In this pull request parent-child relationship for elements generated
with v2 parser is based on actual element IDs instead of IDs baked
somewhere in the HTML script.
With some extra bug fixing it allowed for significantly simplifying json
-> HTML script
## NOTE
`test_unstructured_ingest/expected-structured-output-html` contains all
test HTML fixtures. Original JSON files, from which these HTML fixtures
are generated, were taken from
`test_unstructured_ingest/expected-structured-output`
E.g., now can run:
```bash
# extracts base64 encoded image data for `Table` and `Image` elements
$ unstructured-get-json.sh --trace --verbose --images /t/docs/Captur-1317-5_ENG-p5.pdf
# also extracts `Title` elements (see screenshot)
$ IMAGE_BLOCK_TYPES='"title","table","image"' unstructured-get-json.sh --trace --verbose --images /t/docs/Captur-1317-5_ENG-p5.pdf
```
It was discovered during testing that "narrativetext" does not work,
probably due to camel casing of NarrativeText 😬
Script to render HTML from unstructured elements.
NOTE: This script is not intended to be used as a module.
NOTE: This script is only intended to be used with outputs with
non-empty `metadata.text_as_html`.
TODO: It was noted that unstructured_elements_to_ontology func always
returns a single page
This script is using helper functions to handle multiple pages. I am not
sure if this was intended, or it is a bug - if it is a bug it would
require bit longer debugging - to make it usable fast I used
workarounds.
Usage: test with any outputs with non-empty `metadata.text_as_html`.
Example files attached.
`[Example-Bill-of-Lading-Waste.docx.pdf.json](https://github.com/user-attachments/files/17922898/Example-Bill-of-Lading-Waste.docx.pdf.json)`
[Breast_Cancer1-5.pdf.json](https://github.com/user-attachments/files/17922899/Breast_Cancer1-5.pdf.json)
### Description
Alternative to https://github.com/Unstructured-IO/unstructured/pull/3572
but maintaining all ingest tests, running them by pulling in the latest
version of unstructured-ingest.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
Co-authored-by: Christine Straub <christinemstraub@gmail.com>
Co-authored-by: christinestraub <christinestraub@users.noreply.github.com>
**Summary**
Step 2 in prep for pluggable auto-partitioners, remove `regex_metadata`
field from `ElementMetadata`.
**Additional Context**
- "regex-metadata" was an experimental feature that didn't pan out.
- It's implemented by one of the post-partitioning metadata decorators,
so get rid of it as part of the cleanup before consolidating those
decorators.
**Summary**
In preparation for consolidating post-partitioning metadata decorators,
extract `partition.common` module into a sub-package (directory) and
extract `partition.common.metadata` module to house metadata-specific
object shared by partitioners.
**Additional Context**
- This new module will be the home of the new consolidated metadata
decorator.
- The consolidated decorator is a step toward removing post-processing
decorators from _delegating_ partitioners. A delegating partitioner is
one that convert its file to a different format and "delegates" actual
partitioning to the partitioner for that target format. 10 of the 20
partitioners are delegating partitioners.
- Removing decorators from delegating partitioners will allow us to
avoid "double-decorating", i.e. running those decorators twice, once on
the principal partitioner and again on the proxy partitioner.
- This will allow us to send `**kwargs` to either partitioner, removing
the knowledge of which arguments to send for each file-type from
auto-partition.
- And this will allow pluggable auto-partitioners which all have a
`partition_x(filename, *, file, **kwargs) -> list[Element]` interface.
**Summary**
Remove dead code in `unstructured.file_utils`.
**Additional Context**
These modules were added in 12/2022 and 1/2023 and are not referenced by
any code. Removing to reduce unnecessary complexity. These can of course
be recovered from Git history if we decide we want them again in future.
Adds the bash script `process-pdf-parallel-through-api.sh` that allows
splitting up a PDF into smaller parts (splits) to be processed through
the API concurrently, and is re-entrant. If any of the parts splits fail
to process, one can attempt reprocessing those split(s) by rerunning the
script.
Note: requires the `qpdf` command line utility.
The below command line output shows the scenario where just one split
had to be reprocessed through the API to create the final
`layout-parser-paper_combined.json` output.
```
$ BATCH_SIZE=20 PDF_SPLIT_PAGE_SIZE=6 STRATEGY=hi_res \
./scripts/user/process-pdf-parallel-through-api.sh example-docs/pdf/layout-parser-paper.pdf
> % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
Skipping processing for /Users/cragwolfe/tmp/pdf-splits/layout-parser-paper-output-8a76cb6228e109450992bc097dbd1a51_split-6_strat-hi_res/layout-pars\
er-paper_pages_1_to_6.json as it already exists.
