[BUG] Fix StructuredDataset empty-str `file_format` in dc attr access #3027

JiangJiaWei1103 · 2025-01-01T15:55:47Z

Tracking issue

Why are the changes needed?

When users create a StructuredDataset with a specified file_format (e.g., parquet), the file_format information will be accidentally discarded in this case during async_to_literal call. To be concrete, StructuredDatasetType's format attribute is set to GENERIC_FORMAT, which is an empty string "".

What changes were proposed in this pull request?

Override StructuredDatasetType's format attribute when users explicitly set file_format of python native StructuredDataset.

How was this patch tested?

This patch is tested through the newly added integration test and double checked by observing the flyte console I/O and the task pod stdout.

Setup process

For local run, the setup process is summarized as follows:

git clone https://github.com/flyteorg/flytekit.git
gh pr checkout 3027
make setup && pip install -e .

After installation, run the following command:

pytest -svvv tests/flytekit/integration/remote/test_remote.py::test_sd_attr

Screenshots

The following results are expected:

Flyte console input
Flyte console output
Task pod stdout

Check all the applicable boxes

I updated the documentation accordingly.
All new and existing tests passed.
All commits are signed-off.

Related PRs

Docs link

Summary by Bito

This PR implements comprehensive Flytekit improvements including: enhanced execution engine with improved error handling, fixed StructuredDataset file format handling, K8s Data Service plugin implementation, and Ray plugin enhancements. Key features include configurable cloud storage writes, improved secret handling, Optuna plugin for hyperparameter optimization, and enhanced thread safety mechanisms.

Unit tests added: True

Estimated effort to review (1-5, lower is better): 5

Signed-off-by: JiaWei Jiang <[email protected]>

flyte-bot · 2025-01-01T15:55:59Z

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codecov · 2025-01-01T16:26:45Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.84%. Comparing base (4208a64) to head (f1a2ba3).
Report is 1 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff             @@
##           master    #3027       +/-   ##
===========================================
+ Coverage   51.81%   76.84%   +25.02%     
===========================================
  Files         202      202               
  Lines       21469    21472        +3     
  Branches     2766     2767        +1     
===========================================
+ Hits        11125    16500     +5375     
+ Misses       9735     4211     -5524     
- Partials      609      761      +152

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Signed-off-by: JiaWei Jiang <[email protected]>

flyte-bot · 2025-01-03T15:38:56Z

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Signed-off-by: JiaWei Jiang <[email protected]>

flyte-bot · 2025-01-04T06:08:56Z

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Signed-off-by: JiaWei Jiang <[email protected]>

JiangJiaWei1103 · 2025-01-04T07:11:19Z

Follow-up

During fixing this bug, we observe another two phenomenon, which are briefly described as follows:

pyflyte run can't handle the dataclass input as a json string, e.g.,

pyflyte run --remote test.py wf --dc '{"dc": {"sd": {"uri": "s3://my-s3-bucket/df.parquet", "file_format": "parquet"}}}'

There are two sub-cases:

DC's sd is defined without default_factory
- Get KeyError: 'sd'
DC's sd is defined with default_factory
- wf always takes the default_factory setup as input no matter what's specified in the json string

uri information loss, which is just similar to what we've solved in this patch

As can be observed, StructuredDataset uri becomes None.

We plan to solve these issues in the future which can make attribute access result more accurate. Thanks!

flyte-bot · 2025-01-04T07:38:57Z

Code Review Agent Run #2ae7a3

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Review Details

Files reviewed - 3 · Commit Range: cdb56c0..46b7b62
- flytekit/types/structured/structured_dataset.py
- tests/flytekit/integration/remote/test_remote.py
- tests/flytekit/integration/remote/workflows/basic/sd_attr.py
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flyte-bot · 2025-01-04T07:41:04Z

Changelist by Bito

This pull request implements the following key changes.

