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Connector data source versions should always be string values, however we were using the integer checksum value for the version for fsspec connectors. This casts that value to a string. ## Changes * Cast the checksum value to a string when assigning the version value for fsspec connectors. * Adds test to validate that these connectors will assign a string value when an integer checksum is fetched. ## Testing Unit test added.
This PR is one in a series of PRs for refactoring and fixing the languages parameter so it can address incorrect input by users. #2293 This PR adds _clean_ocr_languages_arg. There are no calls to this function yet, but it will be called in later PRs related to this series.
### Summary Closes #2417. Bumps `unstructured-inference` to pull in the fix implemented in Unstructured-IO/unstructured-inference#317
To test: > cd docs && make html Changelogs: * Fixed sphinx error due to malformed rst table on partition page * Updated API Params, ie. `extract_image_block_types` and `extract_image_block_to_payload` * Updated image filetype supports
FSSpec destination connectors did not use `check_connection`. There was an error when trying to `ls` destination directory - it may not exist at the moment of creation of connector. Now `check_connection` calls `ls` on bucket root and this method is called on `initialize` of destination connector.
### Description
This adds in a destination connector to write content to the Databricks
Unity Catalog Volumes service. Currently there is an internal account
that can be used for testing manually but there is not dedicated account
to use for testing so this is not being added to the automated ingest
tests that get run in the CI.
To test locally:
```shell
#!/usr/bin/env bash
path="testpath/$(uuidgen)"
PYTHONPATH=. python ./unstructured/ingest/main.py local \
--num-processes 4 \
--output-dir azure-test \
--strategy fast \
--verbose \
--input-path example-docs/fake-memo.pdf \
--recursive \
databricks-volumes \
--catalog "utic-dev-tech-fixtures" \
--volume "small-pdf-set" \
--volume-path "$path" \
--username "$DATABRICKS_USERNAME" \
--password "$DATABRICKS_PASSWORD" \
--host "$DATABRICKS_HOST"
```
setup.py is currently pointing to the wrong location for the databricks-volumes extra requirements. This PR updates to point to the correct location. ## Testing Tested by installing from local source with `pip install .`
### Summary Adds a driver with `unstructured` version information to the MongoDB driver. ### Testing, Good to go as long as the MongoDB ingest test run successfully.
When a partitioned or embedded document json has null values, those get converted to a dictionary with None values. This happens in the metadata. I have not see it in other keys. Chroma and Pinecone do not like those None values. `flatten_dict` has been modified with a `remove_none` arg to remove keys with None values. Also, Pinecone has been pinned at 2.2.4 because at 3.0 and above it breaks our code. --------- Co-authored-by: potter-potter <david.potter@gmail.com>
### Summary Closes #2412. Adds support for YAML MIME types and treats them as plain text. In response to `500` errors that the API currently returns if the MIME type is `text/yaml`.
We have added a new version of chipper (Chipperv3), which needs to allow
unstructured to effective work with all the current Chipper versions.
This implies resizing images with the appropriate resolution and make
sure that Chipper elements are not sorted by unstructured.
In addition, it seems that PDFMiner is being called when calling
Chipper, which adds repeated elements from Chipper and PDFMiner.
To evaluate this PR, you can test the code below with the attached PDF.
The code writes a JSON file with the generated elements. The output can
be examined with `cat out.un.json | python -m json.tool`. There are
three things to check:
1. The size of the image passed to Chipper, which can be identiied in
the layout_height and layout_width attributes, which should have values
3301 and 2550 as shown in the example below:
```
[
{
"element_id": "c0493a7872f227e4172c4192c5f48a06",
"metadata": {
"coordinates": {
"layout_height": 3301,
"layout_width": 2550,
```
2. There should be no repeated elements.
3. Order should be closer to reading order.
The script to run Chipper from unstructured is:
```
from unstructured import __version__
print(__version__.__version__)
import json
from unstructured.partition.auto import partition
from unstructured.staging.base import elements_to_json
elements = json.loads(elements_to_json(partition("Huang_Improving_Table_Structure_Recognition_With_Visual-Alignment_Sequential_Coordinate_Modeling_CVPR_2023_paper-p6.pdf", strategy="hi_res", model_name="chipperv3")))
with open('out.un.json', 'w') as w:
json.dump(elements, w)
```
[Huang_Improving_Table_Structure_Recognition_With_Visual-Alignment_Sequential_Coordinate_Modeling_CVPR_2023_paper-p6.pdf](https://github.com/Unstructured-IO/unstructured/files/13817273/Huang_Improving_Table_Structure_Recognition_With_Visual-Alignment_Sequential_Coordinate_Modeling_CVPR_2023_paper-p6.pdf)
---------
Co-authored-by: Antonio Jimeno Yepes <antonio@unstructured.io>
To test: > cd docs && make html Change logs: * Updates the best practice for table extraction to use `skip_infer_table_types` instead of `pdf_infer_table_structure`. * Fixed CSS issue with a duplicate search box. * Fixed RST warning message * Fixed typo on the Intro page.
Formatting of link_texts was breaking metadata storage. Turns out it didn't need any conforming and came in correctly from json. --------- Co-authored-by: potter-potter <david.potter@gmail.com>
- there are multiple places setting the default `hi_res_model_name` in
both `unstructured` and `unstructured-inference`
- they lead to inconsistency and unexpected behaviors
- this fix removes a helper in `unstructured` that tries to set the
default hi_res layout detection model; instead we rely on the
`unstructured-inference` to provide that default when no explicit model
name is passed in
## test
```bash
UNSTRUCTURED_INCLUDE_DEBUG_METADATA=true ipython
```
```python
from unstructured.partition.auto import partition
# find a pdf file
elements = partition("foo.pdf", strategy="hi_res")
assert elements[0].metadata.detection_origin == "yolox"
```
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: badGarnet <badGarnet@users.noreply.github.com>
This PR is the last in a series of PRs for refactoring and fixing the language parameters (`languages` and `ocr_languages` so we can address incorrect input by users. See #2293 It is recommended to go though this PR commit-by-commit and note the commit message. The most significant commit is "update check_languages..."
.heic files are an image filetype we have not supported. #### Testing ``` from unstructured.partition.image import partition_image png_filename = "example-docs/DA-1p.png" heic_filename = "example-docs/DA-1p.heic" png_elements = partition_image(png_filename, strategy="hi_res") heic_elements = partition_image(heic_filename, strategy="hi_res") for i in range(len(heic_elements)): print(heic_elements[i].text == png_elements[i].text) ``` --------- Co-authored-by: christinestraub <christinemstraub@gmail.com>
Update `black` and apply changes to affected files. I separated this PR so we can have a look at the changes and decide whether we want to: 1. Go forward with the new formatting 2. Change the black config to make the old formatting valid 3. Get rid of black entirely and just use `ruff` 4. Do something I haven't thought of
fix typo in makefile: `.PHONE` -> `.PHONY`
Removed `pillow` pin and recompiled. I think it was originally there to address a conflict, which, as far as I can tell, no longer exists. Also a security vulnerability was discovered in the older version of `pillow`. #### Testing: CI should pass.
…#2479) Closes #2480. ### Summary - fixed an error introduced by PR [#2347](#2347) - https://github.com/Unstructured-IO/unstructured/pull/2347/files#diff-cefa2d296ae7ffcf5c28b5734d5c7d506fbdb225c05a0bc27c6b755d5424ffdaL373 - updated `test_partition_pdf_with_model_name()` to test more model names ### Testing The updated test function `test_partition_pdf_with_model_name()` should work on this branch, but fails on the `main` branch.
…ly supported (#2462) This is nice to natively support both Tesseract and Paddle. However, one might already use another OCR and might want to keep using it (for quality reasons, for cost reasons etc...). This PR adds the ability for the user to specify its own OCR agent implementation that is then called by unstructured. I am new to unstructured so don't hesitate to let me know if you would prefer this being done differently and I will rework the PR. --------- Co-authored-by: Yao You <theyaoyou@gmail.com> Co-authored-by: Yao You <yao@unstructured.io>
The purpose of this PR is to pass embedded text through table processing sub-pipeline later later use.
Thanks to Ofer at Vectara, we now have a Vectara destination connector. - There are no dependencies since it is all REST calls to API - --------- Co-authored-by: potter-potter <david.potter@gmail.com>
I accidentally added Vectara to setup and makefile. But there are no dependencies for Vectara This removes Vectara from those files. --------- Co-authored-by: potter-potter <david.potter@gmail.com>
The purpose of this PR is to refactor OCR-related modules to reduce unnecessary module imports to avoid potential issues (most likely due to a "circular import"). ### Summary - add `inference_utils` module (unstructured/partition/pdf_image/inference_utils.py) to define unstructured-inference library related utility functions, which will reduce importing unstructured-inference library functions in other files - add `conftest.py` in `test_unstructured/partition/pdf_image/` directory to define fixtures that are available to all tests in the same directory and its subdirectories ### Testing CI should pass
Small improvement to Vectara requested by Ofer at Vectara In the "Document" construct, every document can have a title. If it's there, in the UI it will show up above the document (otherwise you get "Untitled") --------- Co-authored-by: potter-potter <david.potter@gmail.com>
…text (#3003) Thanks to @erichare from AstraDB Adds support for specifying the indexing options for various columns in Astra DB, allowing users to avoid a situation where long text columns are by-default indexed. Changes to: test_unstructured_ingest/python/test-ingest-astra-output.py are forward looking from AstraDB
…images (#3035) ### Summary Closes #3021 . Turns table extraction for PDFs and images off by default. The default behavior originally changed in #2588 . The reason for reversion is that some users did not realize turning off table extraction was an option and experience long processing times for PDFs and images with the new default behavior. --------- Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com> Co-authored-by: MthwRobinson <MthwRobinson@users.noreply.github.com>
…rameteres (#3014) This PR introduces GLOBAL_WORKING_DIR and GLOBAL_WORKING_PROCESS_DIR controlling where temporary files are stored during partition flow, via tempfile.tempdir. #### Edit: Renamed prefixes from STORAGE_ to UNSTRUCTURED_CACHE_ #### Edit 2: Renamed prefixes from UNSTRUCTURED_CACHE to GLOBAL_WORKING_DIR_
### Summary Closes #3034 and reenables ARM64 in the docker build and publish job. This was taken out in #3039 because we've only build `libreoffice` for AMD64 and not ARM64. If Chainguard publishes an `apk` for `libreoffice`, we can support a Chainguard image for both architectures. The smoke test now differs for both architectures, to reflect differences in the directory structure. ### Testing Build and publish ran successfully for ARM64 (job [here](https://github.com/Unstructured-IO/unstructured/actions/runs/9129712470/job/25104907497)) and AMD64 (job [here](https://github.com/Unstructured-IO/unstructured/actions/runs/9129712470/job/25104907826)).
…eline (#3040) This PR aims to pass `kwargs` through `fast` strategy pipeline, which was missing as part of the previous PR - #3030. I also did some code refactoring in this PR, so I recommend reviewing this PR commit by commit. ### Summary - pass `kwargs` through `fast` strategy pipeline, which will allow users to specify additional params like `sort_mode` - refactor: code reorganization - cut a release for `0.14.0` ### Testing CI should pass
### Summary Closes #2959. Updates the dependency and CI to add support for Python 3.12. The MongoDB ingest tests were disabled due to jobs like [this one](https://github.com/Unstructured-IO/unstructured/actions/runs/9133383127/job/25116767333) failing due to issues with the `bson` package. `bson` is a dependency for the AstraDB connector, but `pymongo` does not work when `bson` is installed from `pip`. This issue is documented by MongoDB [here](https://pymongo.readthedocs.io/en/stable/installation.html). Spun off #3049 to resolve this. Issue seems unrelated to Python 3.12, though unsure why this didn't surface previously. Disables the `argilla` tests because `argilla` does not yet support Python 3.12. We can add the `argilla` tests back in once the PR references below is merged. You can still use the `stage_for_argilla` function if you're on `python<3.12` and you install `argilla` yourself. - argilla-io/argilla#4837 --------- Co-authored-by: Nicolò Boschi <boschi1997@gmail.com>
This PR adds `py.typed`, which will fix issues of the following type: ![Uploading Screenshot 2024-05-17 at 12.13.33.png…]() --------- Co-authored-by: Matt Robinson <mrobinson@unstructured.io>
#2574) Removes this warning: > Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you. Co-authored-by: Matt Robinson <mrobinson@unstructured.io>
This minor change updates the URL of the [Weaviate Docker image](https://weaviate.io/developers/weaviate/installation/docker-compose). Instead of the standard Docker registry, Weaviate now makes use of a custom registry running at `cr.weaviate.io`. Thanks in advance for merging. 🤖 beep boop, the Weaviate bot PS: Please note that the Weaviate Bot automates this PR; apologies if PR formatting is missing. If you have questions, feel free to reach out via our [forum](https://forum.weaviate.io) or [Slack](https://weaviate.io/slack). Co-authored-by: Matt Robinson <mrobinson@unstructured.io>
Just a tiny fix for a broken link that bothered me :) Co-authored-by: Matt Robinson <mrobinson@unstructured.io>
…th_no_strategy` (#3057) ### Summary A `partition_via_api` test that only runs on `main` was [failing](https://github.com/Unstructured-IO/unstructured/actions/runs/9159429513/job/25181600959) with the following output, likely due to the change in the default behavior for `skip_infer_table_types`. This PR explicitly sets the `skip_infer_table_types` param to avoid the failure.. ```python =========================== short test summary info ============================ FAILED test_unstructured/partition/test_api.py::test_partition_via_api_with_no_strategy - AssertionError: assert 'Zejiang Shen® (<), Ruochen Zhang?, Melissa Dell®, Benjamin Charles Germain Lee?, Jacob Carlson®, and Weining Li®' != 'Zejiang Shen® (<), Ruochen Zhang?, Melissa Dell®, Benjamin Charles Germain Lee?, Jacob Carlson®, and Weining Li®' + where 'Zejiang Shen® (<), Ruochen Zhang?, Melissa Dell®, Benjamin Charles Germain Lee?, Jacob Carlson®, and Weining Li®' = <unstructured.documents.elements.Text object at 0x7fb9069fc610>.text + and 'Zejiang Shen® (<), Ruochen Zhang?, Melissa Dell®, Benjamin Charles Germain Lee?, Jacob Carlson®, and Weining Li®' = <unstructured.documents.elements.Text object at 0x7fb90648ad90>.text = 1 failed, 2299 passed, 9 skipped, 2 deselected, 2 xfailed, 9 xpassed, 14 warnings in 1241.64s (0:20:41) = make: *** [Makefile:302: test] Error 1 ``` ### Testing After temporarily removing the "skip if not on `main`" `pytest` mark, the [unit tests pass](https://github.com/Unstructured-IO/unstructured/actions/runs/9163268381/job/25192040902?pr=3057O) on the feature branch.
### Summary Updates GitHub pages to redirect to the new https://docs.unstructured.io page. This will appear on GitHub pages after the next tag. ### Testing 1. From the docs direction, run `make html`. You should not see any errors or warnings 2. Open `unstructured/docs/build/html/index.html`. It should look like the following: <img width="1512" alt="image" src="https://github.com/Unstructured-IO/unstructured/assets/1635179/077626a5-d88a-467e-9e37-273a92e75d30"> 3. Open `unstructured/docs/build/html/404.html`. It should redirect back to `index.html`. Per the [GitHub pages docs](https://docs.github.com/en/pages/getting-started-with-github-pages/creating-a-custom-404-page-for-your-github-pages-site), that page will get served for 404 errors, meaning any links to old docs pages will redirect to `index.html`, which points users to the new docs page.
### Description This refactors the current ingest CLI process to support better granularity in how the steps are ran * Both multiprocessing and async now supported. Given that a lot of the steps are IO-bound, such as downloading and uploading content, we can achieve better parallelization by using async here * Destination step broken up into a stager step and an upload step. This will allow for steps that require manipulation of the data between formats, such as converting the elements json into a csv format to upload for tabular destinations, to be pulled out of the step that does the actual upload. * The process of writing the content to a local destination was now pulled out as it's own dedicated destination connector, meaning you no longer need to persist the content locally once the process is done if the content was uploaded elsewhere. * Quick update to the chunker/partition step to use the python client. * Move the uncompress suppport as a pipeline step since this can arbitrarily apply to any concrete files that have been downloaded, regardless of where they came from. * Leverage last modified date to mark files to be reprocessed, even if the file already exists locally. ### Callouts Retry configs haven't been moved over yet. This is an open question because the intent was for it to wrap potential connection errors but now any of the other steps that leverage an API might run into network connection issues. Should those be isolated in each of the steps and wrapped with the same retry configs? Or do we need to expose a unique retry config for each step? This would bloat the input params even more. ### Testing * If you want to run the new code as an SDK, there's an example file that was added to highlight how to do that: [example.py](https://github.com/Unstructured-IO/unstructured/blob/roman/refactor-ingest/unstructured/ingest/v2/example.py) * If you want to run the new code as an isolated CLI: ```shell PYTHONPATH=. python unstructured/ingest/v2/main.py --help ``` * If you want to see which commands have been migrated to the new version, there's now a `v2` short help text next to those commands when running the current cli: ```shell PYTHONPATH=. python unstructured/ingest/main.py --help Usage: main.py [OPTIONS] COMMAND [ARGS]...main.py --help Options: --help Show this message and exit. Commands: airtable azure biomed box confluence delta-table discord dropbox elasticsearch fsspec gcs github gitlab google-drive hubspot jira local v2 mongodb notion onedrive opensearch outlook reddit s3 v2 salesforce sftp sharepoint slack wikipedia ``` You can run any of the local or s3 specific ingest tests and these should now work. --------- Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com> Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
### Summary Switches to installing `libreoffice` from the Wolfi repository and upgrades the `libreoffice` version to `libreoffice==24.x.x`. Resolves a medium vulnerability in the old `libreoffice` version. Security scanning with `anchore/grype` was also added to the `test_dockerfile` job. Requirements were bumped to resolve a vulnerability in the `requests` library. ### Testing `test_dockerfile` passes with the updates.
This PR adds the ability to fill inferred elements text from embedded text (`pdfminer`) without depending on `unstructured-inference` library. This PR is the second part of moving embedded text related code from `unstructured-inference` to `unstructured` and works together with Unstructured-IO/unstructured-inference#349.
### Summary - Updates the `pinecone-client` from v2 to v4 using the [client migration guide](https://canyon-quilt-082.notion.site/Pinecone-Python-SDK-v3-0-0-Migration-Guide-056d3897d7634bf7be399676a4757c7b#932ad98a2d33432cac4229e1df34d3d5). Version bump was required to [add attribution](https://pinecone-2-partner-integration-guide.mintlify.app/integrations/build-integration/attribute-api-activity) and will also enable use to support [serverless indexes](https://docs.pinecone.io/reference/pinecone-clients#initialize) - Adds `"unstructured.{version}"` as the source tag for the connector ### Testing Destination connection tests [pass](https://github.com/Unstructured-IO/unstructured/actions/runs/9180305080/job/25244484432?pr=3067) with the updates.
**Summary** I preparation for adding DOCX pluggable image extraction, organize a few of the DOCX tests to be parallel to very similar tests for the DOC and ODT partitioners.
Summary: - bump unstructured-inference to `0.7.33` - cut a release for `0.14.2` - add some dependencies that previously came through from the layoutparser extras.
**Summary** Some partitioner test modules are placed in directories by themselves or with one other test module. This unnecessarily obscures where to find the test module corresponding to a partitiner. Move partitioner test modules to mirror the directory structure of `unstructured/partition`.
