Load GO terms in the triplestore
Created: 2009-05-01 14:36:50
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Workflow Components
Authors (1)
Titles (2)
Load GO definition |
Load GO definitions |
Descriptions (0)
Dependencies (0)
Processors (5)
Name |
Type |
Description |
html2uris |
beanshell |
ScriptList split = new ArrayList();
if (!html.equals("")) {
String regexString = "\n";
if (regex != void) {
regexString = regex;
}
String[] result = html.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
import java.util.regex.*;
uris = new ArrayList();
Pattern thePat = Pattern.compile("http://bio2rdf.org/(.*) | ");
int theGroup = 1;
for (Iterator i = split.iterator(); i.hasNext();) {
String item = (String) i.next();
Matcher matcher = thePat.matcher(item);
if (matcher.find()) {
uris.add("http://bio2rdf.org/"+matcher.group(theGroup));
}
}
|
Get_Web_Page_from_URL0 |
localworker |
ScriptURL 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();
|
describe_n3_insert |
workflow |
|
temp |
stringconstant |
Valuetemp |
sparql_get_xGO |
stringconstant |
Valuehttp://localhost:8890/sparql?default-graph-uri=temp&query=SELECT+distinct+%3Fo%0D%0AWHERE+{%0D%0A++%3Fs+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fbio2rdf%23xGO%3E+%3Fo+.%0D%0A++FILTER(%3Fo+!%3D+%3Chttp%3A%2F%2Fbio2rdf.org%2Fgo%3A0009055%3E)+.%0D%0A++FILTER(%3Fo+!%3D+%3Chttp%3A%2F%2Fbio2rdf.org%2Fgo%3A0000166%3E)+.%0D%0A}&format=text%2Fhtml&debug=on |
Beanshells (3)
Name |
Description |
Inputs |
Outputs |
html2uris |
|
html
|
uris
|
sparql_describe_uri |
|
uri
|
output
|
sparql_insert_n3 |
|
n3
graph
|
html
|
Outputs (4)
Name |
Description |
o1 |
|
o3 |
|
o2 |
|
o5 |
|
Datalinks (8)
Source |
Sink |
Get_Web_Page_from_URL0:contents |
html2uris:html |
sparql_get_xGO:value |
Get_Web_Page_from_URL0:url |
html2uris:uris |
describe_n3_insert:uri |
temp:value |
describe_n3_insert:graph |
html2uris:uris |
o1 |
Get_Web_Page_from_URL0:contents |
o3 |
describe_n3_insert:virtuoso_response |
o2 |
describe_n3_insert:query |
o5 |
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licensed under:
Version 1
(of 1)
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