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fix: flaky chunk metadata (#1947) **Executive Summary.** When the elements in a _section_ are combined into a _chunk_, the metadata in each of the elements is _consolidated_ into a single `ElementMetadata` instance. There are two main problems with the current implementation: 1. The current algorithm simply uses the metadata of the first element as the metadata for the chunk. This produces: - **empty chunk metadata** when the first element has no metadata, such as a `PageBreak("")` - **missing chunk metadata** when the first element contains only partial metadata such as a `Header()` or `Footer()` - **misleading metadata** when the first element contains values applicable only to that element, such as `category_depth`, `coordinates` (bounding-box), `header_footer_type`, or `parent_id` 2. Second, list metadata such as `emphasized_text_content`, `emphasized_text_tags`, `link_texts` and `link_urls` is only combined when it is unique within the combined list. These lists are "unzipped" pairs. For example, the first `link_texts` corresponds to the first `link_urls` value. When an item is removed from one (because it matches a prior entry) and not the other (say same text "here" but different URL) the positional correspondence is broken and downstream processing will at best be wrong, at worst raise an exception. ### Technical Discussion Element metadata cannot be determined in the general case simply by sampling that of the first element. At the same time, a simple union of all values is also not sufficient. To effectively consolidate the current variety of metadata fields we need four distinct strategies, selecting which to apply to each field based on that fields provenance and other characteristics. The four strategies are: - `FIRST` - Select the first non-`None` value across all the elements. Several fields are determined by the document source (`filename`, `file_directory`, etc.) and will not change within the output of a single partitioning run. They might not appear in every element, but they will be the same whenever they do appear. This strategy takes the first one that appears, if any, as proxy for the value for the entire chunk. - `LIST` - Consolidate the four list fields like `emphasized_text_content` and `link_urls` by concatenating them in element order (no set semantics apply). All values from `elements[n]` appear before those from `elements[n+1]` and existing order is preserved. - `LIST_UNIQUE` - Combine only unique elements across the (list) values of the elements, preserving order in which a unique item first appeared. - `REGEX` - Regex metadata has its own rules, including adjusting the `start` and `end` offset of each match based its new position in the concatenated text. - `DROP` - Not all metadata can or should appear in a chunk. For example, a chunk cannot be guaranteed to have a single `category_depth` or `parent_id`. Other strategies such as `COORDINATES` could be added to consolidate the bounding box of the chunk from the coordinates of its elements, roughly `min(lefts)`, `max(rights)`, etc. Others could be `LAST`, `MAJORITY`, or `SUM` depending on how metadata evolves. The proposed strategy assignments are these: - `attached_to_filename`: FIRST, - `category_depth`: DROP, - `coordinates`: DROP, - `data_source`: FIRST, - `detection_class_prob`: DROP, # -- ? confirm -- - `detection_origin`: DROP, # -- ? confirm -- - `emphasized_text_contents`: LIST, - `emphasized_text_tags`: LIST, - `file_directory`: FIRST, - `filename`: FIRST, - `filetype`: FIRST, - `header_footer_type`: DROP, - `image_path`: DROP, - `is_continuation`: DROP, # -- not expected, added by chunking, not before -- - `languages`: LIST_UNIQUE, - `last_modified`: FIRST, - `link_texts`: LIST, - `link_urls`: LIST, - `links`: DROP, # -- deprecated field -- - `max_characters`: DROP, # -- unused in code, probably remove from ElementMetadata -- - `page_name`: FIRST, - `page_number`: FIRST, - `parent_id`: DROP, - `regex_metadata`: REGEX, - `section`: FIRST, # -- section unconditionally breaks on new section -- - `sent_from`: FIRST, - `sent_to`: FIRST, - `subject`: FIRST, - `text_as_html`: DROP, # -- not expected, only occurs in TableSection -- - `url`: FIRST, **Assumptions:** - each .eml file is partitioned->chunked separately (not in batches), therefore sent-from, sent-to, and subject will not change within a section. ### Implementation Implementation of this behavior requires two steps: 1. **Collect** all non-`None` values from all elements, each in a sequence by field-name. Fields not populated in any of the elements do not appear in the collection. ```python all_meta = { "filename": ["memo.docx", "memo.docx"] "link_texts": [["here", "here"], ["and here"]] "parent_id": ["f273a7cb", "808b4ced"] } ``` 2. **Apply** the specified strategy to each item in the overall collection to produce the consolidated chunk meta (see implementation). ### Factoring For the following reasons, the implementation of metadata consolidation is extracted from its current location in `chunk_by_title()` to a handful of collaborating methods in `_TextSection`. - The current implementation of metadata consolidation "inline" in `chunk_by_title()` already has too many moving pieces to be understood without extended study. Adding strategies to that would make it worse. - `_TextSection` is the only section type where metadata is consolidated (the other two types always have exactly one element so already exactly one metadata.) - `_TextSection` is already the expert on all the information required to consolidate metadata, in particular the elements that make up the section and their text. Some other problems were also fixed in that transition, such as mutation of elements during the consolidation process. ### Technical Risk: adding new `ElementMetadata` field breaks metadata If each metadata field requires a strategy assignment to be consolidated and a developer adds a new `ElementMetadata` field without adding a corresponding strategy mapping, metadata consolidation could break or produce incorrect results. This risk can be mitigated multiple ways: 1. Add a test that verifies a strategy is defined for each (Recommended). 