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

#!/usr/bin/env bash
# shellcheck disable=SC2317
# NOTE(crag): remove above shellcheck line when the biomed issue is fixed
echo "Skipping test-ingest-biomed-api.sh,"
echo "see https://github.com/Unstructured-IO/unstructured/issues/468"
echo
exit 0

set -e

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

if [[ "$CI" == "true" ]]; then
    if [ "$(( RANDOM % 10))" -lt 1 ] ; then
        echo "Skipping ingest 90% of biomed tests to avoid occaisonal ftp issue."
        exit 0
    fi
fi

if [[ "$(find test_unstructured_ingest/expected-structured-output/biomed-ingest-output-api/ -type f -size +10k | wc -l)" != 2 ]]; then
    echo "The test fixtures in test_unstructured_ingest/expected-structured-output/biomed-ingest-output-api/ 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-api-from "2019-01-02" \
    --biomed-api-until "2019-01-02+00:03:10" \
    --structured-output-dir biomed-ingest-output-api  \
    --num-processes 2 \
    --partition-strategy hi_res \
    --reprocess \
    --verbose \
    --re-download \
    --preserve-downloads

OVERWRITE_FIXTURES=${OVERWRITE_FIXTURES:-false}

set +x

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

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

elif ! diff -ru biomed-ingest-output-api test_unstructured_ingest/expected-structured-output/biomed-ingest-output-api ; 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