Updated CI to shave time off in some conditions with no real downside.
- When the base cache already exists, we don't download it during setup,
and we skip all other steps as well.
- During ingest setup, we check if the ingest cache exists before
downloading the base cache, and if the ingest cache already exists, we
skip everything else.
- `check-deps` doesn't have to wait on `setup` or download a cache, as
the dependencies aren't needed, only `pip`.
### Description
Currently the CI caches the CI dependencies but uses the hash of all
files in `requirements/`. This isn't completely accurate since the
ingest dependencies are installed in a later step and don't affect the
cached environment. As part of this PR:
* ingest dependencies were isolated into their own folder in
`requirements/ingest/`
* A new cache setup was introduced in the CI to restore the base cache
-> install ingest dependencies -> cache it with a new id
* new make target created to install all ingest dependencies via `pip
install -r ...`
* updates to Dockerfile to use `find ...` to install all dependencies,
avoiding the need to update this when new deps are added.
* update to pip-compile script to run over all `*.in` files in
`requirements/`
### Description
Given that many of the options associated with the `Click` based cli
ingest commands are added dynamically from a number of configs, a check
was incorporated to make sure there were no duplicate entries to prevent
new configs from overwriting already added options.
### Issues that were found and fixes:
* duplicate api-key option set on Notion command conflicts with api key
used for unstructured api. Added notion prefix.
* retry logic configs had duplicates in biomed. Removed since this is
not handled by the pipeline.
This moves the setup-python step on ingest job above the cache restore,
otherwise cache is restored and setup-python breaks symlinks. This
matches pattern on other jobs.
PR to support schema changes introduced from [PR
232](https://github.com/Unstructured-IO/unstructured-inference/pull/232)
in `unstructured-inference`.
Specifically what needs to be supported is:
* Change to the way `LayoutElement` from `unstructured-inference` is
structured, specifically that this class is no longer a subclass of
`Rectangle`, and instead `LayoutElement` has a `bbox` property that
captures the location information and a `from_coords` method that allows
construction of a `LayoutElement` directly from coordinates.
* Removal of `LocationlessLayoutElement` since chipper now exports
bounding boxes, and if we need to support elements without bounding
boxes, we can make the `bbox` property mentioned above optional.
* Getting hierarchy data directly from the inference elements rather
than in post-processing
* Don't try to reorder elements received from chipper v2, as they should
already be ordered.
#### Testing:
The following demonstrates that the new version of chipper is inferring
hierarchy.
```python
from unstructured.partition.pdf import partition_pdf
elements = partition_pdf("example-docs/layout-parser-paper-fast.pdf", strategy="hi_res", model_name="chipper")
children = [el for el in elements if el.metadata.parent_id is not None]
print(children)
```
Also verify that running the traditional `hi_res` gives different
results:
```python
from unstructured.partition.pdf import partition_pdf
elements = partition_pdf("example-docs/layout-parser-paper-fast.pdf", strategy="hi_res")
```
---------
Co-authored-by: Sebastian Laverde Alfonso <lavmlk20201@gmail.com>
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: christinestraub <christinemstraub@gmail.com>
This PR:
- defines rbac_data as a SourceMetadata field,
- manages connections to an external api for obtaining rbac data with
ConnectorRBAC class,
- serializes rbac data and saves it to the disk,
- matches the rbac_data in the disk to each IngestDoc, using a common
field,
- forwards rbac data to Elements, via the partition() function
To test the changes, run `examples/ingest/sharepoint/ingest.sh` with the
relevant rbac & connector credentials
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
Currently adding the embedding flag to any unstructured-ingest call
results in this failure:
```
2023-10-11 22:42:14,177 MainProcess ERROR 'b8a98c5d963a9dd75847a8f110cbf7c9'
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Users/ryannikolaidis/.pyenv/versions/3.10.11/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/Users/ryannikolaidis/.pyenv/versions/3.10.11/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/Users/ryannikolaidis/Development/unstructured/unstructured/unstructured/ingest/pipeline/copy.py", line 14, in run
ingest_doc_json = self.pipeline_context.ingest_docs_map[doc_hash]
File "<string>", line 2, in __getitem__
File "/Users/ryannikolaidis/.pyenv/versions/3.10.11/lib/python3.10/multiprocessing/managers.py", line 833, in _callmethod
raise convert_to_error(kind, result)
KeyError: 'b8a98c5d963a9dd75847a8f110cbf7c9'
"""
```
This is because the run method for the embedding node is not adding the
IngestDoc to the context map. This PR adds that logic and adds a test to
validate that the embeddings option works as expected.
