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Use i.s.o. the back quote character, the backspace character as escape c... #25

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Use i.s.o. the back quote character, the backspace character as escape c... #25

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8 changes: 4 additions & 4 deletions ddl/postgres/tm_cz/functions/i2b2_create_concept_counts.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ BEGIN

begin
delete from i2b2demodata.concept_counts
where concept_path like path || '%' escape '`';
where concept_path like path || '%' escape E'\b';
get diagnostics rowCt := ROW_COUNT;
exception
when others then
Expand Down Expand Up @@ -83,9 +83,9 @@ BEGIN
,i2b2metadata.i2b2 la
,i2b2demodata.observation_fact tpm
,i2b2demodata.patient_dimension p
where fa.c_fullname like path || '%' escape '`'
where fa.c_fullname like path || '%' escape E'\b'
and substr(fa.c_visualattributes,2,1) != 'H'
and la.c_fullname like fa.c_fullname || '%' escape '`'
and la.c_fullname like fa.c_fullname || '%' escape E'\b'
and la.c_visualattributes like 'L%'
and tpm.patient_num = p.patient_num
and la.c_basecode = tpm.concept_cd -- outer join in oracle ???
Expand All @@ -110,7 +110,7 @@ BEGIN
begin
update i2b2metadata.i2b2
set c_visualattributes = substr(c_visualattributes,1,1) || 'H' || substr(c_visualattributes,3,1)
where c_fullname like path || '%' escape '`'
where c_fullname like path || '%' escape E'\b'
and (not exists
(select 1 from concept_counts nc
where c_fullname = nc.concept_path)
Expand Down
10 changes: 5 additions & 5 deletions ddl/postgres/tm_cz/functions/i2b2_delete_all_nodes.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ Begin
begin
DELETE FROM i2b2demodata.OBSERVATION_FACT
WHERE
concept_cd IN (SELECT C_BASECODE FROM i2b2metadata.I2B2 WHERE C_FULLNAME LIKE PATH || '%' escape '`');
concept_cd IN (SELECT C_BASECODE FROM i2b2metadata.I2B2 WHERE C_FULLNAME LIKE PATH || '%' escape E'\b');
get diagnostics rowCt := ROW_COUNT;
exception
when others then
Expand All @@ -73,7 +73,7 @@ Begin
--CONCEPT DIMENSION
begin
DELETE FROM i2b2demodata.CONCEPT_DIMENSION
WHERE CONCEPT_PATH LIKE path || '%' escape '`';
WHERE CONCEPT_PATH LIKE path || '%' escape E'\b';
get diagnostics rowCt := ROW_COUNT;
exception
when others then
Expand All @@ -91,7 +91,7 @@ Begin
--I2B2
begin
DELETE FROM i2b2metadata.i2b2
WHERE C_FULLNAME LIKE PATH || '%' escape '`';
WHERE C_FULLNAME LIKE PATH || '%' escape E'\b';
get diagnostics rowCt := ROW_COUNT;
exception
when others then
Expand All @@ -109,7 +109,7 @@ Begin
--i2b2_secure
begin
DELETE FROM i2b2metadata.i2b2_secure
WHERE C_FULLNAME LIKE PATH || '%' escape '`';
WHERE C_FULLNAME LIKE PATH || '%' escape E'\b';
get diagnostics rowCt := ROW_COUNT;
exception
when others then
Expand All @@ -128,7 +128,7 @@ Begin
--concept_counts
begin
DELETE FROM i2b2demodata.concept_counts
WHERE concept_path LIKE PATH || '%' escape '`';
WHERE concept_path LIKE PATH || '%' escape E'\b';
get diagnostics rowCt := ROW_COUNT;
exception
when others then
Expand Down
6 changes: 3 additions & 3 deletions ddl/postgres/tm_cz/functions/i2b2_extend_clinical_data.sql
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Expand Up @@ -62,7 +62,7 @@ Declare
delNodes CURSOR is
select distinct c_fullname
from i2b2metadata.i2b2
where c_fullname like topNode || '%' escape '`'
where c_fullname like topNode || '%' escape E'\b'
and substr(c_visualattributes,2,1) = 'H';

-- cursor to determine if any leaf nodes exist in i2b2 that are not used in this reload (node changes from text to numeric or numeric to text)
Expand All @@ -71,7 +71,7 @@ Declare
select l.c_fullname
from i2b2metadata.i2b2 l
where l.c_visualattributes like 'L%'
and l.c_fullname like topNode || '%' escape '`'
and l.c_fullname like topNode || '%' escape E'\b'
and l.c_fullname not in
(select t.leaf_node
from tm_wz.wt_trial_nodes t
Expand Down Expand Up @@ -1059,7 +1059,7 @@ select count(*) into pExists from i2b2demodata.observation_fact of where (of.pat
and t.leaf_node = i.c_fullname
and not exists -- don't insert if lower level node exists
(select 1 from tm_wz.wt_trial_nodes x
where x.leaf_node like t.leaf_node || '%_' escape '`')
where x.leaf_node like t.leaf_node || '%_' escape E'\b')
and a.data_value is not null;
get diagnostics rowCt := ROW_COUNT;
exception
Expand Down
2 changes: 1 addition & 1 deletion ddl/postgres/tm_cz/functions/i2b2_fill_in_tree.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ Declare
--Trimming off the last node as it would never need to be added.
select distinct substr(c_fullname, 1,instr(c_fullname,'\',-2,1)) as c_fullname
from i2b2metadata.i2b2
where c_fullname like path || '%' escape '`';
where c_fullname like path || '%' escape E'\b';


