peterhambly
commented
5 years ago SQL Server is OK, Postgres fails Test 1005 with a SQL error
JDBC ERROR FETCHING! execute JDBC update query failed in dbSend Update (ERROR: column "nan" does not exist at position: 158)
Querying by JDBC: select * FROM rif40.t_rif40_homogeneity WHERE inv_id =533 AND study_id=561 and adjusted = 0 and genders = 2(attached: TEST 1005 LUNG CANCER 95 96 Risk Analyisis 01 points.json.txt )
Trying JDBC connection using driver class org.postgresql.Driver, lib dir C:\Program Files\Apache Software Foundation\Tomcat 8.5\webapps\rifServices\WEB-INF\lib, URL jdbc:postgresql://localhost:5432/sahsuland, user peter
... JDBC connection established
Querying by JDBC: SELECT rif40_sql_pkg.rif40_startup()
Connected to DB
connectToDb exitValue: 0
About to fetch extract table
JDBC EXTRACT TABLE NAME: rif_studies.s561_extract
Querying by JDBC: select * from rif_studies.s561_extract
JDBC Saving extract frame to: scratchSpace/d501-600/s561/data/tmp_s561_extract.csv
JDBC rif_studies.s561_extract numberOfRows=39160==
About to calculate band data
Covariates: none
About to run homogeneity tests
callRiskAnal exitValue: 0
callRiskAnal() OK: 0
About to save to table
In saveDataFrameToDatabaseTableSaving data frame to: scratchSpace/d501-600/s561/data/tmp_s561_map.csv
Creating temporary table: peter.tmp_s561_map
Replace INF will NA for temporary table: peter.tmp_s561_map
Replace NAN will NA for temporary table: peter.tmp_s561_map
Replace "" will NA for temporary table: peter.tmp_s561_map
About to write temporary table: peter.tmp_s561_map; first 10 rows
area_id gid gid_rowindex username study_id inv_id band_id exposure genders
1 NA NA NA NA 561 533 1 0 1
2 NA NA NA NA 561 533 1 0 2
3 NA NA NA NA 561 533 1 0 3
4 NA NA NA NA 561 533 2 0 1
5 NA NA NA NA 561 533 2 0 2
6 NA NA NA NA 561 533 2 0 3
direct_standardisation adjusted observed expected lower95 upper95
1 0 0 388 418.6505 0.8390080 1.0237504
2 0 0 198 225.8527 0.7626874 1.0077048
3 0 0 586 646.8006 0.8355332 0.9824052
4 0 0 2346 2431.7723 0.9264690 1.0045680
5 0 0 1298 1290.9190 0.9522457 1.0617015
6 0 0 3644 3715.5221 0.9494180 1.0131169
relative_risk smoothed_relative_risk posterior_probability
1 0.9267874 NA NA
2 0.8766777 NA NA
3 0.9059979 NA NA
4 0.9647285 NA NA
5 1.0054853 NA NA
6 0.9807505 NA NA
posterior_probability_upper95 posterior_probability_lower95
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NA
residual_relative_risk residual_rr_lower95 residual_rr_upper95 smoothed_smr
1 NA NA NA NA
2 NA NA NA NA
3 NA NA NA NA
4 NA NA NA NA
5 NA NA NA NA
6 NA NA NA NA
smoothed_smr_lower95 smoothed_smr_upper95
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NA
Creating study_id index on temporary table
SQL> CREATE INDEX s561_ind_study_id ON peter.tmp_s561_map(study_id)Creating area_id index on temporary table
SQL> CREATE INDEX s561_ind_area_id ON peter.tmp_s561_map(area_id)Creating genders index on temporary table
SQL> CREATE INDEX s561_ind_genders ON peter.tmp_s561_map(genders)Created indices on temporary table
saveDataFrameToDatabaseTable finishing
.Primitive("return")
Trying JDBC connection using driver class org.postgresql.Driver, lib dir C:\Program Files\Apache Software Foundation\Tomcat 8.5\webapps\rifServices\WEB-INF\lib, URL jdbc:postgresql://localhost:5432/sahsuland, user peter
