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>
### 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
Modify the logger being used by ingest to leverage a new class
implemented inheriting `logging.Formatter` which adds in some middleware
to update the message being logged to omit any sensitive content. It
does this by dynamically pulled out any valid json from the string being
logged and runs that through a `hide_sensitive_fields` method which
updated any values that are considered sensitive. Replaces the original
json strings with the `json.dumps` version of the new dictionary.
### 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.
Closes#1843
Ingest connector for HubSpot. Supports:
- Calls: Logs from calls related to contacts, companies and tickets
- Communications: Logs from SMS/Whatsapp related to contacts, companies
and tickets
- Notes: Notes related to CRM notes
- Products: CRM products
- Emails: Logs from emails sent to CRM objects.
- Tasks: CRM tasks
From each record, `body/`description`information is grabbed. When a
title property is available, this is registered at the beggining of the
output file. The CLI receives three params:
- `api-token`: [Private
app](https://developers.hubspot.com/docs/api/private-apps) token.
- `object-types: One of the noted supported objects in the form of a
comma separated list: `calls,products,tasks`
- `custom-properties`: Custom properties to grab information from. Must
be in the form
`<object_type>:<custom_property_id>,<object_type>:<custom_property_id>`
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rvztz <rvztz@users.noreply.github.com>
### Description
When passing in a remote path for fsspec-based source connectors, the
base directory was always being included in the output path itself. This
was updated to exclude the base directory any only include any child
directories relative to the base one.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
### Description
There are some source ingest connectors that would be more efficient to
read the content in batches rather than use an entire process per
document. For example, reading from ElasticSearch. Given an index with
possible hundreds of documents, reading each one individually is not as
optimal as reading in batches. To try and maintain as much of the ingest
doc paradigm already being supported, a new class `BaseIngestDocBatch`
was added to handle reading in batches. It produces a list of
`BaseSingleIngestDoc` which is what all current implementations were
renamed to. This list is generated after it runs its `get_files` method.
Past the source node, all other steps in the pipeline should not be
affected, this is just an optimization for the read step.
**Additional Changes:**
* Removed use of jq and instead converted this into a fields filter on
the content to let the database handle the filtering and limit the
amount of data being pulled in.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: rbiseck3 <rbiseck3@users.noreply.github.com>
Currently the `check-diff-evaluation-metrics` only runs when there is
file to perform evaluation on. Add the checking condition to skip the
action when there is none. Additionally, more refactoring and
`visualize` option for both evaluation calculation functions is also
added.
**Summary**
The CI workflow for evaluation previously saved the metric outputs to
the `metrics/` folder. Currently structured in subfolders e.g.
`metrics/text-extraction` `metrics/element-type` for the folder clean up
purpose.
Additionally, Azure connector is also added to
`full_python_matrix_tests` in this PR.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: Klaijan <Klaijan@users.noreply.github.com>
### 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.
Addresses a cluster of HTML-related bugs:
- empty table is identified as bulleted-table
- `partition_html()` emits empty (no text) tables (#1928)
- `.text_as_html` contains inappropriate `<br>` elements in invalid
locations.
- cells enclosed in `<thead>` and `<tfoot>` elements are dropped (#1928)
- `.text_as_html` contains whitespace padding
Each of these is addressed in a separate commit below.
Fixes#1928.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: scanny <scanny@users.noreply.github.com>
Co-authored-by: Yuming Long <63475068+yuming-long@users.noreply.github.com>
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.
When testing ingest tests, one often wants to keep the .json output or
generated metrics files around for inspection after the fact. This
updates the bash condition to actually honor the comment that mentions
# export UNSTRUCTURED_CLEANUP_DEV_FIXTURES=1
** Test Instructions **
Run:
export UNSTRUCTURED_CLEANUP_DEV_FIXTURES=1
./test_unstructured_ingest/src/s3.sh
./test_unstructured_ingest/evaluation-metrics.sh text-extraction
and witness test directories/files do not get cleaned up. E.g.,
`test_unstructured_ingest/metrics-tmp/`. One can also add a `set -x` at
the top of test_unstructured_ingest/cleanup.sh to see what is getting
skipped (it's a lot!).
- Copy script only went through one layer of subdirectory so it did not
found the match between manifest file and structured output. Now edited
to search all subdirectories.
- `set -e` causes the script to exit at any exit rather than `exit 0`,
fix all scripts that needs to run the copy script to be `set +e` right
before the check diff, then back to `set -e` after
- Edit the default evaluation metrics output from `metrics` to
`metrics-tmp` to account for diff check
- Add a script that checks the differences between old eval metric
output (metrics) and new eval metrics output (metrics-tmp)
- allow the overwrite destination to be set to the `OUTPUT_ROOT` instead
of default to script dir.
## test
run
```bash
OVERWRITE_FIXTURES=true OUTPUT_ROOT=/tmp ./test_unstructured_ingest/src/s3.sh
```
with this change we should find new files generated under
`/tmp/expected-structured-output/s3`.