NOTE: until https://github.com/Unstructured-IO/unstructured/pull/1719
goes in, the expected results include the duplicate element bug, however
currently this does at least prove that embeddings are generated and the
function doesn't error.
We’re probably unfairly (to the test) making a large volume of new
connections and requests to test services when all of our ingest tests
run across the full python test matrix and when a lot of PRs a firing at
once. Lets limit the full matrix run to a select few, but still have all
ingest tests run on python v3.10. This is done by checking the version
and skipping in ingest-test.sh.
Bonus: Bumps ingest test fixture workflow to use 3.10. This technically
shouldn't make a difference, but since we're making 3.10 the default of
the matrix strategy, it probably makes sense to use 3.10 for the ingest
fixture generation as well for consistency.
## Testing
-
[example](https://github.com/Unstructured-IO/unstructured/actions/runs/6460319121/job/17537900978?pr=1687)
running all tests in 3.10
-
[example](https://github.com/Unstructured-IO/unstructured/actions/runs/6460319121/job/17537899999?pr=1687)
skipping/running the expected tests in 3.8
This PR adds support for `source` property from
`unstructured_inference`, allowing the user to be able to see the origin
of the data under `detection_origin`field environment variable
UNSTRUCTURED_INCLUDE_DEBUG_METADATA=true
In order to try this feature you can use this code:
```
from unstructured.partition.pdf import partition_pdf_or_image
yolox_elements = partition_pdf_or_image(filename='example-docs/loremipsum-flat.pdf', strategy='hi_res', model_name='yolox')
sources = [e.detection_origin for e in yolox_elements]
print(sources)
```
And will print 'yolox' as source for all the elements
### Description
New [Azure Cognitive
Search](https://azure.microsoft.com/en-us/products/ai-services/cognitive-search)
destination connector added. Writes each json element from the created
json files via partition and writes that content to an index.
**Bonus bug fix:** Due to a recent change where the default version of
python used in the repo was bumped to `3.10` from `3.8`, this means
running `pip-compile` now runs it against that version rather than the
lowest we support which is still `3.8`. This breaks the setup for those
lower versions because some of the versions pulled in by `pip-compile`
exist for `3.10` but not `3.8`. `pip-compile` was updates to run as a
script that checks the version of python being used first, which helps
guarantee that all dependencies meet the minimum python version
requirement.
Closes out https://github.com/Unstructured-IO/unstructured/issues/1466
## Summary
Ingest tests are having paddle OOM issue which cause the tests to hang
forever. The fix here is to remove paddle from ci and set both OCR env
`TABLE_OCR` and `ENTIRE_PAGE_OCR` to `tesseract`. (will have follow up
PR to investigate why this is failing)
## Test
please check ingest tests in CI
This PR ensures the version for `weaviate` is consistent in CI testing.
Latest (3.24.1) is not compatible with our test needs and last version
that run successfully in CI is 3.23.2.
