GT: Database - Master SNP Call Table
Created: 2011-09-10 00:22:14
Either load new Master SNP call data into the database (from an Excel file) or export the master SNP data from the database into an Excel file. NOTE: Running this workflow will take a couple of minutes.
If loading excel data into database, make sure the file is located in the correct directory:
/gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/
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Workflow Components
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Authors (1)
![header=[] body=[These are the descriptive titles embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Titles (1)
GT: Database - Master SNP Call Table |
![header=[] body=[These are the descriptions embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Descriptions (1)
Either load new Master SNP call data into the database (from an Excel file) or export the master SNP data from the database into an Excel file. NOTE: Running this workflow will take a couple of minutes.
If loading excel data into database, make sure the file is located in the correct directory:
/gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/ |
![header=[] body=[These are the listed dependencies of the workflow] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Dependencies (0)
Processors (13)
Name |
Type |
Description |
master_snp_call_database |
externaltool |
|
app_dir |
stringconstant |
Value/gne/research/apps/gcell/prd/arch-indep/bin |
Choose |
localworker |
Scriptimport javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
throw new RuntimeException("selectionValues must be specified and non-empty");
}
ButtonGroup group = new ButtonGroup();
JPanel messagePanel = new JPanel();
messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));
messagePanel.add(new JLabel((message == void ? null : message)));
JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
for (int i = 0; i < buttonArray.length; i++) {
buttonArray[i] = new JRadioButton(selectionValues.get(i));
if (i==0) buttonArray[i].setSelected(true);
group.add(buttonArray[i]);
messagePanel.add(buttonArray[i]);
}
JOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title),
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);
String answer="";
for (JRadioButton button : buttonArray) {
if (button.isSelected()) {
answer=button.getText();
}
}
|
Split_string_into_string_list_by_regular_expression |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
regex_value |
stringconstant |
Value, |
string_value |
stringconstant |
ValueUpload new data (Excel) to database master table,Export Excel file of master table data |
message_value_1 |
stringconstant |
ValueChoose either to upload new data to database, or export master data to an Excel file |
title_value_1 |
stringconstant |
ValueAnalysis Selection |
Tell_2 |
localworker |
Scriptimport javax.swing.JOptionPane;
JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.INFORMATION_MESSAGE);
answer = "answer";
|
tmp_dir |
stringconstant |
Value/gne/research/tmp/ |
Beanshell_2 |
beanshell |
Scriptif (action.equals("Upload new data (Excel) to database master table")) {
perlScriptName = "masterfile2database.pl";
} else if (action.equals("Export Excel file of master table data")) {
perlScriptName = "database2masterfile.pl";
} else {
perlScriptName = "";
}
|
Ask_Beanscript_Edited_2 |
localworker |
Scriptimport javax.swing.JOptionPane;
String title = "Input File Name";
String message = "Type in the file name of your SNP Master Excel file:\n"+
"** IMPORTANT: This is only needed if you selected the option\n"+
"to \"Upload new data (Excel) to database master table.\" If you"+
"selected the \"Export\" option, click OK without entering anything.";
answer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);
|
message_value_3 |
stringconstant |
ValueMaster script has finished |
Beanshells (1)
Name |
Description |
Inputs |
Outputs |
Beanshell_2 |
|
action
|
perlScriptName
|
Outputs (2)
Name |
Description |
database_status |
|
error_report |
|
Datalinks (13)
Source |
Sink |
app_dir:value |
master_snp_call_database:app_dir |
tmp_dir:value |
master_snp_call_database:tmp_dir |
Ask_Beanscript_Edited_2:answer |
master_snp_call_database:input_excel_file |
Beanshell_2:perlScriptName |
master_snp_call_database:perl_script |
Split_string_into_string_list_by_regular_expression:split |
Choose:selectionValues |
message_value_1:value |
Choose:message |
title_value_1:value |
Choose:title |
regex_value:value |
Split_string_into_string_list_by_regular_expression:regex |
string_value:value |
Split_string_into_string_list_by_regular_expression:string |
message_value_3:value |
Tell_2:message |
Choose:answer |
Beanshell_2:action |
master_snp_call_database:STDOUT |
database_status |
master_snp_call_database:STDERR |
error_report |
Coordinations (2)
Controller |
Target |
Choose |
Ask_Beanscript_Edited_2 |
master_snp_call_database |
Tell_2 |
Uploader
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