| EST_reader |
/**
*
* Internet robot, EST_reader, that uses form, located in page
* http://www.ncbi.nlm.nih.gov/entrez/.
* It is your responsibility to find and cite appropriate references
* from this page.
* Generated 2002.8.2 by Sight 2.0, Ulm university.
*
* This robot receives response in XML, transforms using XSLT,
* inserted at the end of this text and then gets the result
* from transformed document.
*/
package impl.rna_analysers;
import Sight.Agents.*;
import Sight.Agents.Redirectors.*;
import Sight.Structures.*;
import Sight.dds.*;
import java.io.*;
import org.w3c.dom.*;
public class EST_reader extends Sight.Agents.Prototypes.xml_based_agent implements Serializable {
/* Data structure to pass query to this robot. */
public class Request extends Sight.Request implements java.io.Serializable {
/** default=22519907 */
public String Id="22519907"; // Parameter
/** Submit request, compute key by SHA digesting algorithm. */
public Sight.Agents.Request submit() { return Sight.Agents.Request.submit(Public, this, getKey()); };
/** Submit request with the known key. */
public Sight.Agents.Request submit(String key)
{ return Sight.Agents.Request.submit(Public, this, key); };
};
/** Get the AMap data structure, required by post method. */
protected AMap getFormParameters(Object req) {
Request request = (Request) req;
AMap map = new AMap();
String Gi = request.Id.toLowerCase();
if (Gi.indexOf("|")>=0)
// if multiple provided, take gi:
{
String left = "gi|";
int a = Gi.indexOf(left);
if (a<0) { Sight.io.Output.e("EST_reader: "+"Invalid gi: "+Gi); return null; }
a = a+left.length();
int b = Gi.indexOf("|",a);
if (b<0) { Sight.io.Output.e("EST_reader: "+"Invalid gi: "+Gi); return null; }
Gi = Gi.substring(a,b);
};
map.add("url:identifier", Gi); // Parameter
map.add("connect:master", "http://www.ncbi.nlm.nih.gov/entrez/"); // connect
map.add("connect:action", "get"); // connect
map.add("url:prefix", "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?view=xml&txt=on&val="); // connect
map.add("url:suffix", ""); // connect
return map; };
/** Get default request for this robot. */
public static Request getDefaultRequest() {
return Public.getRequest(); }
private Request getRequest() { return new Request(); }; // must be non static
/** Type definitions for Request. */
public dStructure getRequestDds() {
return new Sight.dds.Records(false,
new dField[] {
new dField("Id","CharSequence",null,"22519907") }
);
}
/* Record type, used in results for this robot. */
/* The result of this robot is an array of records. */
public static class Record extends Sight.Record implements Serializable {
public CharSequence Id;
public CharSequence Header;
public CharSequence Tissue;
public CharSequence Sequence;
public CharSequence Cell;
};
/** The result of this robot. */
public static class Result extends Sight.Result implements Serializable {
public Record[] a; // array of results.
/** Create report for one record. */
public CharSequence getReportForRecord(Object ro, int level)
{ Record r = (Record) ro;
StringBuffer b = new StringBuffer();
if (r.Id!=null)
{ b.append(r.Id);
};
if (r.Tissue!=null)
{
b.append(' ');
b.append(r.Tissue);
};
if (r.Cell!=null)
{
b.append(' ');
b.append(r.Cell);
};
if (level>=1 && r.Header!=null)
{ b.append(' ');
b.append(r.Header);
};
if (level>=2 && r.Sequence!=null)
{
b.append("<textarea>");
b.append(r.Sequence);
b.append("</textarea>");
};
return b;
};
}
/** Type definitions for Result. */
public dStructure getResultDds() {
return new Sight.dds.Records(true,
new dField[] {
new dField("Id","CharSequence",null,""),
new dField("Header","CharSequence",null,""),
new dField("Tissue","CharSequence",null,""),
new dField("Sequence","CharSequence",null,""),
new dField("Cell","CharSequence",null,"") }
);
}
/* Required structure: parent nodes (name ignored), inside them -
child nodes (can be with parameters), representing fields.
