rrun-z-dp-to-sentence-batch.sh

#!/usr/local/bin/bash

## This script creates sentence annotation files (bionlp) based on the sentences extracted during dependency parsing.

source ./rrun.env.sh

SCRIPT=./scripts/pipelines/sentences/run_dp_to_sentence.sh

########### CHOOSE MEDLINE OR PMCOA
#### MEDLINE
TEXT_PIPELINE_KEY=MEDLINE_XML_TO_TEXT
TEXT_PIPELINE_VERSION='0.1.0'
SUBSET_PREFIX=PUBMED_SUB_
MAX_SUBSET_INDEX=37

#### PMCOA
# PIPELINE_KEY=BIOC_TO_TEXT
# TEXT_PIPELINE_VERSION=
# SUBSET_PREFIX=PMC_SUBSET_
# MAX_SUBSET_INDEX=36

OVERWRITE=YES
OUTPUT_SENTENCE_VERSION='0.3.0'
DP_PIPELINE_VERSION='0.2.1'
JAR_VERSION='0.2.1'

echo "Starting DP-to-sentence pipeline..."
COLLECTION="TEST"
$SCRIPT $PROJECT_ID ${COLLECTION} ${STAGE_LOCATION} ${TEMP_LOCATION} $TEXT_PIPELINE_KEY $TEXT_PIPELINE_VERSION $OUTPUT_SENTENCE_VERSION $DP_PIPELINE_VERSION $JAR_VERSION $OVERWRITE &> "./logs/dp-to-sent-${COLLECTION}.log" &