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#!/usr/bin/env bash
set -e
SRC_PATH=$(dirname "$(realpath "$0")")
SCRIPT_DIR=$(dirname "$SRC_PATH")
cd "$SCRIPT_DIR"/.. || exit 1
OUTPUT_FOLDER_NAME=local-single-file
OUTPUT_ROOT=${OUTPUT_ROOT:-$SCRIPT_DIR}
OUTPUT_DIR=$OUTPUT_ROOT/structured-output/$OUTPUT_FOLDER_NAME
WORK_DIR=$OUTPUT_ROOT/workdir/$OUTPUT_FOLDER_NAME
fix: local connector with input path to single file (#2116) When passed an absolute file path for the input document path, the local connector incorrectly writes the output file to the wrong directory. Also, in the single file input path cases we are currently including parent path as part of the destination writing, instead when a single file is specified as input the output file should be located directly in the specified outputs directory. Note: this change meant that we needed to bump the file path of some expected results. This fixes such that the output in this case is written to `output-dir/input-filename.json`. ## Changes - Fix for incorrect output path of files partitioned via the local connector when the input path is a file path (rather than directory) - Updated single-local-file test to validate the flow where we specify an absolute file path (since this was particularly broken) ## Testing Note: running the updated `local-single-file` test without the changes to the local connector will result in a final output copy of: ``` Copying /Users/ryannikolaidis/Development/unstructured/unstructured/test_unstructured_ingest/workdir/local-single-file/partitioned/a48c2abec07a9a31860429f94e5a6ade.json -> /Users/ryannikolaidis/Development/unstructured/unstructured/test_unstructured_ingest/../example-docs/language-docs/UDHR_first_article_all.txt.json ``` where the output path is the input path and not the expected `output-dir/input-filename.json` Running with this change we can now expect the file at that directory. --------- Co-authored-by: ryannikolaidis <ryannikolaidis@users.noreply.github.com>
2023-11-19 10:21:31 -08:00
# assigning an absolute path to the input file so that we explicitly test passing an absolute path
ABS_INPUT_PATH="$SCRIPT_DIR/../example-docs/language-docs/UDHR_first_article_all.txt"
max_processes=${MAX_PROCESSES:=$(python3 -c "import os; print(os.cpu_count())")}
# shellcheck disable=SC1091
source "$SCRIPT_DIR"/cleanup.sh
# shellcheck disable=SC2317
refactor: unstructured ingest as a pipeline (#1551) ### Description As we add more and more steps to the pipeline (i.e. chunking, embedding, table manipulation), it would help seperate the responsibility of each of these into their own processes, running each in parallel using json files to share data across. This will also help guarantee data is serializable if this code was used in an actual pipeline. Following is a flow diagram of the proposed changes. As part of this change: * A parent pipeline class will be responsible for running each `node`, which can optionally be run via multiprocessing if it supports it, or not. Possible nodes at this moment: * Doc factory: creates all the ingest docs via the source connector * Source: reads/downloads all of the content to process to the local filesystem to the location set by the `download_dir` parameter. * Partition: runs partition on all of the downloaded content in json format. * Any number of reformat nodes that modify the partitioned content. This can include chunking, embedding, etc. * Write: push the final json into the destination via the destination connector * This pipeline relies on the information of the ingest docs to be available via their serialization. An optimization was introduced with the `IngestDocJsonMixin` which adds in all the `@property` fields to the serialized json already being created via the `DataClassJsonMixin` * For all intermediate steps (partitioning, reformatting), the content is saved to a dedicated location on the local filesystem. Right now it's set to `$HOME/.cache/unstructured/ingest/pipeline/STEP_NAME/`. * Minor changes: made sense to move some of the config parameters between the read and partition configs when I explicitly divided the responsibility to download vs partition the content in the pipeline. * The pipeline class only makes the doc factory, source and partition nodes required, keeping with the logic that has been supported so far. All reformatting nodes and write node are optional. * Long term, there should also be some changes to the base configs supported by the CLI to support pipeline specific configs, but for now what exists was used to minimize changes in this PR. * Final step to copy the final output to the location designated by the `_output_filename` value of the ingest doc. * Hashing occurs at each step by hashing the parameters of that step (i.e. partition configs) along with the previous step via the filename used. This allows each step to be the same _if_ all the parameters for it have not changed and the content so far is the same. * The only data that is shared and has writes to across processes is the dictionary of ingest json data. This dict is created using the `multiprocessing.manager.DictProxy` to make sure any interaction with it is behind a lock. ### Minor refactors included: * Utility methods added to extract configs from the click options * Utility method to add common options to click commands. * All writers moved to using the class approach which extracts a lot of the common code so there's less copy-paste when new runners are added. * Use `@property` for source metadata on base ingest doc to add logic to call `update_source_metadata` if it's still `None` at the time it's fetched. ### Additional bug fixes included * Fsspec connectors were not serializable due to the `ingest_doc_cls`. This was removed from the fields captured by the `@dataclass` decorator and added in a `__post_init__` method. * Various reddit connector params were missing. This doesn't have an explicit ingest test at the moment so was never caught. * Fsspec connector had the parent `update_source_metadata` misnamed as `update_source_metadata_metadata` so it was never being called. ### Flow Diagram ![ingest_pipeline](https://github.com/Unstructured-IO/unstructured/assets/136338424/be485606-cfe0-4931-8b81-c2bf569cf1e2)
