Sample Entity Converter
Created: 2009-09-08 15:13:44
Last updated: 2009-09-14 14:14:32
Disclaimer: This workflow is just a simple example designed for academic purposes.
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Authors (0)
Titles (0)
Descriptions (0)
Dependencies (0)
Inputs (2)
| Name |
Description |
| Organism |
Desired Organism
|
| DataType |
The desired Data Type
|
Processors (29)
| Name |
Type |
Description |
| ListDataTypes |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationListDataTypes |
| ListDataTypesIn |
xmlsplitter |
|
| ListDataTypesOut |
xmlsplitter |
|
| ProteinName |
stringconstant |
Valueproteinname |
| SearchOrganism |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationSearchOrganism |
| SearchOrganismIn |
xmlsplitter |
|
| SearchOrganismOut |
xmlsplitter |
|
| SelectDataTypeId |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| DataTypeQuery |
stringconstant |
Value//*[local-name()="DataTypeId"] |
| SelectTaxId |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| TaxIdQuery |
stringconstant |
Value//*[local-name()="TaxonomicId"] |
| SearchProtein |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationSearchProtein |
| SearchProteinIn |
xmlsplitter |
|
| SearchProteinOut |
xmlsplitter |
|
| ConcatTaxIdComma |
localworker |
Scriptoutput = string1 + string2; |
| Comma |
stringconstant |
Value, |
| ConcatTaxIdCommaDataType |
localworker |
Scriptoutput = string1 + string2; |
| Concat2Protein |
localworker |
Scriptoutput = string1 + string2; |
| CommaOne |
stringconstant |
Value,1 |
| ConvertIdentifier |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationConvertIdentifier |
| SelectAlias |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| AliasQuery |
stringconstant |
Value//*[local-name()="Alias"] |
| ListDataTypes2 |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationListDataTypes |
| ListDataTypes2In |
xmlsplitter |
|
| ListDataTypes2Out |
xmlsplitter |
|
| SelectDataType2 |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| ConvertIdentifierIn |
xmlsplitter |
|
| ConvertIdentifierOut |
xmlsplitter |
|
| SelectAlias2 |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
Datalinks (34)
| Source |
Sink |
| ListDataTypesIn:output |
ListDataTypes:parameters |
| ProteinName:value |
ListDataTypesIn:data |
| ListDataTypes:parameters |
ListDataTypesOut:input |
| SearchOrganismIn:output |
SearchOrganism:parameters |
| Organism |
SearchOrganismIn:data |
| SearchOrganism:parameters |
SearchOrganismOut:input |
| DataTypeQuery:value |
SelectDataTypeId:xpath |
| ListDataTypesOut:ListDataTypesResult |
SelectDataTypeId:xml-text |
| TaxIdQuery:value |
SelectTaxId:xpath |
| SearchOrganismOut:SearchOrganismResult |
SelectTaxId:xml-text |
| SearchProteinIn:output |
SearchProtein:parameters |
| Concat2Protein:output |
SearchProteinIn:data |
| SearchProtein:parameters |
SearchProteinOut:input |
| SelectTaxId:nodelist |
ConcatTaxIdComma:string1 |
| Comma:value |
ConcatTaxIdComma:string2 |
| ConcatTaxIdComma:output |
ConcatTaxIdCommaDataType:string1 |
| SelectDataTypeId:nodelist |
ConcatTaxIdCommaDataType:string2 |
| ConcatTaxIdCommaDataType:output |
Concat2Protein:string1 |
| CommaOne:value |
Concat2Protein:string2 |
| ConvertIdentifierIn:output |
ConvertIdentifier:parameters |
| AliasQuery:value |
SelectAlias:xpath |
| SearchProteinOut:SearchProteinResult |
SelectAlias:xml-text |
| ListDataTypes2In:output |
ListDataTypes2:parameters |
| DataType |
ListDataTypes2In:data |
| ListDataTypes2:parameters |
ListDataTypes2Out:input |
| ListDataTypes2Out:ListDataTypesResult |
SelectDataType2:xml-text |
| DataTypeQuery:value |
SelectDataType2:xpath |
| SelectAlias:nodelist |
ConvertIdentifierIn:alias |
| SelectDataType2:nodelist |
ConvertIdentifierIn:datatype |
| SelectTaxId:nodelist |
ConvertIdentifierIn:taxID |
| ConvertIdentifier:parameters |
ConvertIdentifierOut:input |
| AliasQuery:value |
SelectAlias2:xpath |
| ConvertIdentifierOut:ConvertIdentifierResult |
SelectAlias2:xml-text |
| SelectAlias2:nodelist |
Final |
Uploader
License
All versions of this Workflow are
licensed under:
Version 1
(of 1)
Credits (1)
(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
(4)
Only the first 2 workflows that use similar services are shown. View all workflows that use these services.
Get Bioentity from Organism
(1)
GeNS workflow that lists the identifiers corresponding to a given species and data type. For instance, list all OMIM associated with the human species.
Disclaimer: This workflow is just a simple example designed for academic purposes.
Created: 2009-09-08
| Last updated: 2009-09-14
Credits:
Pedro Lopes
Search GeNS BioEntity
(1)
This workflow returns a list of know associations between an organism and a data type. All identifiers correspond to GeNS database identifiers.
Disclaimer: This workflow is just a simple example designed for academic purposes.
Created: 2009-09-15
| Last updated: 2009-09-15
Credits:
Pedro Lopes
Download Workflow
]
Reviews
(0)
No comments yet
Log in to make a comment