Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Support partial deletes #569

Merged
merged 49 commits into from
Jul 9, 2024
Merged

Support partial deletes #569

merged 49 commits into from
Jul 9, 2024

Conversation

Fokko
Copy link
Contributor

@Fokko Fokko commented Apr 2, 2024

This is done through the Iceberg metadata, resulting in efficient deletes if the data is partitioned correctly

@Fokko
Add option to delete datafiles
8d45920 
This is done through the Iceberg metadata, resulting
in efficient deletes if the data is partitioned correctly
@Fokko
Merge branch 'main' of github.com:apache/iceberg-python into fd-add-a…
f6084a6 
…bility-to-delete-full-data-files
@Fokko
Pull in main
87cc065
@Fokko
Merge branch 'main' of github.com:apache/iceberg-python into fd-add-a…
bc9c83e 
…bility-to-delete-full-data-files
jqin61
jqin61 reviewed Apr 3, 2024
View reviewed changes
Copy link
Contributor

@jqin61 jqin61 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This PR looks so nice! It sheds much light on the overwrites. To confirm my understanding, we would use one transaction to build a commit with DeleteFiles and MergeAppend when this PR, #571 and #363 are merged?

pyiceberg/table/__init__.py Outdated Show resolved Hide resolved
pyiceberg/table/__init__.py Show resolved Hide resolved
@Fokko
Merge branch 'main' of github.com:apache/iceberg-python into fd-add-a…
284d05a 
…bility-to-delete-full-data-files
@Fokko
WIP
234d55b
@Fokko
Change DataScan to accept Metadata and io
aadc89c 
For the partial deletes I want to do a scan on in
memory metadata. Changing this API allows this.
@Fokko Fokko changed the title Add option to delete datafiles Support partial deletes Apr 7, 2024
@Fokko Fokko marked this pull request as draft April 7, 2024 20:14
@Fokko Fokko mentioned this pull request Apr 8, 2024
Closed
sungwy
sungwy reviewed May 13, 2024
View reviewed changes
pyiceberg/table/__init__.py Outdated Show resolved Hide resolved
@kevinjqliu kevinjqliu mentioned this pull request May 14, 2024
Open
39 tasks
@enkidulan enkidulan mentioned this pull request Jun 12, 2024
Closed
sungwy
sungwy reviewed Jun 13, 2024
View reviewed changes
pyiceberg/table/__init__.py
filtered_df = df.filter(preserve_row_filter)

# Only rewrite if there are records being deleted
if len(df) != len(filtered_df):
Copy link
Collaborator

@sungwy sungwy Jun 13, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This may be out of scope, but I'm thinking ahead to when we may want to use a Iterator[RecordBatch] to avoid materializing the whole table into memory, and I wonder if there's a way to get around having to use this condition.

Would it be possible to determine which files need to be replaced by evaluating two file plans instead?

If we evaluated:

files_with_records_to_delete = self._scan(row_filter=delete_filter).plan_files()
files_with_records_to_preserve = self._scan(row_filter= preserve_row_filter).plan_files()

Would the intersection of these two lists of files be the ones we would have to rewrite?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is on a file basis, so hopefully, that fits into memory. I do think that iterating over record batches might be an interesting thing to do here.

Would the intersection of these two lists of files be the ones we would have to rewrite?

We don't know for sure. If we're looking for x = 22, and the upper and lower bound are [19, 25], then it will match the evaluator, but we're still not sure if there is a row that matches the predicate until we've gone through the file.

@sungwy
Add docs (#33)
5cdb363 
* docs

* docs
@Fokko Fokko linked an issue Jun 21, 2024 that may be closed by this pull request
Support Partial deletes #554
Closed
@Fokko Fokko requested a review from rdblue June 21, 2024 14:34
@HonahX HonahX self-requested a review June 29, 2024 06:27
HonahX
HonahX reviewed Jun 29, 2024
View reviewed changes
Copy link
Contributor

@HonahX HonahX left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@Fokko Thanks for the great PR! Sorry for the delayed response. It looks great. I have some comments but most of them are minor.

Please let me know what you think!

pyiceberg/table/__init__.py Show resolved Hide resolved
pyiceberg/table/__init__.py Show resolved Hide resolved
tests/integration/test_deletes.py Outdated Show resolved Hide resolved
tests/integration/test_deletes.py Outdated Show resolved Hide resolved
pyiceberg/table/__init__.py Outdated Show resolved Hide resolved
pyiceberg/table/__init__.py Outdated Show resolved Hide resolved
pyiceberg/table/__init__.py Show resolved Hide resolved
pyiceberg/table/__init__.py Show resolved Hide resolved
@Fokko Fokko mentioned this pull request Jul 5, 2024
Closed
@Fokko Fokko requested a review from HonahX July 8, 2024 19:36
HonahX
HonahX approved these changes Jul 9, 2024
View reviewed changes
Copy link
Contributor

@HonahX HonahX left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM! @Fokko Thanks for contributing this great feature! Thanks everyone for reviewing this.

