### 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.
We should be validating the S3 Destination with authenticated requests,
with credentials from a limited test user.
## Changes
- Updates s3 destination test to point to a bucket that requires
authentication.
- Adds authentication to the s3 destination test request
- Bonus: fix deserialization of S3ConnectionConfig for s3 V2 destination
- Bonus: fix S3ConnectionConfig never registered for s3 V2 destination
- Bonus: repair version and changelog version for consistency with -dev
convention
## Testing
Validated by changes to S3 destination ingest test
### 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>
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
This PR:
- Fixes occasional collection deletion failures for AstraDB via putting
collection deletion statements inside a trap statement. It uses click
commands to do this.
Testing:
- Run ingest astradb destination test
The mongodb redact method was created because we wanted part of the url
to be exposed to the user during logging. Thus it did not use the
dataclass `enhanced_field(sensitive=True)` solution.
This changes it to use our standard redacted solution. This also
minimizes the amount of work to be done in platform.
Thanks to @mogith-pn from Clarifai we have a new destination connector!
This PR intends to add Clarifai as a ingest destination connector.
Access via CLI and programmatic.
Documentation and Examples.
Integration test script.
Thanks to Eric Hare @erichare at DataStax we have a new destination
connector.
This Pull Request implements an integration with [Astra
DB](https://datastax.com) which allows for the Astra DB Vector Database
to be compatible with Unstructured's set of integrations.
To create your Astra account and authenticate with your
`ASTRA_DB_APPLICATION_TOKEN`, and `ASTRA_DB_API_ENDPOINT`, follow these
steps:
1. Create an account at https://astra.datastax.com
2. Login and create a new database
3. From the database page, in the right hand panel, you will find your
API Endpoint
4. Beneath that, you can create a Token to be used
Some notes about Astra DB:
- Astra DB is a Vector Database which allows for high-performance
database transactions, and enables modern GenAI apps [See
here](https://docs.datastax.com/en/astra/astra-db-vector/get-started/concepts.html)
- It supports similarity search via a number of methods [See
here](https://docs.datastax.com/en/astra/astra-db-vector/get-started/concepts.html#metrics)
- It also supports non-vector tables / collections
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>
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>
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>
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>
To test:
cd docs && make HTML
changelogs:
point main readme to the correct connector html page
point chroma docs to correct sample code
---------
Co-authored-by: potter-potter <david.potter@gmail.com>
There are several public interface points for chunking and they all
provide a default for arguments like `max_charactes`. These defaults are
provided by literal values. Keeping these synchronized has become a
problem.
Declare constant values for chunking argument default values and use
those wherever a non-trivial default is used in an end-user facing API
function.
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.
This PR updates Pinecone index creation in the ingest test due to a
recent update in Pinecone API.
Due to a change in Pinecone API, it is not allowed anymore to specify
both number of replicas and number of pods:
`Cannot specify both replicas and pods`
We solve it by removing the replica specification while sending the
index creation request.
```
Creating index ingest-test-28418
Index creation success: 201
```
### Description
* Make sure all destination connectors implement the base abstract
methods using the same signatures.
* Also leverage conform dict in the base methods to make sure it's
called in a consistent fashion.
* Additional updates to move the common code into the base destination
connector class
### Description
This PR handles two things:
* Fixes the serialization of the weaviate destination connector since
the client content breaks serialization when present due to `TypeError:
cannot pickle '_thread.lock' object`.
* Set finer auth control rather than generic dictionary on the CLI and
access config.
- 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>
This PR intends to add [Qdrant](https://qdrant.tech/) as a supported
ingestion destination.
- Implements CLI and programmatic usage.
- Documentation update
- Integration test script
---
Clone of #2315 to run with CI secrets
---------
Co-authored-by: Anush008 <anushshetty90@gmail.com>
Co-authored-by: Roman Isecke <136338424+rbiseck3@users.noreply.github.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.
### Description
All other connectors that were not included in
https://github.com/Unstructured-IO/unstructured/pull/2194 are now
updated to follow the new pattern and mark any variables as sensitive
where it makes sense.
Core changes:
* All connectors now support an `AccessConfig` to mark data that's
needed for auth (i.e. username, password) and those that are sensitive
are designated appropriately using the new enhanced field.
* All cli configs on the cli definition now inherit from the base config
in the connector file to reuse the variables set on that dataclass
* The base writer class was updated to better generalize the new
approach given better use of dataclasses
* The base cli classes were refactored to also take into account the
need for a connector and write config when creating the respective
runner/writer classes.
* Any mismatch between the cli field name and the dataclass field name
were updated on the dataclass side to not impact the user but maintain
consistency
* Add custom redaction logic for mongodb URIs since the password is
expected to be a part of it. Now this:
`"mongodb+srv://ingest-test-user:r4hK3BD07b@ingest-test.hgaig.mongodb.net/"`
->
`"mongodb+srv://ingest-test-user:***REDACTED***@ingest-test.hgaig.mongodb.net/"`
in the logs
* Bundle all fsspec based files into their own packages.
* Refactor custom `_decode_dataclass` used for enhanced json mixin by
using a monkey-patch approach. The original approach was breaking on
optional nested dataclasses when serializing since the other methods in
`dataclasses_json_core` weren't using the new method. By monkey-patching
the original method with a new one, all other methods in that library
would use the new one.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
### Description
Given the filtering in the ingest logger, anything going to console
should go through that. This adds a linter that only checks for
`print()` statements in the ingest code and ignored it elsewhere for
now.
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.
### Description
Often times there are tests being skipped either due to missing env vars
or explicitly defined in the base script but these get lost in the logs.
This PR updates the scripts to leverage a custom error code if being
skipped due to missing env vars and this custom error code is being
caught by the base script and logs all files being skipped to a file. At
the end of the script, this file gets logged in the CI output.
### Description
Update any use of OpenAI for generating embeddings in the ingest tests
to use Huggingface
**Bonus Changes:**
* Remove duplicate delta table test
* Delete delta table destination directory at the beginning of the test
to make sure it doesn't exist and prevent the test from breaking.
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>
### Description
This adds the basic implementation of pushing the generated json output
of partition to mongodb. None of this code provisions the mondo db
instance so things like adding a search index around the embedding
content must be done by the user. Any sort of schema validation would
also have to take place via user-specific configuration on the database.
This update makes no assumptions about the configuration of the database
itself.
### Description
To not require additional dependencies on cloud-related CLIs (i.e.
gcloud and az), using python and the existing dependencies already used
to run out code to interact with those providers for overhead work
associated with destination ingest tests.
Intermittently the various destination test will fail with:
```
{noformat}--- Cleanup done ---
gs://utic-test-ingest-fixtures-output/1699377964/example-docs/
deleting gs://utic-test-ingest-fixtures-output/1699377964
Removing objects:
ERROR: (gcloud.storage.rm) The following URLs matched no objects or files:
-gs://utic-test-ingest-fixtures-output/1699377964
Last ran script: gcs.sh
Error: Process completed with exit code 1.{noformat}
```
Reference trace
[here](https://github.com/Unstructured-IO/unstructured/actions/runs/6787927424/job/18452240764?pr=2020)
After some investigation it looks like this error is due to collisions
that occur because we’re assuming 1s date accuracy is sufficient when
generating (and deleting) "unique" test destination location names. The
likelihood is actually pretty high given that we run these tests against
a test matrix.
Instead we should just use a uuid for these unique destinations.
## Changes
- Use uuidgen instead of `date +%s` for unique destinations
### Description
* A full schema was introduced to map the type of all output content
from the json partition output and mapped to a flattened table structure
to leverage table-based destination connectors. The delta table
destination connector was updated at the moment to take advantage of
this.
* Existing method to convert to a dataframe was updated because it had a
bug in it. Object content in the metadata would have the key name
changed when flattened but then this would be omitted since it didn't
exist in the `_get_metadata_table_fieldnames` response.
* Unit test was added to make sure we handle all values possible in an
Element when converting to a table
* Delta table ingest test was split into a source and destination test
(looking ahead to split these up in CI)
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
### Description
Update all destination tests to match pattern:
* Don't omit any metadata to check full schema
* Move azure cognitive dest test from src to dest
* Split delta table test into seperate src and dest tests
* Fix azure cognitive search and add to dest tests being run (wasn't
being run originally)
This PR resolves
[CORE-2453](https://unstructured-ai.atlassian.net/browse/CORE-2453):
- parametrizes the output folder so that ingest output files can be
saved other than the same place where the scripts are; this is set by
env `OUTPUT_ROOT`
- parametrize the python path `PYTHONPATH` to first check existing
definition before default to `.`, the current folder
- parametrize the run script that carries out ingest using `RUN_SCRIPT`,
default is still `./unstructured/ingest/main.py`
These changes allows us to run ingest test with more control. To test:
- run `OUTPUT_ROOT=/tmp
./test_unstructured_ingest/src/local-single-file.sh`: the output now
should be in `/tmp` instead of in the ingest test folder
- run `RUN_SCRIPT=/hope/you/do/not/have/this/folder
./test_unstructured_ingest/src/local-single-file.sh` would raise an
error because system can't find `/hope/you/do/not/have/this/folder`
- run `RUN_SCRIPT=./unstructured/ingest/main.py
./test_unstructured_ingest/src/local-single-file.sh` should run as
normal
- do the following
```bash
cp ./unstructured/ingest/main.py /tmp/main.py
OUTPUT_ROOT=/tmp PYTHONPATH=$(pwd) RUN_SCRIPT=./unstructured/ingest/main.py ./test_unstructured_ingest/src/local-single-file.sh
```
This will run and generate output at `/tmp`
[CORE-2453]:
https://unstructured-ai.atlassian.net/browse/CORE-2453?atlOrigin=eyJpIjoiNWRkNTljNzYxNjVmNDY3MDlhMDU5Y2ZhYzA5YTRkZjUiLCJwIjoiZ2l0aHViLWNvbS1KU1cifQ
### Description
This splits the source ingest tests from the destination ingest tests
since they share a different pattern:
* src tests pull data from a source and compare the partitioned content
to the expected results
* destingation tests leverage the local connector to produce results to
push to a destination and leverages overhead to create temporary
locations at those destinations to write to and delete when done.
Only the src tests create partitioned content that needs to be checked
so the update ingest test CI job only needs to run these.
