ohdsi / studyprotocols Goto Github PK
View Code? Open in Web Editor NEWRepository of OHDSI Collaborative Research Protocols
Repository of OHDSI Collaborative Research Protocols
to find out details about what the CiCalibration study is trying to do, the link seems to be broken.
Constructing treatment and comparator cohorts
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Executing SQL took 2.02 secs
Fetching cohorts from server
Error in data.frame(description = "Original cohorts", treatedPersons =
rawCount$exposedCount[rawCount$treatment == :
arguments imply differing number of rows: 1, 0
Calls: execute ... FUN -> do.call -> getDbCohortMethodData -> data.frame
Execution halted
Greetings,
It seems like the SQL code got a bit garbled up between lines 2500 and 2550 (roughly, it changes depending on Depression, HTN or T2DM SQL files. Some of the statements are throwing errors when I try to execute them AS-IS. I am attaching my fixed version of the files which I fixed using adapting the SQL code found on the MSSQL server version of the files. I successfully ran these files on my Postgres server and calculates the basic summary counts perfectly. Overall, the issue is with the first step of the attrition tables (0. count total persons for attrition table). This might also be found in the Version 2 minCellCount 1 files which I haven't looked at yet.
This seems to be an issue with the Oracle version of the files as well (I haven't checked the other ones) and only the MSSQL server ones seem to be complete. Was the code translated using some kind of automated software package?
Dropbox link to fixed files:
https://dl.dropboxusercontent.com/u/21004832/Study1-V2-MC2-fixedfiles.zip
The settings file that allows generation of several cohort using atlas ID is great.
I used that for a cancer study referenced here
http://forums.ohdsi.org/t/how-to-do-quick-feasibility-counts-from-r-given-public-server-cohort-definition-url-link/2831/3?u=vojtech_huser
It worked fine for 1 cohort.
With two cohorts, I was getting always only one cohort back.
I found a bug in the code:
On this line
https://github.com/OHDSI/StudyProtocols/blob/master/AlendronateVsRaloxifene/R/CreateCohorts.R#L79
part of code that has [i] must be removed.
bad code (current)
counts <- merge(counts, data.frame(cohortDefinitionId = cohortsToCreate$cohortId[i],
cohortName = cohortsToCreate$name[i]))
good code (fixed)
counts <- merge(counts, data.frame(cohortDefinitionId = cohortsToCreate$cohortId,
cohortName = cohortsToCreate$name))
Can anyone tell me which version of FeatureExtraction and CohortMethod was used in this study protocol?
As Feature Extraction becomes upgraded, I don't think current this study can run with the current Feature Extraction or CohortMethod package. (Mine too. I cannot remember the version of the package I used....)
Thanks!
Looks like the SQL cohort code has the restriction of invalid_reason = NULL. Depending on the RDMBS flavor and how the vocabulary files are loaded this will be an issue. Loading the Athena files as-is on PostgreSQL will make invalid reason ='' rather than null.
While this is an easy fix, it might be worth making a note in the vocabulary load instructions that this should be the case. Otherwise, the study runs in a few seconds and gets no patients.
Hello. I'm seojeong, a graduate student of Ajou university in Korea.
I have a issue while I tried to run the GitHub code proposed by this study.
When I executed codes like below,
---------------------------------------------------------------------------------------
execute(connectionDetails = connectionDetails,
cdmDatabaseSchema = "[Camel_DB].[dbo]",
#oracleTempSchema = NULL,
workDatabaseSchema = "[scratch_Shin_SJ].[dbo]",
studyCohortTable = "ohdsi_depression_cohorts",
exposureCohortSummaryTable = "ohdsi_depression_exposure_summary",
workFolder = "c:/temp/LargeScalePopEst",
maxCores = 4,
createCohorts = TRUE,
fetchAllDataFromServer = TRUE,
injectSignals = TRUE,
generateAllCohortMethodDataObjects = TRUE,
runCohortMethod = TRUE)
----------------------------------------------------------------------------------------
I got an error massage about the issue in readChar size. Please check the report I received.