@Fokko Fokko merged commit 3f574d3 into apache:main Jul 9, 2024
7 checks passed
felixscherz added a commit to felixscherz/iceberg-python that referenced this pull request Jul 17, 2024
@felixscherz
chore: merge latest commits on main
6ca85ac 
commit 1ed3abd
Author: Sung Yun <[email protected]>
Date:   Wed Jul 17 02:04:52 2024 -0400

    Allow writing `pa.Table` that are either a subset of table schema or in arbitrary order, and support type promotion on write (apache#921)

    * merge

    * thanks @HonahX :)

    Co-authored-by: Honah J. <[email protected]>

    * support promote

    * revert promote

    * use a visitor

    * support promotion on write

    * fix

    * Thank you @Fokko !

    Co-authored-by: Fokko Driesprong <[email protected]>

    * revert

    * add-files promotiontest

    * support promote for add_files

    * add tests for uuid

    * add_files subset schema test

    ---------

    Co-authored-by: Honah J. <[email protected]>
    Co-authored-by: Fokko Driesprong <[email protected]>

commit 0f2e19e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 15 23:25:08 2024 -0700

    Bump zstandard from 0.22.0 to 0.23.0 (apache#934)

    Bumps [zstandard](https://github.com/indygreg/python-zstandard) from 0.22.0 to 0.23.0.
    - [Release notes](https://github.com/indygreg/python-zstandard/releases)
    - [Changelog](https://github.com/indygreg/python-zstandard/blob/main/docs/news.rst)
    - [Commits](indygreg/python-zstandard@0.22.0...0.23.0)

    ---
    updated-dependencies:
    - dependency-name: zstandard
      dependency-type: direct:production
      update-type: version-update:semver-minor
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit ec73d97
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 15 23:24:47 2024 -0700

    Bump griffe from 0.47.0 to 0.48.0 (apache#933)

    Bumps [griffe](https://github.com/mkdocstrings/griffe) from 0.47.0 to 0.48.0.
    - [Release notes](https://github.com/mkdocstrings/griffe/releases)
    - [Changelog](https://github.com/mkdocstrings/griffe/blob/main/CHANGELOG.md)
    - [Commits](mkdocstrings/griffe@0.47.0...0.48.0)

    ---
    updated-dependencies:
    - dependency-name: griffe
      dependency-type: direct:production
      update-type: version-update:semver-minor
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit d05a423
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 15 23:24:16 2024 -0700

    Bump mkdocs-material from 9.5.28 to 9.5.29 (apache#932)

    Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.5.28 to 9.5.29.
    - [Release notes](https://github.com/squidfunk/mkdocs-material/releases)
    - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG)
    - [Commits](squidfunk/mkdocs-material@9.5.28...9.5.29)

    ---
    updated-dependencies:
    - dependency-name: mkdocs-material
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit e27cd90
Author: Yair Halevi (Spock) <[email protected]>
Date:   Sun Jul 14 22:11:04 2024 +0300

    Allow empty `names` in mapped field of Name Mapping (apache#927)

    * Remove check_at_least_one field validator

    Iceberg spec permits an emtpy list of names in the default name mapping. check_at_least_one is therefore unnecessary.

    * Remove irrelevant test case

    * Fixing pydantic model

    No longer requiring minimum length of names list to be 1.

    * Added test case for empty names in name mapping

    * Fixed formatting error

commit 3f44dfe
Author: Soumya Ghosh <[email protected]>
Date:   Sun Jul 14 00:35:38 2024 +0530

    Lowercase bool values in table properties (apache#924)

commit b11cdb5
Author: Sung Yun <[email protected]>
Date:   Fri Jul 12 16:45:04 2024 -0400

    Deprecate to_requested_schema (apache#918)

    * deprecate to_requested_schema

    * prep for release

commit a3dd531
Author: Honah J <[email protected]>
Date:   Fri Jul 12 13:14:40 2024 -0700

    Glue endpoint config variable, continue apache#530 (apache#920)

