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

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Connector for Biomedical Literature (#345) The implementation involves the introduction of SimpleBiomedConfig, BiomedIngestDoc and BiomedConnector which ingests documents from the PDF Download.
2023-03-11 01:09:54 +00:00
#!/usr/bin/env bash
fix: update ingest test fixtures, disable biomed test (#486) * Update test fixtures that should have been updated in prior commit * Disable biomed ingest tests for now, the fail more often than not * Bonus: echo `tesseract --version` in the update script, since that is a key thing that influences fixture outputs.
2023-04-14 17:07:09 -07:00
# shellcheck disable=SC2317
Connector for Biomedical Literature (#345) The implementation involves the introduction of SimpleBiomedConfig, BiomedIngestDoc and BiomedConnector which ingests documents from the PDF Download.
2023-03-11 01:09:54 +00:00
test: avoid misleading output in ingest tests (#488) Previously, if there was an error (non-zero exit code) in an ingest test script, the script would still complete and echo a warning about mismatched outputs and how to regenerate the fixtures. However, this statement is irrelevant and misleading: if the ingest failed with a non-zero exit code in the first place, that is the failure that should be debugged -- don't confuse the user with a comment about outputs.
2023-04-17 14:57:44 -07:00
set -e
chore: refactor ingest tests (#814) - Adds reusable validation scripts (check-x.sh) to minimize repeated (or near-repeated) code and create one source of truth - Restructures the location of download and output folders such that they are nested in the test_unstructured_ingest directory - Adds gitignore for output folders / files to avoid them accidentally getting checked into the repository - Construct paths as reusable variables declared at top of scripts - Sort order of flag for ingest calls, across all tests (this makes it easier to parse at a glance) - OVERWRITE_FIXTURES removes all old fixtures for path to guarantee no stale results are left behind - Bonus: don't check/exit on expected number of expected outputs when OVERWRITE_FIXTURES is true - Bonus: exclude file_directory from Slack and Discord test scripts (match convention in all others)
2023-06-29 16:13:41 -07:00
SCRIPT_DIR=$(dirname "$(realpath "$0")")
Connector for Biomedical Literature (#345) The implementation involves the introduction of SimpleBiomedConfig, BiomedIngestDoc and BiomedConnector which ingests documents from the PDF Download.
2023-03-11 01:09:54 +00:00
cd "$SCRIPT_DIR"/.. || exit 1
chore: refactor ingest tests (#814) - Adds reusable validation scripts (check-x.sh) to minimize repeated (or near-repeated) code and create one source of truth - Restructures the location of download and output folders such that they are nested in the test_unstructured_ingest directory - Adds gitignore for output folders / files to avoid them accidentally getting checked into the repository - Construct paths as reusable variables declared at top of scripts - Sort order of flag for ingest calls, across all tests (this makes it easier to parse at a glance) - OVERWRITE_FIXTURES removes all old fixtures for path to guarantee no stale results are left behind - Bonus: don't check/exit on expected number of expected outputs when OVERWRITE_FIXTURES is true - Bonus: exclude file_directory from Slack and Discord test scripts (match convention in all others)
2023-06-29 16:13:41 -07:00
OUTPUT_FOLDER_NAME=biomed-path
OUTPUT_DIR=$SCRIPT_DIR/structured-output/$OUTPUT_FOLDER_NAME
DOWNLOAD_DIR=$SCRIPT_DIR/download/$OUTPUT_FOLDER_NAME
Connector for Biomedical Literature (#345) The implementation involves the introduction of SimpleBiomedConfig, BiomedIngestDoc and BiomedConnector which ingests documents from the PDF Download.
2023-03-11 01:09:54 +00:00
chore: refactor ingest tests (#814) - Adds reusable validation scripts (check-x.sh) to minimize repeated (or near-repeated) code and create one source of truth - Restructures the location of download and output folders such that they are nested in the test_unstructured_ingest directory - Adds gitignore for output folders / files to avoid them accidentally getting checked into the repository - Construct paths as reusable variables declared at top of scripts - Sort order of flag for ingest calls, across all tests (this makes it easier to parse at a glance) - OVERWRITE_FIXTURES removes all old fixtures for path to guarantee no stale results are left behind - Bonus: don't check/exit on expected number of expected outputs when OVERWRITE_FIXTURES is true - Bonus: exclude file_directory from Slack and Discord test scripts (match convention in all others)
2023-06-29 16:13:41 -07:00
sh "$SCRIPT_DIR"/check-num-files-expected-output.sh 1 $OUTPUT_FOLDER_NAME 10k
Connector for Biomedical Literature (#345) The implementation involves the introduction of SimpleBiomedConfig, BiomedIngestDoc and BiomedConnector which ingests documents from the PDF Download.