-----------------------------------------------------------------------------------------
DBMS:
sql server
Error:
execute JDBC update query failed in dbSendUpdate
(Arithmetic overflow error converting expression to data type int.)
SQL:
SELECT pair_id,
t_cohort_definition_id,
c_cohort_definition_id,
t_cohort_definition_id * 1000 + pair_id AS tprime_cohort_definition_id,
c_cohort_definition_id * 1000 + pair_id AS cprime_cohort_definition_id,
min_cohort_date,
max_cohort_date
INTO #exposure_cohort_pairs
FROM (
SELECT ROW_NUMBER() OVER (
ORDER BY s1.cohort_definition_id,
s2.cohort_definition_id
) AS pair_id,
s1.cohort_definition_id AS t_cohort_definition_id,
s2.cohort_definition_id AS c_cohort_definition_id,
CASE
WHEN s1.min_cohort_date > s2.min_cohort_date
THEN s1.min_cohort_date
ELSE s2.min_cohort_date
END AS min_cohort_date,
CASE
WHEN s1.max_cohort_date < s2.max_cohort_date
THEN s1.max_cohort_date
ELSE s2.max_cohort_date
END AS max_cohort_date
FROM #exposure_cohort_summary s1,
#exposure_cohort_summary s2
WHERE s1.cohort_definition_id < s2.cohort_definition_id
) t1
-----------------------------------------------------------------------------------------
I think this query should be fixed as follows.
From. -------------------------------------------------------------------
s1.cohort_definition_id AS t_cohort_definition_id,
s2.cohort_definition_id AS c_cohort_definition_id,
-------------------------------------------------------------------------
To. ---------------------------------------------------------------------
CAST(s1.cohort_definition_id AS BIGINT) AS t_cohort_definition_id,
CAST(s2.cohort_definition_id AS BIGINT) AS c_cohort_definition_id,
-------------------------------------------------------------------------
When we tried to run the code with edited version, the result was good.
Could you review this issue and confirm the code that I fixed?
Thank you!
This document claims that value sets are in a folder
Where this folder can be found?
(excellent study btw. The drug-outcome pair was on short-list as well.
@pbr6cornell
I'm still running keppra on Oracle, and ran into another bug.
Here's the error:
No outcome specified so not creating outcome and time variables
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered, :
vmode 'character' not implemented
Calls: execute ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
In addition: Warning message:
replacing previous import ‘Rcpp::LdFlags’ by ‘RcppParallel::LdFlags’ when loading ‘Cyclops’
Execution halted
Full log:
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(KeppraAngioedema)
Loading required package: DatabaseConnector
Loading required package: RJDBC
Loading required package: DBI
Loading required package: rJava
>
> # cohortTable = paste("ohdsi_keppra", Sys.getpid(), sep="_")
> cohortTable = "ohdsi_keppra_19239"
> print(paste("Cohort Table - ", cohortTable))
[1] "Cohort Table - ohdsi_keppra_19239"
>
> # outputDir = paste("/home/chilton/ohdsi_keppra/run", Sys.getpid(), sep="_")
> outputDir = "/home/chilton/ohdsi_keppra/run_19239"
> print(paste("Output Dir - ", outputDir))
[1] "Output Dir - /home/chilton/ohdsi_keppra/run_19239"
>
> connectionDetails <- createConnectionDetails(dbms = "oracle",
+ user = "OHDSI",
+ port = "1521",
+ password = "xxx",
+ server = "sasridg02.uits.iupui.edu/I2B21STG")
>
> execute(connectionDetails,
+ cdmDatabaseSchema = "OMOPV5_DE",
+ workDatabaseSchema = "OHDSI",
+ studyCohortTable = cohortTable,
+ oracleTempSchema = "OHDSI",