2. Define a default strategy, either `DROP` or `FIRST` for scalar types, `LIST` for list types. 3. Raise an exception when an unknown metadata field is encountered. This PR implements option 1 such that a developer will be notified before merge if they add a new metadata field but do not define a strategy for it. ### Other Considerations - If end-users can in-future add arbitrary metadata fields _before_ chunking, then we'll need to define metadata-consolidation behavior for such fields. Depending on how we implement user-defined metadata fields we might: - Require explicit definition of a new metadata field before use, perhaps with a method like `ElementMetadata.add_custom_field()` which requires a consolidation strategy to be defined (and/or has a default value). - Have a default strategy, perhaps `DROP` or `FIRST`, or `LIST` if the field is type `list`. ### Further Context Metadata is only consolidated for `TextSection` because the other two section types (`TableSection` and `NonTextSection`) can only contain a single element. --- ## Further discussion on consolidation strategy by field ### document-static These fields are very likely to be the same for all elements in a single document: - `attached_to_filename` - `data_source` - `file_directory` - `filename` - `filetype` - `last_modified` - `sent_from` - `sent_to` - `subject` - `url` *Consolidation strategy:* `FIRST` - use first one found, if any. ### section-static These fields are very likely to be the same for all elements in a single section, which is the scope we really care about for metadata consolidation: - `section` - an EPUB document-section unconditionally starts new section. *Consolidation strategy:* `FIRST` - use first one found, if any. ### consolidated list-items These `List` fields are consolidated by concatenating the lists from each element that has one: - `emphasized_text_contents` - `emphasized_text_tags` - `link_texts` - `link_urls` - `regex_metadata` - special case, this one gets indexes adjusted too. *Consolidation strategy:* `LIST` - concatenate lists across elements. ### dynamic These fields are likely to hold unique data for each element: - `category_depth` - `coordinates` - `image_path` - `parent_id` *Consolidation strategy:* - `DROP` as likely misleading. - `COORDINATES` strategy could be added to compute the bounding box from all bounding boxes. - Consider allowing if they are all the same, perhaps an `ALL` strategy. ### slow-changing These fields are somewhere in-between, likely to be common between multiple elements but varied within a document: - `header_footer_type` - *strategy:* drop as not-consolidatable - `languages` - *strategy:* take first occurence - `page_name` - *strategy:* take first occurence - `page_number` - *strategy:* take first occurence, will all be the same when `multipage_sections` is `False`. Worst-case semantics are "this chunk began on this page". ### N/A These field types do not figure in metadata-consolidation: - `detection_class_prob` - I'm thinking this is for debug and should not appear in chunks, but need confirmation. - `detection_origin` - for debug only - `is_continuation` - is _produced_ by chunking, never by partitioning (not in our code anyway). - `links` (deprecated, probably should be dropped) - `max_characters` - is unused as far as I can tell, is unreferenced in source code. Should be removed from `ElementMetadata` as far as I can tell. - `text_as_html` - only appears in a `Table` element, each of which appears in its own section so needs no consolidation. Never appears in `TextSection`. *Consolidation strategy:* `DROP` any that appear (several never will)
2023-11-01 18:49:20 -07:00
import dataclasses as dc
import json
from functools import partial
import pytest
from unstructured.cleaners.core import clean_prefix
from unstructured.cleaners.translate import translate_text
from unstructured.documents.coordinates import (
CoordinateSystem,
Orientation,
RelativeCoordinateSystem,
)
from unstructured.documents.elements import (
UUID,
fix: flaky chunk metadata (#1947) **Executive Summary.** When the elements in a _section_ are combined into a _chunk_, the metadata in each of the elements is _consolidated_ into a single `ElementMetadata` instance. There are two main problems with the current implementation: 1. The current algorithm simply uses the metadata of the first element as the metadata for the chunk. This produces: - **empty chunk metadata** when the first element has no metadata, such as a `PageBreak("")` - **missing chunk metadata** when the first element contains only partial metadata such as a `Header()` or `Footer()` - **misleading metadata** when the first element contains values applicable only to that element, such as `category_depth`, `coordinates` (bounding-box), `header_footer_type`, or `parent_id` 2. Second, list metadata such as `emphasized_text_content`, `emphasized_text_tags`, `link_texts` and `link_urls` is only combined when it is unique within the combined list. These lists are "unzipped" pairs. For example, the first `link_texts` corresponds to the first `link_urls` value. When an item is removed from one (because it matches a prior entry) and not the other (say same text "here" but different URL) the positional correspondence is broken and downstream processing will at best be wrong, at worst raise an exception. ### Technical Discussion Element metadata cannot be determined in the general case simply by sampling that of the first element. At the same time, a simple union of all values is also not sufficient. To effectively consolidate the current variety of metadata fields we need four distinct strategies, selecting which to apply to each field based on that fields provenance and other characteristics. The four strategies are: - `FIRST` - Select the first non-`None` value across all the elements. Several fields are determined by the document source (`filename`, `file_directory`, etc.) and will not change within the output of a single partitioning run. They might not appear in every element, but they will be the same whenever they do appear. This strategy takes the first one that appears, if any, as proxy for the value for the entire chunk. - `LIST` - Consolidate the four list fields like `emphasized_text_content` and `link_urls` by