Resolving merge conflicts

Resolved merge conflicts with variable data. Defaulted to previous commit changes.

code/get_nhanes_metadata.R

@@ -266,11 +266,11 @@ get_variables_in_table <- function(table_name, nhanes_data_group) {
             }
           }
         }
-        use_constraints <- ""
+        use_constraints <- "None"
         if(length(table_variables) > 0) {
-          use_constraints <- table_variables[table_variables$Variable.Name == variable_name, 'Use.Constraints']
+          use_constraints <- clean(table_variables[table_variables$Variable.Name == variable_name, 'Use.Constraints'])
           if(length(use_constraints) == 0) {
-            use_constraints <- ""
+            use_constraints <- "None"
           }
         }
         variable_details_vector <- c(toupper(variable_name), toupper(table_name), label, text, instructions, targets, use_constraints)

code/preprocess_metadata.py

@@ -36,7 +36,7 @@ def preprocess(input_file, column_to_process, save_processed_table=False, input_
 
     bl_df = pd.read_csv(BLOCKLIST_TABLE)
     for index, row in bl_df.iterrows():
-        df[PROCESSED_TEXT_COL] = np.where((df["Variable"] == row["names"]) & (df["Table"] == row["tables"]),
+        df[PROCESSED_TEXT_COL] = np.where((df["Variable"] == row["Variable"]) & (df["Table"] == row["Table"]),
                                           "-", df[PROCESSED_TEXT_COL])
     df = _mark_phenotpyes(df)
     df = _replace_synonym_labels(df)