Skipping processing for /Users/cragwolfe/tmp/pdf-splits/layout-parser-paper-output-8a76cb6228e109450992bc097dbd1a51_split-6_strat-hi_res/layout-parser-paper_pages_7_to_12.json as it already exists.
Valid JSON output created: /Users/cragwolfe/tmp/pdf-splits/layout-parser-paper-output-8a76cb6228e109450992bc097dbd1a51_split-6_strat-hi_res/layout-parser-paper_pages_13_to_16.json
Processing complete. Combined JSON saved to /Users/cragwolfe/tmp/pdf-splits/layout-parser-paper-output-8a76cb6228e109450992bc097dbd1a51_split-6_strat-hi_res/layout-parser-paper_combined.json
```
Bonus change to `unstructured-get-json.sh` to point to the standard
hosted Serverless API, but allow using the Free API with --freemium.
This PR aims to remove "unstructured.paddlepaddle" fork. Previously, we
used `unstructured.paddlepaddle` fork to support
`unstructured.paddleocr` on arm64 architecture. But currently,
`unstructured.paddleocr` with `unstructured.paddlepaddle` fails to work
on `arm64` architecture. Also, `unstructured.paddleocr` with the latest
version of the original `paddlepaddle` works on both `amd64` and `arm64`
architectures.
### Testing
```
os.environ["OCR_AGENT"] = "unstructured.partition.utils.ocr_models.paddle_ocr.OCRAgentPaddle"
elements = partition_pdf(
filename=<file_path>,
strategy="hi_res",
infer_table_structure=True,
)
```
### Summary
Adds a CI check to ensure that packages added as dependencies are
appropriately licensed. All of the `.txt` files in the `requirements`
directory are checked with the exception of:
- `constraints.txt`, since those are not installed and are instead
conditions on the other dependency files
- `dev.txt`, since those are for local development and not shipped as
part of the `unstructured` package
- `extra-pdf-image.txt` - the `extra-pdf-image.in` since checking
`extra-pdf-image.txt` pulls in NVIDIA GPU related packages with an
`Other/Proprietary` license type, and there's not a good way to exclude
those without adding `Other/Proprietary` to the allowed licenses list.
### Testing
The new `check-licenses` job should pass in CI.
### Summary
Updates to the latest version of the `wolfi-base` image. Changes
include:
- Version bumps to address CVEs
- `libreoffice` is now included in the `arm64`. `.doc` files are now
supported for `arm64`. `.ppt` do not work with the `libreoffice` package
currently available on `wolfi-os`. We have follow on work to look into
that.
- Updates the location of the `tesseract` `tessdata` files on the
`arm64` build. Closes#3290.
- Closes#3319 and addes `psutil` to the base dependencies.
### Testing
- `test_dockerfile` should continue to pass with the updates.
### Description
In use cases where an external system (such as code being run in a
jupyter notebook) already has a running event loop, run the async code
in a dedicated thread pool to not conflict with the existing event loop.
This also has a variety of fixes that were found when putting together a
demo leveraging the elasticsearch destination connector
Thanks to @tullytim we have a new Kafka source and destination
connector. It also works with hosted Kafka via Confluent.
Documentation will be added to the Docs repo.
This PR aims to fix a docker image publishing error caused by user
changes when pulling the `amd64` image from the `unstructured`
`wolfi-base` image.
(https://github.com/Unstructured-IO/unstructured/pull/3213).
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: christinestraub <christinestraub@users.noreply.github.com>
### Summary
Closes#3173. Removes the `overwrite_schema` kwarg from the Delta Table
connector and bumps the `deltalake` version. Per [this
PR](https://github.com/delta-io/delta-rs/pull/2554) in the `deltalake`
repo, the `overwrite_schema` kwarg is deprecated as of version `0.18.0`.
Users can specify `schema_mode="merge"` to obtain the same behavior.
- `schema_mode="merge"` is equivalent to `overwrite_schema=False`
- `schema_mode="overwrite"` is equivalent to `overwrite_schema=True`
Also adds an `engine` parameter that you can use to set `"rust"` or
`"pyarrow"` as the engine. `engine` defaults to `"pyarrow"` and
`schema_mode` defaults to `None`, which is consistent with the behavior
in `deltalake` documented
[here](https://delta-io.github.io/delta-rs/api/delta_writer/).
### Testing
The Delta Table ingest tests should pass on this PR.
---------
Co-authored-by: Ahmet Melek <39141206+ahmetmeleq@users.noreply.github.com>
### Description
Move over all fsspec connectors to the new framework
Variety of bug fixes found and fixed in this PR as well:
* custom json mixin being used for the enhanced dataclass would break if
typing was quoted. That was fixed. A check was also added to the
enhanced dataclass to prevent `InitVar` from being used in the root
dataclass since this breaks serialization.