concatenating them in element order (no set semantics apply). All values from `elements[n]` appear before those from `elements[n+1]` and existing order is preserved. - `LIST_UNIQUE` - Combine only unique elements across the (list) values of the elements, preserving order in which a unique item first appeared. - `REGEX` - Regex metadata has its own rules, including adjusting the `start` and `end` offset of each match based its new position in the concatenated text. - `DROP` - Not all metadata can or should appear in a chunk. For example, a chunk cannot be guaranteed to have a single `category_depth` or `parent_id`. Other strategies such as `COORDINATES` could be added to consolidate the bounding box of the chunk from the coordinates of its elements, roughly `min(lefts)`, `max(rights)`, etc. Others could be `LAST`, `MAJORITY`, or `SUM` depending on how metadata evolves. The proposed strategy assignments are these: - `attached_to_filename`: FIRST, - `category_depth`: DROP, - `coordinates`: DROP, - `data_source`: FIRST, - `detection_class_prob`: DROP, # -- ? confirm -- - `detection_origin`: DROP, # -- ? confirm -- - `emphasized_text_contents`: LIST, - `emphasized_text_tags`: LIST, - `file_directory`: FIRST, - `filename`: FIRST, - `filetype`: FIRST, - `header_footer_type`: DROP, - `image_path`: DROP, - `is_continuation`: DROP, # -- not expected, added by chunking, not before -- - `languages`: LIST_UNIQUE, - `last_modified`: FIRST, - `link_texts`: LIST, - `link_urls`: LIST, - `links`: DROP, # -- deprecated field -- - `max_characters`: DROP, # -- unused in code, probably remove from ElementMetadata -- - `page_name`: FIRST, - `page_number`: FIRST, - `parent_id`: DROP, - `regex_metadata`: REGEX, - `section`: FIRST, # -- section unconditionally breaks on new section -- - `sent_from`: FIRST, - `sent_to`: FIRST, - `subject`: FIRST, - `text_as_html`: DROP, # -- not expected, only occurs in TableSection -- - `url`: FIRST, **Assumptions:** - each .eml file is partitioned->chunked separately (not in batches), therefore sent-from, sent-to, and subject will not change within a section. ### Implementation Implementation of this behavior requires two steps: 1. **Collect** all non-`None` values from all elements, each in a sequence by field-name. Fields not populated in any of the elements do not appear in the collection. ```python all_meta = { "filename": ["memo.docx", "memo.docx"] "link_texts": [["here", "here"], ["and here"]] "parent_id": ["f273a7cb", "808b4ced"] } ``` 2. **Apply** the specified strategy to each item in the overall collection to produce the consolidated chunk meta (see implementation). ### Factoring For the following reasons, the implementation of metadata consolidation is extracted from its current location in `chunk_by_title()` to a handful of collaborating methods in `_TextSection`. - The current implementation of metadata consolidation "inline" in `chunk_by_title()` already has too many moving pieces to be understood without extended study. Adding strategies to that would make it worse. - `_TextSection` is the only section type where metadata is consolidated (the other two types always have exactly one element so already exactly one metadata.) - `_TextSection` is already the expert on all the information required to consolidate metadata, in particular the elements that make up the section and their text. Some other problems were also fixed in that transition, such as mutation of elements during the consolidation process. ### Technical Risk: adding new `ElementMetadata` field breaks metadata If each metadata field requires a strategy assignment to be consolidated and a developer adds a new `ElementMetadata` field without adding a corresponding strategy mapping, metadata consolidation could break or produce incorrect results. This risk can be mitigated multiple ways: 1. Add a test that verifies a strategy is defined for each (Recommended). 2. Define a default strategy, either `DROP` or `FIRST` for scalar types, `LIST` for list types. 3. Raise an exception when an unknown metadata field is encountered. This PR implements option 1 such that a developer will be notified before merge if they add a new metadata field but do not define a strategy for it. ### Other Considerations - If end-users can in-future add arbitrary metadata fields _before_ chunking, then we'll need to define metadata-consolidation behavior for such fields. Depending on how we implement user-defined metadata fields we might: - Require explicit definition of a new metadata field before use, perhaps with a method like `ElementMetadata.add_custom_field()` which requires a consolidation strategy to be defined (and/or has a default value). - Have a default strategy, perhaps `DROP` or `FIRST`, or `LIST` if the field is type `list`. ### Further Context Metadata is only consolidated for `TextSection` because the other two section types (`TableSection` and `NonTextSection`) can only contain a single element. --- ## Further discussion on consolidation strategy by field ### document-static These fields are very likely to be the same for all elements in a single document: - `attached_to_filename` - `data_source` - `file_directory` - `filename` - `filetype` - `last_modified` - `sent_from` - `sent_to` - `subject` - `url` *Consolidation strategy:* `FIRST` - use first one found, if any. ### section-static These fields are very likely to be the same for all elements in a single section, which is the scope we really care about for metadata consolidation: - `section` - an EPUB document-section unconditionally starts new section. *Consolidation strategy:* `FIRST` - use first one found, if any. ### consolidated list-items These `List` fields are consolidated by concatenating the lists from each element that has one: - `emphasized_text_contents` - `emphasized_text_tags` - `link_texts` - `link_urls` - `regex_metadata` - special case, this one gets indexes adjusted too. *Consolidation strategy:* `LIST` - concatenate lists across elements. ### dynamic These fields are likely to hold unique data for each element: - `category_depth` - `coordinates` - `image_path` - `parent_id` *Consolidation strategy:* - `DROP` as likely misleading. - `COORDINATES` strategy could be added to compute the bounding box from all