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bd8a74d686
Given the tendency for shell scripts to easily enter into a few levels of indentation and long line lengths, update the default to 2 spaces.
35 lines
1.2 KiB
Bash
Executable File
35 lines
1.2 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Processes the Unstructured-IO/unstructured repository
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# through Unstructured's library in 2 processes.
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# Structured outputs are stored in biomed-ingest-output-path/
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# Biomedical documents can be extracted in one of two ways, in this script is the FTP directory approach.
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# The supported ftp directories is:
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# https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf
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# By providing the path, the documents existing therein are downloaded.
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# For example, to download the documents in the path: https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/07/
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# The path needed is oa_pdf/07/
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SCRIPT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" &>/dev/null && pwd)
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cd "$SCRIPT_DIR"/../../.. || exit 1
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# The example below will ingest the PDF from the "oa_pdf/07/07/sbaa031.073.PMC7234218.pdf" path.
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# You can ingest all the documents in the "oa_pdf/07/07" path by passing "oa_pdf/07/07" instead.
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# WARNING: There are many documents in that path.
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PYTHONPATH=. ./unstructured/ingest/main.py \
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biomed \
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--path "oa_pdf/07/07/sbaa031.073.PMC7234218.pdf" \
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--output-dir biomed-ingest-output-path \
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--num-processes 2 \
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--verbose \
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--preserve-downloads
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# Alternatively, you can call it using:
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# unstructured-ingest --biomed-path ...
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