Without this change there will be no such new files.
Canonicalize JSON produced for ingest tests such that incidental changes
is _form_ of the JSON objects (keys moving around) that does not change
the _content_ of that JSON object does not trigger an ingest-test
failure.
Closes#2038.
### Summary
The `fast` strategy should not fall back to a more expensive strategy.
### Testing
For
[9493801-p17.pdf](https://github.com/Unstructured-IO/unstructured/files/13292884/9493801-p17.pdf),
the following code should return an empty list.
```
elements = partition(filename=filename, strategy="fast")
```
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: christinestraub <christinestraub@users.noreply.github.com>
- parametrize the output folder paths and expected output folder paths
in comparison scripts
- now allow user to use env `OUTPUT_ROOT` to control where the output
and expected output is
- currently assumes output from test and expected output are in the same
directory; this may need separation later
## test
run
```bash
OUTPUT_ROOT=/tmp ./test_unstructured_ingest/test-ingest-src.sh
```
and it should show files changed but not able to show diff since there
is no expected output content at `OUTPUT_ROOT`.
Then run
```bash
cp -R test_unstructured_ingest/expected-* /tmp/
OUTPUT_ROOT=/tmp ./test_unstructured_ingest/test-ingest-src.sh
```
we can see (due to CI and local instance producing different results)
actual line by line diff
### Summary
Closes#2011
`languages` was missing from the metadata when partitioning pdfs via
`hi_res` and `fast` strategies and missing from image partitions via
`hi_res`. This PR adds `languages` to the relevant function calls so it
is included in the resulting elements.
### Testing
On the main branch, `partition_image` will include `languages` when
`strategy='ocr_only'`, but not when `strategy='hi_res'`:
```
filename = "example-docs/english-and-korean.png"
from unstructured.partition.image import partition_image
elements = partition_image(filename, strategy="ocr_only", languages=['eng', 'kor'])
elements[0].metadata.languages
elements = partition_image(filename, strategy="hi_res", languages=['eng', 'kor'])
elements[0].metadata.languages
```
For `partition_pdf`, `'ocr_only'` will include `languages` in the
metadata, but `'fast'` and `'hi_res'` will not.
```
filename = "example-docs/korean-text-with-tables.pdf"
from unstructured.partition.pdf import partition_pdf
elements = partition_pdf(filename, strategy="ocr_only", languages=['kor'])
elements[0].metadata.languages
elements = partition_pdf(filename, strategy="fast", languages=['kor'])
elements[0].metadata.languages
elements = partition_pdf(filename, strategy="hi_res", languages=['kor'])
elements[0].metadata.languages
```
On this branch, `languages` is included in the metadata regardless of
strategy
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: Coniferish <Coniferish@users.noreply.github.com>
Page breaks are reliably indicated by `w:lastRenderedPageBreak` elements
present in the document XML. Page breaks are NOT reliably indicated by
"hard" page-breaks inserted by the author and when present are redundant
to a `w:lastRenderedPageBreak` element so cause over-counting if used.
Use rendered page-breaks only.
Closes#1064
When using the `--partition-by-api` flag via unstructured-ingest, none
of the partition arguments are forwarded, meaning that these options are
disregarded. With this change, we now pass through all of the relevant
partition arguments to the api.
## Changes
* parse and pass relevant partition arguments to the api in
unstructured-ingest
* bonus: leverage an existing `partition.api` function to call out to
the api rather than including duplicative request logic in unstructured
ingest
* bonus: --pdf-infer-table-structure is now a flag not an arg (it
defaults false anyways, this is more succinct and consistent with
similar parameters)
* bonus: adds `hi_res_model_name` so a user can specify the model to
leverage when using a hi_res strategy.
## Testing
* update against_api.sh source test script to specify a partition
argument and validates that the response from the api respected the
argument
* manually ran a request and validated that it was processed with
chipper as specified (not sure if we want to bake a chipper request into
the ci tests) (validated that the response leveraged the chipper model):
```
PYTHONPATH=. ./unstructured/ingest/main.py \
local \
--output-dir /tmp/ingest-requests/chipper \
--verbose \
--reprocess \
--strategy hi_res \
--partition-by-api \
--hi-res-model-name chipper \
--api-key "$API_KEY" \
--input-path 'example-docs/layout-parser-paper-with-table.pdf'
```
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
### Summary
Click decorated functions cannot (properly) be called outside of the
click interface. This makes it difficult to reuse the setup
functionality in measure_text_edit_distance or
measure_element_type_accuracy. This PR removes the click decoration and
separates it into a wrapper function purely to execute the command.
### Technical Details
- Changed as suggested in [this StackOverflow
post](https://stackoverflow.com/questions/40091347/call-another-click-command-from-a-click-command)
response
- The locations of these now distinct functions are separate: the
`_command` click-decorated functions stay in ingest/evaluate.py, and the
core functions measure_text_edit_distance and
measure_element_type_accuracy are moved into the unstructured/metrics/
folder (which is a more logical location for them).