+ outputFolder = outputDir,
+ maxCores = 4,
+ createCohorts = FALSE)
Running analyses
*** Creating cohortMethodData objects ***
Loading required package: CohortMethod
Loading required package: Cyclops
Loading required package: FeatureExtraction
Connecting using Oracle driver
Constructing treatment and comparator cohorts
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Analysis took 23.5 secs
Fetching cohorts from server
Fetching cohorts took 0.729 secs
Constructing default covariates
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Analysis took 13.5 hours
Done
Fetching data from server
Loading took 24.8 secs
Removing redundant covariates
Removing redundant covariates took 22.3 secs
Normalizing covariates
Fetching outcomes from server
Fetching outcomes took 0.617 secs
*** Creating study populations ***
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*** Fitting shared propensity score models ***
Removing subject that are in both cohorts (if any)
No outcome specified so skipping removing people with prior outcomes
Removing subjects with less than 1 day(s) at risk (if any)
No outcome specified so not creating outcome and time variables
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered, :
vmode 'character' not implemented
Calls: execute ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
In addition: Warning message:
replacing previous import ‘Rcpp::LdFlags’ by ‘RcppParallel::LdFlags’ when loading ‘Cyclops’
Execution halted
Also, if I rerun it (after it's fixed), can I start from createCohorts = FALSE, or do I need to start over?
Thanks.
Hello,
I'm interested in this study but getting some errors running it.
Warning : the condition has length>1 and only the first element will be used
This warning doesn't look so probelmatic.
There were three chunks of error messages below.
I wonder if this is because I'm using Parallellogger of version 1.0.1 so I'm gonna update and run this package again but please tell me if you know what caused this issue.
Or I suspect that this error is caused becasue my institution hasn't converted some concepts.
Thread 1 returns error : "cannot oppen the connection" when using argument(s) : list(exposureID = NA, outcomeID = NA, modelFolder= NA, covarFileName = c("E:/DPJE001/Desktop/study_results/positiveControlSynthesis/CovarsForModel_gNA", .."
Thread 2 returns error : "argument is of length 0 when using argument(s) : list(exposureID = integer(0), outcomeID = integer(0), modelFolder= character(0), covarFileName = "E:/DPJE001/Desktop/study_results/positiveControlSynthesis/CovarsForModel_g"_, list(exposureID= c(99321,...,)"
Error in ParallelLogger:clusterapply(cluster,tasks,generateOutcomes, : Error(s) when calling function 'fun', see earlier messages for details
Hi,
While esting protocol 2 by running the MainAnalysis.R script configured for our dataset (Oracle >=11g, R 3.0) I ran into error "ORA-03291: Invalid truncate option - missing STORAGE keyword". This issue was triggered because I used a hyphen instead of an underscore in the "sourceName" variable - my bad. However, after correcting this, I found another issue that I think will require a slight change to the code. Specifically, the table prefix 'Depression12mo' leads to table names (e.g. 'Depression12mo_drug_seq_summary') that causes Oracle to trigger 'ORA-00972: identifier is too long'. The character limit on Oracle tables is 30. Going through the MainAnalysis.R and HelperFunctions.R and replacing 'Depression12mo' with 'Depr12mo' fixes this issue.