bounding boxes. - Consider allowing if they are all the same, perhaps an `ALL` strategy. ### slow-changing These fields are somewhere in-between, likely to be common between multiple elements but varied within a document: - `header_footer_type` - *strategy:* drop as not-consolidatable - `languages` - *strategy:* take first occurence - `page_name` - *strategy:* take first occurence - `page_number` - *strategy:* take first occurence, will all be the same when `multipage_sections` is `False`. Worst-case semantics are "this chunk began on this page". ### N/A These field types do not figure in metadata-consolidation: - `detection_class_prob` - I'm thinking this is for debug and should not appear in chunks, but need confirmation. - `detection_origin` - for debug only - `is_continuation` - is _produced_ by chunking, never by partitioning (not in our code anyway). - `links` (deprecated, probably should be dropped) - `max_characters` - is unused as far as I can tell, is unreferenced in source code. Should be removed from `ElementMetadata` as far as I can tell. - `text_as_html` - only appears in a `Table` element, each of which appears in its own section so needs no consolidation. Never appears in `TextSection`. *Consolidation strategy:* `DROP` any that appear (several never will)
2023-11-01 18:49:20 -07:00
ConsolidationStrategy,
CoordinatesMetadata,
Element,
ElementMetadata,
NoID,
fix: chunks break on regex-meta changes and regex-meta start/stop not adjusted (#1779) **Executive Summary.** Introducing strict type-checking as preparation for adding the chunk-overlap feature revealed a type mismatch for regex-metadata between chunking tests and the (authoritative) ElementMetadata definition. The implementation of regex-metadata aspects of chunking passed the tests but did not produce the appropriate behaviors in production where the actual data-structure was different. This PR fixes these two bugs. 1. **Over-chunking.** The presence of `regex-metadata` in an element was incorrectly being interpreted as a semantic boundary, leading to such elements being isolated in their own chunks. 2. **Discarded regex-metadata.** regex-metadata present on the second or later elements in a section (chunk) was discarded. **Technical Summary** The type of `ElementMetadata.regex_metadata` is `Dict[str, List[RegexMetadata]]`. `RegexMetadata` is a `TypedDict` like `{"text": "this matched", "start": 7, "end": 19}`. Multiple regexes can be specified, each with a name like "mail-stop", "version", etc. Each of those may produce its own set of matches, like: ```python >>> element.regex_metadata { "mail-stop": [{"text": "MS-107", "start": 18, "end": 24}], "version": [ {"text": "current: v1.7.2", "start": 7, "end": 21}, {"text": "supersedes: v1.7.0", "start": 22, "end": 40}, ], } ``` *Forensic analysis* * The regex-metadata feature was added by Matt Robinson on 06/16/2023 commit: 4ea71683. The regex_metadata data structure is the same as when it was added. * The chunk-by-title feature was added by Matt Robinson on 08/29/2023 commit: f6a745a7. The mistaken regex-metadata data structure in the tests is present in that commit. Looks to me like a mis-remembering of the regex-metadata data-structure and insufficient type-checking rigor (type-checker strictness level set too low) to warn of the mistake. **Over-chunking Behavior** The over-chunking looked like this: Chunking three elements with regex metadata should combine them into a single chunk (`CompositeElement` object), subject to maximum size rules (default 500 chars). ```python elements: List[Element] = [ Title( "Lorem Ipsum", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="Ipsum", start=6, end=11)]} ), ), Text( "Lorem ipsum dolor sit amet consectetur adipiscing elit.", metadata=ElementMetadata( regex_metadata={"dolor": [RegexMetadata(text="dolor", start=12, end=17)]} ), ), Text( "In rhoncus ipsum sed lectus porta volutpat.", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="ipsum", start=11, end=16)]} ), ), ] chunks = chunk_by_title(elements) assert chunks == [ CompositeElement( "Lorem Ipsum\n\nLorem ipsum dolor sit amet consectetur adipiscing elit.\n\nIn rhoncus" " ipsum sed lectus porta volutpat." ) ] ``` Observed behavior looked like this: ```python chunks => [ CompositeElement('Lorem Ipsum') CompositeElement('Lorem ipsum dolor sit amet consectetur adipiscing elit.') CompositeElement('In rhoncus ipsum sed lectus porta volutpat.') ] ``` The fix changed the approach from breaking on any metadata field not in a specified group (`regex_metadata` was missing from this group) to only breaking on specified fields (whitelisting instead of blacklisting). This avoids overchunking every time we add a new metadata field and is also simpler and easier to understand. This change in approach is discussed in more detail here #1790. **Dropping regex-metadata Behavior** Chunking this section: ```python elements: List[Element] = [ Title( "Lorem Ipsum", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="Ipsum", start=6, end=11)]} ), ), Text( "Lorem ipsum dolor sit amet consectetur adipiscing elit.", metadata=ElementMetadata( regex_metadata={ "dolor": [RegexMetadata(text="dolor", start=12, end=17)], "ipsum": [RegexMetadata(text="ipsum", start=6, end=11)], } ), ), Text( "In rhoncus ipsum sed lectus porta volutpat.", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="ipsum", start=11, end=16)]} ), ), ] ``` ..should produce this regex_metadata on the single produced chunk: ```python assert chunk == CompositeElement( "Lorem Ipsum\n\nLorem ipsum dolor sit amet consectetur adipiscing elit.\n\nIn rhoncus" " ipsum sed lectus porta volutpat." ) assert chunk.metadata.regex_metadata == { "dolor": [RegexMetadata(text="dolor", start=25, end=30)], "ipsum": [ RegexMetadata(text="Ipsum", start=6, end=11), RegexMetadata(text="ipsum", start=19, end=24), RegexMetadata(text="ipsum", start=81, end=86), ], } ``` but instead produced this: ```python regex_metadata == {"ipsum": [{"text": "Ipsum", "start": 6, "end": 11}]} ``` Which is the regex-metadata from the first element only. The fix was to remove the consolidation+adjustment process from inside the "list-attribute-processing" loop (because regex-metadata is not a list) and process regex metadata separately.
