage("A study node has to begin by the character '\\'");
loadDataUI.setIsLoading(false);
return;
}
try {
Class.forName("org.postgresql.Driver");
String connectionString =
"jdbc:postgresql://"
+ PreferencesHandler.getDbServer()
+ ":"
+ PreferencesHandler.getDbPort()
+ "/"
+ PreferencesHandler.getDbName();
Connection con =
DriverManager.getConnection(
connectionString,
PreferencesHandler.getMetadataUser(),
PreferencesHandler.getMetadataPwd());
Statement stmt = con.createStatement();
ResultSet rs =
stmt.executeQuery("select * from table_access where c_name='" + splited[1] + "'");
if (!rs.next()) { // have to add a top node
stmt.executeQuery(
"insert into table_access("
+ "c_table_cd,"
+ "c_table_name,"
+ "c_protected_access,"
+ "c_hlevel,"
+ "c_fullname,"
+ "c_name,"
+ "c_synonym_cd,"
+ "c_visualattributes,"
+ "c_totalnum,"
+ "c_facttablecolumn,"
+ "c_dimtablename,"
+ "c_columnname,"
+ "c_columndatatype,"
+ "c_operator,"
+ "c_dimcode,"
+ "c_tooltip,"
+ "c_status_cd) values("
+ "'"
+ splited[1]
+ "',"
+ "'i2b2',"
+ "'N',"
+ "0,"
+ "'\\"
+ splited[1]
+ "\\',"
+ "'"
+ splited[1]
+ "',"
+ "'N',"
+ "'CA',"
+ "0,"
+ "'concept_cd',"
+ "'concept_dimension',"
+ "'concept_path',"
+ "'T',"
+ "'LIKE',"
+ "'\\"
+ splited[1]
+ "\\',"
+ "'\\"
+ splited[1]
+ "\\',"
+ "'A')");
stmt.executeQuery(
"insert into i2b2 values(0, '\\"
+ splited[1]
+ "\\', '"
+ splited[1]
+ "','N','CA',0,null, null, 'CONCEPT_CD','CONCEPT_DIMENSION','CONCEPT_PATH', 'T', 'LIKE','\\"
+ splited[1]
+ "\\', null, '\\"
+ splited[1]
+ "\\', sysdate, null, null, null, null, null, '@', null, null, null)");
}
con.close();
} catch (SQLException e) {
e.printStackTrace();
loadDataUI.displayMessage("SQL error: " + e.getLocalizedMessage());
loadDataUI.setIsLoading(false);
return;
} catch (ClassNotFoundException e) {
loadDataUI.displayMessage("Java error: Class not found exception");
// TODO Auto-generated catch block
e.printStackTrace();
loadDataUI.setIsLoading(false);
return;
}
// initiate kettle environment
URL kettleUrl = new URL("platform:/plugin/fr.sanofi.fcl4transmart/lib/pentaho");
kettleUrl = FileLocator.toFileURL(kettleUrl);
System.setProperty("KETTLE_PLUGIN_BASE_FOLDERS", kettleUrl.getPath());
KettleEnvironment.init(false);
// find the kettle job to initiate the loading
URL jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_gene_expression_data.kjb");
jobUrl = FileLocator.toFileURL(jobUrl);
String jobPath = jobUrl.getPath();
// create a new job from the kettle file
JobMeta jobMeta = new JobMeta(jobPath, null);
Job job = new Job(null, jobMeta);
// find the other files needed for this job and put them in the cache
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/validate_gene_expression_params.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/validate_gene_expression_columns.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/check_gene_expression_filenames.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_all_gene_expression_files_for_study.kjb");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/run_i2b2_process_mrna_data.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_subject_sample_map_to_lt.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/get_list_of_gene_expression_filenames.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_gene_expression_one_study.kjb");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/set_gene_expression_filename.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/validate_gene_expression_columns.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_gene_expression_data_to_lz.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL("platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/pivot_gene_file.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL("platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/cz_start_audit.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl = new URL("platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/cz_end_audit.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/write_gene_expression_audit.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
