VAMDC Query to Two Nodes using HTML Consumer Service and SpectCol
Created: 2012-03-07 18:48:58
Last updated: 2012-09-12 15:07:33
Workflow to two TAP-XSAMS Node and see results in a HTML view using a Consumer Service. This workflow queries the BaseCol and CDMS Node for MoleculeStoichiometricForumua of 'CO'
VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide
**NOTE an update to the plugin will need to be released later to handle prefixes on certain query nodes and their restrictables. For instance BaseCol expects 'Target.MoleculeStoichiometricFormula' instead of just 'MoleculeStoichiometricFormula'. This is only possible by building the filling out the Query parameter instead of using the helper ports provided by the plugin. This workflow does exactly that for BaseCol.
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Authors (1)
| VAMDC Team: http://www.vamdc.eu
Taverna Workflow Author: Kevin Benson |
Titles (1)
| VAMDC Query to Two Nodes using HTML Consumer Service and SpectCol |
Descriptions (1)
| Workflow to two TAP-XSAMS Node and see results in a HTML view using a Consumer Service. This workflow queries the BaseCol and CDMS Node for MoleculeStoichiometricForumua of 'CO'
VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide
**NOTE an update to the plugin will need to be released later to handle prefixes on certain query nodes and their restrictables. For instance BaseCol expects 'Target.MoleculeStoichiometricFormula' instead of just 'MoleculeStoichiometricFormula'. This is only possible by building the filling out the Query parameter instead of using the helper ports provided by the plugin. This workflow does exactly that for BaseCol. |
Dependencies (0)
Inputs (2)
| Name |
Description |
| Query_Operator |
Mathematical Operator: =, >, <,>=,<=
|
| Restrictable_Value |
Tap XSAMS Restrictable Value. i.e.: MoleculeStoichiometricFormula
|
Processors (16)
| Name |
Type |
Description |
| CDMS_Tap |
vamdc__taverna__suite |
|
| Format_value |
stringconstant |
ValueXSAMS |
| Lang_value |
stringconstant |
ValueVSS2 |
| Reference_value |
stringconstant |
Valuetrue |
| CDMSURL |
vamdc__taverna__suite |
|
| MoleculeStoichiometricFormula |
vamdc__taverna__suite |
|
| Table_views_of_XSAMS |
vamdc__taverna__suite |
|
| Call_Browser |
localworker |
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() );
}
}
} |
| SpectCol |
vamdc__taverna__suite |
|
| BaseCol_URL |
vamdc__taverna__suite |
|
| BaseCol_Tap |
vamdc__taverna__suite |
|
| Query_value |
stringconstant |
ValueSELECT ALL WHERE Target.MoleculeStoichiometricFormula ='CO' |
| Merge_String_List_to_a_String |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| Merge_String_List_to_a_String_2 |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| seperator_value |
stringconstant |
Value |
| seperator_value_1 |
stringconstant |
Value |
Outputs (3)
| Name |
Description |
| HTML_Table_out |
|
| browser_msg |
|
| basecolurl |
|
Datalinks (24)
| Source |
Sink |
| Format_value:value |
CDMS_Tap:Format |
| Lang_value:value |
CDMS_Tap:Lang |
| Reference_value:value |
CDMS_Tap:Reference |
| MoleculeStoichiometricFormula:QueryString |
CDMS_Tap:Query |
| CDMSURL:URLForTapXSAMSQuery |
CDMS_Tap:TAP URL or Registry Ivorn |
| Query_Operator |
MoleculeStoichiometricFormula:Operator |
| Restrictable_Value |
MoleculeStoichiometricFormula:Value |
| Table_views_of_XSAMS:Results |
Call_Browser:inputlist |
| Format_value:value |
BaseCol_Tap:Format |
| Lang_value:value |
BaseCol_Tap:Lang |
| Reference_value:value |
BaseCol_Tap:Reference |
| BaseCol_URL:URLForTapXSAMSQuery |
BaseCol_Tap:TAP URL or Registry Ivorn |
| Query_value:value |
BaseCol_Tap:Query |
| CDMS_Tap:XSamsResult |
Merge_String_List_to_a_String:stringlist |
| seperator_value:value |
Merge_String_List_to_a_String:seperator |
| BaseCol_Tap:XSamsResult |
Merge_String_List_to_a_String_2:stringlist |
| seperator_value_1:value |
Merge_String_List_to_a_String_2:seperator |
| CDMS_Tap:XSamsResult |
Table_views_of_XSAMS:XSAMS URL |
| BaseCol_Tap:XSamsResult |
Table_views_of_XSAMS:XSAMS URL |
| Merge_String_List_to_a_String:concatenated |
SpectCol:Optional URL |
| Merge_String_List_to_a_String_2:concatenated |
SpectCol:Optional URL |
| Table_views_of_XSAMS:Results |
HTML_Table_out |
| Call_Browser:outputmsg |
browser_msg |
| BaseCol_Tap:XSamsResult |
basecolurl |
Uploader
License
All versions of this Workflow are
licensed under:
Version 2 (latest)
(of 2)
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.
Download Workflow
]
Reviews
(0)
No comments yet
Log in to make a comment