2023-10-19 20:16:02 -07:00
RegexMetadata,
Text,
)
2022-06-29 14:35:19 -04:00
def test_text_id():
text_element = Text(text="hello there!")
assert text_element.id == "c69509590d81db2f37f9d75480c8efed"
def test_text_uuid():
text_element = Text(text="hello there!", element_id=UUID())
assert len(text_element.id) == 36
assert text_element.id.count("-") == 4
# Test that the element is JSON serializable. This shold run without an error
json.dumps(text_element.to_dict())
2022-06-29 14:35:19 -04:00
def test_element_defaults_to_blank_id():
element = Element()
assert isinstance(element.id, NoID)
def test_element_uuid():
element = Element(element_id=UUID())
assert isinstance(element.id, UUID)
def test_text_element_apply_cleaners():
text_element = Text(text="[1] A Textbook on Crocodile Habitats")
text_element.apply(partial(clean_prefix, pattern=r"\[\d{1,2}\]"))
assert str(text_element) == "A Textbook on Crocodile Habitats"
def test_text_element_apply_multiple_cleaners():
cleaners = [
partial(clean_prefix, pattern=r"\[\d{1,2}\]"),
partial(translate_text, target_lang="ru"),
]
text_element = Text(text="[1] A Textbook on Crocodile Habitats")
text_element.apply(*cleaners)
assert str(text_element) == "Учебник по крокодильным средам обитания"
def test_apply_raises_if_func_does_not_produce_string():
text_element = Text(text="[1] A Textbook on Crocodile Habitats")
with pytest.raises(ValueError):
text_element.apply(lambda s: 1)
@pytest.mark.parametrize(
("coordinates", "orientation1", "orientation2", "expected_coords"),
[
(
((1, 2), (1, 4), (3, 4), (3, 2)),
Orientation.CARTESIAN,
Orientation.CARTESIAN,
((10, 20), (10, 40), (30, 40), (30, 20)),
),
(
((1, 2), (1, 4), (3, 4), (3, 2)),
Orientation.CARTESIAN,
Orientation.SCREEN,
((10, 1980), (10, 1960), (30, 1960), (30, 1980)),
),
(
((1, 2), (1, 4), (3, 4), (3, 2)),
Orientation.SCREEN,
Orientation.CARTESIAN,
((10, 1980), (10, 1960), (30, 1960), (30, 1980)),
),
(
((1, 2), (1, 4), (3, 4), (3, 2)),
Orientation.SCREEN,
Orientation.SCREEN,
((10, 20), (10, 40), (30, 40), (30, 20)),
),
],
)
def test_convert_coordinates_to_new_system(
coordinates,
orientation1,
orientation2,
expected_coords,
):
coord1 = CoordinateSystem(100, 200)
coord1.orientation = orientation1
coord2 = CoordinateSystem(1000, 2000)
coord2.orientation = orientation2
element = Element(coordinates=coordinates, coordinate_system=coord1)
new_coords = element.convert_coordinates_to_new_system(coord2)
for new_coord, expected_coord in zip(new_coords, expected_coords):
new_coord == pytest.approx(expected_coord)
element.convert_coordinates_to_new_system(coord2, in_place=True)
for new_coord, expected_coord in zip(element.metadata.coordinates.points, expected_coords):
assert new_coord == pytest.approx(expected_coord)
assert element.metadata.coordinates.system == coord2
def test_convert_coordinate_to_new_system_none():
element = Element(coordinates=None, coordinate_system=None)
coord = CoordinateSystem(100, 200)
coord.orientation = Orientation.SCREEN
assert element.convert_coordinates_to_new_system(coord) is None
def test_element_constructor_coordinates_all_present():
coordinates = ((1, 2), (1, 4), (3, 4), (3, 2))
coordinate_system = RelativeCoordinateSystem()
element = Element(coordinates=coordinates, coordinate_system=coordinate_system)
expected_coordinates_metadata = CoordinatesMetadata(
points=coordinates,
system=coordinate_system,
)
assert element.metadata.coordinates == expected_coordinates_metadata
def test_element_constructor_coordinates_points_absent():
with pytest.raises(ValueError) as exc_info:
Element(coordinate_system=RelativeCoordinateSystem())
assert (
str(exc_info.value)
== "Coordinates points should not exist without coordinates system and vice versa."
)
def test_element_constructor_coordinates_system_absent():
with pytest.raises(ValueError) as exc_info:
Element(coordinates=((1, 2), (1, 4), (3, 4), (3, 2)))
assert (
str(exc_info.value)
== "Coordinates points should not exist without coordinates system and vice versa."
