OHDSI Study: Treatment Pathways in Patients with Cancer

rchen · December 19, 2017, 8:27pm

Hi everyone,

As mentioned on the OHDSI community call, we have posted a new study to the OHDSI Research Network:

Treatment Pathways in Patients with Cancer

This study is another variant of the prior Treatment Pathways studies, but includes only patients with cancer. It again investigates treatment pathways for hypertension, type II diabetes, and depression, and uses the shorter required period of 12 months of observation and drug adherence.

The value of this study is two-fold:

treatment pathways are not well characterized in the literature for cancer patients, who are especially vulnerable to developing these co-morbid conditions, particularly depression and diabetes
this is part of a project for NCI (National Cancer Institute) to demonstrate the feasibility of using the OHDSI research network for future cancer studies/funding. We will have our first presentation to NCI in Feb 2018 and would love to have as much data as we can get. So we need your help to run this!

If you would like to join as a contributing investigator, contributing to the analysis and write-up of this work, please let us know. (@Patrick_Ryan, adding you based on our discussions and your enthusiasm from earlier today!) We would also appreciate any feedback/comments on the study or the code, especially from all the experts who put together the initial treatment pathway studies (@jon_duke, @schuemie, @nigam)

Many thanks,
-Ray, George @hripcsa, and Thomas @thomasfalconer

deppen · December 19, 2017, 8:25pm

Our group has pulled a surgical cohort in the VA with known or suspected lung cancer excluding those with metastatic disease (primarily stage 1 and 2 disease). We are interested in participating. I missed today’s collaborator meeting. Please forward the pathway and recruitment criteria to me directly.

rchen · December 19, 2017, 9:46pm

Thanks @deppen ! What is your e-mail? I can send you the protocol via e-mail if you would like. Protocol and the code should all be accessible directly from the study wiki page as well: http://www.ohdsi.org/web/wiki/doku.php?id=research:treatment_pathways_in_cancer_12mo (code and protocol temporarily linked to my Github for now but should be accessible to all)

Basically we’re including all cancer patients, broadly defined as all malignant neoplasms, based on SNOMED codes. So condition criteria for cancer is a diagnosis of Neoplastic disease (55342001), then we exclude:
20376005-Benign neoplastic disease
254827004-Lipomatous tumor

SCYou · December 19, 2017, 11:15pm

@rchen
We have two kinds of database (one from hospital EHR, the other from national insurance)
Please count me in!

And I’m really interested not only variety in treatment pathway but also variety in treatment cost across the world!

cys7like · December 20, 2017, 12:12am

I am a member of Korean OHDSI.
Very interesting topics!
I want to join it!

hscho · December 20, 2017, 12:50am

Hello.
I work at national cancer center. I do research on cancer patient comorbidity and survival. I am very interested in joining the study. I am new to ohdsi. Let me know how I can be involved.

Hyunsoon

ShinSeojeong · December 20, 2017, 1:05am

Hi, I’m a student of Ajou University in Korea. I would like to join in. Let our EHR database to be used in this study!

SCYou · December 20, 2017, 2:28am

Welcome! @hscho We can support you to convert your EHR data and Korean national cancer registry into CDM.
(my e-mail address: applegna@gmail.com)

Now, oncology working group also tries to extend CDM to capture comprehensive oncology data from cancer registries, led by @rimma from MSKCC.

rchen · December 20, 2017, 10:26am

Love the enthusiasm from Korea! And looking forward to the rest of our sites around the world joining in on the excitement!

While NCI may be a bit more US-centric in their interests, I certainly agree that there is a lot we can learn from looking at treatments across different countries and regions, including things such as treatment pathways and cost. Ideally, we can all learn from each other and make novel discoveries that will continue to improve our care of cancer patients

Please review the protocol and wiki, then get the code from Github and try to run it if you are interested. Let us know if you run into any issues or have any questions!

Vojtech_Huser · December 21, 2017, 9:28pm

Just documenting some minor warnings.

conn <- connect(connectionDetails)
Connecting using SQL Server driver using Windows integrated security
executeSql(conn,readSql(htnSqlFile))
|===========================================================================================================================================================================================| 100%
Executing SQL took 25 secs
executeSql(conn,readSql(t2dmSqlFile))
|===========================================================================================================================================================================================| 100%
Executing SQL took 23.3 secs
executeSql(conn,readSql(depSqlFile))
|===========================================================================================================================================================================================| 100%
Executing SQL took 24.4 secs

