fix to target physionet-data

Author: alistairewj

mimic-iv/concepts/copy_concepts_to_versioned_schema.sh

@@ -6,32 +6,32 @@ if [ -z "$$1" ]; then
 fi
 export SOURCE_DATASET=mimiciv_derived
 export TARGET_DATASET=mimiciv_$1_derived
+export PROJECT_ID=physionet-data
 
 # check if the target dataset exists
-if bq ls | grep -q ${TARGET_DATASET}; then
+if bq ls --datasets --project_id ${PROJECT_ID} | grep -q ${TARGET_DATASET}; then
     echo "Using existing dataset ${TARGET_DATASET}."
     # drop the existing tables in the target dataset
     # this includes ones which may not be in the source dataset
-    for TABLE in `bq ls physionet-data:${TARGET_DATASET} | cut -d' ' -f3`;
+    for TABLE in `bq ls ${PROJECT_ID}:${TARGET_DATASET} | cut -d' ' -f3`;
     do
         # skip the first line of dashes
         if [[ "${TABLE:0:2}" == '--' ]]; then
             continue
         fi
-        echo "Dropping table ${TARGET_DATASET}.${TABLE}"
-        bq rm -f -q ${TARGET_DATASET}.${TABLE}
+        bq rm -f -q ${PROJECT_ID}:${TARGET_DATASET}.${TABLE}
     done
 else
-    echo "Creating dataset ${TARGET_DATASET}"
-    bq mk --dataset ${TARGET_DATASET}
+    echo "Creating dataset ${PROJECT_ID}:${TARGET_DATASET}"
+    bq mk --dataset ${PROJECT_ID}:${TARGET_DATASET}
 fi
 
-for TABLE in `bq ls physionet-data:${SOURCE_DATASET} | cut -d' ' -f3`;
+echo "Copying tables from ${SOURCE_DATASET} to ${TARGET_DATASET}."
+for TABLE in `bq ls ${PROJECT_ID}:${SOURCE_DATASET} | cut -d' ' -f3`;
 do
     # skip the first line of dashes
     if [[ "${TABLE:0:2}" == '--' ]]; then
       continue
     fi
-    echo "${SOURCE_DATASET}.${TABLE} -> ${TARGET_DATASET}.${TABLE}"
-    bq cp -f -q ${SOURCE_DATASET}.${TABLE} ${TARGET_DATASET}.${TABLE}
+    bq cp -f -q ${PROJECT_ID}:${SOURCE_DATASET}.${TABLE} ${PROJECT_ID}:${TARGET_DATASET}.${TABLE}
 done