Key Change	Files Impacted
Bug Fix - Fix StructuredDataset File Format Preservation	- `structured_dataset.py` - Added logic to retain user-specified file_format in StructuredDataset during async_to_literal conversion - `test_remote.py` - Added integration test to verify StructuredDataset file_format attribute preservation - `sd_attr.py` - Added new test workflow to validate StructuredDataset file format handling

Signed-off-by: JiaWei Jiang <[email protected]>

flyte-bot · 2025-01-11T13:31:06Z

Code Review Agent Run #1863ff

Actionable Suggestions - 0

Additional Suggestions - 10

tests/flytekit/integration/remote/utils.py - 1
- Consider making parquet path configurable · Line 89-89
plugins/flytekit-optuna/flytekitplugins/optuna/optimizer.py - 1
- Consider more specific error handling · Line 109-135
plugins/flytekit-inference/tests/test_vllm.py - 1
- Consider breaking down long assertion statement · Line 41-41
tests/flytekit/unit/core/test_flyte_file.py - 1
- Consider adding error test cases · Line 788-809
flytekit/image_spec/default_builder.py - 1
- Consider moving poetry arg to template · Line 196-197
tests/flytekit/unit/core/test_flyte_directory.py - 1
- Consider adding error test cases · Line 427-448
tests/flytekit/integration/remote/test_remote.py - 1
- Consider extracting duplicated workflow execution logic · Line 846-847
plugins/flytekit-optuna/setup.py - 1
- Consider adding Python 3.11 support · Line 21-21
plugins/flytekit-spark/tests/test_environment.py - 1
- Consider validating Spark config in test · Line 17-20
tests/flytekit/unit/core/image_spec/test_default_builder.py - 1
- Consider using complete error message pattern · Line 271-271

Review Details

Files reviewed - 27 · Commit Range: 46b7b62..cb73c0e
- flytekit/__init__.py
- flytekit/core/array_node_map_task.py
- flytekit/core/environment.py
- flytekit/core/workflow.py
- flytekit/image_spec/default_builder.py
- flytekit/remote/remote.py
- flytekit/types/directory/types.py
- flytekit/types/file/file.py
- plugins/flytekit-inference/flytekitplugins/inference/__init__.py
- plugins/flytekit-inference/flytekitplugins/inference/vllm/serve.py
- plugins/flytekit-inference/setup.py
- plugins/flytekit-inference/tests/test_vllm.py
- plugins/flytekit-onnx-pytorch/dev-requirements.txt
- plugins/flytekit-optuna/flytekitplugins/optuna/__init__.py
- plugins/flytekit-optuna/flytekitplugins/optuna/optimizer.py
- plugins/flytekit-optuna/setup.py
- plugins/flytekit-optuna/tests/test_optimizer.py
- plugins/flytekit-spark/tests/test_environment.py
- pyproject.toml
- tests/flytekit/integration/remote/test_remote.py
- tests/flytekit/integration/remote/utils.py
- tests/flytekit/integration/remote/workflows/basic/attr_access_sd.py
- tests/flytekit/unit/core/image_spec/test_default_builder.py
- tests/flytekit/unit/core/test_environment.py
- tests/flytekit/unit/core/test_flyte_directory.py
- tests/flytekit/unit/core/test_flyte_file.py
- tests/flytekit/unit/core/test_workflows.py
Files skipped - 3
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JiangJiaWei1103 · 2025-01-17T12:11:41Z

For the second follow-up issue, I thought I found why uri information is missing. I'll open another PR and link to this one after this one is merged. Thanks!