### Summary As seen in [this job](https://github.com/Unstructured-IO/unstructured/actions/runs/9182534479/job/25251583102), the build job for sphinx docs is failing, and has been failing for quite some time. This PR reverts the requirements file back to a [previous good commit](91b892c) for that job, and also moves the `build.in` file so the requirements file doesn't get update on `make pip-compile.` This is fine since those requirements don't get installed as part of the package, and we're deprecated the `sphinx` docs in favor of https://docs.unstructured.io anyway. ### Testing Build was [successful](https://github.com/Unstructured-IO/unstructured/actions/runs/9198605026/job/25301670934?pr=3077) on the feature branch. --------- Co-authored-by: Christine Straub <christinemstraub@gmail.com>
It's pretty basic change, just literally moved the category field to Element class. Can't think of other changes that are needed here, because I think pretty much everything expected the category to be directly in elements list. For local testing, IDE's and linters should see difference in that `category` is now in Element.
### Summary Closes #3078. Sets `resolve_entities=False` for parsing XML with `lxml` in `partition_xml` to avoid text being dynamically injected into the document. ### Testing `pytest test_unstructured/partition/test_xml.py` continues to pass with the update.
**Summary** Allow registration of a custom sub-partitioner that extracts images from a DOCX paragraph. **Additional Context** - A custom image sub-partitioner must implement the `PicturePartitionerT` interface defined in this PR. Basically have an `.iter_elements()` classmethod that takes the paragraph and generates zero or more `Image` elements from it. - The custom image sub-partitioner must be registered by passing the class to `register_picture_partitioner()`. - The default image sub-partitioner is `_NullPicturePartitioner` that does nothing. - The registered picture partitioner is called once for each paragraph.
Thanks to @0xjgv we have upserting instead of adding in Chroma. This will prevent duplicate embeddings. Also including a huggingface example. We had examples for all the other embedders.
This PR aims to add backward compatibility for the deprecated `pdf_infer_table_structure` parameter. A missing part of turning table extraction for PDFs and Images off by default in #3035, which was turned on in #2588. --------- Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com> Co-authored-by: christinestraub <christinestraub@users.noreply.github.com>
A couple of parameters needed for DOCX image extraction were not added as parameters to the `ElementMetadata` constructor when they were added as known fields. Also repair a couple gaps in alphabetical ordering cause by recent additions.
- change some info level logging for per page processing into detail level logging on trace logger - replace the try block in `document_to_element_list` to use `getattr` instead and add comment on the reason why sometimes `type` attribute may not exist for an element
This PR changes the output of table elements: now by default the table
elements' `metadata.table_as_cells` is `None`. The data will only be
populated when the env `EXTRACT_TABLE_AS_CELLS` is set to `true`.
The original design of the `table_as_cells` is for evaluate table
extraction performance. The format itself is not as readable as the
`table_as_html` metadata for human or RAG consumption. Therefore by
default this data is not needed.
Since this output is meant for evaluation use this PR choose to use an
environment variable to control if it should be present in the
partitioned results. This approach avoids adding parameters to the
`partition` function call. Adding a new parameter to the `partition`
interface increases the complexity of the interface and adds more
maintenance cost since there is a long chain of function calls to pass
down this parameter to where it is needed.
## test
running the following code snippet on main vs. this PR
```python
from unstructured.partition.auto import partition
elements = partition("example-docs/layout-parser-paper-with-table.pdf", strategy="hi_res", skip_infer_table_types=[])
table_cells = [element.metadata.table_as_cells, None) for element in elements if element.category == "Table"]
```
on main branch `table_cells` contains cell structured data but on this
branch it is a list of `None`
However if we first set in terminal:
```bash
export EXTRACT_TABLE_AS_CELLS=true
```
then run the same code again with this PR the `table_cells` would
contain actual data, the same as on main branch.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: badGarnet <badGarnet@users.noreply.github.com>
Original PR was #3069. Merged in to a feature branch to fix dependency and linting issues. Application code changes from the original PR were already reviewed and approved. ------------ Original PR description: Adding VoyageAI embeddings Voyage AI’s embedding models and rerankers are state-of-the-art in retrieval accuracy. --------- Co-authored-by: fzowl <160063452+fzowl@users.noreply.github.com> Co-authored-by: Liuhong99 <39693953+Liuhong99@users.noreply.github.com>
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