chore: drop sqlfluff/sqlite hunks moved to #2148/#2149

Author: Chessing234

.github/workflows/lint_sqlfluff.yml

@@ -6,9 +6,6 @@ on:
 jobs:
   lint-mimic-iv:
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      checks: write
     steps:
       - name: checkout
         uses: actions/checkout@v7
@@ -38,10 +35,8 @@ jobs:
         shell: bash
         run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json
       - name: Annotate
-        if: steps.get_files_to_lint.outputs.lintees != ''
         uses: yuzutech/annotations-action@v0.6.0
         with:
           repo-token: "${{ secrets.GITHUB_TOKEN }}"
           title: "SQLFluff Lint"
-          input: "./annotations.json"
-          ignore-unauthorized-error: true
+          input: "./annotations.json"

mimic-iii/buildmimic/sqlite/import.py

@@ -26,16 +26,9 @@ def _table_name_from_csv(filename: str) -> str:
     print(msg)
     sys.exit()
 
-# Prefer .csv.gz when both exist for the same table; also load plain .csv
-# (import.sh already accepts both).
-files_by_table = {}
-for f in glob("*.csv"):
-    files_by_table[_table_name_from_csv(f)] = f
 for f in glob("*.csv.gz"):
-    files_by_table[_table_name_from_csv(f)] = f
-
-for table, f in sorted(files_by_table.items()):
     print("Starting processing {}".format(f))
+    table = _table_name_from_csv(f)
     if os.path.getsize(f) < THRESHOLD_SIZE:
         df = pd.read_csv(f, index_col="ROW_ID")
         df.to_sql(table, CONNECTION_STRING)

mimic-iii/buildmimic/sqlite/import.sh

@@ -28,19 +28,19 @@ for FILE in *; do
     TABLE_NAME=$(echo "${FILE%%.*}" | tr "[:upper:]" "[:lower:]")
     case "$FILE" in
         *csv)
-            IMPORT_CMD=".import \"$FILE\" $TABLE_NAME"
+            IMPORT_CMD=".import $FILE $TABLE_NAME"
         ;;
         # need to decompress csv before load
         *csv.gz)
-            IMPORT_CMD=".import \"|gzip -dc \\\"$FILE\\\"\" $TABLE_NAME"
+            IMPORT_CMD=".import \"|gzip -dc $FILE\" $TABLE_NAME"
         ;;
         # not a data file so skip
         *)
             continue
         ;;
     esac
     echo "Loading $FILE."
-    sqlite3 "$OUTFILE" <<EOF
+    sqlite3 $OUTFILE <<EOF
 .headers on
 .mode csv
 $IMPORT_CMD

mimic-iv/buildmimic/sqlite/import.py

@@ -110,7 +110,7 @@ def main():
     if args.limit > 0:
         for f in data_files:
             if 'patients' in f.name:
-                pt = pd.read_csv(f, low_memory=False)
+                pt = pd.read_csv(f)
                 break
         if pt is None:
             raise FileNotFoundError('Unable to find a patients file in current folder.')
@@ -158,7 +158,7 @@ def main():
             tablename = tablenames[i]
             print("Starting processing {}".format(tablename), end='.. ')
             if os.path.getsize(f) < THRESHOLD_SIZE:
-                df = pd.read_csv(f, dtype=mimic_dtypes, low_memory=False)
+                df = pd.read_csv(f, dtype=mimic_dtypes)
                 df = process_dataframe(df, subjects=subjects)
                 df.to_sql(tablename, connection, index=False)
                 row_counts[tablename] += len(df)

mimic-iv/buildmimic/sqlite/import.sh

@@ -29,19 +29,19 @@ for FILE in */**.csv*; do
       TABLE_NAME=$(echo "${BASENAME%%.*}" | tr "[:upper:]" "[:lower:]")
       case "$FILE" in
           *csv)
-              IMPORT_CMD=".import \"$FILE\" $TABLE_NAME"
+              IMPORT_CMD=".import $FILE $TABLE_NAME"
           ;;
           # need to decompress csv before load
           *csv.gz)
-              IMPORT_CMD=".import \"|gzip -dc \\\"$FILE\\\"\" $TABLE_NAME"
+              IMPORT_CMD=".import \"|gzip -dc $FILE\" $TABLE_NAME"
           ;;
           # not a data file so skip
           *)
               continue
           ;;
       esac
       echo "Loading $FILE."
-      sqlite3 "$OUTFILE" <<EOF
+      sqlite3 $OUTFILE <<EOF
 .headers on
 .mode csv
 $IMPORT_CMD