34047007@qq.com
a6cd99a4ca
OncoLit: a multi-tenant oncology literature search, feed, and collaboration platform. Built with FastAPI + Vue 3 + PostgreSQL. Includes PubMed pipeline, drug approvals, AI summaries, and systematic review tools.
76 lines
2.3 KiB
Bash
76 lines
2.3 KiB
Bash
#!/bin/bash
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# PubMed 基线 —— aria2 下载 + 流水线（下载/导入并行）
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set -e
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STATE_FILE="/tmp/pubmed_import_state.txt"
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BATCH_DIR="/tmp/pubmed_batch"
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SCRIPT="/app/scripts/pubmed_baseline.py"
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BASE_URL="https://ftp.ncbi.nlm.nih.gov/pubmed/baseline"
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TOTAL=1334
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mkdir -p "$BATCH_DIR"
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CURRENT=$(cat "$STATE_FILE" 2>/dev/null || echo 0)
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echo "[$(date)] Resuming from file $((CURRENT+1)), total $TOTAL"
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aria2c --version | head -1
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for ((i = CURRENT+1; i <= TOTAL; i++)); do
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fnum=$(printf "%04d" $i)
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filename="pubmed26n${fnum}.xml.gz"
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filepath="$BATCH_DIR/$filename"
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# Download if not cached
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if [ ! -f "$filepath" ]; then
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echo "[$(date)] [$i] Downloading $filename ..."
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aria2c -x 5 -s 5 -k 1M --connect-timeout=30 --timeout=60 \
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--console-log-level=warn --summary-interval=0 \
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-d "$BATCH_DIR" -o "$filename" \
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"${BASE_URL}/${filename}" 2>&1 | tail -3
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if [ ! -s "$filepath" ]; then
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echo "[$(date)] [$i] Retrying..."
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sleep 3
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aria2c -x 5 -s 5 -k 1M --connect-timeout=30 --timeout=60 \
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--console-log-level=warn --summary-interval=0 \
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-d "$BATCH_DIR" -o "$filename" \
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"${BASE_URL}/${filename}" 2>&1 | tail -3
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fi
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if [ ! -s "$filepath" ]; then
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echo "[$(date)] [$i] Download failed, skipping"
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rm -f "$filepath"
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continue
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fi
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fi
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SIZE=$(stat -c%s "$filepath" 2>/dev/null)
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if [ "$SIZE" -lt 1000000 ]; then
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echo "[$(date)] [$i] File too small ($SIZE bytes), skipping"
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rm -f "$filepath"
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continue
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fi
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echo "[$(date)] [$i] Importing $filename ($SIZE bytes)..."
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START=$(date +%s)
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# Copy to container and import
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docker cp "$filepath" scilit-backend-1:/tmp/pubmed_batch/ 2>/dev/null
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docker exec -w /app scilit-backend-1 python "$SCRIPT" --dir /tmp/pubmed_batch 2>&1 | tail -1
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END=$(date +%s)
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DURATION=$((END - START))
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# Update state and log
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echo "$i" > "$STATE_FILE"
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echo "[$i] ${DURATION}s" >> /tmp/pubmed_import.log
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echo "[$(date)] [$i] Done (${DURATION}s)"
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# Clean up
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rm -f "$filepath"
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docker exec scilit-backend-1 rm -f "/tmp/pubmed_batch/$filename" 2>/dev/null
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done
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echo "[$(date)] Done! All files processed."
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