Skip to content

Commit

Permalink
database consistency
Browse files Browse the repository at this point in the history 
- editing setting_id to be float
- moving tables/columns in resulttables.sql to be consistent with resultsdatamodelspecifications.csv
  • Loading branch information
@jreps
jreps committed Jul 30, 2024
1 parent 66efbde commit a395a76
Show file tree
Hide file tree
Showing 2 changed files with 45 additions and 49 deletions.
12 changes: 6 additions & 6 deletions inst/settings/resultsDataModelSpecification.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ dechallenge_rechallenge,pct_rechallenge_attempt,float,Yes,No,No,No,The percentag
dechallenge_rechallenge,pct_rechallenge_success,float,Yes,No,No,No,The percentage of rechallenge success
dechallenge_rechallenge,pct_rechallenge_fail,float,Yes,No,No,No,The percentage of rechallenge fails
analysis_ref,database_id,varchar(100),Yes,Yes,No,No,The database identifier
analysis_ref,setting_id,int,Yes,Yes,No,No,The run identifier
analysis_ref,setting_id,float,Yes,Yes,No,No,The run identifier
analysis_ref,analysis_id,int,Yes,Yes,No,No,The analysis identifier
analysis_ref,analysis_name,varchar,Yes,No,No,No,The analysis name
analysis_ref,domain_id,varchar,Yes,No,No,No,The domain id
Expand All @@ -54,15 +54,15 @@ analysis_ref,end_day,int,Yes,No,No,No,The end day
analysis_ref,is_binary,varchar(1),Yes,No,No,No,Is this a binary analysis
analysis_ref,missing_means_zero,varchar(1),Yes,No,No,No,Missing means zero
covariate_ref,database_id,varchar(100),Yes,Yes,No,No,The database identifier
covariate_ref,setting_id,int,Yes,Yes,No,No,The run identifier
covariate_ref,setting_id,float,Yes,Yes,No,No,The run identifier
covariate_ref,covariate_id,bigint,Yes,Yes,No,No,The covariate identifier
covariate_ref,covariate_name,varchar,Yes,No,No,No,The covariate name
covariate_ref,analysis_id,int,Yes,No,No,No,The analysis identifier
covariate_ref,concept_id,bigint,Yes,No,No,No,The concept identifier
covariate_ref,value_as_concept_id,int,N,N,N,N,The value as concept_id for features created from observation or measurement values
covariate_ref,collisions,int,N,N,N,N,The number of collisions found for the covariate_id
covariates,database_id,varchar(100),Yes,Yes,No,No,The database identifier
covariates,setting_id,int,Yes,Yes,No,No,The run identifier
covariates,setting_id,float,Yes,Yes,No,No,The run identifier
covariates,cohort_type,varchar(10),Yes,Yes,No,No,The cohort type
covariates,target_cohort_id,int,Yes,Yes,No,No,The target cohort id
covariates,outcome_cohort_id,int,Yes,Yes,No,No,The outcome cohort id
Expand All @@ -71,7 +71,7 @@ covariates,covariate_id,bigint,Yes,Yes,No,No,The covaraite id
covariates,sum_value,int,Yes,No,No,No,The sum value
covariates,average_value,float,Yes,No,No,No,The average value
covariates_continuous,database_id,varchar(100),Yes,Yes,No,No,The database identifier
covariates_continuous,setting_id,int,Yes,Yes,No,No,The run identifier
covariates_continuous,setting_id,float,Yes,Yes,No,No,The run identifier
covariates_continuous,cohort_type,varchar(10),Yes,Yes,No,No,The cohort type
covariates_continuous,target_cohort_id,int,Yes,Yes,No,No,The target cohort id
covariates_continuous,outcome_cohort_id,int,Yes,Yes,No,No,The outcome cohort id
Expand All @@ -86,7 +86,7 @@ covariates_continuous,p_10_value,float,Yes,No,No,No,The 10th percentile
covariates_continuous,p_25_value,float,Yes,No,No,No,The 25th percentile
covariates_continuous,p_75_value,float,Yes,No,No,No,The 75th percentile
covariates_continuous,p_90_value,float,Yes,No,No,No,The 90th percentile
settings,setting_id,int,Yes,Yes,No,No,The run identifier
settings,setting_id,float,Yes,Yes,No,No,The run identifier
settings,database_id,varchar(100),Yes,Yes,No,No,The database identifier
settings,covariate_setting_json,varchar,Yes,No,No,No,The covariate settings JSON
settings,case_covariate_setting_json,varchar,Yes,No,No,No,The during covariate settings JSON
Expand All @@ -99,7 +99,7 @@ settings,end_anchor,varchar(15),No,No,No,No,The end anchor
settings,case_pre_target_duration,int,No,No,No,No,How far to look back before index for case features
settings,case_post_outcome_duration,int,No,No,No,No,How far to look forward after outcome for case features
cohort_details,database_id,varchar(100),Yes,Yes,No,No,The database identifier
cohort_details,setting_id,int,Yes,Yes,No,No,The run identifier
cohort_details,setting_id,float,Yes,Yes,No,No,The run identifier
cohort_details,cohort_type,varchar(10),Yes,Yes,No,No,The cohort type
cohort_details,target_cohort_id,int,Yes,Yes,No,No,The target cohort id
cohort_details,outcome_cohort_id,int,Yes,Yes,No,No,The outcome cohort id
Expand Down
82 changes: 39 additions & 43 deletions inst/sql/sql_server/ResultTables.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -59,37 +59,9 @@ CREATE TABLE @my_schema.@table_prefixdechallenge_rechallenge (
outcome_cohort_definition_id)
);