2023-10-06 14:49:29 -04:00
function cleanup() {
cleanup_dir "$OUTPUT_DIR"
cleanup_dir "$WORK_DIR"
refactor: unstructured ingest as a pipeline (#1551) ### Description As we add more and more steps to the pipeline (i.e. chunking, embedding, table manipulation), it would help seperate the responsibility of each of these into their own processes, running each in parallel using json files to share data across. This will also help guarantee data is serializable if this code was used in an actual pipeline. Following is a flow diagram of the proposed changes. As part of this change: * A parent pipeline class will be responsible for running each `node`, which can optionally be run via multiprocessing if it supports it, or not. Possible nodes at this moment: * Doc factory: creates all the ingest docs via the source connector * Source: reads/downloads all of the content to process to the local filesystem to the location set by the `download_dir` parameter. * Partition: runs partition on all of the downloaded content in json format. * Any number of reformat nodes that modify the partitioned content. This can include chunking, embedding, etc. * Write: push the final json into the destination via the destination connector * This pipeline relies on the information of the ingest docs to be available via their serialization. An optimization was introduced with the `IngestDocJsonMixin` which adds in all the `@property` fields to the serialized json already being created via the `DataClassJsonMixin` * For all intermediate steps (partitioning, reformatting), the content is saved to a dedicated location on the local filesystem. Right now it's set to `$HOME/.cache/unstructured/ingest/pipeline/STEP_NAME/`. * Minor changes: made sense to move some of the config parameters between the read and partition configs when I explicitly divided the responsibility to download vs partition the content in the pipeline. * The pipeline class only makes the doc factory, source and partition nodes required, keeping with the logic that has been supported so far. All reformatting nodes and write node are optional. * Long term, there should also be some changes to the base configs supported by the CLI to support pipeline specific configs, but for now what exists was used to minimize changes in this PR. * Final step to copy the final output to the location designated by the `_output_filename` value of the ingest doc. * Hashing occurs at each step by hashing the parameters of that step (i.e. partition configs) along with the previous step via the filename used. This allows each step to be the same _if_ all the parameters for it have not changed and the content so far is the same. * The only data that is shared and has writes to across processes is the dictionary of ingest json data. This dict is created using the `multiprocessing.manager.DictProxy` to make sure any interaction with it is behind a lock. ### Minor refactors included: * Utility methods added to extract configs from the click options * Utility method to add common options to click commands. * All writers moved to using the class approach which extracts a lot of the common code so there's less copy-paste when new runners are added. * Use `@property` for source metadata on base ingest doc to add logic to call `update_source_metadata` if it's still `None` at the time it's fetched. ### Additional bug fixes included * Fsspec connectors were not serializable due to the `ingest_doc_cls`. This was removed from the fields captured by the `@dataclass` decorator and added in a `__post_init__` method. * Various reddit connector params were missing. This doesn't have an explicit ingest test at the moment so was never caught. * Fsspec connector had the parent `update_source_metadata` misnamed as `update_source_metadata_metadata` so it was never being called. ### Flow Diagram ![ingest_pipeline](https://github.com/Unstructured-IO/unstructured/assets/136338424/be485606-cfe0-4931-8b81-c2bf569cf1e2)
2023-10-06 14:49:29 -04:00
}
trap cleanup EXIT
RUN_SCRIPT=${RUN_SCRIPT:-./unstructured/ingest/main.py}
PYTHONPATH=${PYTHONPATH:-.} "$RUN_SCRIPT" \
local \
--num-processes "$max_processes" \
--metadata-exclude coordinates,filename,file_directory,metadata.data_source.date_created,metadata.data_source.date_modified,metadata.data_source.date_processed,metadata.last_modified,metadata.detection_class_prob,metadata.parent_id,metadata.category_depth \
--output-dir "$OUTPUT_DIR" \
--additional-partition-args '{"strategy":"ocr_only", "languages":["ind", "est"]}' \
--verbose \
--reprocess \
--input-path "$ABS_INPUT_PATH" \
--work-dir "$WORK_DIR"
set +e
"$SCRIPT_DIR"/check-diff-expected-output.sh $OUTPUT_FOLDER_NAME
EXIT_CODE=$?
set -e
if [ "$EXIT_CODE" -ne 0 ]; then
echo "The last script run exited with a non-zero exit code: $EXIT_CODE."
# Handle the error or exit
fi
"$SCRIPT_DIR"/evaluation-ingest-cp.sh "$OUTPUT_DIR" "$OUTPUT_FOLDER_NAME"
exit $EXIT_CODE