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rrun-j2-chem_gene-sentence-extraction-batch.sh
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#!/bin/sh
source ./rrun.env.sh
SCRIPT=./scripts/pipelines/sentences/run_sentence_extraction.sh
# TEXT_PIPELINE_KEY=MEDLINE_XML_TO_TEXT
# TEXT_PIPELINE_VERSION="recent"
# SECTION_PIPELINE_KEY=MEDLINE_XML_TO_TEXT
# SECTION_PIPELINE_VERSION="recent"
# MAX_SUBSET_INDEX=38
# SUBSET_PREFIX=PUBMED_SUB_
TEXT_PIPELINE_KEY=FILTER_UNACTIONABLE_TEXT
TEXT_PIPELINE_VERSION="recent"
SECTION_PIPELINE_KEY=BIOC_TO_TEXT
SECTION_PIPELINE_VERSION="recent"
SUBSET_PREFIX=PMC_SUBSET_
MAX_SUBSET_INDEX=41
SENTENCE_PIPELINE_KEY=SENTENCE_SEGMENTATION
SENTENCE_PIPELINE_VERSION="recent"
CONCEPT_POST_PROCESS_VERSION="0.3.0"
# For chemical/drug to gene sentences
ASSOCIATION="bl_chemical_to_gene"
PREFIX_X="CHEBI|DRUGBANK"
PLACEHOLDER_X="@CHEMICAL$"
PREFIX_Y="PR"
PLACEHOLDER_Y="@GENE$"
OUTPUT_VERSION="0.2.0" # v0.2.0 is a run after large concept recognition error analysis and updates
# # # ---------------------------------------------
# # # process a single collection
# COLLECTION="PMC_SUBSET_0"
# OUTPUT_COLLECTION=$COLLECTION
# $SCRIPT $PROJECT_ID ${COLLECTION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $SECTION_PIPELINE_KEY $SECTION_PIPELINE_VERSION $SENTENCE_PIPELINE_KEY $SENTENCE_PIPELINE_VERSION $CONCEPT_POST_PROCESS_VERSION $ASSOCIATION $PREFIX_X $PLACEHOLDER_X $PREFIX_Y $PLACEHOLDER_Y ${STAGE_LOCATION} ${TEMP_LOCATION} ${WORK_BUCKET} $JAR_VERSION ${OUTPUT_VERSION} ${OUTPUT_COLLECTION} &> "./logs/sentence-extraction-${COLLECTION}-${ASSOCIATION}.log" &
# # ---------------------------------------------
# # use the below for bulk processing
# #
for INDEX in $(seq 1 4 $MAX_SUBSET_INDEX)
do
ind=$(($INDEX + 0))
if (( ind <= $MAX_SUBSET_INDEX)); then
echo "Starting sentence extraction pipeline... ${ind} $(date)"
COLLECTION="${SUBSET_PREFIX}${ind}"
OUTPUT_COLLECTION=$COLLECTION
$SCRIPT $PROJECT_ID ${COLLECTION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $SECTION_PIPELINE_KEY $SECTION_PIPELINE_VERSION $SENTENCE_PIPELINE_KEY $SENTENCE_PIPELINE_VERSION $CONCEPT_POST_PROCESS_VERSION $ASSOCIATION $PREFIX_X $PLACEHOLDER_X $PREFIX_Y $PLACEHOLDER_Y ${STAGE_LOCATION} ${TEMP_LOCATION} ${WORK_BUCKET} $JAR_VERSION ${OUTPUT_VERSION} ${OUTPUT_COLLECTION} &> "./logs/sentence-extraction-${COLLECTION}-${ASSOCIATION}-${OUTPUT_VERSION}.log" &
sleep 120
fi
ind=$(($INDEX + 1))
if (( ind <= $MAX_SUBSET_INDEX)); then
echo "Starting sentence extraction pipeline... ${ind} $(date)"
COLLECTION="${SUBSET_PREFIX}${ind}"
OUTPUT_COLLECTION=$COLLECTION
$SCRIPT $PROJECT_ID ${COLLECTION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $SECTION_PIPELINE_KEY $SECTION_PIPELINE_VERSION $SENTENCE_PIPELINE_KEY $SENTENCE_PIPELINE_VERSION $CONCEPT_POST_PROCESS_VERSION $ASSOCIATION $PREFIX_X $PLACEHOLDER_X $PREFIX_Y $PLACEHOLDER_Y ${STAGE_LOCATION} ${TEMP_LOCATION} ${WORK_BUCKET} $JAR_VERSION ${OUTPUT_VERSION} ${OUTPUT_COLLECTION} &> "./logs/sentence-extraction-${COLLECTION}-${ASSOCIATION}-${OUTPUT_VERSION}.log" &
sleep 120
fi
ind=$(($INDEX + 2))
if (( ind <= $MAX_SUBSET_INDEX)); then
echo "Starting sentence extraction pipeline... ${ind} $(date)"
COLLECTION="${SUBSET_PREFIX}${ind}"
OUTPUT_COLLECTION=$COLLECTION
$SCRIPT $PROJECT_ID ${COLLECTION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $SECTION_PIPELINE_KEY $SECTION_PIPELINE_VERSION $SENTENCE_PIPELINE_KEY $SENTENCE_PIPELINE_VERSION $CONCEPT_POST_PROCESS_VERSION $ASSOCIATION $PREFIX_X $PLACEHOLDER_X $PREFIX_Y $PLACEHOLDER_Y ${STAGE_LOCATION} ${TEMP_LOCATION} ${WORK_BUCKET} $JAR_VERSION ${OUTPUT_VERSION} ${OUTPUT_COLLECTION} &> "./logs/sentence-extraction-${COLLECTION}-${ASSOCIATION}-${OUTPUT_VERSION}.log" &
sleep 120
fi
ind=$(($INDEX + 3))
if (( ind <= $MAX_SUBSET_INDEX)); then
echo "Starting sentence extraction pipeline... ${ind} $(date)"
COLLECTION="${SUBSET_PREFIX}${ind}"
OUTPUT_COLLECTION=$COLLECTION
$SCRIPT $PROJECT_ID ${COLLECTION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $SECTION_PIPELINE_KEY $SECTION_PIPELINE_VERSION $SENTENCE_PIPELINE_KEY $SENTENCE_PIPELINE_VERSION $CONCEPT_POST_PROCESS_VERSION $ASSOCIATION $PREFIX_X $PLACEHOLDER_X $PREFIX_Y $PLACEHOLDER_Y ${STAGE_LOCATION} ${TEMP_LOCATION} ${WORK_BUCKET} $JAR_VERSION ${OUTPUT_VERSION} ${OUTPUT_COLLECTION} &> "./logs/sentence-extraction-${COLLECTION}-${ASSOCIATION}-${OUTPUT_VERSION}.log" &
fi
wait
done