fix offset column in cdm ddl

darwin-eu · Jan 29, 2024 · dc00900 · dc00900
1 parent 61fb719
commit dc00900
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/extras/package_maintenance.R b/extras/package_maintenance.R
@@ -54,11 +54,11 @@ spec_cdm_table_54 <-  cdm_tables_src_54 %>%
          group_default = cdmTableName %in% default_tables)
 
 
-
 spec_cdm_field_54 <-  cdm_fields_src_54 %>%
   select(1:4) %>%
   mutate(across(everything(), tolower)) %>%
-  mutate(isRequired = case_when(isRequired == "yes" ~ TRUE, isRequired == "no" ~ FALSE))
+  mutate(isRequired = case_when(isRequired == "yes" ~ TRUE, isRequired == "no" ~ FALSE)) %>%
+  mutate(cdmFieldName = ifelse(cdmFieldName == '"offset"', "offset", cdmFieldName))
 
 
 spec_cdm_table_53 <-  cdm_tables_src_53 %>%
@@ -74,12 +74,12 @@ spec_cdm_table_53 <-  cdm_tables_src_53 %>%
 spec_cdm_field_53 <-  cdm_fields_src_53 %>%
   select(1:4) %>%
   mutate(across(everything(), tolower)) %>%
-  mutate(isRequired = case_when(isRequired == "yes" ~ TRUE, isRequired == "no" ~ FALSE))
+  mutate(isRequired = case_when(isRequired == "yes" ~ TRUE, isRequired == "no" ~ FALSE)) %>%
+  mutate(cdmFieldName = ifelse(cdmFieldName == '"offset"', "offset", cdmFieldName))
 
 spec_cdm_table <- list("5.4" = spec_cdm_table_54, "5.3" = spec_cdm_table_53)
 spec_cdm_field <- list("5.4" = spec_cdm_field_54, "5.3" = spec_cdm_field_53)
 
-
 readr::write_csv(spec_cdm_field_54, file.path("inst", "csv", "OMOP_CDMv5.4_Field_Level.csv"))
 readr::write_csv(spec_cdm_table_54, file.path("inst", "csv", "OMOP_CDMv5.4_Table_Level.csv"))
 

diff --git a/inst/csv/OMOP_CDMv5.3_Field_Level.csv b/inst/csv/OMOP_CDMv5.3_Field_Level.csv
@@ -189,7 +189,7 @@ note_nlp,note_nlp_id,TRUE,integer
 note_nlp,note_id,TRUE,integer
 note_nlp,section_concept_id,FALSE,integer
 note_nlp,snippet,FALSE,varchar(250)
-note_nlp,"""offset""",FALSE,varchar(50)
+note_nlp,offset,FALSE,varchar(50)
 note_nlp,lexical_variant,TRUE,varchar(250)
 note_nlp,note_nlp_concept_id,FALSE,integer
 note_nlp,note_nlp_source_concept_id,FALSE,integer

diff --git a/inst/csv/OMOP_CDMv5.4_Field_Level.csv b/inst/csv/OMOP_CDMv5.4_Field_Level.csv
@@ -203,7 +203,7 @@ note_nlp,note_nlp_id,TRUE,integer
 note_nlp,note_id,TRUE,integer
 note_nlp,section_concept_id,FALSE,integer
 note_nlp,snippet,FALSE,varchar(250)
-note_nlp,"""offset""",FALSE,varchar(50)
+note_nlp,offset,FALSE,varchar(50)
 note_nlp,lexical_variant,TRUE,varchar(250)
 note_nlp,note_nlp_concept_id,FALSE,integer
 note_nlp,note_nlp_source_concept_id,FALSE,integer