[MOBY-guts] biomoby commit
Martin Senger
senger at pub.open-bio.org
Mon Nov 7 07:03:49 UTC 2005
senger
Mon Nov 7 02:03:49 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/test
In directory pub.open-bio.org:/tmp/cvs-serv16438/src/main/org/biomoby/registry/rdfagent/test
Modified Files:
RDFAgentTestSuite.java
Log Message:
moby-live/Java/src/main/org/biomoby/registry/rdfagent/test RDFAgentTestSuite.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/test/RDFAgentTestSuite.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/test/RDFAgentTestSuite.java 2005/11/06 16:47:10 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/test/RDFAgentTestSuite.java 2005/11/07 07:03:49 1.3
@@ -353,8 +353,6 @@
public void performTest2() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test two ####");
println("Adding another simple output DNASequence(myDNASequence) with no namespace.");
println("Changing the signature url to point to 2.rdf");
@@ -371,8 +369,6 @@
public void performTest3() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test three ####");
println("Adding another simple input DNASequence(myDNASequence) with no namespace.");
println("Changing the signature url to point to 3.rdf");
@@ -389,8 +385,6 @@
public void performTest4() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test four ####");
println("Modified the simple output 'myString' to be called 'myNewString'.");
println("Changing the signature url to point to 4.rdf");
@@ -407,8 +401,6 @@
public void performTest5() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test five ####");
println("Modified the simple input 'myDNASequence' to be called 'myNewDNASequence'.");
println("Changing the signature url to point to 5.rdf");
@@ -425,8 +417,6 @@
public void performTest6() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test six ####");
println("Modified the simple output 'myDNASequence' contain a namespace EC\nand I removed the namespace from the simple output 'myNewString'.");
println("Changing the signature url to point to 6.rdf");
@@ -443,8 +433,6 @@
public void performTest7() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test seven ####");
println("Swapped the input 'myNewString' with the output 'myKeyword'.");
println("Changing the signature url to point to 7.rdf");
@@ -461,8 +449,6 @@
public void performTest8() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test eight ####");
println("removed the simple output 'myKeyword'.");
println("Changing the signature url to point to 8.rdf");
@@ -479,8 +465,6 @@
public void performTest9() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test nine ####");
println("Removed the very last simple output 'myDNASequence'.");
println("Changing the signature url to point to 9.rdf");
@@ -497,8 +481,6 @@
public void performTest10() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test ten ####");
println("removed the simple input 'myNewDNASequence'.");
println("Changing the signature url to point to 10.rdf");
@@ -515,8 +497,6 @@
public void performTest11() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test eleven ####");
println("Added a simple output of type BasicGFFSequenceFeature and articlename 'myGFF'.");
println("Changing the signature url to point to 11.rdf");
@@ -533,8 +513,6 @@
public void performTest12() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twelve ####");
println("appended a 'blah blah blah' to the description.");
println("Changing the signature url to point to 12.rdf");
@@ -551,8 +529,6 @@
public void performTest13() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirteen ####");
println("changed the contact email address to be kawas7 at yahoo.com");
println("Changing the signature url to point to 13.rdf");
@@ -569,8 +545,6 @@
public void performTest14() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test fourteen ####");
println("Chagned the service type to be analysis.");
println("Changing the signature url to point to 14.rdf");
@@ -587,8 +561,6 @@
public void performTest15() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test fifteen ####");
println("added a secondary input, called pseudocount of type integer with a\nmin/max of (-)2147483648 and a default value of 9");
println("Changing the signature url to point to 15.rdf");
@@ -605,8 +577,6 @@
public void performTest16() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test sixteen ####");
println("Added a duplicate secondary input as in test 15 called 'second'");
println("Changing the signature url to point to 16.rdf");
@@ -623,8 +593,6 @@
public void performTest17() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test seventeen ####");
println("removed the simple output 'myGFF'.");
println("Changing the signature url to point to 17.rdf");
@@ -641,8 +609,6 @@
public void performTest17a() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test seventeen a ####");
println("Removed the last remaining simple input.\nTHIS SHOULD NOT WORK!");
println("Changing the signature url to point to 17a.rdf");
@@ -659,8 +625,6 @@
public void performTest17b() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test seventeen b ####");
println("Changed the pre-existing simple input to be an input of datatype Integer called myInt with no namespace declared.");
println("Changing the signature url to point to 17b.rdf");
@@ -677,8 +641,6 @@
public void performTest18() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test eighteen ####");
println("removed the secondary input 'pseudocount'. Note that there is an mobyPred:produces element that contains an empty bag.");
println("Changing the signature url to point to 18.rdf");
@@ -695,8 +657,6 @@
public void performTest19() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test nineteen ####");
println("Added another secondary input that handles floats.");
println("The name is 'expectation_value' and is of type Float.\nNo min/max, but an enumeration of the 8 values(.0001,.01,.001,.1,10,.000001,.00001,1\nand a default of 10.0.");
@@ -714,8 +674,6 @@
public void performTest20() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty ####");
println("Added an enum value to expectation value of 101.1.");
println("Changing the signature url to point to 20.rdf");
@@ -732,8 +690,6 @@
public void performTest21() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-one ####");
println("changed the default value of expectation_value to be 47.2");
println("Changing the signature url to point to 21.rdf");
@@ -750,8 +706,6 @@
public void performTest22() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-two ####");
println("removed all enums except 101.1 from the secondary input 'expectation_value'");
println("Changing the signature url to point to 22.rdf");
@@ -768,8 +722,6 @@
public void performTest23() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-three ####");
println("added a min value to the secondary input expectation value of .000001");
println("Changing the signature url to point to 23.rdf");
@@ -786,8 +738,6 @@
public void performTest24() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-four ####");
