### Description
Pivot from using the retry logic as a decorator as this posed too many
limitations on what can be passed in as a parameter at runtime. Moved
this to be a class approach and now that can be instantiated with
appropriate loggers leveraging the `--verbose` flag to set the log
level. This also mitigates how much new code is being forked from the
backoff library. The existing notion client that was using the previous
decorator has been refactored to use the new class approach and the
airtable connector was updated to support retry logic as well. Default
log handlers were introduced which applies to all instances of the retry
handler when it starts, backs off, and gives up.
A generic approach was added to configuring the retry parameters in the
CLI and was added to the running number of common configs across all CLI
commands.
Omitted CHANGELOG entry as this is mostly just a refactor of the retry
code. All other connectors will be updated to support retry in another
PR but this helps limit the number of changes to review in this one.
### Extra fixes
* Updated local and salesforce source connector to set `ingest_doc_cls`
in a `__post_init__` method since this variable can't be serialized.
### Testing
Both the airtable and notion ingest tests can be run locally. While they
might not pass due to text changes (to be expected when running
locally), the process can be viewed in the logs to validate.
Associated issue: #1488
The current code assumes the first line of csv and tsv files are a
header line. Most csv and tsv files don't have a header line, and even
for those that do, dropping this line may not be the desired behavior.
Here is a snippet of code that demonstrates the current behavior and the
proposed fix
```
import pandas as pd
from lxml.html.soupparser import fromstring as soupparser_fromstring
c1 = """
Stanley Cups,,
Team,Location,Stanley Cups
Blues,STL,1
Flyers,PHI,2
Maple Leafs,TOR,13
"""
f = "./test.csv"
with open(f, 'w') as ff:
ff.write(c1)
print("Suggested Improvement Keep First Line")
table = pd.read_csv(f, header=None)
html_text = table.to_html(index=False, header=False, na_rep="")
text = soupparser_fromstring(html_text).text_content()
print(text)
print("\n\nOriginal Looses First Line")
table = pd.read_csv(f)
html_text = table.to_html(index=False, header=False, na_rep="")
text = soupparser_fromstring(html_text).text_content()
print(text)
```
---------
Co-authored-by: cragwolfe <crag@unstructured.io>
Co-authored-by: Yao You <theyaoyou@gmail.com>
Co-authored-by: Yao You <yao@unstructured.io>
### Description
As we add more and more steps to the pipeline (i.e. chunking, embedding,
table manipulation), it would help seperate the responsibility of each
of these into their own processes, running each in parallel using json
files to share data across. This will also help guarantee data is
serializable if this code was used in an actual pipeline. Following is a
flow diagram of the proposed changes. As part of this change:
* A parent pipeline class will be responsible for running each `node`,
which can optionally be run via multiprocessing if it supports it, or
not. Possible nodes at this moment:
* Doc factory: creates all the ingest docs via the source connector
* Source: reads/downloads all of the content to process to the local
filesystem to the location set by the `download_dir` parameter.
* Partition: runs partition on all of the downloaded content in json
format.
* Any number of reformat nodes that modify the partitioned content. This
can include chunking, embedding, etc.
* Write: push the final json into the destination via the destination
connector
* This pipeline relies on the information of the ingest docs to be
available via their serialization. An optimization was introduced with
the `IngestDocJsonMixin` which adds in all the `@property` fields to the
serialized json already being created via the `DataClassJsonMixin`
* For all intermediate steps (partitioning, reformatting), the content
is saved to a dedicated location on the local filesystem. Right now it's
set to `$HOME/.cache/unstructured/ingest/pipeline/STEP_NAME/`.
* Minor changes: made sense to move some of the config parameters
between the read and partition configs when I explicitly divided the
responsibility to download vs partition the content in the pipeline.
* The pipeline class only makes the doc factory, source and partition
nodes required, keeping with the logic that has been supported so far.
All reformatting nodes and write node are optional.
* Long term, there should also be some changes to the base configs
supported by the CLI to support pipeline specific configs, but for now
what exists was used to minimize changes in this PR.
* Final step to copy the final output to the location designated by the
`_output_filename` value of the ingest doc.
* Hashing occurs at each step by hashing the parameters of that step
(i.e. partition configs) along with the previous step via the filename
used. This allows each step to be the same _if_ all the parameters for
it have not changed and the content so far is the same.
