Triplify LSRN record name list [myexperiment:lsrn_xref_namespace2rdf]
Created: 2009-12-01 06:24:54
Last updated: 2009-12-01 06:27:20
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Authors (1)
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Titles (1)
Triplify LSRN record name list [myexperiment:lsrn_xref_namespace2rdf] |
![header=[] body=[These are the descriptions embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Descriptions (6)
test values:
bmuri = http://bio2rdf.orf/geneid:15275 |
Triplify LSRN record name list [myexperiment:lsrn_xref_namespace2rdf]
Get LSRN list from http://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf
TAG: banff_manifesto, lsrn, xref, bio2rdf, rdf |
|
test values:
bmuri = http://bio2rdf.org/geneid:15275 |
Get LSRN list from http://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf
TAG: banff_manifesto, lsrn, xref, bio2rdf, rdf |
Get LSRN list from http://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf
TAG: banff_manifesto, lsrn, xref, bio2rdf, rdf |
![header=[] body=[These are the listed dependencies of the workflow] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Dependencies (0)
Processors (9)
Name |
Type |
Description |
get_lsrn_rdf |
beanshell |
Scriptimport com.hp.hpl.jena.rdf.model.*;
Model model = ModelFactory.createDefaultModel();
model.read(url, "RDF/XML");
StringWriter writer = new StringWriter () ;
model.write( writer, "N-TRIPLE");
ntriples_size = "<" + bmuri + "> \"" + model.size() + "\" .";
model.close();
ntriples = writer.toString () ;
|
lsrn_rdf_url |
stringconstant |
Valuehttp://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf |
eol |
stringconstant |
Value\n |
Normalise_predicate |
beanshell |
Scriptimport java.util.regex.*;
String line;
namespace = "";
line = in;
line = line.replace("", "");
line = line.replace("", "");
line = line.replace("", "");
line = line.replace("", "");
line = line.replace("", "");
line = line.replace("");
Matcher matcher = thePat.matcher(line);
if (matcher.find()) {
String parm = matcher.group(1);
line = line.replace(" ", " ");
}
Pattern thePat1 = Pattern.compile("^ .(.*)...");
Matcher matcher1 = thePat1.matcher(line);
if (matcher1.find()) {
String id = matcher1.group(1);
namespace = id;
String desc = matcher1.group(2);
line = line + "\n \"bm:ns:"+id+"\" .";
line = line + "\n \""+id+"\" .";
line = line + "\n \""+desc+" [bm:ns:"+id+"]\".";
line = line + "\n .";
line = line + "\n";
}
ntriples = line; |
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();
|
Split_string_into_string_list_by_regular_expression |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
LSRN_ntriples |
beanshell |
ScriptString id = "lsrn";
String title = "Life Science Record Name";
ntriples = "\n .";
ntriples = ntriples + "\n \"bm:ns:"+id+"\" .";
ntriples = ntriples + "\n \"" + title + " [bm:ns:"+id+"]\" .";
ntriples = ntriples + "\n \"" + title + "\" .";
ntriples = ntriples + "\n \""+id+"\" .";
ntriples = ntriples + "\n";
|
Concatenate_two_strings |
localworker |
Scriptoutput = string1 + string2; |
Remove_String_Duplicates |
localworker |
ScriptList strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (strippedlist.contains(item) == false) {
strippedlist.add(item);
}
}
|
Beanshells (3)
Name |
Description |
Inputs |
Outputs |
get_lsrn_rdf |
|
url
|
ntriples
|
Normalise_predicate |
|
in
|
ntriples
namespace
|
LSRN_ntriples |
|
|
ntriples
|
Outputs (3)
Name |
Description |
lsrn_xref_namespace_ntriples |
|
url |
|
namespace_list |
|
Datalinks (11)
Source |
Sink |
lsrn_rdf_url:value |
get_lsrn_rdf:url |
Split_string_into_string_list_by_regular_expression:split |
Normalise_predicate:in |
Normalise_predicate:ntriples |
Merge_String_List_to_a_String:stringlist |
eol:value |
Split_string_into_string_list_by_regular_expression:regex |
get_lsrn_rdf:ntriples |
Split_string_into_string_list_by_regular_expression:string |
LSRN_ntriples:ntriples |
Concatenate_two_strings:string1 |
Merge_String_List_to_a_String:concatenated |
Concatenate_two_strings:string2 |
Normalise_predicate:namespace |
Remove_String_Duplicates:stringlist |
Concatenate_two_strings:output |
lsrn_xref_namespace_ntriples |
lsrn_rdf_url:value |
url |
Remove_String_Duplicates:strippedlist |
namespace_list |
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