println("added a max value to the secondary input expectation_value of 885858.01.");
println("Changing the signature url to point to 24.rdf");
@@ -804,8 +754,6 @@
public void performTest25() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-five ####");
println("removed the max value from the secondary input expectation_value.");
println("Changing the signature url to point to 25.rdf");
@@ -822,8 +770,6 @@
public void performTest26() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-six ####");
println("changed the datatype of the secondary input expecation_value to be String.");
println("Changing the signature url to point to 26.rdf");
@@ -840,8 +786,6 @@
public void performTest27() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-seven ####");
println("removed the min value from the secondary input 'expectation_value'.");
println("Changing the signature url to point to 27.rdf");
@@ -858,8 +802,6 @@
public void performTest28() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-eight ####");
println("removed the secondary input 'expectation_value'");
println("Changing the signature url to point to 28.rdf");
@@ -876,8 +818,6 @@
public void performTest29() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test twenty-nine ####");
println("removing the last secondary input 'second'");
println("Changing the signature url to point to 29.rdf");
@@ -894,8 +834,6 @@
public void performTest30() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty ####");
println("Adding a simple output called 'Jim', of type DNASequence, and ns EBI");
println("Changing the signature url to point to 30.rdf");
@@ -912,8 +850,6 @@
public void performTest31() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-one ####");
println("Added an output collection, 'myOutputCollection', containing a simple <GO_Term, null, [GO]>");
println("Changing the signature url to point to 31.rdf");
@@ -930,8 +866,6 @@
public void performTest32() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-two ####");
println("Added to the output collection, 'myOutputCollection', a simple <String, 'myNewString', []>");
println("Changing the signature url to point to 32.rdf");
@@ -948,8 +882,6 @@
public void performTest33() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-three ####");
println("Modified the simple output DNASequence is now an object, ns = EC and articlename JimIII>");
println("Changing the signature url to point to 33.rdf");
@@ -966,8 +898,6 @@
public void performTest34() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-four ####");
println("Modified the simple output object: added another ns to object EMBL, and added a ns, EC, to 'myNewString' contained in the output collection.");
println("Changing the signature url to point to 34.rdf");
@@ -984,8 +914,6 @@
public void performTest35() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-five ####");
println("Modified the output collection: added another ns, EC, to the GO_Term");
println("Changing the signature url to point to 35.rdf");
@@ -1020,8 +948,6 @@
public void performTest37() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-seven ####");
println("Cloned the output collection and placed it as an input. Article Name is myInputCollection.");
println("Changing the signature url to point to 37.rdf");
@@ -1038,8 +964,6 @@
public void performTest38() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-eight ####");
println("Removed the output collection 'myOutputCollection'");
println("Changing the signature url to point to 38.rdf");
@@ -1056,8 +980,6 @@
public void performTest39() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test thirty-nine ####");
println("Removed the last output collection.");
println("Changing the signature url to point to 39.rdf");
@@ -1074,8 +996,6 @@
public void performTest40() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty ####");
println("Removed Go_Term from myInputCollection.");
println("Changing the signature url to point to 40.rdf");
@@ -1092,8 +1012,6 @@
public void performTest41() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-one ####");
println("Changed the name of the simple and changed its type (myOldString, Object) in the collection input.\nALso added a new ns EMBL.\nThe simple input 'myNewString' has a new ns EC.");
println("Changing the signature url to point to 41.rdf");
@@ -1110,8 +1028,6 @@
public void performTest42() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-two ####");
println("Added a simple to the input collection <GFF,'myGFF', [EBI,EMBL]>");
println("Changing the signature url to point to 42.rdf");
@@ -1128,8 +1044,6 @@
public void performTest43a() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-three a####");
println("Cloning the input collection and adding it as input twice with articleName myClonedCollection and no article name.");
println("Changing the signature url to point to 43a.rdf");
@@ -1146,8 +1060,6 @@
public void performTest43() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-three ####");
println("Removed myOldString from the input collection. TODO more tests with 43a as starting point");
println("Changing the signature url to point to 43.rdf");
@@ -1164,8 +1076,6 @@
public void performTest44() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-four ####");
println("Removed a ns (EMBL) from the simple in the input collection.");
println("Changing the signature url to point to 44.rdf");
@@ -1182,8 +1092,6 @@
public void performTest45() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-five ####");
println("Removed the last remaining ns from the simple in the input collection");
println("Changing the signature url to point to 45.rdf");
@@ -1200,8 +1108,6 @@
public void performTest46() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-six ####");
println("Removed the article name of the simple in the collection.");
println("Changing the signature url to point to 46.rdf");
@@ -1218,8 +1124,6 @@
public void performTest47() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-seven ####");
println("Removed the articlename from the input collection.");
println("Changing the signature url to point to 47.rdf");
@@ -1236,8 +1140,6 @@
public void performTest48() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-eight ####");
println("Removed the simple input. All that is left is the collection.");
println("Changing the signature url to point to 48.rdf");
@@ -1254,8 +1156,6 @@
public void performTest49() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test forty-nine ####");
println("Removed the last remaining input.");
println("Changing the signature url to point to 49.rdf");
@@ -1272,8 +1172,6 @@
public void performTest50() throws TestException {
/* all variable used should be declared here */
String signatureUrlLocation = "";
- String name = "";
- ServSignature service = null;
println("#### Test fifty ####");
println("Added an input collection containing a datatype GFF2.");
println("Changing the signature url to point to 50.rdf");
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