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rrun-b-sentence-segmentation-batch.sh
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#!/bin/sh
source ./rrun.env.sh
# #### PUBMED
# TEXT_PIPELINE_KEY=MEDLINE_XML_TO_TEXT
# TEXT_PIPELINE_VERSION="recent"
# SUBSET_PREFIX=PUBMED_SUB_
# MAX_SUBSET_INDEX=36
### PMCOA
TEXT_PIPELINE_KEY=FILTER_UNACTIONABLE_TEXT
TEXT_PIPELINE_VERSION="0.1.0"
SUBSET_PREFIX=PMC_SUBSET_
MAX_SUBSET_INDEX=41
SCRIPT=./scripts/pipelines/sentences/run_sentence_segment.sh
OVERWRITE=YES
# use the below to run a single collection
COLLECTION="2023-11-26"
echo "Starting SENTENCE SEGMENTATION pipeline... ${COLLECTION}"
$SCRIPT $PROJECT_ID ${COLLECTION} ${STAGE_LOCATION} ${TEMP_LOCATION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $OVERWRITE $JAR_VERSION &> "./logs/sentence-${COLLECTION}.log" &
# for INDEX in $(seq 0 4 $MAX_SUBSET_INDEX)
# do
# ind=$(($INDEX + 0))
# if (( ind <= $MAX_SUBSET_INDEX)); then
# echo "Starting SENTENCE SEGMENTATION pipeline... ${ind} $(date)"
# $SCRIPT $PROJECT_ID ${SUBSET_PREFIX}${ind} ${STAGE_LOCATION} ${TEMP_LOCATION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $OVERWRITE $JAR_VERSION &> "./logs/sentence-${SUBSET_PREFIX}${ind}.log" &
# sleep 120
# fi
# ind=$(($INDEX + 1))
# if (( ind <= $MAX_SUBSET_INDEX)); then
# echo "Starting SENTENCE SEGMENTATION pipeline... ${ind} $(date)"
# $SCRIPT $PROJECT_ID ${SUBSET_PREFIX}${ind} ${STAGE_LOCATION} ${TEMP_LOCATION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $OVERWRITE $JAR_VERSION &> "./logs/sentence-${SUBSET_PREFIX}${ind}.log" &
# sleep 120
# fi
# ind=$(($INDEX + 2))
# if (( ind <= $MAX_SUBSET_INDEX)); then
# echo "Starting SENTENCE SEGMENTATION pipeline... ${ind} $(date)"
# $SCRIPT $PROJECT_ID ${SUBSET_PREFIX}${ind} ${STAGE_LOCATION} ${TEMP_LOCATION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $OVERWRITE $JAR_VERSION &> "./logs/sentence-${SUBSET_PREFIX}${ind}.log" &
# sleep 120
# fi
# ind=$(($INDEX + 3))
# if (( ind <= $MAX_SUBSET_INDEX)); then
# echo "Starting SENTENCE SEGMENTATION pipeline... ${ind} $(date)"
# $SCRIPT $PROJECT_ID ${SUBSET_PREFIX}${ind} ${STAGE_LOCATION} ${TEMP_LOCATION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $OVERWRITE $JAR_VERSION &> "./logs/sentence-${SUBSET_PREFIX}${ind}.log" &
# fi
# wait
# done