... JDBC connection established
Querying by JDBC: SELECT rif40_sql_pkg.rif40_startup()
Connected to DB
connectToDb exitValue: 0
SQL> UPDATE rif_studies.s561_map a
SET direct_standardisation=b.direct_standardisation,adjusted=b.adjusted,observed=b.observed,expected=b.expected,lower95=b.lower95,upper95=b.upper95,relative_risk=b.relative_risk,smoothed_relative_risk=CASE WHEN b.smoothed_relative_risk = "NAN" THEN NULL ELSE b.smoothed_relative_risk END, posterior_probability=CASE WHEN b.posterior_probability = "NAN" THEN NULL ELSE b.posterior_probability END, posterior_probability_upper95=CASE WHEN b.posterior_probability_upper95 = "NAN" THEN NULL ELSE b.posterior_probability_upper95 END, posterior_probability_lower95=CASE WHEN b.posterior_probability_lower95 = "NAN" THEN NULL ELSE b.posterior_probability_lower95 END, residual_relative_risk=CASE WHEN b.residual_relative_risk = "NAN" THEN NULL ELSE b.residual_relative_risk END, residual_rr_lower95=CASE WHEN b.residual_rr_lower95 = "NAN" THEN NULL ELSE b.residual_rr_lower95 END, residual_rr_upper95=CASE WHEN b.residual_rr_upper95 = "NAN" THEN NULL ELSE b.residual_rr_upper95 END, smoothed_smr=CASE WHEN b.smoothed_smr = "NAN" THEN NULL ELSE b.smoothed_smr END, smoothed_smr_lower95=CASE WHEN b.smoothed_smr_lower95 = "NAN" THEN NULL ELSE b.smoothed_smr_lower95 END, smoothed_smr_upper95=CASE WHEN b.smoothed_smr_upper95 = "NAN" THEN NULL ELSE b.smoothed_smr_upper95 END
FROM peter.tmp_s561_map b WHERE a.study_id=b.study_id AND a.band_id=b.band_id AND a.inv_id=b.inv_id AND a.genders=b.genders
Trying JDBC connection using driver class org.postgresql.Driver, lib dir C:\Program Files\Apache Software Foundation\Tomcat 8.5\webapps\rifServices\WEB-INF\lib, URL jdbc:postgresql://localhost:5432/sahsuland, user peter
... JDBC connection established
Querying by JDBC: SELECT rif40_sql_pkg.rif40_startup()
Connected to DB
connectToDb exitValue: 0
Saving data frame to: scratchSpace/d501-600/s561/data/tmp_s561_Homog.csv
Querying by JDBC: select * FROM rif40.t_rif40_homogeneity WHERE inv_id =533 AND study_id=561 and adjusted = 0 and genders = 1
Stack tracer >>>
.handleSimpleError(function (obj)
{
calls = sys.calls()
calls = ca stop("execute JDBC update query failed in dbSendUpdate (", .jcall(x, "S", " .local(conn, statement, ...) dbSendUpdate(connection, updateStmt) JdbcHandler.R#530: dbSendUpdate(connection, updateStmt) Statistics_Common.R#178: withVisible(expr) Statistics_Common.R#178: withCallingHandlers(withVisible(expr), error = err JdbcHandler.R#530: withErrorTracing({
dbSendUpdate(connection, updateSt doTryCatch(return(expr), name, parentenv, handler) tryCatchOne(expr, names, parentenv, handlers[[1]]) tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) doTryCatch(return(expr), name, parentenv, handler) tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names tryCatchList(expr, classes, parentenv, handlers) JdbcHandler.R#529: tryCatch({
withErrorTracing({
dbSendUpdate(c insertHomogeneityResults(resultHomog) tryCatch({
withErrorTracing({
cat(paste0("About to fetch extrac eval(expr, pf) eval(expr, pf) withVisible(eval(expr, pf)) evalVis(expr) Statistics_JRI.R#280: capture.output({
tryCatch({
withErrorTrac runRRiskAnalFunctions()
<<< End of stack tracer.