)
def test_coordinate_metadata_serdes():
coordinates = ((1, 2), (1, 4), (3, 4), (3, 2))
coordinate_system = RelativeCoordinateSystem()
coordinates_metadata = CoordinatesMetadata(points=coordinates, system=coordinate_system)
expected_schema = {
"layout_height": 1,
"layout_width": 1,
"points": ((1, 2), (1, 4), (3, 4), (3, 2)),
"system": "RelativeCoordinateSystem",
}
coordinates_metadata_dict = coordinates_metadata.to_dict()
assert coordinates_metadata_dict == expected_schema
assert CoordinatesMetadata.from_dict(coordinates_metadata_dict) == coordinates_metadata
def test_element_to_dict():
coordinates = ((1, 2), (1, 4), (3, 4), (3, 2))
coordinate_system = RelativeCoordinateSystem()
element = Element(
element_id="awt32t1",
coordinates=coordinates,
coordinate_system=coordinate_system,
)
expected = {
"metadata": {
"coordinates": {
"layout_height": 1,
"layout_width": 1,
"points": ((1, 2), (1, 4), (3, 4), (3, 2)),
"system": "RelativeCoordinateSystem",
},
},
"type": None,
"element_id": "awt32t1",
}
assert element.to_dict() == expected
fix: chunks break on regex-meta changes and regex-meta start/stop not adjusted (#1779) **Executive Summary.** Introducing strict type-checking as preparation for adding the chunk-overlap feature revealed a type mismatch for regex-metadata between chunking tests and the (authoritative) ElementMetadata definition. The implementation of regex-metadata aspects of chunking passed the tests but did not produce the appropriate behaviors in production where the actual data-structure was different. This PR fixes these two bugs. 1. **Over-chunking.** The presence of `regex-metadata` in an element was incorrectly being interpreted as a semantic boundary, leading to such elements being isolated in their own chunks. 2. **Discarded regex-metadata.** regex-metadata present on the second or later elements in a section (chunk) was discarded. **Technical Summary** The type of `ElementMetadata.regex_metadata` is `Dict[str, List[RegexMetadata]]`. `RegexMetadata` is a `TypedDict` like `{"text": "this matched", "start": 7, "end": 19}`. Multiple regexes can be specified, each with a name like "mail-stop", "version", etc. Each of those may produce its own set of matches, like: ```python >>> element.regex_metadata { "mail-stop": [{"text": "MS-107", "start": 18, "end": 24}], "version": [ {"text": "current: v1.7.2", "start": 7, "end": 21}, {"text": "supersedes: v1.7.0", "start": 22, "end": 40}, ], } ``` *Forensic analysis* * The regex-metadata feature was added by Matt Robinson on 06/16/2023 commit: 4ea71683. The regex_metadata data structure is the same as when it was added. * The chunk-by-title feature was added by Matt Robinson on 08/29/2023 commit: f6a745a7. The mistaken regex-metadata data structure in the tests is present in that commit. Looks to me like a mis-remembering of the regex-metadata data-structure and insufficient type-checking rigor (type-checker strictness level set too low) to warn of the mistake. **Over-chunking Behavior** The over-chunking looked like this: Chunking three elements with regex metadata should combine them into a single chunk (`CompositeElement` object), subject to maximum size rules (default 500 chars). ```python elements: List[Element] = [ Title( "Lorem Ipsum", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="Ipsum", start=6, end=11)]} ), ), Text( "Lorem ipsum dolor sit amet consectetur adipiscing elit.", metadata=ElementMetadata( regex_metadata={"dolor": [RegexMetadata(text="dolor", start=12, end=17)]} ), ), Text( "In rhoncus ipsum sed lectus porta volutpat.", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="ipsum", start=11, end=16)]} ), ), ] chunks = chunk_by_title(elements) assert chunks == [ CompositeElement( "Lorem Ipsum\n\nLorem ipsum dolor sit amet consectetur adipiscing elit.\n\nIn rhoncus" " ipsum sed lectus porta volutpat." ) ] ``` Observed behavior looked like this: ```python chunks => [ CompositeElement('Lorem Ipsum') CompositeElement('Lorem ipsum dolor sit amet consectetur adipiscing elit.') CompositeElement('In rhoncus ipsum sed lectus porta volutpat.') ] ``` The fix changed the approach from breaking on any metadata field not in a specified group (`regex_metadata` was missing from this group) to only breaking on specified fields (whitelisting instead of blacklisting). This avoids overchunking every time we add a new metadata field and is also simpler and easier to understand. This change in approach is discussed in more detail here #1790. **Dropping regex-metadata Behavior** Chunking this section: ```python elements: List[Element] = [ Title( "Lorem Ipsum", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="Ipsum", start=6, end=11)]} ), ), Text( "Lorem ipsum dolor sit amet consectetur adipiscing elit.", metadata=ElementMetadata( regex_metadata={ "dolor": [RegexMetadata(text="dolor", start=12, end=17)], "ipsum": [RegexMetadata(text="ipsum", start=6, end=11)], } ), ), Text( "In rhoncus ipsum sed lectus porta volutpat.", metadata=ElementMetadata( regex_metadata={"ipsum": [RegexMetadata(text="ipsum", start=11, end=16)]} ), ), ] ``` ..should produce this regex_metadata on the single produced chunk: ```python assert chunk == CompositeElement( "Lorem Ipsum\n\nLorem ipsum dolor sit amet consectetur adipiscing elit.\n\nIn rhoncus" " ipsum sed lectus porta volutpat." ) assert chunk.metadata.regex_metadata == { "dolor": [RegexMetadata(text="dolor", start=25, end=30)], "ipsum": [ RegexMetadata(text="Ipsum", start=6, end=11), RegexMetadata(text="ipsum", start=19, end=24), RegexMetadata(text="ipsum", start=81, end=86), ], } ``` but instead produced this: ```python regex_metadata == {"ipsum": [{"text": "Ipsum", "start": 6, "end": 11}]} ``` Which is the regex-metadata from the first element only. The fix was to remove the consolidation+adjustment process from inside the "list-attribute-processing" loop (because regex-metadata is not a list) and process regex metadata separately.
