Created
March 25, 2015 15:03
-
-
Save forus/86839b651c42dba931b9 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
From a00dd10787880368f2243e709dd219872476fa2a Mon Sep 17 00:00:00 2001 | |
From: Ruslan Forostianov <ruslan@thehyve.nl> | |
Date: Wed, 25 Mar 2015 16:01:47 +0100 | |
Subject: [PATCH 1/1] Fixes in favour of constraints | |
--- | |
data/common/i2b2metadata/i2b2_secure.tsv | 1 - | |
.../functions/i2b2_create_security_for_trial.sql | 68 ---------------------- | |
.../tm_cz/functions/i2b2_process_mrna_data.sql | 2 +- | |
3 files changed, 1 insertion(+), 70 deletions(-) | |
diff --git a/data/common/i2b2metadata/i2b2_secure.tsv b/data/common/i2b2metadata/i2b2_secure.tsv | |
index dc3a930..e69de29 100644 | |
--- a/data/common/i2b2metadata/i2b2_secure.tsv | |
+++ b/data/common/i2b2metadata/i2b2_secure.tsv | |
@@ -1 +0,0 @@ | |
-"0" "\Public Studies\" "Public Studies" "N" "CA " "365" "CONCEPT_CD" "CONCEPT_DIMENSION" "CONCEPT_PATH" "T" "LIKE" "\Public Studies\" "\Public Studies\" "2012-07-03 10:19:17.625681" "2012-07-03 10:19:17.625681" "2012-07-03 10:19:17.625681" "EXP:PUBLIC" | |
diff --git a/ddl/postgres/tm_cz/functions/i2b2_create_security_for_trial.sql b/ddl/postgres/tm_cz/functions/i2b2_create_security_for_trial.sql | |
index 4f1f022..9a1c097 100644 | |
--- a/ddl/postgres/tm_cz/functions/i2b2_create_security_for_trial.sql | |
+++ b/ddl/postgres/tm_cz/functions/i2b2_create_security_for_trial.sql | |
@@ -58,74 +58,6 @@ BEGIN | |
stepCt := 0; | |
- begin | |
- delete from i2b2demodata.observation_fact | |
- where sourcesystem_cd = TrialID | |
- and concept_cd = 'SECURITY'; | |
- get diagnostics rowCt := ROW_COUNT; | |
- exception | |
- when others then | |
- errorNumber := SQLSTATE; | |
- errorMessage := SQLERRM; | |
- --Handle errors. | |
- select tm_cz.cz_error_handler (jobID, procedureName, errorNumber, errorMessage) into rtnCd; | |
- --End Proc | |
- select tm_cz.cz_end_audit (jobID, 'FAIL') into rtnCd; | |
- return -16; | |
- end; | |
- stepCt := stepCt + 1; | |
- select tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Delete security records for trial from I2B2DEMODATA observation_fact',rowCt,stepCt,'Done') into rtnCd; | |
- | |
- begin | |
- insert into i2b2demodata.observation_fact | |
- (encounter_num | |
- ,patient_num | |
- ,concept_cd | |
- ,start_date | |
- ,provider_id | |
- ,modifier_cd | |
- ,valtype_cd | |
- ,tval_char | |
- ,valueflag_cd | |
- ,location_cd | |
- ,update_date | |
- ,download_date | |
- ,import_date | |
- ,sourcesystem_cd | |
- ,instance_num | |
- ) | |
- select patient_num | |
- ,patient_num | |
- ,'SECURITY' | |
- ,current_timestamp | |
- ,'@' | |
- ,TrialId | |
- ,'T' | |
- ,case when securedStudy = 'N' then 'EXP:PUBLIC' else 'EXP:' || trialID end | |
- ,'@' | |
- ,'@' | |
- ,current_timestamp | |
- ,current_timestamp | |
- ,current_timestamp | |
- --,sourcesystem_cd | |
- ,TrialId | |
- ,1 | |
- from i2b2demodata.patient_dimension | |
- where sourcesystem_cd like TrialID || ':%'; | |
- get diagnostics rowCt := ROW_COUNT; | |
- exception | |
- when others then | |
- errorNumber := SQLSTATE; | |
- errorMessage := SQLERRM; | |
- --Handle errors. | |
- select tm_cz.cz_error_handler (jobID, procedureName, errorNumber, errorMessage) into rtnCd; | |
- --End Proc | |
- select tm_cz.cz_end_audit (jobID, 'FAIL') into rtnCd; | |
- return -16; | |
- end; | |
- stepCt := stepCt + 1; | |
- select tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Insert security records for trial from I2B2DEMODATA observation_fact',rowCt,stepCt,'Done') into rtnCd; | |
- | |
-- insert patients to patient_trial table | |
begin | |
diff --git a/ddl/postgres/tm_cz/functions/i2b2_process_mrna_data.sql b/ddl/postgres/tm_cz/functions/i2b2_process_mrna_data.sql | |
index 5615ca0..a6edae4 100755 | |
--- a/ddl/postgres/tm_cz/functions/i2b2_process_mrna_data.sql | |
+++ b/ddl/postgres/tm_cz/functions/i2b2_process_mrna_data.sql | |
@@ -931,7 +931,7 @@ BEGIN | |
) | |
select distinct m.patient_id | |
,m.concept_code | |
- ,m.trial_name | |
+ ,'@' | |
,'T' -- Text data type | |
,'E' --Stands for Equals for Text Types | |
,m.trial_name | |
-- | |
1.8.5.2 (Apple Git-48) | |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment