VAMDC VALD query with SME processing
Created: 2012-03-07 18:03:01
Last updated: 2012-11-29 11:56:21
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
![header=[] body=[This is the author information extracted from the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Authors (1)
VAMDC Team: http://www.vamdc.eu
Taverna Workflow Author: Kevin Benson |
![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)
VAMDC VALD query with SME processing |
![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)
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 |
![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)
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 |
Vald_Moscow |
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 >= 0 AND IonCharge <= 1))"; |
TAP URL or Registry Ivorn_value |
stringconstant |
Valuehttp://vald.inasan.ru/vald-node/tap/sync |
Xsams2SME |
vamdc__taverna__suite |
|
SME_App-simple |
vamdc__taverna__suite |
|
EchoAndSleep |
localworker |
ScriptThread.sleep(8000);
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() );
}
}
}
|
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 |
Vald_Moscow:Reference |
Format_value:value |
Vald_Moscow:Format |
Lang_value:value |
Vald_Moscow:Lang |
CreateQuery:output |
Vald_Moscow:Query |
TAP URL or Registry Ivorn_value:value |
Vald_Moscow:TAP URL or Registry Ivorn |
GetWavelengthBegin:split |
CreateQuery:string1 |
GetWavlengthEnd:split |
CreateQuery:string2 |
Vald_Moscow:XSamsResult |
Xsams2SME:XSAMS URL |
EchoAndSleep:outputstring |
SME_App-simple:SMEURL |
ObservationFileURL |
SME_App-simple:ObsFileURL |
Logg |
SME_App-simple:Logg |
Teff |
SME_App-simple:Teff |
Xsams2SME:Results |
EchoAndSleep:inputstring |
SME_App-simple:report.ps |
Call_Browser:inputlist |
SME_App-simple:report.txt |
Call_Browser:inputlist |
Xsams2SME:Results |
XSAMS2SMEOut |
SME_App-simple:report.txt |
reporttxt |
SME_App-simple:report.ps |
reportps |
Call_Browser:outputmsg |
BrowserMsg |
Uploader
License
All versions of this Workflow are
licensed under:
Version 2
(of 4)
Credits (2)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (0)
None
Featured In Packs (0)
None
Log in to add to one of your Packs
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Statistics
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
No comments yet
Log in to make a comment