    Co-authored-by: Seb Pretzer <[email protected]>

commit 32e8f88
Author: Sung Yun <[email protected]>
Date:   Fri Jul 12 15:26:00 2024 -0400

    support PyArrow timestamptz with Etc/UTC (apache#910)

    Co-authored-by: Fokko Driesprong <[email protected]>

commit f6d56e9
Author: Sung Yun <[email protected]>
Date:   Fri Jul 12 05:31:06 2024 -0400

    fix invalidation logic (apache#911)

commit 6488ad8
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Jul 11 22:56:48 2024 -0700

    Bump coverage from 7.5.4 to 7.6.0 (apache#917)

    Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.5.4 to 7.6.0.
    - [Release notes](https://github.com/nedbat/coveragepy/releases)
    - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
    - [Commits](nedbat/coveragepy@7.5.4...7.6.0)

    ---
    updated-dependencies:
    - dependency-name: coverage
      dependency-type: direct:development
      update-type: version-update:semver-minor
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit dceedfa
Author: Sung Yun <[email protected]>
Date:   Thu Jul 11 20:32:14 2024 -0400

    Check if schema is compatible in `add_files` API (apache#907)

    Co-authored-by: Fokko Driesprong <[email protected]>

commit aceed2a
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Jul 11 15:52:06 2024 +0200

    Bump mypy-boto3-glue from 1.34.136 to 1.34.143 (apache#912)

    Bumps [mypy-boto3-glue](https://github.com/youtype/mypy_boto3_builder) from 1.34.136 to 1.34.143.
    - [Release notes](https://github.com/youtype/mypy_boto3_builder/releases)
    - [Commits](https://github.com/youtype/mypy_boto3_builder/commits)

    ---
    updated-dependencies:
    - dependency-name: mypy-boto3-glue
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit 1b9b884
Author: Fokko Driesprong <[email protected]>
Date:   Thu Jul 11 12:45:20 2024 +0200

    PyArrow: Don't enforce the schema when reading/writing (apache#902)

    * PyArrow: Don't enforce the schema

    PyIceberg struggled with the different type of arrow, such as
    the `string` and `large_string`. They represent the same, but are
    different under the hood.

    My take is that we should hide these kind of details from the user
    as much as possible. Now we went down the road of passing in the
    Iceberg schema into Arrow, but when doing this, Iceberg has to
    decide if it is a large or non-large type.

    This PR removes passing down the schema in order to let Arrow decide
    unless:

     - The type should be evolved
     - In case of re-ordering, we reorder the original types

    * WIP

    * Reuse Table schema

    * Make linter happy

    * Squash some bugs

    * Thanks Sung!

    Co-authored-by: Sung Yun <[email protected]>

    * Moar code moar bugs

    * Remove the variables wrt file sizes

    * Linting

    * Go with large ones for now

    * Missed one there!

    ---------

    Co-authored-by: Sung Yun <[email protected]>

commit 8f47dfd
Author: Soumya Ghosh <[email protected]>
Date:   Thu Jul 11 11:52:55 2024 +0530

    Move determine_partitions and helper methods to io.pyarrow (apache#906)

commit 5aa451d
Author: Soumya Ghosh <[email protected]>
Date:   Thu Jul 11 07:57:05 2024 +0530

    Rename data_sequence_number to sequence_number in ManifestEntry (apache#900)

commit 77a07c9
Author: Honah J <[email protected]>
Date:   Wed Jul 10 03:56:13 2024 -0700

    Support MergeAppend operations (apache#363)

    * add ListPacker + tests

    * add merge append

    * add merge_append

    * fix snapshot inheritance

    * test manifest file and entries

    * add doc

    * fix lint

    * change test name

    * address review comments

    * rename _MergingSnapshotProducer to _SnapshotProducer

    * fix a serious bug

    * update the doc

    * remove merge_append as public API

    * make default to false

    * add test description

    * fix merge conflict

    * fix snapshot_id issue

commit 66b92ff
Author: Fokko Driesprong <[email protected]>
Date:   Wed Jul 10 10:09:20 2024 +0200

    GCS: Fix incorrect token description (apache#909)

commit c25e080
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Jul 9 20:50:29 2024 -0700

    Bump zipp from 3.17.0 to 3.19.1 (apache#905)

    Bumps [zipp](https://github.com/jaraco/zipp) from 3.17.0 to 3.19.1.
    - [Release notes](https://github.com/jaraco/zipp/releases)
    - [Changelog](https://github.com/jaraco/zipp/blob/main/NEWS.rst)
    - [Commits](jaraco/zipp@v3.17.0...v3.19.1)

