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Partial solve to issue #13

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Paul W. Egeler, MS, GStat 2019-07-26 12:02:20 -04:00 committed by pegeler
parent 7eb7d5b459
commit a2dcdc73a9
1 changed files with 128 additions and 91 deletions
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103
SAS/REDCap_split.sas
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@ -2,7 +2,7 @@
*
* FILE: REDCap_split.sas
*
* VERSION: 0.0.0
* VERSION: 0.1.0
*
* PURPOSE: Take a REDCap dataset with multiple events and make into several
* tables with primary and foreign keys
@ -50,10 +50,27 @@
%MACRO REDCAP_SPLIT(
DATA_SET = REDCAP /* The name of the SAS dataset created by REDCap */,
DATA_DICTIONARY = REDCAP_DATA_DICTIONARY /* The name of the SAS dataset of the data dictionary */
DATA_DICTIONARY = REDCAP_DATA_DICTIONARY /* The name of the SAS dataset of the data dictionary */,
NUMERIC_SUBTABLES = N /* Y/N: Should the subtables be numbered (Y) or should the be based on the name of the repeating instrument (N)? */
);
/* Find the key that links the base table to child tables */
/* Also check that REDCAP_REPEAT_INSTRUMENT is present in the data */
%LET DSID = %SYSFUNC(OPEN(&DATA_SET));
%LET KEY = %SYSFUNC(VARNAME(&DSID, 1));
%LET CHECK = %SYSFUNC(VARNUM(&DSID, REDCAP_REPEAT_INSTRUMENT));
%LET RC = %SYSFUNC(CLOSE(&DSID));
%IF &CHECK EQ 0 %THEN %DO;
%PUT ERROR: The dataset &DATA_SET does not contain repeating instruments.;
%PUT ERROR: Stopping MACRO.;
%GOTO FINISH;
%END;
/* Remove formatting from repeat instrument field */
%PUT NOTE: Removing formatting from REDCAP_REPEAT_INSTRUMENT in &DATA_SET..;
DATA &DATA_SET.;
SET &DATA_SET.;
FORMAT REDCAP_REPEAT_INSTRUMENT;
@ -73,14 +90,20 @@
%LET N_SUBTABLES = &SQLOBS;
%PUT INSTRUMENTS: %LEFT(&INSTRUMENTS);
%PUT INSTRUMENT LIST: %LEFT(&INSTRUMENT_LIST);
%PUT N SUBTABLES: %LEFT(&N_SUBTABLES);
QUIT;
%IF &N_SUBTABLES GT 0 %THEN %DO;
%IF &N_SUBTABLES EQ 0 %THEN %DO;
%PUT WARNING: There were no records containing repeating instruments in the dataset %LEFT(&DATA_SET).;
%PUT WARNING: No action was taken.;
%GOTO FINISH;
%END;
%PUT N SUBTABLES: %LEFT(&N_SUBTABLES);
%PUT INSTRUMENTS: %LEFT(&INSTRUMENTS);
%PUT INSTRUMENT LIST: %LEFT(%BQUOTE(&INSTRUMENT_LIST));
/* Get information on the variables in the dataset */
PROC CONTENTS
@ -89,15 +112,6 @@
NOPRINT;
RUN;
/* Find the key that links the base table to child tables */
DATA _NULL_;
SET REDCAP_VARNAMES;
IF VARNUM EQ 1 THEN DO;
CALL SYMPUT("KEY", NAME);
STOP;
END;
RUN;
/* Make a list of fields and their associated forms based on data dictionary */
DATA REDCAP_FIELDS(KEEP=VAR_NAME FORM_NAME);
SET &DATA_DICTIONARY.;
@ -119,7 +133,7 @@
CREATE TABLE REDCAP_INSTRUMENT_STATUS_FIELDS AS
SELECT DISTINCT TRIM(FORM_NAME)!!"_complete" AS VAR_NAME LENGTH=200, FORM_NAME
FROM REDCAP_DATA_DICTIONARY;
FROM &DATA_DICTIONARY.;
QUIT;
@ -128,6 +142,17 @@
DATA=REDCAP_INSTRUMENT_STATUS_FIELDS;
RUN;
DATA REDCAP_FIELDS;
SET REDCAP_FIELDS;
IF LENGTH(VAR_NAME) GT 32 THEN DO;
PUT "WARNING: The variable " VAR_NAME "is too long (MAX 32 CHARACTERS).";
PUT "WARNING: " VAR_NAME "will not be included in the output dataset.";
DELETE;
END;
RUN;
/* Sort out the field names */
PROC SQL NOPRINT;
@ -143,21 +168,19 @@
%LET INSTRUMENT_I = %SCAN(&INSTRUMENTS,&I,%STR( ));
SELECT VAR_NAME
INTO :VARS_&INSTRUMENT_I. SEPARATED BY ' '
INTO :VARS_&I. SEPARATED BY ' '
FROM REDCAP_FIELDS AS A
WHERE FORM_NAME EQ "&INSTRUMENT_I.";
%put &INSTRUMENT_I. vars: &&VARS_&INSTRUMENT_I;
%PUT &INSTRUMENT_I. vars: &&VARS_&I;
%END;
QUIT;
/* Make new data sets based on field names above */
DATA &DATA_SET._BASE (KEEP = &VARS_BASE);
SET &DATA_SET;
IF MISSING(REDCAP_REPEAT_INSTRUMENT);
RUN;
@ -165,13 +188,35 @@
%LET INSTRUMENT_I = %SCAN(&INSTRUMENTS,&I,%STR( ));
DATA &DATA_SET._&INSTRUMENT_I. (KEEP = &KEY redcap_repeat_instance &&VARS_&INSTRUMENT_I);
/* Create either numeric table name or name based on repeating instrument name (see issue #12) */
%IF &NUMERIC_SUBTABLES EQ N %THEN %DO;
%LET SUBTABLE_NAME = &DATA_SET._&INSTRUMENT_I.;
%IF %LENGTH(&SUBTABLE_NAME) GT 32 %THEN %DO;
%PUT ERROR: The table name &SUBTABLE_NAME is %LENGTH(&SUBTABLE_NAME) characters long (MAX 32 CHARACTERS).;
%PUT ERROR: &SUBTABLE_NAME will be skipped. Consider setting NUMERIC_SUBTABLES = Y.;
%GOTO SKIP;
%END;
%END;
%ELSE %DO;
%LET SUBTABLE_NAME = &DATA_SET._&I.;
%END;
DATA &SUBTABLE_NAME (KEEP = &KEY redcap_repeat_instance &&VARS_&I);
SET &DATA_SET;
IF REDCAP_REPEAT_INSTRUMENT EQ "&INSTRUMENT_I.";
RUN;
%PUT NOTE: Records from instrument &INSTRUMENT_I have been placed in &SUBTABLE_NAME;
%SKIP:
%END;
/* Clean up temporary datasets */
@ -179,14 +224,6 @@
DELETE REDCAP_FIELDS REDCAP_VARNAMES REDCAP_INSTRUMENT_STATUS_FIELDS;
RUN;
%END;
%ELSE %DO;
%PUT THERE WERE NO REPEAT INSTRUMENTS IN THE DATASET %LEFT(&DATA_SET);
%PUT NO ACTION WAS TAKEN;
%END;
%FINISH:
%MEND REDCAP_SPLIT;