VAMDC VALD query with SME processing
Created: 2012-03-07 18:03:01
Last updated: 2012-11-29 11:56:21
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Authors (1)
VAMDC Team: http://www.vamdc.eu
Taverna Workflow Author: Kevin Benson |
Titles (1)
VAMDC VALD query with SME processing |
Descriptions (1)
VAMDC workflow that queries the VALD Atomic database in Moscow and runs SME (Spectroscopy Made Easy)
VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide |
Dependencies (0)
Inputs (3)
Name |
Description |
Logg |
Logg
|
Teff |
Temperature
|
ObservationFileURL |
Observation File on a public url
|
Processors (16)
Name |
Type |
Description |
SME_Extract_Wavelength_Range-simple |
vamdc__taverna__suite |
|
GetWavelengthRangeResult |
localworker |
Scriptif ((url == void) || (url == null)) {
throw new RuntimeException("The url must be specified");
}
URL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
}
else {
inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();
StringBuffer result = new StringBuffer();
BufferedReader reader;
String encoding = con.getContentEncoding();
if (encoding == null) {
reader = new BufferedReader(new InputStreamReader(in));
} else {
reader = new BufferedReader(new InputStreamReader(in, encoding));
}
String line = null;
String NEWLINE = System.getProperty("line.separator");
while ((line = reader.readLine()) != null) {
result.append(line);
result.append(NEWLINE);
}
reader.close();
contents = result.toString();
|
GetWavelengthBegin |
localworker |
Scriptif (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
split = result[1].trim();
}
|
regex_value |
stringconstant |
Value |
GetWavlengthEnd |
localworker |
Scriptif (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
split = result[2].trim();
}
|
regex_value_1 |
stringconstant |
Value |
VAMDC_TAP |
vamdc__taverna__suite |
|
Reference_value |
stringconstant |
Valuetrue |
Format_value |
stringconstant |
ValueXSAMS |
Lang_value |
stringconstant |
ValueVSS2 |
CreateQuery |
localworker |
Scriptoutput = "select * where (RadTransWavelength >= " + string1 + " AND RadTransWavelength <= " + string2 + " AND lower.StateEnergy >= 0.0 AND lower.StateEnergy <= 80655.4429 ) AND IonCharge<=1 AND RadTransProbabilityLog10WeightedOscillatorStrength > -3"; |
SME_App-simple |
vamdc__taverna__suite |
|
EchoAndSleep |
localworker |
ScriptThread.sleep(20000);
outputstring = inputstring; |
Call_Browser |
beanshell |
Script
if( !java.awt.Desktop.isDesktopSupported() ) {
System.err.println( "Desktop is not supported cannot open browser" );
outputmsg = "Desktop is not supported, cannot open browser";
}
if(inputlist.size() == 0) {
outputmsg = "No Input to call Browser.";
}else {
java.awt.Desktop desktop = java.awt.Desktop.getDesktop();
outputmsg = "";
for (Iterator i = inputlist.iterator(); i.hasNext();) {
String item = new String(i.next());
try {
if(item.startsWith("http")) {
java.net.URI uri = new java.net.URI( item );
desktop.browse( uri );
outputmsg += "Success: " + item;
}
}
catch ( Exception e ) {
System.err.println( e.getMessage() );
}
}
}
|
URL |
vamdc__taverna__suite |
VALD Uppsala
|
Convert_to_SME-format |
vamdc__taverna__suite |
|
Beanshells (1)
Name |
Description |
Inputs |
Outputs |
Call_Browser |
|
inputlist
|
outputmsg
|
Outputs (4)
Name |
Description |
XSAMS2SMEOut |
|
reporttxt |
|
reportps |
|
BrowserMsg |
|
Datalinks (25)
Source |
Sink |
ObservationFileURL |
SME_Extract_Wavelength_Range-simple:ObsFileURL |
SME_Extract_Wavelength_Range-simple:wave.txt |
GetWavelengthRangeResult:url |
GetWavelengthRangeResult:contents |
GetWavelengthBegin:string |
regex_value:value |
GetWavelengthBegin:regex |
GetWavelengthRangeResult:contents |
GetWavlengthEnd:string |
regex_value_1:value |
GetWavlengthEnd:regex |
Reference_value:value |
VAMDC_TAP:Reference |
Format_value:value |
VAMDC_TAP:Format |
Lang_value:value |
VAMDC_TAP:Lang |
CreateQuery:output |
VAMDC_TAP:Query |
URL:URLForTapXSAMSQuery |
VAMDC_TAP:TAP URL or Registry Ivorn |
GetWavelengthBegin:split |
CreateQuery:string1 |
GetWavlengthEnd:split |
CreateQuery:string2 |
EchoAndSleep:outputstring |
SME_App-simple:SMEURL |
ObservationFileURL |
SME_App-simple:ObsFileURL |
Logg |
SME_App-simple:Logg |
Teff |
SME_App-simple:Teff |
Convert_to_SME-format:Results |
EchoAndSleep:inputstring |
VAMDC_TAP:XSamsResult |
Convert_to_SME-format:XSAMS URL |
SME_App-simple:report.ps |
Call_Browser:inputlist |
SME_App-simple:report.txt |
Call_Browser:inputlist |
Convert_to_SME-format:Results |
XSAMS2SMEOut |
SME_App-simple:report.txt |
reporttxt |
SME_App-simple:report.ps |
reportps |
Call_Browser:outputmsg |
BrowserMsg |
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License
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licensed under:
Version 4 (latest)
(of 4)
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