* The only data that is shared and has writes to across processes is the
dictionary of ingest json data. This dict is created using the
`multiprocessing.manager.DictProxy` to make sure any interaction with it
is behind a lock.
### Minor refactors included:
* Utility methods added to extract configs from the click options
* Utility method to add common options to click commands.
* All writers moved to using the class approach which extracts a lot of
the common code so there's less copy-paste when new runners are added.
* Use `@property` for source metadata on base ingest doc to add logic to
call `update_source_metadata` if it's still `None` at the time it's
fetched.
### Additional bug fixes included
* Fsspec connectors were not serializable due to the `ingest_doc_cls`.
This was removed from the fields captured by the `@dataclass` decorator
and added in a `__post_init__` method.
* Various reddit connector params were missing. This doesn't have an
explicit ingest test at the moment so was never caught.
* Fsspec connector had the parent `update_source_metadata` misnamed as
`update_source_metadata_metadata` so it was never being called.
### Flow Diagram
Fixes
docker exec unstructured-smoke-test /bin/bash -c
/home/notebook-user/test_unstructured_ingest/test-ingest-wikipedia.sh
/home/notebook-user/test_unstructured_ingest/test-ingest-wikipedia.sh:
line 10: python: command not found
in
https://github.com/Unstructured-IO/unstructured/blob/6ad4971/scripts/docker-smoke-test.sh#L43
that was preventing docker images from being built.
## **Summary**
By adding hierarchy to unstructured elements, users will have more
information for implementing vector db/LLM chunking strategies. For
example, text elements could be queried by their preceding title
element. The hierarchy is implemented by a parent_id tag in the
element's metadata.
### Features
- Introduces a parent_id to ElementMetadata (The id of the parent
element, not a pointer)
- Creates a rule set for assigning hierarchies. Sensible default is
assigned, with an optional override parameter
- Sets element parent ids if there isn't an existing parent id or
matches the ruleset
### How it works
Hierarchies are assigned via a parent id field in element metadata.
Elements are read sequentially and evaluated against a ruleset. For
example take the following elements:
1. Title, "This is the Title"
2. Text, "this is the text"
And the ruleset: `{"title": ["text"]}`. When evaluated, the parent_id of
2 will be the id of 1. The algorithm for determining this is more
complex and resolves several edge cases, so please read the code for
further details.
### Schema Changes
```
@dataclass
class ElementMetadata:
coordinates: Optional[CoordinatesMetadata] = None
data_source: Optional[DataSourceMetadata] = None
filename: Optional[str] = None
file_directory: Optional[str] = None
last_modified: Optional[str] = None
filetype: Optional[str] = None
attached_to_filename: Optional[str] = None
+ parent_id: Optional[Union[str, uuid.UUID, NoID, UUID]] = None
+ category_depth: Optional[int] = None
...
```
### Testing
```
from unstructured.partition.auto import partition
from typing import List
elements = partition(filename="./unstructured/example-docs/fake-html.html", strategy="auto")
for element in elements:
print(
f"Category: {getattr(element, 'category', '')}\n"\
f"Text: {getattr(element, 'text', '')}\n"
f"ID: {element.id}\n" \
f"Parent ID: {element.metadata.parent_id}\n"\
f"Depth: {element.metadata.category_depth}\n" \
)
```
### Additional Notes
Implementing this feature revealed a possibly undesired side-effect in
how element metadata are processed. In
`unstructured/partition/common.py` the `_add_element_metadata` is
invoked as part of the `add_metadata_with_filetype` decorator for
filetype partitioning. This method is intended to add additional
information to the metadata generated with the element including
filename and filetype, however the existing metadata is merged into a
newly created metadata object rather than the other way around. Because
of the way it's structured, new metadata fields can easily be forgotten
and pose debugging challenges to developers. This likely warrants a new
issue.
I'm guessing that the implementation is done this way to avoid issues
with deserializing elements, but could be wrong.
---------
Co-authored-by: Benjamin Torres <benjats07@users.noreply.github.com>
### Description
Update all other connectors to use the new downstream architecture that
was recently introduced for the s3 connector.
Closes#1313 and #1311
If a layout model is used from unstructured-inference, you get back
class probabilities in the element metadata from partition.
extra-pdf-image-in in requirements already has the newest version of
unstructured-inference in there without a pinned version. Is there any
place else that the unstructured-inference version needs to be updated
to the required release version, 0.5.22?
* 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>