BEGIN
Expand Down
16 changes: 9 additions & 7 deletions ddl/postgres/tm_cz/functions/i2b2_load_clinical_data.sql
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Expand Up @@ -55,7 +55,7 @@ Declare
delNodes CURSOR is
select distinct c_fullname
from i2b2metadata.i2b2
where c_fullname like topNode || '%' escape '`'
where c_fullname like topNode || '%' escape E'\b'
and substr(c_visualattributes,2,1) = 'H';

-- cursor to determine if any leaf nodes exist in i2b2 that are not used in this reload (node changes from text to numeric or numeric to text)
Expand All @@ -64,7 +64,7 @@ Declare
select l.c_fullname
from i2b2metadata.i2b2 l
where l.c_visualattributes like 'L%'
and l.c_fullname like topNode || '%' escape '`'
and l.c_fullname like topNode || '%' escape E'\b'
and l.c_fullname not in
(select t.leaf_node
from tm_wz.wt_trial_nodes t
Expand Down Expand Up @@ -512,11 +512,13 @@ BEGIN
select tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Set visit_name to null when only DATALABE in category_cd',rowCt,stepCt,'Done') into rtnCd;

-- change any % to Pct and & and + to ' and ' and _ to space in data_label only
-- change any % to Pct and & and + to ' and ' and \ to space in data_value only
-- -- changing \ to space is to prevent data value to be interpreteted as a (sub)path

begin
update tm_wz.wrk_clinical_data
set data_label=replace(replace(replace(replace(data_label,'%',' Pct'),'&',' and '),'+',' and '),'_',' ')
,data_value=replace(replace(replace(data_value,'%',' Pct'),'&',' and '),'+',' and ')
,data_value=replace(replace(replace(replace(data_value,'%',' Pct'),'&',' and '),'+',' and '),'\',' ')
,category_cd=replace(replace(category_cd,'%',' Pct'),'&',' and ')
,category_path=replace(replace(category_path,'%',' Pct'),'&',' and ');
exception
Expand Down Expand Up @@ -1136,7 +1138,7 @@ BEGIN
and t.leaf_node = i.c_fullname
and not exists -- don't insert if lower level node exists
(select 1 from tm_wz.wt_trial_nodes x
where x.leaf_node like t.leaf_node || '%_' escape '`')
where x.leaf_node like t.leaf_node || '%_' escape E'\b')
and a.data_value is not null;
get diagnostics rowCt := ROW_COUNT;
exception
Expand All @@ -1158,8 +1160,8 @@ BEGIN
with upd as (select p.c_fullname, count(*) as nbr_children
from i2b2metadata.i2b2 p
,i2b2metadata.i2b2 c
where p.c_fullname like topNode || '%' escape '`'
and c.c_fullname like p.c_fullname || '%' escape '`'
where p.c_fullname like topNode || '%' escape E'\b'
and c.c_fullname like p.c_fullname || '%' escape E'\b'
group by p.c_fullname)
update i2b2metadata.i2b2 b
set c_visualattributes=case when upd.nbr_children = 1
Expand All @@ -1173,7 +1175,7 @@ BEGIN
where b.c_fullname = upd.c_fullname
and b.c_fullname in
(select x.c_fullname from i2b2 x
where x.c_fullname like topNode || '%' escape '`');
where x.c_fullname like topNode || '%' escape E'\b');
get diagnostics rowCt := ROW_COUNT;
exception
when others then
Expand Down
2 changes: 1 addition & 1 deletion ddl/postgres/tm_cz/functions/i2b2_process_acgh_data.sql
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Expand Up @@ -74,7 +74,7 @@ Declare
delNodes CURSOR is
select distinct c_fullname
from i2b2metadata.i2b2
where c_fullname like topNode || '%' escape '`'
where c_fullname like topNode || '%' escape E'\b'
and substr(c_visualattributes,2,1) = 'H';

BEGIN
Expand Down
2 changes: 1 addition & 1 deletion ddl/postgres/tm_cz/functions/i2b2_process_mrna_data.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ Declare
delNodes CURSOR is
select distinct c_fullname
from i2b2metadata.i2b2
where c_fullname like topNode || '%' escape '`'
where c_fullname like topNode || '%' escape E'\b'
and substr(c_visualattributes,2,1) = 'H';

BEGIN
Expand Down
2 changes: 1 addition & 1 deletion ddl/postgres/tm_cz/functions/i2b2_process_rnaseq_data.sql
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Expand Up @@ -76,7 +76,7 @@ Declare
delNodes CURSOR is
select distinct c_fullname
from i2b2metadata.i2b2
where c_fullname like topNode || '%' escape '`'
where c_fullname like topNode || '%' escape E'\b'
and substr(c_visualattributes,2,1) = 'H';

BEGIN
Expand Down