unstructured/test_unstructured_ingest/test-ingest-biomed-path.sh

#!/usr/bin/env bash
# shellcheck disable=SC2317

set -e

SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
cd "$SCRIPT_DIR"/.. || exit 1

if [[ "$(find test_unstructured_ingest/expected-structured-output/biomed-ingest-output-path/ -type f -size +10k | wc -l)" -ne 1 ]]; then
    echo "The test fixtures in test_unstructured_ingest/expected-structured-output/biomed-ingest-output-path/ look suspicious. At least one of the files is too small."
    echo "Did you overwrite test fixtures with bad outputs?"
    exit 1
fi

PYTHONPATH=. ./unstructured/ingest/main.py \
    --metadata-exclude filename,file_directory,metadata.data_source.date_processed \
    --biomed-path "oa_pdf/07/07/sbaa031.073.PMC7234218.pdf" \
    --biomed-max-retries 5 \
    --biomed-max-request-time 30 \
    --biomed-decay .3 \
    --structured-output-dir biomed-ingest-output-path \
    --num-processes 2 \
    --partition-strategy hi_res \
    --reprocess \
    --download-dir files-ingest-download/biomed-path \
    --preserve-downloads \
    --verbose


OVERWRITE_FIXTURES=${OVERWRITE_FIXTURES:-false}

set +e

# to update ingest test fixtures, run scripts/ingest-test-fixtures-update.sh on x86_64
if [[ "$OVERWRITE_FIXTURES" != "false" ]]; then

    OWNER_GROUP=$(stat -c "%u:%g" test_unstructured_ingest/expected-structured-output/biomed-ingest-output-path)
    rsync -rv --chown="$OWNER_GROUP" biomed-ingest-output-path/ test_unstructured_ingest/expected-structured-output/biomed-ingest-output-path

elif ! diff -ru biomed-ingest-output-path test_unstructured_ingest/expected-structured-output/biomed-ingest-output-path ; then
    echo
    echo "There are differences from the previously checked-in structured outputs."
    echo
    echo "If these differences are acceptable, overwrite by the fixtures by setting the env var:"
    echo
    echo "  export OVERWRITE_FIXTURES=true"
    echo
    echo "and then rerun this script."
    echo
    echo "NOTE: You'll likely just want to run scripts/ingest-test-fixtures-update.sh on x86_64 hardware"
    echo "to update fixtures for CI."
    echo
    exit 1
fi