This connector:
- takes a Jira Cloud URL, user email and api token; to authenticate into
Jira Cloud
- ingests:
- either all issues in all projects in a Jira Cloud Organization
- or
- issues in user specified projects, boards
- user specified issues
- processes this kind of data:
- text fields such as issue summary, description, and comments
- dropdown fields such as issue type, status, priority, assignee,
reporter, labels, and components
- other data such as issue id, issue key, project id, information on
subtasks
- notes down attachment URLs, however does not process attachments
- stores each downloaded issue in a txt file, in a predefined template
form (consisting of the data above)
- then processes each downloaded issue document into elements using
unstructured library
- related to: https://github.com/Unstructured-IO/unstructured/issues/263
To test the changes, make the necessary setups and run the relevant
ingest test scripts.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
### Description
Add delta table connector and test against a delta table generated via
delta.io and uploaded to s3. Shows an example of how to use the
connection options to leverage s3.
I was able to get this to work with s3 if I pass in the access and
secret keys as storage options. Even though the s3 bucket being used is
public, would not work without those.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
### Description
* Add ingest test for Notion docs
* Update default cache dir for connectors to include connector name.
Makes debugging the cached content easier.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
**Summary**
Closes#747
* Create CI Pipeline for running text, xml, email, and html doc tests
against the library installed without extras
* Create CI Pipeline for running each library extra against their
respective tests
* add the first version of airtable connector
* change imports as inline to fail gracefully in case of lacking dependency
* parse tables as csv rather than plain text
* add relevant logic to be able to use --airtable-list-of-paths
* add script for creation of reseources for testing, add test script (large) for testing with a large number of tables to validate scroll functionality, update test script (diff) based on the new settings
* fix ingest test names
* add scripts for the large table test
* remove large table test from diff test
* make base and table ids explicit
* add and remove comments
* use -ne instead of !=
* update code based on the recent ingest refactor, update changelog and version
* shellcheck fix
* update comments
* update check-num-rows-and-columns-output error message
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
* update help comments
* update help comments
* update help comments
* update workflows to set auth tokens and to run make install
* add comments on create_scale_test_components
* separate component ids from the test script, add comments to document test component creation
* add LARGE_BASE test, implement LARGE_BASE component creation, replace component id
* shellcheck fixes
* shellcheck fixes
* update docs
* update comment
* bump version
* add wrongly deleted file
* sort columns before saving to process
* Update ingest test fixtures (#1098)
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* Add confluence connector and an example script
* add test script, add dependency installations
* add authentication secret variables for ci tests and actions
* add dependency installation commands for workflows
* add dependency installation commands for workflows
* Update ingest test fixtures (#907)
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* add add ingest test fixtures update workflow for python 3.10, update example script with dummy values
* change workflow name to avoid confusion
* change workflow name to avoid confusion
* only leave 3.8 in ingest test matrix to test consistent partitioning among python versions, remove 3.10 workflow for the test fixtures update
* only leave 3.8 in ingest test matrix to test consistent partitioning among python versions
* Update ingest test fixtures (#911)
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* revert back the test python version matrix
* recompile dependencies
* modifications for shellcheck
* update changelog and version
* changelog and version
* remove comments
* Update ingest test fixtures (#915)
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* add the option to state the number of spaces to be fetched
* add scroll functionality, expose --confluence-num-of-spaces, --confluence-list-of-spaces and --confluence-num-of-docs-from-each-space to users
* add help message
* add docstrings for two tests, validate grabbing every doc in the fetched spaces, count number of files instead of diffing for confluence2 test
* change test names
* rename connector arg
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
* change arg name for connector
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
* add comment to example
* change arg names
* add new tests to ingest test
* shellcheck remove redundant statement
* Update ingest test fixtures (#932)
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* Update ingest test fixtures (#936)
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* linting
* change file extensions to parse as html
* Update ingest test fixtures (#943)
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* remove old fixtures
* update version to 0.8.2-dev3
* change file to trigger CI
* change file to trigger CI
* change file to trigger CI
* change file to trigger CI
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
* remove argilla; bump reqs
* enable py 3.11
* add 3.11 to setup.py
* make pip-compile
* ignore cli mypy errors
* install argilla
* fix constraints
* install argilla
* changelog and version
* skip argilla in docker
* dont import argilla in docker
* skip all of argilla if in container
* only import argilla if outside docker
* more docker skips
* remove weird pypi settings