JDBC ERROR FETCHING! execute JDBC update query failed in dbSendUpdate (ERROR: column "nan" does not exist
Position: 158)
Querying by JDBC: select * FROM rif40.t_rif40_homogeneity WHERE inv_id =533 AND study_id=561 and adjusted = 0 and genders = 2
Stack tracer >>>
.handleSimpleError(function (obj)
{
calls = sys.calls()
calls = ca stop("execute JDBC update query failed in dbSendUpdate (", .jcall(x, "S", " .local(conn, statement, ...) dbSendUpdate(connection, updateStmt) JdbcHandler.R#530: dbSendUpdate(connection, updateStmt) Statistics_Common.R#178: withVisible(expr) Statistics_Common.R#178: withCallingHandlers(withVisible(expr), error = err JdbcHandler.R#530: withErrorTracing({
dbSendUpdate(connection, updateSt doTryCatch(return(expr), name, parentenv, handler) tryCatchOne(expr, names, parentenv, handlers[[1]]) tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) doTryCatch(return(expr), name, parentenv, handler) tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names tryCatchList(expr, classes, parentenv, handlers) JdbcHandler.R#529: tryCatch({
withErrorTracing({
dbSendUpdate(c insertHomogeneityResults(resultHomog) tryCatch({
withErrorTracing({
cat(paste0("About to fetch extrac eval(expr, pf) eval(expr, pf) withVisible(eval(expr, pf)) evalVis(expr) Statistics_JRI.R#280: capture.output({
tryCatch({
withErrorTrac runRRiskAnalFunctions()
<<< End of stack tracer.
JDBC ERROR FETCHING! execute JDBC update query failed in dbSendUpdate (ERROR: column "nan" does not exist
Position: 159)
Querying by JDBC: select * FROM rif40.t_rif40_homogeneity WHERE inv_id =533 AND study_id=561 and adjusted = 0 and genders = 3
Stack tracer >>>
.handleSimpleError(function (obj)
{
calls = sys.calls()
calls = ca stop("execute JDBC update query failed in dbSendUpdate (", .jcall(x, "S", " .local(conn, statement, ...) dbSendUpdate(connection, updateStmt) JdbcHandler.R#530: dbSendUpdate(connection, updateStmt) Statistics_Common.R#178: withVisible(expr) Statistics_Common.R#178: withCallingHandlers(withVisible(expr), error = err JdbcHandler.R#530: withErrorTracing({
dbSendUpdate(connection, updateSt doTryCatch(return(expr), name, parentenv, handler) tryCatchOne(expr, names, parentenv, handlers[[1]]) tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) doTryCatch(return(expr), name, parentenv, handler) tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names tryCatchList(expr, classes, parentenv, handlers) JdbcHandler.R#529: tryCatch({
withErrorTracing({
dbSendUpdate(c insertHomogeneityResults(resultHomog) tryCatch({
withErrorTracing({
cat(paste0("About to fetch extrac eval(expr, pf) eval(expr, pf) withVisible(eval(expr, pf)) evalVis(expr) Statistics_JRI.R#280: capture.output({
tryCatch({
withErrorTrac runRRiskAnalFunctions()
<<< End of stack tracer.
JDBC ERROR FETCHING! execute JDBC update query failed in dbSendUpdate (ERROR: column "nan" does not exist
Position: 159)
Trying JDBC connection using driver class org.postgresql.Driver, lib dir C:\Program Files\Apache Software Foundation\Tomcat 8.5\webapps\rifServices\WEB-INF\lib, URL jdbc:postgresql://localhost:5432/sahsuland, user peter
... JDBC connection established
Querying by JDBC: SELECT rif40_sql_pkg.rif40_startup()
Connected to DB
connectToDb exitValue: 0
.Primitive("return")
----------------- End of Statistics failure details -------------------
devilgate
Implementing linearity test with exposure