--- output before fix ---
> source("MainAnalysis.R")
Loading required package: RJDBC
Loading required package: DBI
Loading required package: rJava
Created file 'TxPath autoTranslate oracle HTN12mo.sql'
Created file 'TxPath autoTranslate oracle T2DM12mo.sql'
Created file 'TxPath autoTranslate oracle Depression12mo.sql'
Connecting using Oracle driver
|============ | 17%Error executing SQL: Error in .local(conn, statement, ...): execute JDBC update query failed in dbSendUpdate (ORA-00972: identifier is too long
ORA-06512: at line 7
)
An error report has been created at /home/rdb20/OHDSI-code/StudyProtocols/Study 2 - Treatment Pathways 12mo/R Version/errorReport.txt
Error in value[[3L]](cond) : no loop for break/next, jumping to top level
after
> source("MainAnalysis.R")
Created file 'TxPath autoTranslate oracle HTN12mo.sql'
Created file 'TxPath autoTranslate oracle T2DM12mo.sql'
Created file 'TxPath autoTranslate oracle Depr12mo.sql'
Connecting using Oracle driver
|======================================================================| 100%
Analysis took 19.8 secs
|======================================================================| 100%
Analysis took 16.9 secs
|======================================================================| 100%
Analysis took 16.8 secs
Created file 'HTN12mo_GOHDSI_summary.csv'
Created file 'HTN12mo_GOHDSI_person_cnt.csv'
Created file 'HTN12mo_GOHDSI_seq_cnt.csv'
Created file 'T2DM12mo_GOHDSI_summary.csv'
Created file 'T2DM12mo_GOHDSI_person_cnt.csv'
Created file 'T2DM12mo_GOHDSI_seq_cnt.csv'
Created file 'Depr12mo_GOHDSI_summary.csv'
Created file 'Depr12mo_GOHDSI_person_cnt.csv'
Created file 'Depr12mo_GOHDSI_seq_cnt.csv'
Hi,
We're trying to run Keppra Angiodema on Oracle, and I'm having issues when it is trying to create/select into cohort_person. It looks like it is creating the temp table in the CDM schema, and it should be coming from the workDatabaseSchema, right? Here's the error. It seems like it might be coming from a SELECT...INTO.
DBMS:
oracle
Error:
execute JDBC update query failed in dbSendUpdate (ORA-01031: insufficient privileges
)
SQL:
CREATE TABLE OMOPV5_DE.pwpkmcrscohort_person
AS
SELECT
ROW_NUMBER() OVER (ORDER BY person_id, cohort_start_date) AS row_id,
subject_id,
cohort_definition_id,
cohort_start_date,
( cohort_start_date - observation_period_start_date) AS days_from_obs_start,
( cohort_end_date - cohort_start_date)
AS days_to_cohort_end,
( observation_period_end_date - cohort_start_date)
AS days_to_obs_end
FROM
(SELECT subject_id,
cohort_definition_id,
cohort_start_date,
cohort_end_date
FROM OHDSI.ohdsi_keppra_19239 exposure_table
WHERE cohort_definition_id IN (1, 2)
) raw_cohorts
INNER JOIN OMOPV5_DE.observation_period
ON subject_id = person_id
WHERE cohort_start_date <= observation_period_end_date
AND cohort_start_date >= observation_period_start_date
R version:
R version 3.3.0 (2016-05-03)
Platform:
x86_64-pc-linux-gnu
Attached base packages:
- stats
- graphics
- grDevices
- utils
- datasets
- methods
- base
Other attached packages:
- CohortMethod (2.0.2)
- FeatureExtraction (1.0.0)
- Cyclops (1.2.0)
- KeppraAngioedema (0.1.0)
- DatabaseConnector (1.4.0)
- RJDBC (0.2-5)
- rJava (0.9-8)
- DBI (0.4-1)
Hello, I'm Seojeong, a graduate student of Ajou university in Korea.
I got a issue while I running the LargeScalePopEst Code.
I was trying to execute "injectionSignals" parameter especially for comfirming whether each step working rightly and then an error message was shown just like below. (Note that the parameters "createCohorts" and "fetchAllDataFromServer" worked well although one warning message poped up during executing the "createCohorts" step.)
↓ The warning message during "createCohort" step.
↓ The Error message during "injectSignals" step.
And I figured out that the length of [ unique(data$outcomeId) ] and [ negativeControlIds ] is different each other.
So I ask if it is possible that the code of LargeScalePopEst protocols can be altered.
↓ The Create outcomes file CODE
I think it would be better that the code should allow or skip the absent of some "outcomeId".