jobUrl =
new URL(
"platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/write_study_id_to_audit.ktr");
jobUrl = FileLocator.toFileURL(jobUrl);
job.getJobMeta().setParameterValue("DATA_FILE_PREFIX", "raw");
job.getJobMeta().setParameterValue("DATA_LOCATION", path);
job.getJobMeta()
.setParameterValue(
"MAP_FILENAME", ((GeneExpressionData) dataType).getStsmf().getName());
job.getJobMeta().setParameterValue("DATA_TYPE", "R");
job.getJobMeta().setParameterValue("LOG_BASE", "2");
job.getJobMeta().setParameterValue("FilePivot_LOCATION", "");
job.getJobMeta().setParameterValue("LOAD_TYPE", "I");
job.getJobMeta().setParameterValue("SAMPLE_REMAP_FILENAME", "NOSAMPLEREMAP");
job.getJobMeta().setParameterValue("SAMPLE_SUFFIX", ".rma-Signal");
if (loadDataUI.getSecurity()) {
job.getJobMeta().setParameterValue("SECURITY_REQUIRED", "Y");
} else {
job.getJobMeta().setParameterValue("SECURITY_REQUIRED", "N");
}
job.getJobMeta().setParameterValue("SOURCE_CD", "STD");
File sort = new File(sortName);
if (!sort.exists()) {
FileUtils.forceMkdir(sort);
}
path = sort.getAbsolutePath();
job.getJobMeta().setParameterValue("SORT_DIR", path);
job.getJobMeta().setParameterValue("STUDY_ID", dataType.getStudy().toString());
job.getJobMeta().setParameterValue("TOP_NODE", topNode);
// job.getJobMeta().setParameterValue("JAVA_HOME", "/usr/local/jdk1.6.0_31");
job.getJobMeta().setParameterValue("TM_CZ_DB_SERVER", PreferencesHandler.getDbServer());
job.getJobMeta().setParameterValue("TM_CZ_DB_NAME", PreferencesHandler.getDbName());
job.getJobMeta().setParameterValue("TM_CZ_DB_PORT", PreferencesHandler.getDbPort());
job.getJobMeta().setParameterValue("TM_CZ_DB_USER", PreferencesHandler.getTm_czUser());
job.getJobMeta().setParameterValue("TM_CZ_DB_PWD", PreferencesHandler.getTm_czPwd());
job.getJobMeta().setParameterValue("TM_LZ_DB_SERVER", PreferencesHandler.getDbServer());
job.getJobMeta().setParameterValue("TM_LZ_DB_NAME", PreferencesHandler.getDbName());
job.getJobMeta().setParameterValue("TM_LZ_DB_PORT", PreferencesHandler.getDbPort());
job.getJobMeta().setParameterValue("TM_LZ_DB_USER", PreferencesHandler.getTm_lzUser());
job.getJobMeta().setParameterValue("TM_LZ_DB_PWD", PreferencesHandler.getTm_lzPwd());
job.getJobMeta().setParameterValue("DEAPP_DB_SERVER", PreferencesHandler.getDbServer());
job.getJobMeta().setParameterValue("DEAPP_DB_NAME", PreferencesHandler.getDbName());
job.getJobMeta().setParameterValue("DEAPP_DB_PORT", PreferencesHandler.getDbPort());
job.getJobMeta().setParameterValue("DEAPP_DB_USER", PreferencesHandler.getDeappUser());
job.getJobMeta().setParameterValue("DEAPP_DB_PWD", PreferencesHandler.getDeappPwd());
if (loadDataUI.getIndexes()) {
// drop indexes
String connectionString =
"jdbc:oracle:thin:@"
+ PreferencesHandler.getDbServer()
+ ":"
+ PreferencesHandler.getDbPort()
+ ":"
+ PreferencesHandler.getDbName();
Connection con =
DriverManager.getConnection(
connectionString,
PreferencesHandler.getTm_czUser(),
PreferencesHandler.getTm_czPwd());
String sql = "{call i2b2_mrna_index_maint(?)}";
CallableStatement call = con.prepareCall(sql);
call.setString(1, "DROP");
call.execute();
con.close();
System.out.println("Indexes dropped");
}
job.start();
job.waitUntilFinished();
System.out.println("Job finished");
if (loadDataUI.getIndexes()) {
// add indexes
String connectionString =
"jdbc:postgresql://"
+ PreferencesHandler.getDbServer()
+ ":"
+ PreferencesHandler.getDbPort()
+ "/"