- Initial test added for measure_text_edit_distance
### Test
`sh ./test_unstructured_ingest/evaluation-metrics.sh text-extraction`
functionality is unchanged.
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: shreyanid <shreyanid@users.noreply.github.com>
Co-authored-by: Trevor Bossert <37596773+tabossert@users.noreply.github.com>
Closes#1782
This PR:
- Extends ingest pipeline so that it is possible to select an embedding
provider from a range of providers
- Modifies the ingest embedding test to be a diff test, since the
embedding vectors are reproducible after supporting multiple providers
Additional info on the chosen provider for the test:
- Found `langchain.embeddings.HuggingFaceEmbeddings` to be deterministic
even when there's no seed set
- Took 6.84s to pass a unit test with the provider (without cache,
including model download)
- `langchain.embeddings.HuggingFaceEmbeddings` runs in local, making it
zero cost
For all these reasons, testing embedding modules with the Huggingface
model seems to be making sense
---------
Co-authored-by: cragwolfe <crag@unstructured.io>
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
### 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
To always support the latest changed to the partition method and the
possible kwargs it supports, the ingest CLI has been refactored to take
in a valid json string to represent those values to allow a user more
flexibility with controlling the partition method.
### Summary
To combine ingest and holistic metrics efforts, add the `doctype` field
to the results from the functions in evaluate.py for use in subsequent
aggregation functions.
### Test
Run `sh ./test_unstructured_ingest/evaluation-metrics.sh
text-extraction` and there will be a new doctype column with the file's
doctype extension.
<img width="508" alt="Screenshot 2023-11-01 at 2 23 11 PM"
src="https://github.com/Unstructured-IO/unstructured/assets/42684285/44583da9-e7ef-4142-be72-c2247b954bcf">
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: shreyanid <shreyanid@users.noreply.github.com>
### 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.
Refactor the evaluation scripts including
`unstructured/ingest/evaluation.py`
`test_unstructured_ingest/evaluation-metrics.sh` for more structured
code and usage.
- The script is now only use one python script call with param
- Adds function to build string for output_args (`--output_dir
--output_list) and source_args (`--source_dir --source_args`)
- Now accepts evaluation to call as a param, currently only accepts
`text-extraction` and `element-type`
Example to call the function:
```sh evaluation-metrics.sh text-extraction```
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: Klaijan <Klaijan@users.noreply.github.com>
### Description
### Google Drive
The existing service account parameter was expanded to support either a
file path or a json value to generate the credentials when instantiating
the google drive client.
### GCS
Google Cloud Storage already supports the value being passed in, from
their docstring:
> - you may supply a token generated by the
[gcloud](https://cloud.google.com/sdk/docs/)
utility; this is either a python dictionary, the name of a file
containing the JSON returned by logging in with the gcloud CLI tool,
or a Credentials object.
I tested this locally:
```python
from gcsfs import GCSFileSystem
import json
with open("/Users/romanisecke/.ssh/google-cloud-unstructured-ingest-test-d4fc30286d9d.json") as json_file:
json_data = json.load(json_file)
print(json_data)
fs = GCSFileSystem(token=json_data)
print(fs.ls(path="gs://utic-test-ingest-fixtures/"))
```
`['utic-test-ingest-fixtures/ideas-page.html',
'utic-test-ingest-fixtures/nested-1',
'utic-test-ingest-fixtures/nested-2']`
Closes: #1891 (check the issue for more info)
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: ahmetmeleq <ahmetmeleq@users.noreply.github.com>
Co-authored-by: Yao You <yao@unstructured.io>
### Summary
Update `ocr_only` strategy in `partition_pdf()`. This PR adds the
functionality to get accurate coordinate data when partitioning PDFs and
Images with the `ocr_only` strategy.
- Add functionality to perform OCR region grouping based on the OCR text
taken from `pytesseract.image_to_string()`
- Add functionality to get layout elements from OCR regions (ocr_layout)
for both `tesseract` and `paddle`
- Add functionality to determine the `source` of merged text regions
when merging text regions in `merge_text_regions()`
- Merge multiple test functions related to "ocr_only" strategy into
`test_partition_pdf_with_ocr_only_strategy()`
- This PR also fixes [issue
#1792](https://github.com/Unstructured-IO/unstructured/issues/1792)
### Evaluation
```
# Image
PYTHONPATH=. python examples/custom-layout-order/evaluate_natural_reading_order.py example-docs/double-column-A.jpg ocr_only xy-cut image
# PDF
PYTHONPATH=. python examples/custom-layout-order/evaluate_natural_reading_order.py example-docs/multi-column-2p.pdf ocr_only xy-cut pdf
```
### Test
- **Before update**
All elements have the same coordinate data
- **After update**
All elements have accurate coordinate data
---------
Co-authored-by: ryannikolaidis <1208590+ryannikolaidis@users.noreply.github.com>
Co-authored-by: christinestraub <christinestraub@users.noreply.github.com>
