[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Tue Aug 2 05:19:57 UTC 2005
kawas
Tue Aug 2 01:19:57 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier
In directory pub.open-bio.org:/tmp/cvs-serv30997/org/biomoby/registry/rdfagent/verifier
Modified Files:
DataMngr.java ServiceDescrParser.java
Log Message:
Fixed the all the bugs detected by my driver, except for the ability to remove all inputs when no outputs exist when a secondary input exists.
Ed
moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier DataMngr.java,1.11,1.12 ServiceDescrParser.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/DataMngr.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/DataMngr.java 2005/07/29 22:19:05 1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/DataMngr.java 2005/08/02 05:19:57 1.12
@@ -216,7 +216,7 @@
public static void processService(Hashtable servSign, Hashtable servInp,
Hashtable servOut, String servname, String authURI, String signURL) {
-
+
Connection con = DBConnector.getConnection();
String servName = "";
String cat = "moby";
@@ -333,30 +333,7 @@
|| !authoritative.equals(signature.getAuthoritative())
|| !authuri.equals(authURI)) {
- //TODO
- Log.info("Updating the service '" + servName
- + "' since the RDF document has been modified.");
if (signatureURL.equals("NNN")) {
- Log.info("sig == NNN" + signURL);
- Log
- .info("<servName,cat,stype,authuri,url,email,desc,authoritative,signURL>=<"
- + servName
- + ","
- + cat
- + ","
- + stype
- + ","
- + authuri
- + ","
- + url
- + ","
- + email
- + ","
- + desc
- + ","
- + authoritative
- + ","
- + signURL + ">");
int res = updSign(servName, cat, stype, authuri, url,
email, desc, authoritative, signURL);
if (res == 1) {
@@ -372,7 +349,6 @@
}
} else {
- Log.info("sig != NNN");
int res = updSign(servName, cat, stype, authuri, url,
email, desc, authoritative, signatureURL);
if (res == 1) {
@@ -412,10 +388,13 @@
if (delRow("simple_input", servInstId) == 1)
dels = 1;
}
+
+ // check if there is at lease one simple input
if (!servInp.containsKey("siminp1")) {
if (delRow("simple_input", servInstId) == 1)
dels = 1;
}
+ // check if there is at least one collection input
if (!servInp.containsKey("colinp1")) {
delCollectionMember("input", servInstId);
if (delRow("collection_input", servInstId) == 1)
@@ -568,6 +547,8 @@
Report.doWrite("collection_input_id: " + colId);
// Log.info("collection_input_id: "+colId);
}
+ // TODO - made this change to clear the collection input id
+ colId = 0;
}
Report.doWrite("service_instance_id: " + servInstId);
@@ -628,7 +609,6 @@
Report.doWrite("Simple output " + so);
Report.add("Simple output " + so + ":");
- //TODO bug #13 here?
if (delsout == 0) {
delRow("simple_output", servInstId); // delete from
// simple_output table
@@ -652,23 +632,23 @@
if (col_art.equals(" ")) {
col_art = null;
}
- }
+ } else
if (ob1.equals("articleName")) {
art = simple.get(ob1).toString();
if (art.equals(" ")) {
art = null;
}
- }
+ } else
if (ob1.equals("object_type_uri")) {
obt = simple.get(ob1).toString();
- }
+ } else
if (ob1.equals("namespace_type_uris")) {
nst = simple.get(ob1).toString();
}
}
if (simcol.equals("colout")) {
-
+ //TODO bug 36 here?
insIntoCol("collection_output", col_art, servInstId); // insert
// the row
// into
@@ -681,6 +661,7 @@
art = null;
obt = null;
nst = null;
+ col_art = null;
}
// TODO bug #11 here - fixed
if (simcol.equals("simout")) {
@@ -694,6 +675,7 @@
Report.doWrite("collection_output_id: " + colOutId);
// Log.info("collection_output_id: "+coloutId);
}
+ colOutId = null;
}
// return serv;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java 2005/07/29 22:17:39 1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java 2005/08/02 05:19:57 1.9
@@ -377,6 +377,7 @@
| type.equals(RDF.Bag)) {
// if (l3Res.hasProperty(RDF.type,RDF.Bag) &&
// l3Res.hasProperty(RDF.li(1))){
+
if (l3Res.hasProperty(RDF.li(1))) {
StmtIterator p34iter = l3Res.listProperties();
if (l3Res.hasProperty(MP.articleName)) {
@@ -385,6 +386,8 @@
String[] rezNode = col_artName.split(":http:");
col_artName = rezNode[0];
colinp.put("col_articleName", col_artName);
+ } else if (colinp.containsKey("col_articleName")) {
+ colinp.remove("col_articleName");
}
while (p34iter.hasNext()) {
Statement l4iter = p34iter.nextStatement();
@@ -446,20 +449,21 @@
.toString());
colinp.put(name, lsid_nsp);
} else if (name.equals("articleName")) {
- colinp.put(name, l5Node.getName());
+ colinp.put(name, rezNode[0]);
}else {
colinp.put(name, l5Node);
}
}
- input.put("colinp" + cin, colinp);
- cin += 1;
+ input.put("colinp" + cin++, colinp);
Enumeration num = colinp.keys();
- String col_name = (String)colinp.get("col_articleName");
+ String col_name = null;
+ if (colinp.containsKey("col_articleName"))
+ col_name = (String)colinp.get("col_articleName");
colinp = new Hashtable();
- colinp.put("col_articleName", col_name);
+ if (col_name != null)
+ colinp.put("col_articleName", col_name);
}
}
-
}
} else {
collection = "error";
@@ -647,6 +651,8 @@
String[] rezNode = col_artName.split(":http:");
col_artName = rezNode[0];
colout.put("col_articleName", col_artName);
+ } else if (colout.containsKey("col_articleName")) {
+ colout.remove("col_articleName");
}
while (p34iter.hasNext()) {
Statement l4iter = p34iter.nextStatement();
@@ -713,13 +719,14 @@
colout.put(name, l5Node);
}
}
- //TODO BUG here. colout should be 'new' and not recycled
- output.put("colout" + co, colout);
- co += 1;
- Enumeration num = colout.keys();
- String col_name = (String)colout.get("col_articleName");
+ output.put("colout" + co++, colout);
+ Enumeration num = colout.keys(); //why?
+ String col_name = null;
+ if (colout.containsKey("col_articleName"))
+ col_name = (String)colout.get("col_articleName");
colout = new Hashtable();
- colout.put("col_articleName", col_name);
+ if (col_name != null)
+ colout.put("col_articleName", col_name);
}
}
@@ -742,7 +749,6 @@
} catch (Exception e) {
Log.warning("Failed (ServiceDescrParser.java-getOutput): " + e);
}
- //System.out.println("output = "+output);
return output;
}
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