+ PreferencesHandler.getDbName();
Connection con =
DriverManager.getConnection(
connectionString,
PreferencesHandler.getTm_czUser(),
PreferencesHandler.getTm_czPwd());
String sql = "{call i2b2_mrna_index_maint(?)}";
CallableStatement call = con.prepareCall(sql);
call.setString(1, "ADD");
call.execute();
con.close();
System.out.println("Indexes added");
}
@SuppressWarnings("unused")
Result result = job.getResult();
Display.getDefault()
.asyncExec(
new Runnable() {
public void run() {
loadDataUI.displayMessage(
"Loading process is over.\n Please check monitoring step.");
}
});
Log4jBufferAppender appender = CentralLogStore.getAppender();
String logText = appender.getBuffer(job.getLogChannelId(), false).toString();
Pattern pattern =
Pattern.compile(
".*Finished job entry \\[run i2b2_process_mrna_data\\].*", Pattern.DOTALL);
Matcher matcher = pattern.matcher(logText);
if (matcher.matches()) {
String connectionString =
"jdbc:postgresql://"
+ PreferencesHandler.getDbServer()
+ ":"
+ PreferencesHandler.getDbPort()
+ "/"
+ PreferencesHandler.getDbName();
Connection con =
DriverManager.getConnection(
connectionString,
PreferencesHandler.getTm_czUser(),
PreferencesHandler.getTm_czPwd());
Statement stmt = con.createStatement();
// remove rows for this study before adding new ones
ResultSet rs =
stmt.executeQuery(
"select max(JOB_ID) from CZ_JOB_AUDIT where STEP_DESC='Starting i2b2_process_mrna_data'");
int jobId;
if (rs.next()) {
jobId = rs.getInt(1);
} else {
con.close();
loadDataUI.setIsLoading(false);
return;
}
logText += "\nOracle job id:\n" + String.valueOf(jobId);
con.close();
}
writeLog(logText);
CentralLogStore.discardLines(job.getLogChannelId(), false);
} catch (Exception e1) {
// this.write(e1.getMessage());
messageException = e1.getLocalizedMessage();
Display.getDefault()
.asyncExec(
new Runnable() {
public void run() {
loadDataUI.displayMessage("Error: " + messageException);
}
});
loadDataUI.setIsLoading(false);
e1.printStackTrace();
}
loadDataUI.setIsLoading(false);
}
}.start();
this.loadDataUI.waitForThread();
WorkPart.updateSteps();
WorkPart.addFiles(this.dataType);
}
@Override
public void handleEvent(Event event) {
Vector<File> rawFiles = ((ClinicalData) this.dataType).getRawFiles();
Vector<String> siteIds = this.setOtherIdsUI.getSiteIds();
Vector<String> visitNames = this.setOtherIdsUI.getVisitNames();
// write in a new file
File file =
new File(
this.dataType.getPath().toString()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".columns.tmp");
try {
FileWriter fw = new FileWriter(file);
BufferedWriter out = new BufferedWriter(fw);
out.write(
"Filename\tCategory Code\tColumn Number\tData Label\tData Label Source\tControlled Vocab Code\n");
for (int i = 0; i < rawFiles.size(); i++) {
// site identifier
if (siteIds.elementAt(i).compareTo("") != 0) {
int columnNumber =
FileHandler.getHeaderNumber(rawFiles.elementAt(i), siteIds.elementAt(i));
if (columnNumber != -1) {
out.write(rawFiles.elementAt(i).getName() + "\t\t" + columnNumber + "\tSITE_ID\t\t\n");
}
}
// visit name
if (visitNames.elementAt(i).compareTo("") != 0) {
int columnNumber =
FileHandler.getHeaderNumber(rawFiles.elementAt(i), visitNames.elementAt(i));
if (columnNumber != -1) {
out.write(
rawFiles.elementAt(i).getName() + "\t\t" + columnNumber + "\tVISIT_NAME\t\t\n");
}
}
}
// add lines from existing CMF
try {
BufferedReader br =
new BufferedReader(new FileReader(((ClinicalData) this.dataType).getCMF()));
String line = br.readLine();
while ((line = br.readLine()) != null) {
String[] s = line.split("\t", -1);
if (s[3].compareTo("SITE_ID") != 0 && s[3].compareTo("VISIT_NAME") != 0) {
out.write(line + "\n");
}
}
br.close();
} catch (Exception e) {
this.setOtherIdsUI.displayMessage("Error: " + e.getLocalizedMessage());
e.printStackTrace();
