Upload restore_hitraj_backup.sh with huggingface_hub

restore_hitraj_backup.sh

@@ -0,0 +1,172 @@
+#!/usr/bin/env bash
+# =============================================================================
+#  HiReT / Clinical-Reasoning backup - restore helper
+#
+#  Backup repo : https://huggingface.co/datasets/Xin-Rui/Med_Reason
+#  Archive     : hitraj_backup_20260929.7z.001 ... .061   (AES-256, header-encrypted)
+#  Contents    : 444,063 files / 7,249 folders / 325.6 GB uncompressed
+#
+#  WHAT THIS SCRIPT DOES
+#    1. download the 61 encrypted volumes, the checksum list and RESTORE.md
+#    2. verify every volume against the published SHA256 list
+#    3. optional: concatenate the volumes into one single .7z file
+#    4. extract the archive into /root (the original absolute paths come back)
+#    5. print the command that rebuilds the Python environment
+#
+#  THE PASSPHRASE
+#    * It is NOT in this script and NOT in the repository.
+#    * You are prompted for it in STEP 4 (extraction). If you also run the
+#      optional full integrity test you are prompted again there. Nothing else
+#      needs it.
+#    * Keep it in a password manager and in one offline copy. Without it the
+#      backup can never be opened again.
+#
+#  RESOURCES
+#    download: about 310 GB; extraction: another ~326 GB. Budget ~700 GB free.
+#
+#  USAGE
+#    bash restore_hitraj_backup.sh                     # download + verify + extract
+#    bash restore_hitraj_backup.sh --skip-download     # volumes already on disk
+#    bash restore_hitraj_backup.sh --skip-verify       # trust volumes already verified
+#    bash restore_hitraj_backup.sh --single-file       # also build one single .7z
+#    bash restore_hitraj_backup.sh --only "autodl-tmp/backup_meta/*"
+#                                                      # restore only a subset (quick test)
+#    DEST=/data/restore bash restore_hitraj_backup.sh  # custom download directory
+# =============================================================================
+
+set -Eeuo pipefail
+
+REPO="Xin-Rui/Med_Reason"
+REPO_TYPE="dataset"
+VOL_PREFIX="hitraj_backup_20260929.7z"
+SHA_FILE="${VOL_PREFIX}.volumes.sha256"
+DEST="${DEST:-/root/autodl-tmp/restore}"
+EXTRACT_ROOT="${EXTRACT_ROOT:-/root}"
+SKIP_DOWNLOAD=0
+SKIP_VERIFY=0
+SINGLE_FILE=0
+ONLY_PATTERN=""
+
+while [ $# -gt 0 ]; do
+  case "$1" in
+    --skip-download) SKIP_DOWNLOAD=1 ;;
+    --skip-verify)   SKIP_VERIFY=1 ;;
+    --single-file)   SINGLE_FILE=1 ;;
+    --dest)          DEST="$2"; shift ;;
+    --only)          ONLY_PATTERN="$2"; shift ;;
+    *) echo "unknown option: $1"; exit 2 ;;
+  esac
+  shift
+done
+
+log() { printf "\n=== %s\n" "$*"; }
+
+# ------------------------------------------------------------------ step 0 --
+log "STEP 0  checking tools"
+for t in sha256sum cat; do
+  command -v "$t" >/dev/null || { echo "missing tool: $t"; exit 1; }
+done
+if ! command -v 7z >/dev/null; then
+  echo "7z is missing. Install it first, for example:"
+  echo "   apt-get update && apt-get install -y p7zip-full"
+  exit 1
+fi
+HF_CLI=""
+for c in hf huggingface-cli; do
+  if command -v "$c" >/dev/null; then HF_CLI="$c"; break; fi
+done
+echo "7z      : $(7z | sed -n 2p)"
+echo "hf cli  : ${HF_CLI:-not found (only needed for the download step)}"
+
+mkdir -p "$DEST"
+
+# ------------------------------------------------------------------ step 1 --
+if [ "$SKIP_DOWNLOAD" = 0 ]; then
+  log "STEP 1  downloading volumes from https://huggingface.co/datasets/$REPO"
+  if [ -z "$HF_CLI" ]; then
+    echo "huggingface cli not found. Install it with:  pip install -U huggingface_hub"
+    exit 1
+  fi
+  # HF_HUB_DISABLE_XET=1 keeps the classic transfer path. On machines with a
+  # small memory cgroup the xet backend buffers about 1.3 GB per file and can
+  # be OOM-killed, which is exactly what happened when this backup was made.