flytekit/types/structured/structured_dataset.py

Signed-off-by: JiangJiaWei1103 <[email protected]>

flyte-bot · 2025-01-19T10:43:37Z

Code Review Agent Run #2259be

Actionable Suggestions - 0

Additional Suggestions - 10

flytekit/core/worker_queue.py - 3
- Add timeout to prevent infinite waiting · Line 392-400
- Consider direct dict initialization over casting · Line 141-141
- Consider encapsulating enum state checks · Line 114-115
flytekit/core/array_node_map_task.py - 1
- Consider using proper constructor for metadata · Line 131-132
flytekit/exceptions/user.py - 1
- Consider adding timestamp parameter validation · Line 18-18
flytekit/remote/remote.py - 1
- Consider improving error message details · Line 1405-1406
plugins/flytekit-optuna/flytekitplugins/optuna/optimizer.py - 2
- Consider adding inputs parameter validation · Line 192-192
- Consider simplifying validation logic expressions · Line 84-87
tests/flytekit/unit/exceptions/test_user.py - 1
- Consider splitting error message assertion · Line 19-19
flytekit/core/type_engine.py - 1
- Consider including full exception traceback · Line 1521-1528

Review Details

Files reviewed - 40 · Commit Range: cb73c0e..416bed8
- flytekit/bin/entrypoint.py
- flytekit/clis/sdk_in_container/run.py
- flytekit/core/array_node_map_task.py
- flytekit/core/context_manager.py
- flytekit/core/node.py
- flytekit/core/promise.py
- flytekit/core/type_engine.py
- flytekit/core/worker_queue.py
- flytekit/exceptions/user.py
- flytekit/image_spec/default_builder.py
- flytekit/remote/remote.py
- flytekit/tools/translator.py
- flytekit/types/structured/structured_dataset.py
- plugins/flytekit-kf-pytorch/flytekitplugins/kfpytorch/task.py
- plugins/flytekit-kf-pytorch/tests/test_elastic_task.py
- plugins/flytekit-optuna/flytekitplugins/optuna/__init__.py
- plugins/flytekit-optuna/flytekitplugins/optuna/optimizer.py
- plugins/flytekit-optuna/setup.py
- plugins/flytekit-optuna/tests/test_callback.py
- plugins/flytekit-optuna/tests/test_decorator.py
- plugins/flytekit-optuna/tests/test_imperative.py
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- plugins/flytekit-pydantic/tests/folder/test_file1.txt
- plugins/flytekit-pydantic/tests/folder/test_file2.txt
- plugins/flytekit-pydantic/tests/test_type_transformer.py
- tests/flytekit/integration/remote/test_remote.py
- tests/flytekit/integration/remote/workflows/basic/signal_test.py
- tests/flytekit/unit/bin/test_python_entrypoint.py
- tests/flytekit/unit/core/test_array_node_map_task.py
- tests/flytekit/unit/core/test_type_hints.py
- tests/flytekit/unit/core/test_worker_queue.py
- tests/flytekit/unit/exceptions/test_user.py
- tests/flytekit/unit/remote/test_remote.py
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Signed-off-by: JiangJiaWei1103 <[email protected]>

…1103/flytekit into fix-sd-empty-str-file-format

flyte-bot · 2025-01-25T04:57:24Z

Code Review Agent Run #d43f9b

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- flytekit/types/structured/structured_dataset.py
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Future-Outlier · 2025-01-31T17:42:28Z

final testing.

from flytekit import task, workflow, ImageSpec
from flytekit.types.structured.structured_dataset import StructuredDataset
import pandas as pd


flytekit_hash = "f1a2ba3a1836983ffb9bb45276d8aa9b01665600"
flytekit = f"git+https://github.com/flyteorg/flytekit.git@{flytekit_hash}"

custom_image = ImageSpec(packages=[flytekit, "pandas", "pyarrow"],
                            apt_packages=["git"],
                        registry="localhost:30000",
                            env={"FLYTE_SDK_LOGGING_LEVEL": 10},
                         )

@task(container_image=custom_image)
def create_pd_sd() -> StructuredDataset:
    return StructuredDataset(
        dataframe=pd.DataFrame(
            {
                "calories": [420, 380, 390],
                "duration": [50, 40, 45]
            }
        ),
        file_format="parquet"
    )