out.close();
}
out.close();
try {
String fileName = ((ClinicalData) this.dataType).getCMF().getName();
((ClinicalData) this.dataType).getCMF().delete();
File fileDest = new File(this.dataType.getPath() + File.separator + fileName);
FileUtils.moveFile(file, fileDest);
((ClinicalData) this.dataType).setCMF(fileDest);
} catch (IOException ioe) {
this.setOtherIdsUI.displayMessage("File error: " + ioe.getLocalizedMessage());
return;
}
} catch (Exception e) {
this.setOtherIdsUI.displayMessage("Error: " + e.getLocalizedMessage());
e.printStackTrace();
}
this.setOtherIdsUI.displayMessage("Column mapping file updated");
WorkPart.updateSteps();
WorkPart.updateFiles();
UsedFilesPart.sendFilesChanged(dataType);
}
@Override
public Composite createUI(Composite parent) {
this.display = WorkPart.display();
Shell shell = new Shell(this.display);
shell.setSize(50, 100);
GridLayout gridLayout = new GridLayout();
gridLayout.numColumns = 1;
shell.setLayout(gridLayout);
ProgressBar pb = new ProgressBar(shell, SWT.HORIZONTAL | SWT.INDETERMINATE);
pb.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
Label searching = new Label(shell, SWT.NONE);
searching.setText("Searching...");
shell.open();
this.isSearching = true;
new Thread() {
public void run() {
testTm_cz = RetrieveData.testTm_czConnection();
testTm_lz = RetrieveData.testTm_lzConnection();
testDeapp = RetrieveData.testDeappConnection();
root = new TreeNode("Dataset explorer", null, false);
studyTree = new StudyTree(root);
topNodeController = new TopNodeController(root, dataType, studyTree);
root = topNodeController.buildTree();
topNode = dataType.getStudy().getTopNode();
isSearching = false;
}
}.start();
this.display = WorkPart.display();
while (this.isSearching) {
if (!display.readAndDispatch()) {
display.sleep();
}
}
shell.close();
Composite composite = new Composite(parent, SWT.NONE);
GridLayout gd = new GridLayout();
gd.numColumns = 1;
gd.horizontalSpacing = 0;
gd.verticalSpacing = 0;
composite.setLayout(gd);
composite.setLayoutData(new GridData(GridData.FILL_BOTH));
ScrolledComposite scroller = new ScrolledComposite(composite, SWT.H_SCROLL | SWT.V_SCROLL);
scroller.setLayoutData(new GridData(GridData.FILL_BOTH));
gd = new GridLayout();
gd.numColumns = 1;
gd.horizontalSpacing = 0;
gd.verticalSpacing = 0;
scroller.setLayout(gd);
scroller.setLayoutData(new GridData(GridData.FILL_BOTH));
Composite scrolledComposite = new Composite(scroller, SWT.NONE);
scroller.setContent(scrolledComposite);
GridLayout layout = new GridLayout();
layout.numColumns = 1;
layout.verticalSpacing = 10;
scrolledComposite.setLayout(layout);
scrolledComposite.setLayoutData(new GridData(GridData.FILL_BOTH));
this.topNode = this.dataType.getStudy().getTopNode();
if (topNode != null && topNode.compareTo("") != 0) {
viewer = new TreeViewer(scrolledComposite, SWT.SINGLE | SWT.H_SCROLL | SWT.V_SCROLL);
viewer.setContentProvider(new StudyContentProvider());
viewer.setAutoExpandLevel(AbstractTreeViewer.ALL_LEVELS);
viewer.setInput(this.studyTree);
GridData gridData = new GridData(GridData.FILL_BOTH);
gridData.horizontalAlignment = SWT.FILL;
gridData.verticalAlignment = SWT.FILL;
gridData.grabExcessHorizontalSpace = true;
gridData.grabExcessVerticalSpace = true;
gridData.heightHint = 300;
gridData.widthHint = 250;
this.viewer.getControl().setLayoutData(gridData);
viewer.setLabelProvider(
new ColumnLabelProvider() {
@Override
public String getText(Object element) {
return element.toString();
}
@Override
public Color getBackground(Object element) {
if (((TreeNode) element).isStudyRoot()) {
return new Color(Display.getCurrent(), 237, 91, 67);
}
if (((TreeNode) element).isLabel()) {
return new Color(Display.getCurrent(), 212, 212, 212);
}
return null;
}
});
securityButton = new Button(scrolledComposite, SWT.CHECK);