* hashing for partitioner was using the filename of the raw file being
partitioned rather than the file name of the file data generated from
indexing. This means that mutliple files could result in the same
partition hash when recursive flag is passed in. This was updated to use
the file data file name instead.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@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>
### 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
Updates the `Dockerfile` to use the Chainguard `wolfi-base` image to
reduce CVEs. Also adds a step in the docker publish job that scans the
images and checks for CVEs before publishing. The job will fail if there
are high or critical vulnerabilities.
### Testing
Run `make docker-run-dev` and then `python3.11` once you're in. And that
point, you can try:
```python
from unstructured.partition.auto import partition
elements = partition(filename="example-docs/DA-1p.pdf", skip_infer_table_types=["pdf"])
elements
```
Stop the container once you're done.
### Description
* The `consistent-deps.sh` was fixed to take into account the ingest
dependencies, causing some errors to show up. New constriants were added
to make that script pass.
* Update all requirements without constraint on pydantic, allowing the
latest version to be pulled in.
* `pikepdf` is causing a conflict but there's a fix on their `main`
branch, just need for the next release to be published. Opened up a
question here to see if we can get that out any sooner: [Do releases
happen on a
schedule?](https://github.com/pikepdf/pikepdf/discussions/574). For now
added `lxml<5` to the constraints.
A couple optimizations:
* `constraints.in` renamed to `constraints.txt` since the whole point is
all dependencies are already pinned and the file never gets compiled
* `constraints.txt` moved to a `requirements/deps` directory as this
never gets compiled by `pip-compile`
* Other dependency files updated to reference the new location of
`base.in` and `constraints.txt`
* make file updated since it was originally written to avoid the
`base.in` and `constraints.in` file
### Description
Currently the requirements associated with an extra in the `setup.py` is
being dynamically generated using the `load_requirements()` method in
the same file. This is being passed in all the `.in` files which then
get read line by line to generate the requirements associated with an
extra. Unless the `.in` file itself has a version pin, this will never
respect the `.txt` files being generated by `pip-compile`. This fix
updates all the inputs to `load_requirements()` to use the `.txt` files
themselves.
change opensearch port to see if fixes CI. We think there may be a
conflict with the elasticsearch docker port.
Also adding simple retry to vector query.
---------
Co-authored-by: potter-potter <david.potter@gmail.com>
Adds OpenSearch as a source and destination.
Since OpenSearch is a fork of Elasticsearch, these connectors rely
heavily on inheriting the Elasticsearch connectors whenever possible.
- Adds OpenSearch source connector to be able to ingest documents from
OpenSearch.
- Adds OpenSearch destination connector to be able to ingest documents
from any supported source, embed them and write the embeddings /
documents into OpenSearch.
- Defines an example unstructured elements schema for users to be able
to setup their unstructured OpenSearch indexes easily.
---------
Co-authored-by: potter-potter <david.potter@gmail.com>
Currently in the Elasticsearch Destination ingest test we are writing
the embeddings to a "float" type field. In order to leverage this field
for similarity search it should be mapped as "dense_vector" with the
respective dimensions assigned.
This PR updates that mapping and adds a test query to validate that this
works as expected.
- Adds a destination connector to upload processed output into a
PostgreSQL/Sqlite database instance.
- Users are responsible to provide their instances. This PR includes a
couple of configuration examples.
- Defines the scripts required to setup a PostgreSQL instance with the
unstructured elements schema.
- Validates postgres/pgvector embedding storage and retrieval
---------
Co-authored-by: potter-potter <david.potter@gmail.com>
Closes https://github.com/Unstructured-IO/unstructured/issues/1842
Closes https://github.com/Unstructured-IO/unstructured/issues/2202
Closes https://github.com/Unstructured-IO/unstructured/issues/2203
This PR:
- Adds Elasticsearch destination connector to be able to ingest
documents from any supported source, embed them and write the embeddings
/ documents into Elasticsearch.
- Defines an example unstructured elements schema for users to be able
to setup their unstructured elasticsearch indexes easily.
- Includes parallelized upload and lazy processing for elasticsearch
destination connector.
- Rearranges elasticsearch test helpers to source, destination, and
common folders.
- Adds util functions to be able to batch iterables in a lazy way for
uploads
- Fixes a bug where removing the optional parameter `--fields` broke the
connector due to an integer processing error.
- Fixes a bug where using an [elasticsearch
config](8fa5cbf036/unstructured/ingest/connector/elasticsearch.py (L26-L35))
for a destination connector resulted in a serialization issue when
optional parameter `--fields` was not provided.
Adds Chroma (also known as ChromaDB) as a vector destination.
Currently Chroma is an in-memory single-process oriented library with
plans of a hosted and/or more production ready solution
-https://docs.trychroma.com/deployment
Though they now claim to support multiple Clients hitting the database
at once, I found that it was inconsistent. Sometimes multiprocessing
worked (maybe 1 out of 3 times) But the other times I would get
different errors. So I kept it single process.