2023-10-19 20:16:02 -07:00
def test_regex_metadata_round_trips_through_JSON():
"""metadata.regex_metadata should appear at full depth in JSON."""
regex_metadata = {
"mail-stop": [RegexMetadata(text="MS-107", start=18, end=24)],
"version": [
RegexMetadata(text="current=v1.7.2", start=7, end=21),
RegexMetadata(text="supersedes=v1.7.2", start=22, end=40),
],
}
metadata = ElementMetadata(regex_metadata=regex_metadata)
metadata_json = json.dumps(metadata.to_dict())
deserialized_metadata = ElementMetadata.from_dict(json.loads(metadata_json))
reserialized_metadata_json = json.dumps(deserialized_metadata.to_dict())
assert reserialized_metadata_json == metadata_json
def test_metadata_from_dict_extra_fields():
"""
Assert that the metadata classes ignore nonexistent fields.
This can be an issue when elements_from_json gets a schema
from the future.
"""
element_metadata = {
"new_field": "hello",
"data_source": {
"new_field": "world",
},
"coordinates": {
"new_field": "foo",
},
}
metadata = ElementMetadata.from_dict(element_metadata)
metadata_dict = metadata.to_dict()
assert "new_field" not in metadata_dict
assert "new_field" not in metadata_dict["coordinates"]
assert "new_field" not in metadata_dict["data_source"]
fix: flaky chunk metadata (#1947) **Executive Summary.** When the elements in a _section_ are combined into a _chunk_, the metadata in each of the elements is _consolidated_ into a single `ElementMetadata` instance. There are two main problems with the current implementation: 1. The current algorithm simply uses the metadata of the first element as the metadata for the chunk. This produces: - **empty chunk metadata** when the first element has no metadata, such as a `PageBreak("")` - **missing chunk metadata** when the first element contains only partial metadata such as a `Header()` or `Footer()` - **misleading metadata** when the first element contains values applicable only to that element, such as `category_depth`, `coordinates` (bounding-box), `header_footer_type`, or `parent_id` 2. Second, list metadata such as `emphasized_text_content`, `emphasized_text_tags`, `link_texts` and `link_urls` is only combined when it is unique within the combined list. These lists are "unzipped" pairs. For example, the first `link_texts` corresponds to the first `link_urls` value. When an item is removed from one (because it matches a prior entry) and not the other (say same text "here" but different URL) the positional correspondence is broken and downstream processing will at best be wrong, at worst raise an exception. ### Technical Discussion Element metadata cannot be determined in the general case simply by sampling that of the first element. At the same time, a simple union of all values is also not sufficient. To effectively consolidate the current variety of metadata fields we need four distinct strategies, selecting which to apply to each field based on that fields provenance and other characteristics. The four strategies are: - `FIRST` - Select the first non-`None` value across all the elements. Several fields are determined by the document source (`filename`, `file_directory`, etc.) and will not change within the output of a single partitioning run. They might not appear in every element, but they will be the same whenever they do appear. This strategy takes the first one that appears, if any, as proxy for the value for the entire chunk. - `LIST` - Consolidate the four list fields like `emphasized_text_content` and `link_urls` by concatenating them in element order (no set semantics apply). All values from `elements[n]` appear before those from `elements[n+1]` and existing order is preserved. - `LIST_UNIQUE` - Combine only unique elements across the (list) values of the elements, preserving order in which a unique item first appeared. - `REGEX` - Regex metadata has its own rules, including adjusting the `start` and `end` offset of each match based its new position in the concatenated text. - `DROP` - Not all metadata can or should appear in a chunk. For example, a chunk cannot be guaranteed to have a single `category_depth` or `parent_id`. Other strategies such as `COORDINATES` could be added to consolidate the bounding box of the chunk from the coordinates of its elements, roughly `min(lefts)`, `max(rights)`, etc. Others could be `LAST`, `MAJORITY`, or `SUM` depending on how metadata evolves. The proposed strategy assignments are these: - `attached_to_filename`: FIRST, - `category_depth`: DROP, - `coordinates`: DROP, - `data_source`: FIRST, - `detection_class_prob`: DROP, # -- ? confirm -- - `detection_origin`: DROP, # -- ? confirm -- - `emphasized_text_contents`: LIST, - `emphasized_text_tags`: LIST, - `file_directory`: FIRST, - `filename`: FIRST, - `filetype`: FIRST, - `header_footer_type`: DROP, - `image_path`: DROP, - `is_continuation`: DROP, # -- not expected, added by chunking, not before -- - `languages`: LIST_UNIQUE, - `last_modified`: FIRST, - `link_texts`: LIST, - `link_urls`: LIST, - `links`: DROP, # -- deprecated field -- - `max_characters`: DROP, # -- unused in code, probably remove from ElementMetadata -- - `page_name`: FIRST, - `page_number`: FIRST, - `parent_id`: DROP, - `regex_metadata`: REGEX, - `section`: FIRST, # -- section unconditionally breaks on new section -- - `sent_from`: FIRST, - `sent_to`: FIRST, - `subject`: FIRST, - `text_as_html`: DROP, # -- not expected, only occurs in TableSection -- - `url`: FIRST, **Assumptions:** - each .eml file is partitioned->chunked separately (not in batches), therefore sent-from, sent-to, and subject will not change within a section. ### Implementation Implementation of this behavior requires two steps: 1. **Collect** all non-`None` values from all elements, each in a sequence by field-name. Fields not populated