securityButton.setText("Security required");
securityButton.addListener(
SWT.Selection,
new Listener() {
@Override
public void handleEvent(Event event) {
security = securityButton.getSelection();
}
});
/*indexesButton=new Button(scrolledComposite, SWT.CHECK);
indexesButton.setText("Turn off the indexes during loaded (only for large datasets)");
indexesButton.addListener(SWT.Selection, new Listener(){
@Override
public void handleEvent(Event event) {
indexes=indexesButton.getSelection();
}
})*/ ;
} else {
Label label = new Label(scrolledComposite, SWT.NONE);
label.setText("Please first choose a study node in the description data type");
}
Button button = new Button(scrolledComposite, SWT.PUSH);
button.setText("Load");
if (topNode != null && topNode.compareTo("") != 0) {
if (this.testTm_cz && this.testTm_lz && this.testDeapp) {
button.addListener(SWT.Selection, new LoadGeneExpressionDataListener(this, this.dataType));
Label dbLabel = new Label(scrolledComposite, SWT.NONE);
dbLabel.setText("You are connected to database '" + PreferencesHandler.getDb() + "'");
} else {
button.setEnabled(false);
Label warn = new Label(scrolledComposite, SWT.NONE);
warn.setText("Warning: connection to database is not possible");
}
} else {
button.setEnabled(false);
}
scrolledComposite.setSize(scrolledComposite.computeSize(SWT.DEFAULT, SWT.DEFAULT));
return composite;
}
@Override
public void handleEvent(Event event) {
this.selectRawFilesUI.openLoadingShell();
new Thread() {
public void run() {
String[] paths = selectRawFilesUI.getPath().split(File.pathSeparator, -1);
for (int i = 0; i < paths.length; i++) {
String path = paths[i];
if (path == null) {
selectRawFilesUI.setIsLoading(false);
return;
}
File rawFile = new File(path);
if (rawFile.exists()) {
if (rawFile.isFile()) {
if (path.contains("%")) {
selectRawFilesUI.setMessage("File name can not contain percent ('%') symbol.");
selectRawFilesUI.setIsLoading(false);
return;
}
String newPath =
dataType.getPath().getAbsolutePath() + File.separator + rawFile.getName();
if (selectRawFilesUI.getFormat().compareTo("Tab delimited raw file") != 0
&& selectRawFilesUI.getFormat().compareTo("SOFT") != 0) {
selectRawFilesUI.setMessage("File format does not exist");
selectRawFilesUI.setIsLoading(false);
return;
}
if (selectRawFilesUI.getFormat().compareTo("SOFT") == 0) {
File newFile = new File(newPath);
if (newFile.exists()) {
selectRawFilesUI.setMessage("File has already been added");
selectRawFilesUI.setIsLoading(false);
return;
} else {
if (createTabFileFromSoft(rawFile, newFile)) {
((ClinicalData) dataType).addRawFile(newFile);
selectRawFilesUI.setMessage("File has been added");
}
}
} else if (selectRawFilesUI.getFormat().compareTo("Tab delimited raw file") == 0) {
if (!checkTabFormat(rawFile)) {
selectRawFilesUI.setIsLoading(false);
return;
}
File copiedRawFile = new File(newPath);
if (!copiedRawFile.exists()) {
try {
FileUtils.copyFile(rawFile, copiedRawFile);
((ClinicalData) dataType).addRawFile(copiedRawFile);
selectRawFilesUI.setMessage("File has been added");
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
selectRawFilesUI.setMessage("File error: " + e.getLocalizedMessage());
selectRawFilesUI.setIsLoading(false);
return;
}
} else {
selectRawFilesUI.setMessage("File has already been added");
selectRawFilesUI.setIsLoading(false);
return;
}
}
} else {
selectRawFilesUI.setMessage("File is a directory");
selectRawFilesUI.setIsLoading(false);
return;
}
} else {
selectRawFilesUI.setMessage("Path does no exist");
selectRawFilesUI.setIsLoading(false);
return;
}
}
selectRawFilesUI.setIsLoading(false);
}
}.start();
this.selectRawFilesUI.waitForThread();
selectRawFilesUI.updateViewer();
WorkPart.updateSteps();
UsedFilesPart.sendFilesChanged(dataType);
}