    ---
    updated-dependencies:
    - dependency-name: zipp
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit 301e336
Author: Sung Yun <[email protected]>
Date:   Tue Jul 9 23:35:11 2024 -0400

    Cast 's', 'ms' and 'ns' PyArrow timestamp to 'us' precision on write (apache#848)

commit 3f574d3
Author: Fokko Driesprong <[email protected]>
Date:   Tue Jul 9 11:36:43 2024 +0200

    Support partial deletes (apache#569)

    * Add option to delete datafiles

    This is done through the Iceberg metadata, resulting
    in efficient deletes if the data is partitioned correctly

    * Pull in main

    * WIP

    * Change DataScan to accept Metadata and io

    For the partial deletes I want to do a scan on in
    memory metadata. Changing this API allows this.

    * fix name-mapping issue

    * WIP

    * WIP

    * Moar tests

    * Oops

    * Cleanup

    * WIP

    * WIP

    * Fix summary generation

    * Last few bits

    * Fix the requirement

    * Make ruff happy

    * Comments, thanks Kevin!

    * Comments

    * Append rather than truncate

    * Fix merge conflicts

    * Make the tests pass

    * Add another test

    * Conflicts

    * Add docs (apache#33)

    * docs

    * docs

    * Add a partitioned overwrite test

    * Fix comment

    * Skip empty manifests

    ---------

    Co-authored-by: HonahX <[email protected]>
    Co-authored-by: Sung Yun <[email protected]>

commit cdc3e54
Author: Fokko Driesprong <[email protected]>
Date:   Tue Jul 9 08:28:27 2024 +0200

    Disallow writing empty Manifest files (apache#876)

    * Disallow writing empty Avro files/blocks

    Raising an exception when doing this might look extreme, but
    there is no real good reason to allow this.

    * Relax the constaints a bit

commit b68e109
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 8 22:16:23 2024 -0700

    Bump fastavro from 1.9.4 to 1.9.5 (apache#904)

    Bumps [fastavro](https://github.com/fastavro/fastavro) from 1.9.4 to 1.9.5.
    - [Release notes](https://github.com/fastavro/fastavro/releases)
    - [Changelog](https://github.com/fastavro/fastavro/blob/master/ChangeLog)
    - [Commits](fastavro/fastavro@1.9.4...1.9.5)

    ---
    updated-dependencies:
    - dependency-name: fastavro
      dependency-type: direct:development
      update-type: version-update:semver-patch
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit 90547bb
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 8 22:15:39 2024 -0700

    Bump moto from 5.0.10 to 5.0.11 (apache#903)

    Bumps [moto](https://github.com/getmoto/moto) from 5.0.10 to 5.0.11.
    - [Release notes](https://github.com/getmoto/moto/releases)
    - [Changelog](https://github.com/getmoto/moto/blob/master/CHANGELOG.md)
    - [Commits](getmoto/moto@5.0.10...5.0.11)

    ---
    updated-dependencies:
    - dependency-name: moto
      dependency-type: direct:development
      update-type: version-update:semver-patch
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit 7dff359
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Jul 7 07:50:19 2024 +0200

    Bump tenacity from 8.4.2 to 8.5.0 (apache#898)

commit 4aa469e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Jul 6 22:30:59 2024 +0200

    Bump certifi from 2024.2.2 to 2024.7.4 (apache#899)

    Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.2.2 to 2024.7.4.
    - [Commits](certifi/python-certifi@2024.02.02...2024.07.04)

    ---
    updated-dependencies:
    - dependency-name: certifi
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit aa7ad78
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Jul 6 20:37:51 2024 +0200

    Bump deptry from 0.16.1 to 0.16.2 (apache#897)

    Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.16.1 to 0.16.2.
    - [Release notes](https://github.com/fpgmaas/deptry/releases)
    - [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md)
    - [Commits](fpgmaas/deptry@0.16.1...0.16.2)

    ---
    updated-dependencies:
    - dependency-name: deptry
      dependency-type: direct:development
      update-type: version-update:semver-patch
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jqin61 jqin61 jqin61 left review comments

@HonahX HonahX HonahX approved these changes

@sungwy sungwy sungwy left review comments

@MehulBatra MehulBatra MehulBatra left review comments

@kevinjqliu kevinjqliu kevinjqliu left review comments

@rdblue rdblue Awaiting requested review from rdblue

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
PyIceberg 0.7.0 release
Development

Successfully merging this pull request may close these issues.

Support Partial deletes
6 participants
@Fokko @kevinjqliu @MehulBatra @sungwy @HonahX @jqin61