Retrieve UniSTS numerical UID from name of genetic marker
Created: 2009-08-19 13:48:47
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Authors (1)
Steffen Möller <moeller@inb.uni-luebeck.de> |
Titles (1)
Search for details of genetic marker. |
Descriptions (1)
The UniSTS database is queried with the marker name. |
Dependencies (0)
Inputs (1)
Name |
Description |
MarkerName |
The name of the marker to search for.
|
Processors (6)
Name |
Type |
Description |
Get_Web_Page_from_URL |
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();
|
UniSTS_URL |
stringconstant |
Valuehttp://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=unists&term= |
Concatenate_two_strings |
localworker |
Scriptoutput = string1 + string2; |
UniSTS_UID_access_URL |
stringconstant |
Valuehttp://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid= |
Escaped_UniSTD_UID_URL_as_RegEx |
stringconstant |
Value.*www.ncbi.nlm.nih.gov.*genom.*uid=([0-9]+)"> |
Nested_workflow |
workflow |
|
Outputs (4)
Name |
Description |
UniSTS_FirstSearchResult |
|
Matching_Lines_with_UniSTS_UID_URLs |
|
UniSTS_FirstSearchResult_as_Lines |
|
UniSTS_UIDs_for_marker_given |
|
Datalinks (9)
Source |
Sink |
Concatenate_two_strings:output |
Get_Web_Page_from_URL:url |
UniSTS_URL:value |
Concatenate_two_strings:string1 |
MarkerName |
Concatenate_two_strings:string2 |
Get_Web_Page_from_URL:contents |
Nested_workflow:string_with_lines_to_be_filtered |
Escaped_UniSTD_UID_URL_as_RegEx:value |
Nested_workflow:regex_to_filter_lines_for |
Get_Web_Page_from_URL:contents |
UniSTS_FirstSearchResult |
Nested_workflow:filtered_lines |
Matching_Lines_with_UniSTS_UID_URLs |
Nested_workflow:lines |
UniSTS_FirstSearchResult_as_Lines |
Nested_workflow:filtered_values |
UniSTS_UIDs_for_marker_given |
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License
All versions of this Workflow are
licensed under:
Version 2 (latest)
(of 2)
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