*/
public Sight.Record createRecord(Node xml)
{
Record r = new Record();
r. Id = getXMLField("Id", xml);
r. Header = getXMLField("Header", xml);
r. Tissue = getXMLField("Tissue", xml);
r. Sequence = getXMLField("Sequence", xml);
r. Cell = getXMLField("Cell", xml);
return r;
};
/** main(..) method provided to check robot quickly, launching it
* as standalone program. */
public static void main(String[] args) {
try {
Request request = getDefaultRequest();
// (now you can modify 'request' fields if required)
Sight.Agents.Request submission = request.submit();
// processing now started in separate thread:
Result response = (Result) submission.getResult();
try {
// to format report, we need an agent itself, because
// Document cannot be easily extended by extra methods.
String html = EST_reader .getAvailableAgent().getReport(response, 2);
System.out.println("Report: "+html);
}
catch (java.lang.UnsupportedOperationException ui)
{ System.out.println(ui.getMessage()); };
} catch (Exception exc)
{ if (exc!=null) System.out.println(exc.getMessage());
exc.printStackTrace();
};
}
public EST_reader() {
setDescription("Reads NCBI EST records.");
setFormURL("http://www.ncbi.nlm.nih.gov/entrez/");
setMasterURL("http://www.ncbi.nlm.nih.gov/entrez/");
// define pre scan section.
preScan = new preScan();
cn_maxConnectionLength = 80000000; // abort after 8000 Mb by default.
}
/** Public instance of agent for user. */
public static EST_reader Public = new EST_reader();
public static Agent getAvailableAgent() { return Public; };
public Class getRecordClass() { return Record.class; };
/** Get result from the given XML document */
public Sight.Result resultFromDocument(Document node) throws Exception {
Result r = new Result();
r.a = (Record[]) createResultArray(node);
return r;
};
public String getXSLT() {
return getXMLFromSelf("Sight:xml-xsl-insert-1");
};
// This insert will be loaded runtime:
/* <Sight:xml-xsl-insert-1>
<?xml version="1.0"?>
<!-- See http://www.w3.org/TR/1999/REC-xslt-19991116 and http://www.w3.org/TR/1999/REC-xpath-19991116
for transform language description. -->
<!-- $comment -->
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:output method="xml" indent="yes"/>
<!-- This will add required starting and closing tags. -->
<xsl:template match="/">
<Sight>
<xsl:apply-templates/>
</Sight>
</xsl:template>
<xsl:template match="text()|@*"></xsl:template>
<!-- // mathes the path anywhere in the document: -->
<xsl:template match="//SubSource/SubSource_subtype[@value='tissue-type']">
<Sight-record>
<Tissue>
<xsl:copy-of select="following-sibling::SubSource_name/text()"/>
</Tissue>
</Sight-record>
</xsl:template>
<xsl:template match="//SubSource/SubSource_subtype[@value='cell-type']">
<Sight-record>
<Cell>
<xsl:copy-of select="following-sibling::SubSource_name/text()"/>
</Cell>
</Sight-record>
</xsl:template>
<xsl:template match="//SubSource/SubSource_subtype[@value='sex']">
<Sight-record>
<Sex>
<xsl:copy-of select="following-sibling::SubSource_name/text()"/>
</Sex>
</Sight-record>
</xsl:template>
<xsl:template match="//SubSource/SubSource_subtype[@value='dev-stage']">
<Sight-record>
<Stage>
<xsl:copy-of select="following-sibling::SubSource_name/text()"/>
</Stage>
</Sight-record>
</xsl:template>
<xsl:template match="//Bioseq/Bioseq_id/Seq-id/Seq-id_gi">
<Sight-record>
<Id>
<xsl:copy-of select="text()"/>
</Id>
</Sight-record>
</xsl:template>
<xsl:template match="//IUPACna">
<Sight-record>
<Sequence>
<xsl:copy-of select="text()"/>
</Sequence>
</Sight-record>
</xsl:template>
<xsl:template match="//Seqdesc_title">
<Sight-record>
<Header>
<xsl:copy-of select="text()"/>
</Header>
</Sight-record>
</xsl:template>
</xsl:stylesheet>
</Sight:xml-xsl-insert-1> */
}
| EST_reader |