Extract tables to CSV files:

extractAndWriteToFile(conn, “summary”, resultsSchema, sourceName, “HTN12mo_ca”, dbms)
Created file ‘HTN12mo_ca_txpath12mo_ca_summary.csv’
Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema = resultsSchema, :
Parameter ‘cdmSchema’ not found in SQL
2: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
sourceDialect argument is deprecated in the translateSql function in SqlRender. Please update your code
extractAndWriteToFile(conn, “person_cnt”, resultsSchema, sourceName, “HTN12mo_ca”, dbms)
Created file ‘HTN12mo_ca_txpath12mo_ca_person_cnt.csv’
Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema = resultsSchema, :
Parameter ‘cdmSchema’ not found in SQL
2: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
sourceDialect argument is deprecated in the translateSql function in SqlRender. Please update your code
extractAndWriteToFile(conn, “seq_cnt”, resultsSchema, sourceName, “HTN12mo_ca”, dbms)
Created file ‘HTN12mo_ca_txpath12mo_ca_seq_cnt.csv’
Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema = resultsSchema, :
Parameter ‘cdmSchema’ not found in SQL
2: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
sourceDialect argument is deprecated in the translateSql function in SqlRender. Please update your code

rchen · December 21, 2017, 10:03pm

Thank you @Vojtech_Huser! We based our code on the treatment pathways code from the studies 3 years ago, hence there will probably be some warnings. But I don’t think they affect the analysis; we will take a deeper dive into our data to double check and try to be sure

Also a big thank you to @rohitv and @nigam for running it on Stanford’s data! Had a call with NCI and they’re very excited about how open and collaborative our community is!

rkboyce · December 23, 2017, 12:01am

Hi,

I am interested in participating in the study. The population is a
relatively small nursing home patient population of ~5,000 folks. The
data is stored in Oracle. I tried to run the study package and ran into
several difficulties with table names and characters (see listing
below). Did you have success with Oracle CDMs in your last study? Any
suggestions for how to proceed?

Thanks,
-Rich

 > # Create the parameterized SQL files:
 > htnSqlFile <-
renderStudySpecificSql("HTN12mo",minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
Created file 'TxPath autoTranslate oracle HTN12mo.sql'
Warning messages:
1: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   sourceDialect argument is deprecated in the translateSql function in
SqlRender. Please update your code
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#HTN12mo_drug_seq_summary' is too long. Temp table
names should be shorter than 22 characters to prevent Oracle from crashing.
 > t2dmSqlFile <-
renderStudySpecificSql("T2DM12mo",minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
Created file 'TxPath autoTranslate oracle T2DM12mo.sql'
Warning messages:
1: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   sourceDialect argument is deprecated in the translateSql function in
SqlRender. Please update your code
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#T2DM12mo_drug_seq_summary' is too long. Temp table
names should be shorter than 22 characters to prevent Oracle from crashing.
 > depSqlFile <-
renderStudySpecificSql("Depression12mo",minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
Created file 'TxPath autoTranslate oracle Depression12mo.sql'
Warning messages:
1: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   sourceDialect argument is deprecated in the translateSql function in
SqlRender. Please update your code
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#Depression12mo_drug_seq_summary' is too long. Temp
table names should be shorter than 22 characters to prevent Oracle from
crashing.
3: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#Depression12mo_IndexCohort' is too long. Temp table
names should be shorter than 22 characters to prevent Oracle from crashing.
4: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#Depression12mo_indexcohort' is too long. Temp table
names should be shorter than 22 characters to prevent Oracle from crashing.
5: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#Depression12mo_drug_seq' is too long. Temp table
names should be shorter than 22 characters to prevent Oracle from crashing.
6: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#Depression12mo_matchcohort' is too long. Temp table
names should be shorter than 22 characters to prevent Oracle from crashing.
7: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :
   Temp table name '#Depression12mo_MatchCohort' is too long. Temp table
names should be shorter than 22 characters to prevent Oracle from crashing.
 >
 > # Execute the SQL:
 > conn <- connect(connectionDetails)
Connecting using Oracle driver
- using THIN to connect
 > executeSql(conn,readSql(htnSqlFile))
|== |   2%Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00911: invalid character
ORA-06512: at line 7

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
 > executeSql(conn,readSql(t2dmSqlFile))
|== |   2%Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00911: invalid character
ORA-06512: at line 7

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
 > executeSql(conn,readSql(depSqlFile))
|== |   2%Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00911: invalid character
ORA-06512: at line 7

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
 >
 > # Extract tables to CSV files:
 > extractAndWriteToFile(conn, "summary", resultsSchema, sourceName,
"HTN12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
extractAndWriteToFile(conn, "person_cnt", resultsSchema, sourceName,
"HTN12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
extractAndWriteToFile(conn, "seq_cnt", resultsSchema, sourceName,
"HTN12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
 > extractAndWriteToFile(conn, "summary", resultsSchema, sourceName,
"T2DM12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
extractAndWriteToFile(conn, "person_cnt", resultsSchema, sourceName,
"T2DM12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
extractAndWriteToFile(conn, "seq_cnt", resultsSchema, sourceName,
"T2DM12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
 > extractAndWriteToFile(conn, "summary", resultsSchema, sourceName,
"Depression12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
extractAndWriteToFile(conn, "person_cnt", resultsSchema, sourceName,
"Depression12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
extractAndWriteToFile(conn, "seq_cnt", resultsSchema, sourceName,
"Depression12mo", dbms)
Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt
In addition: Warning messages:
1: In renderSql(parameterizedSql, cdmSchema = cdmSchema, resultsSchema =
resultsSchema,  :
   Parameter 'cdmSchema' not found in SQL
2: In translateSql(renderedSql, sourceDialect = "sql server",
targetDialect = dbms) :

  Show Traceback

  Rerun with Debug
  Error: Error executing SQL:
java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

An error report has been created at  C:/Users/boycerd_adm/Study 2 -
Treatment Pathways 12mo/R Version/errorReport.txt >
 > dbDisconnect(conn)
Error: could not find function "dbDisconnect"

ShinSeojeong · December 26, 2017, 9:32am

Hi, I’m seojeong of Ajou University in Korea.
I ran the code but there are some problems.

