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Merge pull request #836 from virtualcell/834-refine-database-logging
refine database logging, and Biomodel saves
2 parents 75037aa + 92d098a commit aca89dd

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‎docker/build/vcell-api.log4j.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
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</Root>
1919
<!-- <Logger name="org.vcell" level="warn" />-->
2020
<!-- <Logger name="cbit.vcell" level="warn" />-->
21-
<!-- <Logger name="cbit.vcell.modeldb" level="warn" />-->
21+
<Logger name="cbit.vcell.modeldb" level="debug" />
2222
<!-- <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
2323
<!-- <Logger name="org.vcell.util.exe" level="debug" />-->
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<!-- <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

‎docker/build/vcell-data.log4j.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
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</Root>
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<!-- <Logger name="org.vcell" level="warn" />-->
2020
<!-- <Logger name="cbit.vcell" level="warn" />-->
21-
<!-- <Logger name="cbit.vcell.modeldb" level="warn" />-->
21+
<Logger name="cbit.vcell.modeldb" level="debug" />
2222
<!-- <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
2323
<!-- <Logger name="org.vcell.util.exe" level="debug" />-->
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<!-- <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

‎docker/build/vcell-db.log4j.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
1818
</Root>
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<!-- <Logger name="org.vcell" level="warn" />-->
2020
<!-- <Logger name="cbit.vcell" level="warn" />-->
21-
<!-- <Logger name="cbit.vcell.modeldb" level="warn" />-->
21+
<Logger name="cbit.vcell.modeldb" level="debug" />
2222
<!-- <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
2323
<!-- <Logger name="org.vcell.util.exe" level="debug" />-->
2424
<!-- <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

‎docker/build/vcell-sched.log4j.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
1818
</Root>
1919
<!-- <Logger name="org.vcell" level="warn" />-->
2020
<!-- <Logger name="cbit.vcell" level="warn" />-->
21-
<!-- <Logger name="cbit.vcell.modeldb" level="warn" />-->
21+
<Logger name="cbit.vcell.modeldb" level="debug" />
2222
<!-- <Logger name="cbit.vcell.message.server.cmd" level="warn" />-->
2323
<!-- <Logger name="org.vcell.util.exe" level="warn" />-->
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<!-- <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

‎docker/build/vcell-submit.log4j.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@
2222
<!-- <Logger name="cbit.vcell.mongodb" level="trace" />-->
2323
<!-- <Logger name="org.vcell" level="warn" />-->
2424
<!-- <Logger name="cbit.vcell" level="warn" />-->
25-
<!-- <Logger name="cbit.vcell.modeldb" level="warn" />-->
25+
<Logger name="cbit.vcell.modeldb" level="debug" />
2626
<!-- <Logger name="cbit.vcell.message.server.cmd" level="warn" />-->
2727
<!-- <Logger name="org.vcell.util.exe" level="warn" />-->
2828
<!-- <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

‎docker/build/vcell-web.log4j.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
1818
</Root>
1919
<!-- <Logger name="org.vcell" level="warn" />-->
2020
<!-- <Logger name="cbit.vcell" level="warn" />-->
21-
<!-- <Logger name="cbit.vcell.modeldb" level="warn" />-->
21+
<Logger name="cbit.vcell.modeldb" level="debug" />
2222
<!-- <Logger name="cbit.vcell.message.server.cmd" level="debug" />-->
2323
<!-- <Logger name="org.vcell.util.exe" level="debug" />-->
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<!-- <Logger name="org.vcell.util.CommentStringTokenizer" level="warn" />-->

‎vcell-admin/src/main/java/org/vcell/stochtest/StochtestDbUtils.java‎

Lines changed: 32 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,9 @@
33
import java.sql.ResultSet;
44
import java.sql.SQLException;
55

6+
import cbit.vcell.modeldb.DbDriver;
7+
import org.apache.logging.log4j.LogManager;
8+
import org.apache.logging.log4j.Logger;
69
import org.vcell.db.ConnectionFactory;
710
import org.vcell.stochtest.TimeSeriesMultitrialData.SummaryStatistics;
811
import org.vcell.util.DataAccessException;
@@ -14,6 +17,7 @@
1417
import cbit.vcell.modeldb.StochtestTable;
1518

1619
public class StochtestDbUtils {
20+
private static final Logger lg = LogManager.getLogger(StochtestDbUtils.class);
1721

1822
public static StochtestRun getStochtestRun(ConnectionFactory conFactory, KeyValue stochtestRunKey) throws IllegalArgumentException, SQLException, DataAccessException {
1923