2023-03-11 01:09:54 +00:00
PYTHONPATH=. ./unstructured/ingest/main.py \
Roman/ingest refactor (#978) * Pull out s3 code as subcommand * Pull out dropbox code as subcommand * Pull out azure code as subcommand * Pull out fsspec code as subcommand * Pull out github code as subcommand * Pull out gitlab code as subcommand * Pull out reddit code as subcommand * Pull out slack code as subcommand * Pull out discord code as subcommand * Pull out wikipedia code as subcommand * Pull out gdrive code as subcommand * Pull out biomed code as subcommand * rename parameters * Pull out onedrive code as subcommand * Pull out outlook code as subcommand * Pull out local code as subcommand * Pull out elasticsearch code as subcommand * Pull out confluence code as subcommand * Drop previous main file * update changelog * Add back in mp.Pool * Fix mypy issues with click * Make sure all tests run with verbose flag * refactor approach to dynamically add common options to each subcommand, scrub logging of options for sensitive data * Pull out some more shared options * Support running code via python as well as cli * update ingest readme and move it to the ingest folder * update usage in connector docs * move local command arg in test * Seperate out cli code from logic running unstructured * Make some cli fields required rather than optional * rename process -> processor * Improve logger to avoid duplicate handlers --------- Co-authored-by: Ryan Nikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
2023-07-31 13:20:10 -04:00
biomed \
chore: refactor ingest tests (#814) - Adds reusable validation scripts (check-x.sh) to minimize repeated (or near-repeated) code and create one source of truth - Restructures the location of download and output folders such that they are nested in the test_unstructured_ingest directory - Adds gitignore for output folders / files to avoid them accidentally getting checked into the repository - Construct paths as reusable variables declared at top of scripts - Sort order of flag for ingest calls, across all tests (this makes it easier to parse at a glance) - OVERWRITE_FIXTURES removes all old fixtures for path to guarantee no stale results are left behind - Bonus: don't check/exit on expected number of expected outputs when OVERWRITE_FIXTURES is true - Bonus: exclude file_directory from Slack and Discord test scripts (match convention in all others)
2023-06-29 16:13:41 -07:00
--download-dir "$DOWNLOAD_DIR" \
chore: rename Element's "date" field to "last_modified" (#997) Change the Element's date field name to the more specific last_modified so there is less room for confusion of what that field represents.
2023-07-31 19:55:43 -07:00
--metadata-exclude coordinates,filename,file_directory,metadata.last_modified,metadata.data_source.date_processed \
Connector for Biomedical Literature (#345) The implementation involves the introduction of SimpleBiomedConfig, BiomedIngestDoc and BiomedConnector which ingests documents from the PDF Download.
2023-03-11 01:09:54 +00:00
--num-processes 2 \
Chore(ingest): Add `--partition-strategy` parameter in CLI (#582) * change strategy arg defalut to auto in partition * passing --partition-strategy down * add strategy="hi_res" to test (default changed) * made an error on param name, added note
2023-05-15 15:26:53 -04:00
--partition-strategy hi_res \
test: avoid misleading output in ingest tests (#488) Previously, if there was an error (non-zero exit code) in an ingest test script, the script would still complete and echo a warning about mismatched outputs and how to regenerate the fixtures. However, this statement is irrelevant and misleading: if the ingest failed with a non-zero exit code in the first place, that is the failure that should be debugged -- don't confuse the user with a comment about outputs.
2023-04-17 14:57:44 -07:00
--preserve-downloads \
chore: refactor ingest tests (#814) - Adds reusable validation scripts (check-x.sh) to minimize repeated (or near-repeated) code and create one source of truth - Restructures the location of download and output folders such that they are nested in the test_unstructured_ingest directory - Adds gitignore for output folders / files to avoid them accidentally getting checked into the repository - Construct paths as reusable variables declared at top of scripts - Sort order of flag for ingest calls, across all tests (this makes it easier to parse at a glance) - OVERWRITE_FIXTURES removes all old fixtures for path to guarantee no stale results are left behind - Bonus: don't check/exit on expected number of expected outputs when OVERWRITE_FIXTURES is true - Bonus: exclude file_directory from Slack and Discord test scripts (match convention in all others)
2023-06-29 16:13:41 -07:00
--reprocess \
--structured-output-dir "$OUTPUT_DIR" \
Roman/ingest refactor (#978) * Pull out s3 code as subcommand * Pull out dropbox code as subcommand * Pull out azure code as subcommand * Pull out fsspec code as subcommand * Pull out github code as subcommand * Pull out gitlab code as subcommand * Pull out reddit code as subcommand * Pull out slack code as subcommand * Pull out discord code as subcommand * Pull out wikipedia code as subcommand * Pull out gdrive code as subcommand * Pull out biomed code as subcommand * rename parameters * Pull out onedrive code as subcommand * Pull out outlook code as subcommand * Pull out local code as subcommand * Pull out elasticsearch code as subcommand * Pull out confluence code as subcommand * Drop previous main file * update changelog * Add back in mp.Pool * Fix mypy issues with click * Make sure all tests run with verbose flag * refactor approach to dynamically add common options to each subcommand, scrub logging of options for sensitive data * Pull out some more shared options * Support running code via python as well as cli * update ingest readme and move it to the ingest folder * update usage in connector docs * move local command arg in test * Seperate out cli code from logic running unstructured * Make some cli fields required rather than optional * rename process -> processor * Improve logger to avoid duplicate handlers --------- Co-authored-by: Ryan Nikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
2023-07-31 13:20:10 -04:00
--verbose \
--decay .3 \
--max-request-time 30 \
--max-retries 5 \
--path "oa_pdf/07/07/sbaa031.073.PMC7234218.pdf" \
Connector for Biomedical Literature (#345) The implementation involves the introduction of SimpleBiomedConfig, BiomedIngestDoc and BiomedConnector which ingests documents from the PDF Download.
2023-03-11 01:09:54 +00:00
chore: refactor ingest tests (#814) - Adds reusable validation scripts (check-x.sh) to minimize repeated (or near-repeated) code and create one source of truth - Restructures the location of download and output folders such that they are nested in the test_unstructured_ingest directory - Adds gitignore for output folders / files to avoid them accidentally getting checked into the repository - Construct paths as reusable variables declared at top of scripts - Sort order of flag for ingest calls, across all tests (this makes it easier to parse at a glance) - OVERWRITE_FIXTURES removes all old fixtures for path to guarantee no stale results are left behind - Bonus: don't check/exit on expected number of expected outputs when OVERWRITE_FIXTURES is true - Bonus: exclude file_directory from Slack and Discord test scripts (match convention in all others)
2023-06-29 16:13:41 -07:00
sh "$SCRIPT_DIR"/check-diff-expected-output.sh $OUTPUT_FOLDER_NAME
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