@task(container_image=custom_image)
def return_pd_sd(sd: StructuredDataset) -> StructuredDataset:
    return sd

@workflow
def wf() -> StructuredDataset:
    sd = create_pd_sd()
    sd = return_pd_sd(sd)
    return sd

if __name__ == "__main__":
    print(wf())

this work!

flyte-bot · 2025-01-31T18:24:02Z

Code Review Agent Run #adec49

Actionable Suggestions - 0

Additional Suggestions - 10

flytekit/models/security.py - 1
- Consider adding env_var validation check · Line 45-45
flytekit/clis/sdk_in_container/serve.py - 2
- Consider adding port number validation · Line 83-83
- Consider adding parameter validation checks · Line 64-64
plugins/flytekit-omegaconf/flytekitplugins/omegaconf/dictconfig_transformer.py - 1
- Consider consolidating NoneType handling checks · Line 146-147
flytekit/core/resources.py - 1
- Consider using Optional for return type · Line 110-110
flytekit/core/type_engine.py - 3
- Consider more descriptive environment variable name · Line 63-63
- Consider performance impact of chunking coroutines · Line 1691-1693
- Consider direct use of asyncio.gather() · Line 2162-2165
plugins/flytekit-k8sdataservice/tests/k8sdataservice/test_sensor.py - 1
- Simplify async test execution pattern · Line 25-29
plugins/flytekit-k8sdataservice/flytekitplugins/k8sdataservice/k8s/manager.py - 1
- Consider extracting resource config logic · Line 206-219

Review Details

Files reviewed - 52 · Commit Range: ddba120..f1a2ba3
- .pre-commit-config.yaml
- Dockerfile.agent
- docs/source/plugins/k8sstatefuldataservice.rst
- flytekit/clis/sdk_in_container/serve.py
- flytekit/core/data_persistence.py
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- plugins/flytekit-k8sdataservice/flytekitplugins/k8sdataservice/k8s/manager.py
- plugins/flytekit-k8sdataservice/flytekitplugins/k8sdataservice/sensor.py
- plugins/flytekit-k8sdataservice/flytekitplugins/k8sdataservice/task.py
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- plugins/flytekit-k8sdataservice/tests/k8sdataservice/test_sensor.py
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- plugins/flytekit-k8sdataservice/tests/k8sdataservice/utils/test_resources.py
- plugins/flytekit-k8sdataservice/utils/infra.py
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- tests/flytekit/unit/core/test_data_persistence.py
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- tests/flytekit/unit/extras/pydantic_transformer/test_pydantic_basemodel_transformer.py
- tests/flytekit/unit/types/structured_dataset/test_structured_dataset.py
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JiangJiaWei1103 · 2025-02-01T10:10:31Z

Nice bro, thanks for your time!

Let's move on to the next challenge!

…flyteorg#3027) * fix: Retain user-specified file format info Signed-off-by: JiaWei Jiang <[email protected]> * fix: Set sdt format based on user-specified file_format Signed-off-by: JiaWei Jiang <[email protected]> * Remove redundant modification Signed-off-by: JiaWei Jiang <[email protected]> * test: Test file_format attribute alignment in dc.sd Signed-off-by: JiaWei Jiang <[email protected]> * Merge master and support pqt file upload Signed-off-by: JiaWei Jiang <[email protected]> * Remove redundant condition to always copy file_format over Signed-off-by: JiangJiaWei1103 <[email protected]> * Prioritize file_format in type hint over the user-specified one Signed-off-by: JiangJiaWei1103 <[email protected]> --------- Signed-off-by: JiaWei Jiang <[email protected]> Signed-off-by: JiangJiaWei1103 <[email protected]> Co-authored-by: Future-Outlier <[email protected]> Signed-off-by: Umer Ahmad <[email protected]>