Warning messages during creating the paramerterized SQL files
Progress bar stopped in 21% during executing SQL (for more 3 days)

Please check this state and let me know what is problem.

setwd(folder)

source(“HelperFunctions.R”)

Create the parameterized SQL files:

htnSqlFile <- renderStudySpecificSql(“HTN12mo_ca”,minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
Created file ‘TxPath autoTranslate sql server HTN12mo_ca.sql’
경고메시지(들):
1: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
sourceDialect argument is deprecated in the translateSql function in SqlRender. Please update your code
2: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#HTN12mo_ca_IndexCohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
3: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#HTN12mo_ca_indexcohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
4: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#HTN12mo_ca_drug_seq_summary’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
5: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#HTN12mo_ca_matchcohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
6: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#HTN12mo_ca_MatchCohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
7: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ HTN12mo_ca_txpath12mo_ca_person_cnt’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.
8: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ HTN12mo_ca_txpath12mo_ca_seq_cnt’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.
9: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ HTN12mo_ca_txpath12mo_ca_summary’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.

t2dmSqlFile <- renderStudySpecificSql(“T2DM12mo_ca”,minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
Created file ‘TxPath autoTranslate sql server T2DM12mo_ca.sql’
경고메시지(들):
1: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
sourceDialect argument is deprecated in the translateSql function in SqlRender. Please update your code
2: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#T2DM12mo_ca_matchcohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
3: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#T2DM12mo_ca_indexcohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
4: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#T2DM12mo_ca_IndexCohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
5: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#T2DM12mo_ca_drug_seq_summary’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
6: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#T2DM12mo_ca_MatchCohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
7: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ T2DM12mo_ca_txpath12mo_ca_summary’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.
8: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ T2DM12mo_ca_txpath12mo_ca_seq_cnt’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.
9: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ T2DM12mo_ca_txpath12mo_ca_person_cnt’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.

depSqlFile <- renderStudySpecificSql(“Depression12mo_ca”,minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
Created file ‘TxPath autoTranslate sql server Depression12mo_ca.sql’
경고메시지(들):
1: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
sourceDialect argument is deprecated in the translateSql function in SqlRender. Please update your code
2: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#Depression12mo_ca_matchcohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
3: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#Depression12mo_ca_indexcohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
4: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#Depression12mo_ca_MatchCohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
5: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#Depression12mo_ca_drug_seq’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
6: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#Depression12mo_ca_drug_seq_summary’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
7: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Temp table name ‘#Depression12mo_ca_IndexCohort’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.
8: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ Depression12mo_ca_txpath12mo_ca_seq_cnt’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.
9: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ Depression12mo_ca_txpath12mo_ca_person_cnt’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.
10: In translateSql(renderedSql, sourceDialect = “sql server”, targetDialect = dbms) :
Table name ’ Depression12mo_ca_txpath12mo_ca_summary’ is too long. Table names should be shorter than 30 characters to prevent Oracle from crashing.

Execute the SQL:

conn <- connect(connectionDetails)
Connecting using SQL Server driver

executeSql(conn,readSql(htnSqlFile))
|=========================== | 21%

vhonavar · December 26, 2017, 9:48am

I would love to contribute, as needed to data analyses and modeling (using machine learning and causal inference techniques). Please email me additional information about the goals of the project, data available for analyses, etc.

Thanks,
Vasant

rchen · December 27, 2017, 6:41pm

Hi Rich, I think we may need to update the temp table names with Oracle… I’m not sure whether or not it was run on Oracle for the last iteration, but I can try to get a working version. Can you send me an e-mail at rc3179@cumc.columbia.edu and we can try some updated files? Thanks!

rchen · December 27, 2017, 6:46pm

Hi Seojeong, do you happen to have the errorReport.txt file that is generated with this? All of the messages above look like warning messages (which we also get while running due to some old code) but not hard-stop error messages. If you have an errorReport file, that would help. Please feel free to post here or e-mail me (rc3179@cumc.columbia.edu). Thanks for participating!

rchen · January 22, 2018, 5:15pm

Hi everyone, if anyone is still interested in participating, please go ahead and try to run the code as soon as you can. I’ve updated some of the code and there should be less warnings now, although it all should still produce the same results.

We will be presenting this data to the National Cancer Institute in 3 weeks, so this will probably be the last week that we can run code/share data in order to have enough time to package and present it to NCI. Thanks for all your help!