[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Fri Jul 29 22:17:40 UTC 2005
kawas
Fri Jul 29 18:17:39 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-serv12281/org/biomoby/registry/rdfagent/verifier
Modified Files:
ServiceDescrParser.java
Log Message:
fixed some bugs that were due to the scope of certain variables.
formatted the code.
fixed a bug that ignored article names of collections.
fixed a bug that over wrote preexisting simples in collections with new ones even though both should exist.
fixed a bug that caused pre-existing ns to be associated with simples without ns.
...
moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier ServiceDescrParser.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java 2005/07/28 15:26:13 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java 2005/07/29 22:17:39 1.8
@@ -78,20 +78,16 @@
servSign = getServSignature(resource);
if (!servSign.isEmpty()) { // a valid MOBY RDF
- servName = servSign.get("servicename").toString();
+ servName = servSign.get("servicename").toString()+"";
auth_URI = servSign.get("authURI").toString();
resources.addElement(servName);
Hashtable servInp = new Hashtable();
- servInp = getInput(resource);
+ servInp = getInput(resource); //TODO modify collections and simples like getOutput();
Hashtable servOut = new Hashtable();
servOut = getOutput(resource);
- for (int i = 0; i < ver.length; i++) { // a clearance of the
- // array ver[]
- ver[i] = 0;
-
- }
+ ver = new int[]{0,0,0,0,0,0,0,0};
if (servInp.containsValue("error")
| servOut.containsValue("error")) {
servError += 1;
@@ -302,7 +298,7 @@
Hashtable input = new Hashtable();
Resource si = servDescrMd.getResource(resource);
-
+ if (si.hasProperty(MP.consumes))
try {
Resource consumes = si.getRequiredProperty(MP.consumes)
.getResource();
@@ -375,7 +371,7 @@
// to Input
sin += 1;
Enumeration num = siminp.keys();
-
+ siminp= new Hashtable();
}
} else if (type.equals(MP.Collection)
| type.equals(RDF.Bag)) {
@@ -383,9 +379,9 @@
// l3Res.hasProperty(RDF.li(1))){
if (l3Res.hasProperty(RDF.li(1))) {
StmtIterator p34iter = l3Res.listProperties();
- if (l3Res.hasProperty(MP.article_name)) {
+ if (l3Res.hasProperty(MP.articleName)) {
String col_artName = l3Res.getProperty(
- MP.article_name).getObject().toString();
+ MP.articleName).getObject().toString();
String[] rezNode = col_artName.split(":http:");
col_artName = rezNode[0];
colinp.put("col_articleName", col_artName);
@@ -449,13 +445,18 @@
String lsid_nsp = switchURItoLSID(l5Node
.toString());
colinp.put(name, lsid_nsp);
- } else {
+ } else if (name.equals("articleName")) {
+ colinp.put(name, l5Node.getName());
+ }else {
colinp.put(name, l5Node);
}
}
input.put("colinp" + cin, colinp);
cin += 1;
Enumeration num = colinp.keys();
+ String col_name = (String)colinp.get("col_articleName");
+ colinp = new Hashtable();
+ colinp.put("col_articleName", col_name);
}
}
@@ -529,7 +530,7 @@
input.put("input", "error");
}
} catch (Exception e) {
- Log.warning("Failed:" + e);
+ Log.warning("Failed (ServiceDescrParser.java - getInput): " + e);
}
// }
//System.out.println("input= "+input);
@@ -558,8 +559,9 @@
Hashtable output = new Hashtable();
Resource si = servDescrMd.getResource(resource);
-
+ if (si.hasProperty(MP.produces))
try {
+
Resource consumes = si.getRequiredProperty(MP.produces)
.getResource();
StmtIterator p23iter = consumes.listProperties();
@@ -628,7 +630,7 @@
// to Output
so += 1;
Enumeration num = simout.keys();
-
+ simout = new Hashtable();
}
}
@@ -636,12 +638,12 @@
// if (l3Res.hasProperty(RDF.type,RDF.Bag) &&
// l3Res.hasProperty(RDF.li(1))){
- if (l3Res.hasProperty(RDF.li(1))) {
+ if (l3Res.hasProperty(RDF.li(1))) { //TODO is this right? probably should iterate through the anon nodes, breaking when the hasProperty() fails.
StmtIterator p34iter = l3Res.listProperties();
- if (l3Res.hasProperty(MP.article_name)) {
+ if (l3Res.hasProperty(MP.articleName)) {
String col_artName = l3Res.getProperty(
- MP.article_name).getObject().toString();
+ MP.articleName).getObject().toString();
String[] rezNode = col_artName.split(":http:");
col_artName = rezNode[0];
colout.put("col_articleName", col_artName);
@@ -705,13 +707,19 @@
String lsid_nsp = switchURItoLSID(l5Node
.toString());
colout.put(name, lsid_nsp);
- } else {
+ } else if (name.equals("articleName")) {
+ colout.put(name, rezNode[0]);
+ }else {
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");
+ colout = new Hashtable();
+ colout.put("col_articleName", col_name);
}
}
@@ -732,7 +740,7 @@
output.put("output", "error");
}
} catch (Exception e) {
- Log.warning("Failed:" + e);
+ Log.warning("Failed (ServiceDescrParser.java-getOutput): " + e);
}
//System.out.println("output = "+output);
return output;
@@ -845,6 +853,7 @@
return res;
}
+ //TODO - need to fix this to make it portable
public String switchURItoLSID(String uri) {
String lsid = "";
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