Could you modify this Code for us?
Please review this issue.
Thank you!
I am getting this for a few of the packages (on Windows):
Warning in install.packages :
cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://OHDSI.github.io/drat/bin/windows/contrib/3.2:
cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://cloudyr.github.io/drat/bin/windows/contrib/3.2:
cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES'
Running Oracle. First two exports work fine:
extractAndWriteToFile(conn, "person_count", resultsSchema, sourceName, "T2DM", dbms)
extractAndWriteToFile(conn, "person_count_year", resultsSchema, sourceName, "T2DM", dbms)
Last two exports throw an error:
extractAndWriteToFile(conn, "seq_count", resultsSchema, sourceName, "T2DM", dbms)
Error executing SQL: Error in .jcall(rp, "I", "fetch", stride): java.lang.OutOfMemoryError: Java heap space
Error in value[3L] : no loop for break/next, jumping to top levelextractAndWriteToFile(conn, "seq_count_year", resultsSchema, sourceName, "T2DM", dbms)
Error executing SQL: Error in .jcall(rp, "I", "fetch", stride): java.lang.OutOfMemoryError: Java heap space
Any ideas?
Hi. I`m Minseok, a graduate student in Ajou univ.
I executed CelecoxibVsNsNSAIDs analysis R code and have some trouble.
My error message is
//Error in ff::ff(1, length = nrow(covariates)) : unable to open
In addition: There were 17 warnings (use warnings() to see them) //
and 17 warnings are almost
//In readChar(pathToSql, file.info(pathToSql)$size) :
can only read in bytes in a non-UTF-8 MBCS locale execute//
//In lowLevelQuerySql.ffdf(connection, sql) :
Data has zero rows, returning an empty data frame execute//
But I don`t know what the error is with just that text.
I attach running code log
execute(connectionDetails,
cdmDatabaseSchema = "Camel_DB.dbo",
workDatabaseSchema = "Camel_nsnsaids_result.dbo",
studyCohortTable = "celecoxib_vs_nsnsaids",
oracleTempSchema = NULL,
outputFolder = "E:/R/OHDSI/study_results",
cdmVersion = "5")
execute(connectionDetails,
cdmDatabaseSchema = "Camel_DB.dbo",
workDatabaseSchema = "Camel_nsnsaids_result.dbo",
studyCohortTable = "celecoxib_vs_nsnsaids",
oracleTempSchema = NULL,
outputFolder = "E:/R/OHDSI/study_results",
cdmVersion = "5")
Creating exposure and outcome cohorts
Connecting using SQL Server driver
Constructing treatment and comparator cohorts
Executing multiple queries. This could take a while
|==================================================================================================================================================| 100%
Analysis took 56.5 secs
Fetching data from server
Loading took 0.521 secs
Constructing baseline covariates
Constructing covariates
|==================================================================================================================================================| 100%
Analysis took 21.4 secs
Done
Fetching data from server
Loading took 0.11 secs
Removing redundant covariates
Error in ff::ff(1, length = nrow(covariates)) : unable to open
In addition: There were 17 warnings (use warnings() to see them)
I am attempting to run CiCalibration::execute
function by following the instructions at
https://github.com/OHDSI/StudyProtocols/tree/master/CiCalibration
I have installed the dependencies R packages, installed PostgreSQL server and created the database, as well as the cdm_data
and results
schemas. When I ran the code shown at the web page, I get this error
Creating exposure and outcome cohorts Connecting using PostgreSQL driver Creating cohort: DabigatranSouthworth |== | 3%Error: Error executing SQL: org.postgresql.util.PSQLException: ERROR: relation "cdm_data.concept" does not exist Position: 155
Am I supposed to setup other tables before I can run CiCalibration::execute
?
Thanks!
Return median time-to-event and its 95%CI for T and C cohorts in StudyResults
artifacts.
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