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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter GAMEAdapter.java,1.30.2.19,1.30.2.20
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From: Nomi H. <no...@us...> - 2002-01-30 22:56:32
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Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter
In directory usw-pr-cvs1:/tmp/cvs-serv20172
Modified Files:
Tag: sanger_branch
GAMEAdapter.java
Log Message:
I'm a little reluctant to commit this because there is some slightly kludgey stuff
for testing different ways to select a datafile without actually having a GUI for it
yet, so you can type into the file selection box things like "gene=cact" or "band=34A"
and it will find the relevant XML file via a cgi. (In the case of a query that spans
more than one scaffold, it will just use the FIRST one it finds.)
Index: GAMEAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/GAMEAdapter.java,v
retrieving revision 1.30.2.19
retrieving revision 1.30.2.20
diff -C2 -d -r1.30.2.19 -r1.30.2.20
*** GAMEAdapter.java 2002/01/30 19:29:36 1.30.2.19
--- GAMEAdapter.java 2002/01/30 22:56:28 1.30.2.20
***************
*** 78,86 ****
public String getName() {
! return "GAME Adapter";
}
public String getType() {
! return "GAME XML Filename or URL";
}
--- 78,86 ----
public String getName() {
! return "GAME XML Adapter";
}
public String getType() {
! return "GAME XML source (filename, URL, gene=cact, band=34A, or sequence=ACGT)";
}
***************
*** 100,106 ****
public GAMEAdapter(String xmlsource) {
! if (xmlsource.startsWith("http"))
setURL(xmlsource);
else {
System.out.println("Setting filename: " + xmlsource); // DEL
setFilename(xmlsource);
--- 100,109 ----
public GAMEAdapter(String xmlsource) {
! if (xmlsource.startsWith("http")) {
! setFilename((String) null);
setURL(xmlsource);
+ }
else {
+ setURL((String) null);
System.out.println("Setting filename: " + xmlsource); // DEL
setFilename(xmlsource);
***************
*** 110,117 ****
public void setFilename(String filename) {
// !! This is just while debugging
! if (filename.startsWith("http"))
setURL(filename);
! else
this.filename = filename;
}
--- 113,124 ----
public void setFilename(String filename) {
// !! This is just while debugging
! if (filename.startsWith("http")) {
! setFilename((String) null);
setURL(filename);
! }
! else {
! setURL((String) null);
this.filename = filename;
+ }
}
***************
*** 125,128 ****
--- 132,139 ----
public void setURL(String urlstring) {
+ if (urlstring == null) {
+ this.url = null;
+ return;
+ }
try {
this.url = new URL(urlstring);
***************
*** 134,137 ****
--- 145,159 ----
}
+ public URL getURL() {
+ return url;
+ }
+
+ public String getInputName() {
+ if (url != null)
+ return (url.toString());
+ else
+ return filename;
+ }
+
public Properties getStateInformation() {
Properties props = new Properties();
***************
*** 948,955 ****
ex2.printStackTrace();
}
! String message = "Couldn't read " + filename;
! if (url != null)
! message = "Couldn't read " + url;
! throw new DataAdapterException(message);
}
return curation;
--- 970,974 ----
ex2.printStackTrace();
}
! throw new DataAdapterException(ex2.getMessage());
}
return curation;
***************
*** 970,977 ****
}
else if ((filename != null) && !(filename.equals(""))) {
! // !! FOR DEBUGGING--assume that a SHORT filename is actually a GENE NAME
! if (filename.length() < 6) { // DEL
! System.out.println("Assuming " + filename + " is actually a gene name you're searching for");
! url = getURLForGene(filename);
if (url == null) {
System.err.println("Couldn't find url for " + filename);
--- 989,1041 ----
}
else if ((filename != null) && !(filename.equals(""))) {
! // !! FOR DEBUGGING--filename that starts with gene= is a GENE NAME
! if (filename.startsWith("gene=")) {
! String gene = filename.substring(5);
! url = getURLForGene(gene);
! if (url == null) {
! String message = "Couldn't find url for " + filename;
! System.err.println(message);
! stream = null;
! throw new DataAdapterException(message);
! }
! if (url != null) {
! try {
! System.err.println("Trying to open url " + url + " for reading");
! stream = url.openStream();
! } catch (Exception e) {
! String message = "Gene " + gene + " not found";
! System.err.println(message);
! stream = null;
! throw new DataAdapterException(message);
! }
! }
! }
! // !! FOR DEBUGGING--"filename" that starts with "band=" is a cytological location
! else if (filename.startsWith("band=")) {
! String band = filename.substring(5);
! url = getURLForBand(band);
! if (url == null) {
! String message = "Couldn't find url for " + filename;
! System.err.println(message);
! stream = null;
! throw new DataAdapterException(message);
! }
! if (url != null) {
! try {
! System.err.println("Trying to open url " + url + " for reading");
! stream = url.openStream();
! } catch (Exception e) {
! String message = "Couldn't find scaffold for cytological location " + band;
! System.err.println(message);
! stream = null;
! throw new DataAdapterException(message);
! }
! }
! }
!
