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parse_apps.sh
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parse_apps.sh
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#!/bin/bash
#
#SBATCH --job-name=app_prs
#SBATCH --output=parse_apps.out
#
#SBATCH --partition=hlwill
#SBATCH --time=7-00:00:00
#SBATCH --mem=0
#SBATCH --cpus-per-task=23
#
#SBATCH --mail-type=ALL
#SBATCH [email protected]
module load python/3.9.0
module load libxml2
module load libxslt
# Ensure packages are up-to-date
pip3 install --upgrade -r requirements.txt
OAK="/oak/stanford/groups/hlwill"
TEMP="$SCRATCH/app_parse_temp"
ZIP_DIR="$OAK/raw/USPTO_applications/data"
DTDS="$OAK/raw/USPTO_applications/python/patent_processor/config/applications/DTDs"
OUTPUT="output/applications"
rm -r $TEMP
rm -r $OUTPUT
mkdir $TEMP
mkdir $OUTPUT
# 2001-2005
for i in $ZIP_DIR/pa0[1-4]*.zip; do unzip "$i" -d $TEMP & done
wait
python3 patent_xml_to_csv.py --verbose \
--xml-input $TEMP/*.{xml,XML} \
--recurse \
--config config/uspto-applications.2001-2004.yaml \
--output-path $OUTPUT \
--output-type sqlite \
--dtd-path $DTDS \
--continue-on-error
rm -r $TEMP
mkdir $TEMP
# 2005-2006
for i in $ZIP_DIR/ipa05*.zip; do unzip "$i" -d $TEMP & done
wait
python3 patent_xml_to_csv.py --verbose \
--xml-input $TEMP/*.{xml,XML} \
--recurse \
--config config/uspto-applications.2005.yaml \
--output-path $OUTPUT \
--output-type sqlite \
--dtd-path $DTDS \
--continue-on-error
rm -r $TEMP
mkdir $TEMP
#2006-2013
for i in $ZIP_DIR/ipa0[6-9]*.zip; do unzip "$i" -d $TEMP & done
for i in $ZIP_DIR/ipa1[0-3]*.zip; do unzip "$i" -d $TEMP & done
wait
python3 patent_xml_to_csv.py --verbose \
--xml-input $TEMP/*.{xml,XML} \
--recurse \
--config config/uspto-applications.2006-2013.yaml \
--output-path $OUTPUT \
--output-type sqlite \
--dtd-path $DTDS \
--continue-on-error
rm -r $TEMP
mkdir $TEMP
#2013-present
for i in $ZIP_DIR/ipa1[4-9]*.zip; do unzip "$i" -d $TEMP & done
for i in $ZIP_DIR/ipa2*.zip; do unzip "$i" -d $TEMP & done
wait
python3 patent_xml_to_csv.py --verbose \
--xml-input $TEMP/*.{xml,XML} \
--recurse \
--config config/uspto-applications.2014+.yaml \
--output-path $OUTPUT \
--output-type sqlite \
--dtd-path $DTDS \
--continue-on-error
rm -r $TEMP