+  HF_HUB_DISABLE_XET=1 "$HF_CLI" download "$REPO" \
+      --repo-type "$REPO_TYPE" \
+      --local-dir "$DEST" \
+      --include "${VOL_PREFIX}.0*" \
+      --include "$SHA_FILE" \
+      --include "RESTORE.md"
+else
+  log "STEP 1  skipped (--skip-download)"
+fi
+
+cd "$DEST"
+if ! ls -1 "${VOL_PREFIX}".0* >/dev/null 2>&1; then
+  echo "no volumes found in $DEST"
+  exit 1
+fi
+echo "volumes present: $(ls -1 ${VOL_PREFIX}.0* | wc -l)"
+
+# ------------------------------------------------------------------ step 2 --
+log "STEP 2  verifying every volume (SHA256)"
+if [ "$SKIP_VERIFY" = 1 ]; then
+  echo "skipped (--skip-verify). Note: this step reads all volumes and takes a while."
+else
+  sha256sum -c "$SHA_FILE"
+fi
+
+# ------------------------------------------------------------------ step 3 --
+if [ "$SINGLE_FILE" = 1 ]; then
+  log "STEP 3  concatenating the volumes into one single .7z"
+  cat "${VOL_PREFIX}".0* > "${VOL_PREFIX}"
+  sha256sum "${VOL_PREFIX}" | tee "${VOL_PREFIX}.sha256"
+  ARCHIVE="${VOL_PREFIX}"
+else
+  log "STEP 3  skipped - keeping the volume set (7z reads all volumes automatically)"
+  ARCHIVE="${VOL_PREFIX}.001"
+fi
+
+# ------------------------------------------------------------------ step 4 --
+log "STEP 4  extracting  >>>  THE PASSPHRASE IS REQUIRED HERE  <<<"
+printf "archive passphrase: "
+read -rs ARCHIVE_PASS
+echo
+if [ -z "$ARCHIVE_PASS" ]; then
+  echo "empty passphrase - aborting"
+  exit 1
+fi
+
+cd "$EXTRACT_ROOT"
+if [ -n "$ONLY_PATTERN" ]; then
+  echo "restoring subset only: $ONLY_PATTERN"
+  7z x -p"$ARCHIVE_PASS" -y "$DEST/$ARCHIVE" "$ONLY_PATTERN"
+else
+  7z x -p"$ARCHIVE_PASS" -y "$DEST/$ARCHIVE"
+fi
+unset ARCHIVE_PASS
+
+echo
+echo "extracted into $EXTRACT_ROOT"
+echo "restored layout: $EXTRACT_ROOT/autodl-tmp/Clinical_Reasoning/..."
+echo "                 $EXTRACT_ROOT/autodl-tmp/ClinicalReasoning-ICLR/..."
+echo "                 $EXTRACT_ROOT/autodl-tmp/backup_meta/..."
+echo
+echo "optional, end-to-end integrity test of the archive (asks for the passphrase again):"
+echo "   7z t -p\"<passphrase>\" \"$DEST/${VOL_PREFIX}.001\""
+
+# ------------------------------------------------------------------ step 5 --
+log "STEP 5  rebuilding the Python environment"
+cat <<EOT
+with conda:
+   /root/miniconda3/bin/conda env create -f ${EXTRACT_ROOT}/autodl-tmp/backup_meta/env_llama-fac-wxr.yml
+
+without conda:
+   pip install -r ${EXTRACT_ROOT}/autodl-tmp/backup_meta/pip_freeze.txt
+
+Full notes, including what is deliberately not included and how the embedding
+caches were produced, are in ${EXTRACT_ROOT}/autodl-tmp/backup_meta/RESTORE.md.
+
+Reminder: Datasets/, per-sample predictions and the embedding caches are
+MIMIC-IV derived. Keep repository access restricted and keep the passphrase
+private even though the archive itself is encrypted.
+EOT