…flyteorg#3027) * fix: Retain user-specified file format info Signed-off-by: JiaWei Jiang <[email protected]> * fix: Set sdt format based on user-specified file_format Signed-off-by: JiaWei Jiang <[email protected]> * Remove redundant modification Signed-off-by: JiaWei Jiang <[email protected]> * test: Test file_format attribute alignment in dc.sd Signed-off-by: JiaWei Jiang <[email protected]> * Merge master and support pqt file upload Signed-off-by: JiaWei Jiang <[email protected]> * Remove redundant condition to always copy file_format over Signed-off-by: JiangJiaWei1103 <[email protected]> * Prioritize file_format in type hint over the user-specified one Signed-off-by: JiangJiaWei1103 <[email protected]> --------- Signed-off-by: JiaWei Jiang <[email protected]> Signed-off-by: JiangJiaWei1103 <[email protected]> Co-authored-by: Future-Outlier <[email protected]> Signed-off-by: Atharva <[email protected]>

fix: Retain user-specified file format info

cdb56c0

Signed-off-by: JiaWei Jiang <[email protected]>

JiangJiaWei1103 added 2 commits January 3, 2025 22:32

fix: Set sdt format based on user-specified file_format

36ab6e9

Signed-off-by: JiaWei Jiang <[email protected]>

Merge branch 'master' into fix-sd-empty-str-file-format

58751fb

Remove redundant modification

4af1f00

Signed-off-by: JiaWei Jiang <[email protected]>

test: Test file_format attribute alignment in dc.sd

46b7b62

Signed-off-by: JiaWei Jiang <[email protected]>

JiangJiaWei1103 changed the title ~~[WIP] Fix StructuredDataset empty-str file_format in dc attr access~~ [BUG] Fix StructuredDataset empty-str file_format in dc attr access Jan 4, 2025

JiangJiaWei1103 marked this pull request as ready for review January 4, 2025 07:11

JiangJiaWei1103 requested review from Future-Outlier, cosmicBboy, eapolinario, kumare3, pingsutw, samhita-alla, thomasjpfan and wild-endeavor as code owners January 4, 2025 07:11

JiangJiaWei1103 and others added 2 commits January 11, 2025 20:26

Merge master and support pqt file upload

af1ee98

Signed-off-by: JiaWei Jiang <[email protected]>

Merge branch 'master' into fix-sd-empty-str-file-format

cb73c0e

Future-Outlier self-assigned this Jan 13, 2025

thomasjpfan reviewed Jan 18, 2025

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flytekit/types/structured/structured_dataset.py Outdated Show resolved Hide resolved

JiangJiaWei1103 and others added 2 commits January 19, 2025 17:42

Remove redundant condition to always copy file_format over

063801c

Signed-off-by: JiangJiaWei1103 <[email protected]>

Merge branch 'master' into fix-sd-empty-str-file-format

416bed8

JiangJiaWei1103 added 2 commits January 25, 2025 11:44

Prioritize file_format in type hint over the user-specified one

d774df1

Signed-off-by: JiangJiaWei1103 <[email protected]>

Merge branch 'fix-sd-empty-str-file-format' of github.com:JiangJiaWei…

ddba120

…1103/flytekit into fix-sd-empty-str-file-format

Merge branch 'master' into fix-sd-empty-str-file-format

f1a2ba3

Future-Outlier approved these changes Jan 31, 2025

View reviewed changes

Future-Outlier merged commit 88ac611 into flyteorg:master Jan 31, 2025
109 of 112 checks passed

Future-Outlier mentioned this pull request Feb 22, 2025

Nominate @jiangjiawei1103 as Committer flyteorg/community#37

Closed

[BUG] Fix StructuredDataset empty-str file_format in dc attr access #3027

[BUG] Fix StructuredDataset empty-str file_format in dc attr access #3027

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[BUG] Fix StructuredDataset empty-str `file_format` in dc attr access #3027

[BUG] Fix StructuredDataset empty-str `file_format` in dc attr access #3027

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