---------
Co-authored-by: potter-potter <david.potter@gmail.com>
### Description
Given all the shell files that now exist in the repo, would be nice to
have linting/formatting around them (in addition to the existing
shellcheck which doesn't do anything to format the shell code). This PR
introduces `shfmt` to both check for changes and apply formatting when
the associated make targets are called.
Adds source connector for SFTP which uses fsspec and paramiko via
fsspec. Paramiko is the standard sftp package for python used in pysftp
etc...
```
--username foo \
--password bar \
--remote-url sftp://localhost:47474/upload/
```
Will only download a specifically requested file if it has an extension.
(i.e. `--remote-url sftp://localhost:47474/upload/bob.zip`) It will
treat any other remote_url as a folder path. This is intentional.
---------
Co-authored-by: potter-potter <david.potter@gmail.com>
### Description
Building off of PR
https://github.com/Unstructured-IO/unstructured/pull/2179, updating
fsspec based connectors to use better authentication field handling.
This PR adds in the following changes:
* Update the base classes to inherit from the enhanced json mixin
* Add in a new access config dataclass that should be used as a nest
dataclass in the connector configs
* Update the code extracting configs out of the cli options dictionary
to support the nested access config if it exists on the parent config
* Update all fsspec connectors with explicit access configs given what
each one's SDKs support
* Update the json mixin and enhanced field to support a name override
when serializing/deserializing from json/dicts. This allows a different
name to be used for the CLI option than what the name of the field is on
the dataclass.
* Update all the writes to use class-based approach and share the same
structure of the runner classes
* Above update allowed for better code to be used in the base source and
destination CLI commands
* Add in utility code around paring a flat dictionary (coming from the
click based options) into dataclass-based configs with potentially
nested dataclasses.
**Slightly unrelated changes:**
* session handle removed from pinecone connector as this was breaking
the serialization of the write config and didn't have any benefit as a
connection was never being shared, the index used simply makes a new
http call each time it's invoked.
* Dedicated write configs were created for all destination connectors to
better support serialization
* Refactor of Elasticsearch connector included, with update to ingest
test to use auth
**TODOs**
* Left a `#TODO` in the code but the way session handler is implemented
right now, it breaks serialization since it adds a generic variable
based on the library being used for a connector (i.e.
`googleapiclient.discovery.Resource`) which is not serializable. This
will need to be updated to omit that from serialization but still
support the current workflow.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
Closes#1781.
- Adds a Weaviate destination connector
- The connector receives a host for the weaviate instance and a weaviate
class name.
- Defines a weaviate schema for json elements.
- Defines the pre-processing to conform unstructured's schema to the
proposed weaviate schema.
**Executive Summary**
Eyeballing or saving html in a Table element (in the
`metadata.text_as_html` field) takes some manual effort. This script
provides a quick way to do so given an unstructured .json file that
adheres to the usual schema (i.e., that's returned by the Unstructured
API).
**Testing Instructions**
Get some unstructured output that includes a table. E.g.
[124_PDFsam_Basel III - Finalising post-crisis
reforms.pdf](https://github.com/Unstructured-IO/unstructured/files/13407404/124_PDFsam_Basel.III.-.Finalising.post-crisis.reforms.pdf)
```
./unstructured-get-json.sh --tables --hi-res \
124_PDFsam_Basel\ III\ -\ Finalising\ post-crisis\ reforms.pdf
````
Then use this the following script to view the structure and content of
the tables: (note that output file was copied to the clipboard from
prior command):
```
./u-tables-inspect.sh \
"<snip>/tmp/unst-outputs/124_PDFsam_Basel III - Finalising post-crisis reforms.pdf-hi-res.json"
```
Usage: ./unstructured-get-json.sh [options] <file>"
Options:
--api-key KEY Specify the API key for authentication. Set the env var $UNST_API_KEY to skip providing this option.
--hi-res hi_res strategy: Enable high-resolution processing, with layout segmentation and OCR
--fast fast strategy: No OCR, just extract embedded text
--ocr-only ocr_only strategy: Perform OCR (Optical Character Recognition) only. No layout segmentation.
--tables Enable table extraction: tables are represented as html in metadata
--coordinates Include coordinates in the output
--trace Enable trace logging for debugging, useful to cut and paste the executed curl call
--verbose Enable verbose logging including printing first 8 elements to stdout
--s3 Write the resulting output to s3 (like a pastebin)
--help Display this help and exit.
Arguments:
<file> File to send to the API.
The script requires a <file>, the document to post to the Unstructured API.
The .json result is written to ~/tmp/unst-outputs/ -- this path is echoed and copied to your clipboard.