code/resources/allowlist.csv

@@ -0,0 +1,103 @@
+Variable,Table,SASLabel
+DR1ICALC,DR1IFF_C,Calcium (mg)
+DR1ICALC,DR1IFF_D,Calcium (mg)
+DR1ICALC,DR1IFF_E,Calcium (mg)
+DR1ICALC,DR1IFF_F,Calcium (mg)
+DR1ICALC,DR1IFF_G,Calcium (mg)
+DR1ICALC,DR1IFF_H,Calcium (mg)
+DR1ICALC,DR1IFF_I,Calcium (mg)
+DR1ICALC,DR1IFF_J,Calcium (mg)
+DR1TCALC,DR1TOT_C,Calcium (mg)
+DR1TCALC,DR1TOT_D,Calcium (mg)
+DR1TCALC,DR1TOT_E,Calcium (mg)
+DR1TCALC,DR1TOT_F,Calcium (mg)
+DR1TCALC,DR1TOT_G,Calcium (mg)
+DR1TCALC,DR1TOT_H,Calcium (mg)
+DR1TCALC,DR1TOT_I,Calcium (mg)
+DR1TCALC,DR1TOT_J,Calcium (mg)
+DR2ICALC,DR2IFF_C,Calcium (mg)
+DR2ICALC,DR2IFF_D,Calcium (mg)
+DR2ICALC,DR2IFF_E,Calcium (mg)
+DR2ICALC,DR2IFF_F,Calcium (mg)
+DR2ICALC,DR2IFF_G,Calcium (mg)
+DR2ICALC,DR2IFF_H,Calcium (mg)
+DR2ICALC,DR2IFF_I,Calcium (mg)
+DR2ICALC,DR2IFF_J,Calcium (mg)
+DR2TCALC,DR2TOT_C,Calcium (mg)
+DR2TCALC,DR2TOT_D,Calcium (mg)
+DR2TCALC,DR2TOT_E,Calcium (mg)
+DR2TCALC,DR2TOT_F,Calcium (mg)
+DR2TCALC,DR2TOT_G,Calcium (mg)
+DR2TCALC,DR2TOT_H,Calcium (mg)
+DR2TCALC,DR2TOT_I,Calcium (mg)
+DR2TCALC,DR2TOT_J,Calcium (mg)
+DRXICALC,DRXIFF,Calcium (mg)
+DRXICALC,DRXIFF_B,Calcium (mg)
+DRXTCALC,DRXTOT,Calcium (mg)
+DRXTCALC,DRXTOT_B,Calcium (mg)
+DS1ICALC,DS1IDS_E,Calcium (mg)
+DS1ICALC,DS1IDS_F,Calcium (mg)
+DS1ICALC,DS1IDS_G,Calcium (mg)
+DS1ICALC,DS1IDS_H,Calcium (mg)
+DS1ICALC,DS1IDS_I,Calcium (mg)
+DS1ICALC,DS1IDS_J,Calcium (mg)
+DS1TCALC,DS1TOT_E,Calcium (mg)
+DS1TCALC,DS1TOT_F,Calcium (mg)
+DS1TCALC,DS1TOT_G,Calcium (mg)
+DS1TCALC,DS1TOT_H,Calcium (mg)
+DS1TCALC,DS1TOT_I,Calcium (mg)
+DS1TCALC,DS1TOT_J,Calcium (mg)
+DS2ICALC,DS2IDS_E,Calcium (mg)
+DS2ICALC,DS2IDS_F,Calcium (mg)
+DS2ICALC,DS2IDS_G,Calcium (mg)
+DS2ICALC,DS2IDS_H,Calcium (mg)
+DS2ICALC,DS2IDS_I,Calcium (mg)
+DS2ICALC,DS2IDS_J,Calcium (mg)
+DS2TCALC,DS2TOT_E,Calcium (mg)
+DS2TCALC,DS2TOT_F,Calcium (mg)
+DS2TCALC,DS2TOT_G,Calcium (mg)
+DS2TCALC,DS2TOT_H,Calcium (mg)
+DS2TCALC,DS2TOT_I,Calcium (mg)
+DS2TCALC,DS2TOT_J,Calcium (mg)
+DSQICALC,DSQIDS_E,Calcium (mg)
+DSQICALC,DSQIDS_F,Calcium (mg)
+DSQICALC,DSQIDS_G,Calcium (mg)
+DSQICALC,DSQIDS_H,Calcium (mg)
+DSQICALC,DSQIDS_I,Calcium (mg)
+DSQICALC,DSQIDS_J,Calcium (mg)
+DSQTCALC,DSQTOT_E,Calcium (mg)
+DSQTCALC,DSQTOT_F,Calcium (mg)
+DSQTCALC,DSQTOT_G,Calcium (mg)
+DSQTCALC,DSQTOT_H,Calcium (mg)
+DSQTCALC,DSQTOT_I,Calcium (mg)
+DSQTCALC,DSQTOT_J,Calcium (mg)
+DR1ICALC,P_DR1IFF,Calcium (mg)
+DR1TCALC,P_DR1TOT,Calcium (mg)
+DR2ICALC,P_DR2IFF,Calcium (mg)
+DR2TCALC,P_DR2TOT,Calcium (mg)
+DS1ICALC,P_DS1IDS,Calcium (mg)
+DS1TCALC,P_DS1TOT,Calcium (mg)
+DS2ICALC,P_DS2IDS,Calcium (mg)
+DS2TCALC,P_DS2TOT,Calcium (mg)
+DSQICALC,P_DSQIDS,Calcium (mg)
+DSQTCALC,P_DSQTOT,Calcium (mg)
+URXTLC,EPHPP_H,Urinary Triclocarban (ng/mL)
+URXTLC,EPHPP_I,Urinary Triclocarban (ng/mL)
+LBXALC,L06VIT_B,a-carotene(ug/dL)
+LBXALC,L45VIT_C,a-Carotene(ug/dL)
+LB2ALC,VIT_2_B,alpha-carotene(ug/dL)
+LBXCLC,L45VIT_C,cis-Lycopene(ug/dL)
+SSK_FLC,SSOL_A,Kappa FLC
+SSK_FLC,SSOL_B,Kappa FLC
+SSK_FLC,SSOL_C,Kappa FLC
+SSL_FLC,SSOL_A,Lambda FLC
+SSL_FLC,SSOL_B,Lambda FLC
+SSL_FLC,SSOL_C,Lambda FLC
+TBXRUULC,TBX_G,PPDS ulceration
+LBXALC,VITAEC_D,Alpha-carotene (ug/dL)
+LBXALC,VITAEC_J,alpha-carotene (ug/dL)
+VIXPLC,VIX,Prescription left cylinder
+VIXPLC,VIX_B,Prescription left cylinder
+VIXPLC,VIX_C,Prescription left cylinder
+VIXPLC,VIX_D,Prescription left cylinder
+VIXPLC,VIX_E,Prescription left cylinder

code/resources/blocklist_regexps.txt

@@ -9,6 +9,7 @@
 .*[Cc]omment [Cc]ode$
 .*[Cc]omment$
 [Cc]omment [Cc]ode for.*
+.*[Ii]nterview\\??$
 Reasons for Not Done
 Pool identification number
 Respondent sequence number