in any of the elements do not appear in the collection. ```python all_meta = { "filename": ["memo.docx", "memo.docx"] "link_texts": [["here", "here"], ["and here"]] "parent_id": ["f273a7cb", "808b4ced"] } ``` 2. **Apply** the specified strategy to each item in the overall collection to produce the consolidated chunk meta (see implementation). ### Factoring For the following reasons, the implementation of metadata consolidation is extracted from its current location in `chunk_by_title()` to a handful of collaborating methods in `_TextSection`. - The current implementation of metadata consolidation "inline" in `chunk_by_title()` already has too many moving pieces to be understood without extended study. Adding strategies to that would make it worse. - `_TextSection` is the only section type where metadata is consolidated (the other two types always have exactly one element so already exactly one metadata.) - `_TextSection` is already the expert on all the information required to consolidate metadata, in particular the elements that make up the section and their text. Some other problems were also fixed in that transition, such as mutation of elements during the consolidation process. ### Technical Risk: adding new `ElementMetadata` field breaks metadata If each metadata field requires a strategy assignment to be consolidated and a developer adds a new `ElementMetadata` field without adding a corresponding strategy mapping, metadata consolidation could break or produce incorrect results. This risk can be mitigated multiple ways: 1. Add a test that verifies a strategy is defined for each (Recommended). 2. Define a default strategy, either `DROP` or `FIRST` for scalar types, `LIST` for list types. 3. Raise an exception when an unknown metadata field is encountered. This PR implements option 1 such that a developer will be notified before merge if they add a new metadata field but do not define a strategy for it. ### Other Considerations - If end-users can in-future add arbitrary metadata fields _before_ chunking, then we'll need to define metadata-consolidation behavior for such fields. Depending on how we implement user-defined metadata fields we might: - Require explicit definition of a new metadata field before use, perhaps with a method like `ElementMetadata.add_custom_field()` which requires a consolidation strategy to be defined (and/or has a default value). - Have a default strategy, perhaps `DROP` or `FIRST`, or `LIST` if the field is type `list`. ### Further Context Metadata is only consolidated for `TextSection` because the other two section types (`TableSection` and `NonTextSection`) can only contain a single element. --- ## Further discussion on consolidation strategy by field ### document-static These fields are very likely to be the same for all elements in a single document: - `attached_to_filename` - `data_source` - `file_directory` - `filename` - `filetype` - `last_modified` - `sent_from` - `sent_to` - `subject` - `url` *Consolidation strategy:* `FIRST` - use first one found, if any. ### section-static These fields are very likely to be the same for all elements in a single section, which is the scope we really care about for metadata consolidation: - `section` - an EPUB document-section unconditionally starts new section. *Consolidation strategy:* `FIRST` - use first one found, if any. ### consolidated list-items These `List` fields are consolidated by concatenating the lists from each element that has one: - `emphasized_text_contents` - `emphasized_text_tags` - `link_texts` - `link_urls` - `regex_metadata` - special case, this one gets indexes adjusted too. *Consolidation strategy:* `LIST` - concatenate lists across elements. ### dynamic These fields are likely to hold unique data for each element: - `category_depth` - `coordinates` - `image_path` - `parent_id` *Consolidation strategy:* - `DROP` as likely misleading. - `COORDINATES` strategy could be added to compute the bounding box from all bounding boxes. - Consider allowing if they are all the same, perhaps an `ALL` strategy. ### slow-changing These fields are somewhere in-between, likely to be common between multiple elements but varied within a document: - `header_footer_type` - *strategy:* drop as not-consolidatable - `languages` - *strategy:* take first occurence - `page_name` - *strategy:* take first occurence - `page_number` - *strategy:* take first occurence, will all be the same when `multipage_sections` is `False`. Worst-case semantics are "this chunk began on this page". ### N/A These field types do not figure in metadata-consolidation: - `detection_class_prob` - I'm thinking this is for debug and should not appear in chunks, but need confirmation. - `detection_origin` - for debug only - `is_continuation` - is _produced_ by chunking, never by partitioning (not in our code anyway). - `links` (deprecated, probably should be dropped) - `max_characters` - is unused as far as I can tell, is unreferenced in source code. Should be removed from `ElementMetadata` as far as I can tell. - `text_as_html` - only appears in a `Table` element, each of which appears in its own section so needs no consolidation. Never appears in `TextSection`. *Consolidation strategy:* `DROP` any that appear (several never will)
2023-11-01 18:49:20 -07:00
def test_there_is_a_consolidation_strategy_for_every_ElementMetadata_field():
metadata_field_names = sorted(f.name for f in dc.fields(ElementMetadata))
consolidation_strategies = ConsolidationStrategy.field_consolidation_strategies()
for field_name in metadata_field_names:
assert field_name in consolidation_strategies, (
f"ElementMetadata field `.{field_name}` does not have a consolidation strategy."
f" Add one in `ConsolidationStrategy.field_consolidation_strategies()."
)