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https://github.com/Unstructured-IO/unstructured.git
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63861f537e
### Description Given that many of the options associated with the `Click` based cli ingest commands are added dynamically from a number of configs, a check was incorporated to make sure there were no duplicate entries to prevent new configs from overwriting already added options. ### Issues that were found and fixes: * duplicate api-key option set on Notion command conflicts with api key used for unstructured api. Added notion prefix. * retry logic configs had duplicates in biomed. Removed since this is not handled by the pipeline.
42 lines
1.3 KiB
Bash
Executable File
42 lines
1.3 KiB
Bash
Executable File
#!/usr/bin/env bash
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# shellcheck disable=SC2317
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set -e
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SCRIPT_DIR=$(dirname "$(realpath "$0")")
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cd "$SCRIPT_DIR"/.. || exit 1
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OUTPUT_FOLDER_NAME=biomed-api
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OUTPUT_DIR=$SCRIPT_DIR/structured-output/$OUTPUT_FOLDER_NAME
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WORK_DIR=$SCRIPT_DIR/workdir/$OUTPUT_FOLDER_NAME
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DOWNLOAD_DIR=$SCRIPT_DIR/download/$OUTPUT_FOLDER_NAME
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max_processes=${MAX_PROCESSES:=$(python3 -c "import os; print(os.cpu_count())")}
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# shellcheck disable=SC1091
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source "$SCRIPT_DIR"/cleanup.sh
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function cleanup() {
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cleanup_dir "$OUTPUT_DIR"
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cleanup_dir "$WORK_DIR"
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}
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trap cleanup EXIT
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"$SCRIPT_DIR"/check-num-files-expected-output.sh 2 $OUTPUT_FOLDER_NAME 10k
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PYTHONPATH=. ./unstructured/ingest/main.py \
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biomed \
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--download-dir "$DOWNLOAD_DIR" \
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--metadata-exclude coordinates,filename,file_directory,metadata.last_modified,metadata.data_source.date_processed,metadata.detection_class_prob,metadata.parent_id,metadata.category_depth \
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--num-processes "$max_processes" \
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--strategy hi_res \
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--preserve-downloads \
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--re-download \
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--reprocess \
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--output-dir "$OUTPUT_DIR" \
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--verbose \
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--api-from "2019-01-02" \
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--api-until "2019-01-02+00:03:10" \
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--max-request-time 30 \
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--max-retries 5 \
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--work-dir "$WORK_DIR"
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"$SCRIPT_DIR"/check-diff-expected-output.sh $OUTPUT_FOLDER_NAME
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