Cross-references search, duplicated genes search, cross-reference fetch

None

filteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (item.matches(regex)) {
		filteredlist.add(item);
	}
}

filteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (item.matches(regex)) {
		filteredlist.add(item);
	}
}

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();

InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);

StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
  buf.append((char)ch);
}
inReader.close();
contents = buf.toString();


//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
//	inputURL = new URL(new URL(base), url);
//} else {
//	inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
//	result.append(line);
//	result.append(NEWLINE);
//}
//
//contents = result.toString();

filteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (item.matches(regex)) {
		filteredlist.add(item);
	}
}

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();

InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);

StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
  buf.append((char)ch);
}
inReader.close();
contents = buf.toString();


//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
//	inputURL = new URL(new URL(base), url);
//} else {
//	inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
//	result.append(line);
//	result.append(NEWLINE);
//}
//
//contents = result.toString();

Name	Type	Description
XrefSearch	wsdl	Wsdl http://webservices.genouest.org/typedservices/Xref.wsdl Wsdl Operation launchJobBlocking
XrefSearch_launchJobBlockingInput	xmlsplitter
launchJobBlockingInput_input	xmlsplitter
XrefSearch_launchJobBlockingOutput	xmlsplitter
launchJobBlockingOutput_jobOut	xmlsplitter
xrefSearch_Output_filter	localworker	Script filteredlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (item.matches(regex)) { filteredlist.add(item); } }
xrefSearch_mode	stringconstant	Value get_ens
xrefSearch_inputFileName	stringconstant	Value askedGenes.txt
regex_filter	stringconstant	Value .*output.tsv
DGDFetchByEnsIds	wsdl	Wsdl http://webservices.genouest.org/typedservices/DGD.wsdl Wsdl Operation launchJobBlocking
DGDFetchByEnsIds_launchJobBlockingInput	xmlsplitter
launchJobBlockingInput_inputEnsids	xmlsplitter
DGDFetchByEnsIds_launchJobBlockingOutput	xmlsplitter
launchJobBlockingOutput_jobOut_2	xmlsplitter
DGDFetch_inputFileName	stringconstant	Value inputDGD.txt
DGDFetch_Output_filter	localworker	Script filteredlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (item.matches(regex)) { filteredlist.add(item); } }
Get_Web_Page_from_URL	localworker	Script 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(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
location_searchTerms	stringconstant	Value http://dgd.genouest.org/images/dgd/tutorial/ws_example.txt
jobOut_outputFile	xmlsplitter
2_outputFile	xmlsplitter
XrefFetch	wsdl	Wsdl http://webservices.genouest.org/typedservices/Xref.wsdl Wsdl Operation launchJobBlocking
XrefFetch_launchJobBlockingInput	xmlsplitter
launchJobBlockingInput_input_2	xmlsplitter
xrefFetch_inputFileName	stringconstant	Value inputXrefFetch.txt
XrefFetch_launchJobBlockingOutput	xmlsplitter
launchJobBlockingOutput_jobOut_3	xmlsplitter
3_outputFile	xmlsplitter
XrefFetch_Output_filter	localworker	Script filteredlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (item.matches(regex)) { filteredlist.add(item); } }
Get_Web_Page_from_URL_2	localworker	Script 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(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
launchJobBlockingInput_xrefsrcs	xmlsplitter
location_askedXrefs	stringconstant	Value http://dgd.genouest.org/images/dgd/tutorial/ws_example_xrefs.txt
xrefFetch_SrcsFileName	stringconstant	Value askedXrefs.txt
xrefFetch_value	stringconstant	Value get_xrefs

Name	Description
Found_genes_by_xref
Xrefs_Fetched

Source	Sink
XrefSearch_launchJobBlockingInput:output	XrefSearch:launchJobBlockingInput
launchJobBlockingInput_input:output	XrefSearch_launchJobBlockingInput:input
xrefSearch_mode:value	XrefSearch_launchJobBlockingInput:mode
xrefSearch_inputFileName:value	launchJobBlockingInput_input:name
location_searchTerms:value	launchJobBlockingInput_input:location
XrefSearch:launchJobBlockingOutput	XrefSearch_launchJobBlockingOutput:input
XrefSearch_launchJobBlockingOutput:jobOut	launchJobBlockingOutput_jobOut:input
jobOut_outputFile:url	xrefSearch_Output_filter:stringlist
regex_filter:value	xrefSearch_Output_filter:regex
DGDFetchByEnsIds_launchJobBlockingInput:output	DGDFetchByEnsIds:launchJobBlockingInput
launchJobBlockingInput_inputEnsids:output	DGDFetchByEnsIds_launchJobBlockingInput:inputEnsids
xrefSearch_Output_filter:filteredlist	launchJobBlockingInput_inputEnsids:location
DGDFetch_inputFileName:value	launchJobBlockingInput_inputEnsids:name
DGDFetchByEnsIds:launchJobBlockingOutput	DGDFetchByEnsIds_launchJobBlockingOutput:input
DGDFetchByEnsIds_launchJobBlockingOutput:jobOut	launchJobBlockingOutput_jobOut_2:input
regex_filter:value	DGDFetch_Output_filter:regex
2_outputFile:url	DGDFetch_Output_filter:stringlist
DGDFetch_Output_filter:filteredlist	Get_Web_Page_from_URL:url
launchJobBlockingOutput_jobOut:outputFile	jobOut_outputFile:input
launchJobBlockingOutput_jobOut_2:outputFile	2_outputFile:input
XrefFetch_launchJobBlockingInput:output	XrefFetch:launchJobBlockingInput
launchJobBlockingInput_input_2:output	XrefFetch_launchJobBlockingInput:input
launchJobBlockingInput_xrefsrcs:output	XrefFetch_launchJobBlockingInput:xrefsrcs
xrefFetch_value:value	XrefFetch_launchJobBlockingInput:mode
xrefFetch_inputFileName:value	launchJobBlockingInput_input_2:name
xrefSearch_Output_filter:filteredlist	launchJobBlockingInput_input_2:location
XrefFetch:launchJobBlockingOutput	XrefFetch_launchJobBlockingOutput:input
XrefFetch_launchJobBlockingOutput:jobOut	launchJobBlockingOutput_jobOut_3:input
launchJobBlockingOutput_jobOut_3:outputFile	3_outputFile:input
3_outputFile:url	XrefFetch_Output_filter:stringlist
regex_filter:value	XrefFetch_Output_filter:regex
XrefFetch_Output_filter:filteredlist	Get_Web_Page_from_URL_2:url
location_askedXrefs:value	launchJobBlockingInput_xrefsrcs:location
xrefFetch_SrcsFileName:value	launchJobBlockingInput_xrefsrcs:name
Get_Web_Page_from_URL:contents	Found_genes_by_xref
Get_Web_Page_from_URL_2:contents	Xrefs_Fetched

Cross-references search, duplicated genes search, cross-reference fetch

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Script

Value

Value

Value

Wsdl

Wsdl Operation

Value

Script

Script

Value

Wsdl

Wsdl Operation

Value

Script

Script

Value

Value

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (0)