fix errors due to order of make

Author: alistairewj

mimic-iv/concepts/make_concepts.sh

@@ -1,17 +1,25 @@
 #!/bin/bash
 # This script generates the concepts in the BigQuery table mimic_derived.
-export TARGET_DATASET=mimic_derived
+export TARGET_DATASET=mimiciv_derived
 
 # specify bigquery query command options
 # note: max_rows=1 *displays* only one row, but all rows are inserted into the destination table
 BQ_OPTIONS='--quiet --headless --max_rows=0 --use_legacy_sql=False --replace'
 
+# generate a few tables first as the desired order isn't alphabetical
+for table_path in demographics/icustay_times;
+do
+  table=`echo $table_path | rev | cut -d/ -f1 | rev`
+  echo "Generating ${TARGET_DATASET}.${table}"
+  bq query ${BQ_OPTIONS} --destination_table=${TARGET_DATASET}.${table} < ${table_path}.sql
+done
+
 # generate tables in subfolders
 # order is important for a few tables here:
 # * firstday should go last
 # * sepsis depends on score (sofa.sql in particular)
 # * organfailure depends on measurement
-for d in comorbidity demographics measurement medication organfailure treatment score sepsis firstday;
+for d in demographics comorbidity measurement medication organfailure treatment firstday score sepsis;
 do
     for fn in `ls $d`;
     do
@@ -20,9 +28,9 @@ do
             # table name is file name minus extension
             tbl=`echo $fn | rev | cut -d. -f2- | rev`
 
-            # skip certain tables where order matters - generated at the end of the script
+            # skip certain tables where order matters
             skip=0
-            for skip_table in first_day_sofa kdigo_stages vasoactive_agent norepinephrine_eqivalent_dose
+            for skip_table in meld icustay_times first_day_sofa kdigo_stages vasoactive_agent norepinephrine_eqivalent_dose
             do
               if [[ "${tbl}" == "${skip_table}" ]]; then
                 skip=1
@@ -42,10 +50,10 @@ done
 
 echo "Now generating tables which were skipped due to depending on other tables."
 # generate tables after the above, and in a specific order to ensure dependencies are met
-for table_path in firstday/first_day_sofa organfailure/kdigo_stages medication/vasoactive_agent medication/norepinephrine_equivalent_dose;
+for table_path in firstday/first_day_sofa organfailure/kdigo_stages organfailure/meld medication/vasoactive_agent medication/norepinephrine_equivalent_dose;
 do
   table=`echo $table_path | rev | cut -d/ -f1 | rev`
 
   echo "Generating ${TARGET_DATASET}.${table}"
   bq query ${BQ_OPTIONS} --destination_table=${TARGET_DATASET}.${table} < ${table_path}.sql
-done
+done