! // !! FOR DEBUGGING--"filename" that starts with "sequence=" is a DNA string to search for with BLAST
! else if (filename.startsWith("sequence=")) {
! String seq = filename.substring(9);
! url = getURLForSequence(seq);
if (url == null) {
System.err.println("Couldn't find url for " + filename);
***************
*** 995,999 ****
stream = new FileInputStream (filename);
} catch (Exception e) {
- System.err.println("Error: could not open file " + filename + " for reading.");
stream = null;
// If we couldn't find filename, and it's a relative, rather than absolute, path,
--- 1059,1062 ----
***************
*** 1002,1006 ****
String rootdir = System.getProperty("APOLLO_ROOT");
setFilename(rootdir + "/" + filename);
! System.err.println("Trying " + getFilename()); // DEL
try {
InputStream newstream = XMLInputStream();
--- 1065,1069 ----
String rootdir = System.getProperty("APOLLO_ROOT");
setFilename(rootdir + "/" + filename);
! System.err.println("Trying to open " + getFilename()); // DEL
try {
InputStream newstream = XMLInputStream();
***************
*** 1008,1019 ****
}
catch (DataAdapterException e2) {
! System.err.println(getFilename() + " didn't work either, oh well"); // DEL
throw new DataAdapterException("Error: could not open file " + filename + " for reading.");
}
}
! throw new DataAdapterException("Error: could not open file " + filename + " for reading.");
}
}
}
return stream;
}
--- 1071,1084 ----
}
catch (DataAdapterException e2) {
! // System.err.println(getFilename() + " didn't work either, oh well"); // DEL
throw new DataAdapterException("Error: could not open file " + filename + " for reading.");
}
}
! throw new DataAdapterException("Error: could not open " + getInputName() + " for reading.");
}
}
}
+ fireProgressEvent(new ProgressEvent(this, new Double(65.0),
+ "Reading GAME XML..."));
return stream;
}
***************
*** 1023,1027 ****
* returns an Curation derived from the XML document
*/
! private void readXML(InputStream istream) {
element_chain = new Stack();
--- 1088,1093 ----
* returns an Curation derived from the XML document
*/
! private void readXML(InputStream istream)
! throws DataAdapterException {
element_chain = new Stack();
***************
*** 1045,1051 ****
xml_parser.parse(new InputSource(istream));
} catch (Exception e) {
! System.err.println("Fatal Error near element # " +
element_count + " : " + e.getMessage());
! e.printStackTrace();
}
}
--- 1111,1117 ----
xml_parser.parse(new InputSource(istream));
} catch (Exception e) {
! System.err.println("Fatal Error in xml parse near element # " +
element_count + " : " + e.getMessage());
! throw new DataAdapterException("Fatal error while trying to parse xml from " + getInputName());
}
}
***************
*** 1906,1910 ****
public URL getURLForGene(String gene) {
! // This CGI actually does a redirect to the relevant XML
String query = "http://www.fruitfly.org:90/cgi-bin/annot/which-xml.pl?namesearch=" + gene;
try {
--- 1972,1977 ----
public URL getURLForGene(String gene) {
! // This CGI actually does a redirect to the relevant XML, so the URL we return here
! // will yield the XML when opened.
String query = "http://www.fruitfly.org:90/cgi-bin/annot/which-xml.pl?namesearch=" + gene;
try {
***************
*** 1916,1919 ****
--- 1983,2021 ----
return(null);
}
+ fireProgressEvent(new ProgressEvent(this, new Double(12.0),
+ "Searching for location of " + gene + "..."));
+ return(url);
+ }
+
+ public URL getURLForBand(String band) {
+ // Returns the URL for the xml of the FIRST scaffold in the requested band
+ String query = "http://www.fruitfly.org:90/cgi-bin/annot/which-xml.pl?band=" + band;
+ try {
+ this.url = new URL(query);
+ } catch ( Exception ex ) {
+ System.err.println("caught exception creating URL " + query);
+ System.out.println(ex.getMessage());
+ ex.printStackTrace();
+ return(null);
+ }
+ fireProgressEvent(new ProgressEvent(this, new Double(10.0),
+ "Searching for FIRST scaffold at cytological location " + band + "..."));
+ return(url);
+ }
+
+ // ! Proof-of-concept method gets the URL for the XML for the scaffold that has the
+ // best blast hit to the given sequence (uses the fruitfly blast server)
+ public URL getURLForSequence(String seq) {
+ String query = "http://www.fruitfly.org:90/cgi-bin/annot/which-xml.pl?sequence=" + seq;
+ try {
+ this.url = new URL(query);
+ } catch ( Exception ex ) {
+ System.err.println("caught exception creating URL " + query);
+ System.out.println(ex.getMessage());
+ ex.printStackTrace();
+ return(null);
+ }
+ fireProgressEvent(new ProgressEvent(this, new Double(5.0),
+ "Running BLAST query--please be patient..."));
return(url);
}
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