@@ -112,11 +116,13 @@ public static void finalizeAcceptedStochtestRun(ConnectionFactory conFactory, St
112116
stochtestRunTable.networkGenProbs.getUnqualifiedColName() + " = " + networkGenProbsRHS + " " +
113117
" WHERE "+stochtestRunTable.id.getUnqualifiedColName()+" = " + acceptedStochtestRun.key.toString();
114118
stmt = con.createStatement();
115-
System.out.println(sql);
116-
int numrows = stmt.executeUpdate(sql);
117-
if (numrows != 1){
118-
throw new DataAccessException("failed to update mathgen status for id = "+acceptedStochtestRun.key);
119-
}
119+
if (lg.isDebugEnabled()) {
120+
lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
121+
}
122+
int numrows = stmt.executeUpdate(sql); // jcs: added logging
123+
if (numrows != 1) {
124+
throw new DataAccessException("failed to update mathgen status for id = " + acceptedStochtestRun.key);
125+
}
120126
} finally {
121127
if (stmt != null) {
122128
stmt.close();
@@ -171,11 +177,13 @@ public static void finalizeAcceptedStochtestCompare(ConnectionFactory conFactory
171177
}
172178
sql += " WHERE "+stochtestCompareTable.id.getUnqualifiedColName()+" = " + acceptedStochtestCompare.key.toString();
173179
stmt = con.createStatement();
174-
System.out.println(sql);
175-
int numrows = stmt.executeUpdate(sql);
176-
if (numrows != 1){
177-
throw new DataAccessException("failed to update mathgen status for id = "+acceptedStochtestCompare.key);
178-
}
180+
if (lg.isDebugEnabled()) {
181+
lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
182+
}
183+
int numrows = stmt.executeUpdate(sql); // jcs: added logging
184+
if (numrows != 1) {
185+
throw new DataAccessException("failed to update mathgen status for id = " + acceptedStochtestCompare.key);
186+
}
179187
} finally {
180188
if (stmt != null) {
181189
stmt.close();
@@ -262,11 +270,13 @@ public static StochtestRun acceptNextWaitingStochtestRun(ConnectionFactory conFa
262270
" SET "+stochtestRunTable.status.getUnqualifiedColName() + " = " + "'"+StochtestRun.StochtestRunStatus.accepted+"'" +
263271
" WHERE "+stochtestRunTable.id.getUnqualifiedColName()+" = " + stochtestRun.key.toString();
264272
stmt = con.createStatement();
265-
System.out.println(sql);
266-
int numrows = stmt.executeUpdate(sql);
267-
if (numrows != 1){
268-
throw new DataAccessException("failed to update mathgen status for id = "+stochtestRun.key);
269-
}
273+
if (lg.isDebugEnabled()) {
274+
lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
275+
}
276+
int numrows = stmt.executeUpdate(sql); // jcs: added logging
277+
if (numrows != 1) {
278+
throw new DataAccessException("failed to update mathgen status for id = " + stochtestRun.key);
279+
}
270280
} finally {
271281
if (stmt != null) {
272282
stmt.close();
@@ -341,11 +351,13 @@ public static StochtestCompare acceptNextWaitingStochtestCompare(ConnectionFacto
341351
" SET "+stochtestCompareTable.status.getUnqualifiedColName() + " = " + "'"+StochtestCompare.StochtestCompareStatus.accepted+"'" +
342352
" WHERE "+stochtestCompareTable.id.getUnqualifiedColName()+" = " + stochtestCompare.key.toString();
343353
stmt = con.createStatement();
344-
System.out.println(sql);
345-
int numrows = stmt.executeUpdate(sql);
346-
if (numrows != 1){
347-
throw new DataAccessException("failed to update mathgen status for id = "+stochtestCompare.key);
348-
}
354+
if (lg.isDebugEnabled()) {
355+
lg.debug("executeUpdate() SQL: '" + sql + "'", new DbDriver.StackTraceGenerationException());
356+
}
357+
int numrows = stmt.executeUpdate(sql); // jcs: added logging
358+
if (numrows != 1) {
359+
throw new DataAccessException("failed to update mathgen status for id = " + stochtestCompare.key);
360+
}
349361
} finally {
350362
if (stmt != null) {
351363
stmt.close();

‎vcell-api/src/main/java/org/vcell/rest/UserVerifier.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -169,7 +169,7 @@ public AuthenticationStatus verify(ChallengeResponse challengeResponse) {
169169
return AuthenticationStatus.valid;
170170
}
171171
}catch (Exception e){
172-
lg.error(e);
172+
lg.error(e.getMessage(), e);
173173
return AuthenticationStatus.invalid;
174174
}
175175
}else{

‎vcell-api/src/main/java/org/vcell/rest/VCellCookieAuthenticator.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -85,7 +85,7 @@ protected int logout(Request request, Response response) {
8585
}
8686

8787
}catch (Exception e){
88-
lg.error(e);
88+
lg.error(e.getMessage(), e);
8989
getLogger().log(Level.SEVERE,"MyCookieAuthenticator.logout(request,response) - exception while invalidating '"+CustomAuthHelper.ACCESS_TOKEN+"'",e);
9090
}
9191

‎vcell-api/src/main/java/org/vcell/rest/admin/AdminJobsRestlet.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -112,7 +112,7 @@ public void handle(Request req, Response response) {
112112

113113
} catch (Exception e) {
114114
getLogger().severe("failed to retrieve job status: "+e.getMessage());
115-
lg.error(e);
115+
lg.error(e.getMessage(), e);
116116
response.setStatus(Status.SERVER_ERROR_INTERNAL);
117117
response.setEntity("failed to retrieve job status: "+e.getMessage(), MediaType.TEXT_PLAIN);
118118
}

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