-- covariateSettings
CREATE TABLE @my_schema.@table_prefixsettings (
setting_id int NOT NULL,
database_id varchar(100) NOT NULL,
covariate_setting_json varchar(MAX),
case_covariate_setting_json varchar(MAX),
min_prior_observation int,
outcome_washout_days int,
risk_window_start int,
start_anchor varchar(15),
risk_window_end int,
end_anchor varchar(15),
case_pre_target_duration int,
case_post_outcome_duration int,
PRIMARY KEY (setting_id, database_id)
);

-- added this table
CREATE TABLE @my_schema.@table_prefixcohort_details (
setting_id int NOT NULL,
database_id varchar(100) NOT NULL,
target_cohort_id int,
outcome_cohort_id int,
cohort_type varchar(10),
PRIMARY KEY (setting_id, database_id,target_cohort_id,outcome_cohort_id,cohort_type)
);

CREATE TABLE @my_schema.@table_prefixanalysis_ref (
setting_id int NOT NULL,
database_id varchar(100) NOT NULL,
setting_id float NOT NULL,
analysis_id int NOT NULL,
analysis_name varchar(max) NOT NULL,
domain_id varchar(30),
Expand All @@ -101,8 +73,8 @@ CREATE TABLE @my_schema.@table_prefixanalysis_ref (
);

CREATE TABLE @my_schema.@table_prefixcovariate_ref (
setting_id int NOT NULL,
database_id varchar(100) NOT NULL,
setting_id float NOT NULL,
covariate_id bigint NOT NULL,
covariate_name varchar(max) NOT NULL,
analysis_id int NOT NULL,
Expand All @@ -113,24 +85,24 @@ CREATE TABLE @my_schema.@table_prefixcovariate_ref (
);

CREATE TABLE @my_schema.@table_prefixcovariates (
setting_id int NOT NULL,
database_id varchar(100) NOT NULL,
setting_id float NOT NULL,
cohort_type varchar(10),
target_cohort_id int,
outcome_cohort_id int,
cohort_type varchar(10),
min_characterization_mean float,
covariate_id bigint NOT NULL,
sum_value int NOT NULL,
average_value float NOT NULL,
min_characterization_mean float,
PRIMARY KEY (database_id, setting_id, target_cohort_id, outcome_cohort_id, cohort_type , covariate_id)
);

CREATE TABLE @my_schema.@table_prefixcovariates_continuous (
setting_id int NOT NULL,
database_id varchar(100) NOT NULL,
setting_id float NOT NULL,
cohort_type varchar(10),
target_cohort_id int,
outcome_cohort_id int,
cohort_type varchar(10),
covariate_id bigint NOT NULL,
count_value int NOT NULL,
min_value float,
Expand All @@ -145,23 +117,47 @@ CREATE TABLE @my_schema.@table_prefixcovariates_continuous (
PRIMARY KEY (database_id, setting_id, target_cohort_id, outcome_cohort_id, cohort_type , covariate_id)
);

CREATE TABLE @my_schema.@table_prefixcohort_counts(
-- covariateSettings
CREATE TABLE @my_schema.@table_prefixsettings (
setting_id float NOT NULL,
database_id varchar(100) NOT NULL,
target_cohort_id int,
outcome_cohort_id int,
cohort_type varchar(10),
covariate_setting_json varchar(MAX),
case_covariate_setting_json varchar(MAX),
min_prior_observation int,
outcome_washout_days int,
risk_window_start int,
risk_window_end int,
start_anchor varchar(15),
end_anchor varchar(15),
case_pre_target_duration int,
case_post_outcome_duration int,
PRIMARY KEY (setting_id, database_id)
);

-- added this table
CREATE TABLE @my_schema.@table_prefixcohort_details (
database_id varchar(100) NOT NULL,
setting_id float NOT NULL,
cohort_type varchar(10),
target_cohort_id int,
outcome_cohort_id int,
PRIMARY KEY (setting_id, database_id,target_cohort_id,outcome_cohort_id,cohort_type)
);

CREATE TABLE @my_schema.@table_prefixcohort_counts(
database_id varchar(100) NOT NULL,
cohort_type varchar(10),
target_cohort_id int,
outcome_cohort_id int,
risk_window_start int,
risk_window_end int,
start_anchor varchar(15),
end_anchor varchar(15),
min_prior_observation int,
outcome_washout_days int,
row_count int NOT NULL,
person_count int NOT NULL,
min_exposure_time int,
mean_exposure_time int,
max_exposure_time int--,
--PRIMARY KEY (database_id, target_cohort_id,outcome_cohort_id,
--cohort_type, min_prior_observation, outcome_washout_days,
--risk_window_start, start_anchor, risk_window_end, end_anchor)
max_exposure_time int
);

0 comments on commit a395a76

Please sign in to comment.