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Issues: mmcdermott/MEDS_transforms

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#35 opened Jul 16, 2024 by mmcdermott
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57 Open 83 Closed
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Issues list

Should consider integration with other workflow management softwares Pipeline Configuration and Stage Management Issues relating to proper definition and usability of different stages in a pipeline priority:low A low priority issue. Runner For things about the multi-stage, single-script Runner
#234 opened Jan 15, 2025 by mmcdermott
If a time format is provided but the column is already a datetime type it should not throw an error and should instead warn the user bug Something isn't working good first issue Good for newcomers MEDS-Extract priority:medium A medium priority issue. Usability / Interface
#232 opened Dec 4, 2024 by mmcdermott
You should be able to re-type columns during extraction dynamically MEDS-Extract priority:low A low priority issue.
#231 opened Dec 4, 2024 by mmcdermott
Boolean additional columns should be supported during extraction good first issue Good for newcomers MEDS-Extract priority:high A high priority issue.
#230 opened Dec 4, 2024 by mmcdermott
Should update log tests with pytest-loguru priority:low A low priority issue. Testing
#226 opened Nov 18, 2024 by mmcdermott
Error case integration tests should check for the right error message. priority:medium A medium priority issue. Testing
#220 opened Nov 8, 2024 by mmcdermott
File paths with spaces in them break the runner Blocking External Tools For issues actively blocking external tools, such as ACES, MEDS-torch, MEDS-tab, etc. priority:high A high priority issue. Runner For things about the multi-stage, single-script Runner
#217 opened Nov 4, 2024 by mmcdermott
Get test coverage to 100% priority:medium A medium priority issue. Testing
#216 opened Oct 30, 2024 by mmcdermott
1 of 4 tasks
Shoud add a test with non-standard splits priority:low A low priority issue. Testing
#215 opened Oct 30, 2024 by mmcdermott
Single stage tester is likely not checking for the right kinds of errors when should_error is True priority:medium A medium priority issue. Testing
#213 opened Oct 30, 2024 by mmcdermott
We should be able to convert between different ontological code vocabularies.
#204 opened Oct 11, 2024 by mmcdermott
1
@prenc
4
add_time_derived_measurements breaks if you use _script in the meds_transform_runner bug Something isn't working priority:medium A medium priority issue. Runner For things about the multi-stage, single-script Runner
#202 opened Sep 3, 2024 by Oufattole
1
All stages must have unique names or an error should be thrown. Pipeline Configuration and Stage Management Issues relating to proper definition and usability of different stages in a pipeline priority:medium A medium priority issue. Runner For things about the multi-stage, single-script Runner Usability / Interface
#201 opened Sep 2, 2024 by mmcdermott
Stages that depend on code metadata having been recently computed (e.g., filter_measurements) should be better documented documentation Improvements or additions to documentation priority:high A high priority issue. Usability / Interface
#200 opened Sep 2, 2024 by mmcdermott
1
Should distribute / package typing information too priority:low A low priority issue.
#195 opened Aug 30, 2024 by mmcdermott
1
Lock files should be pipeline ID specific in some way -- this will enable pipelines to flag when old run locks are present. Computational Performance Issues relating to efficient computational performance of MEDS_transforms pipelines Pipeline Configuration and Stage Management Issues relating to proper definition and usability of different stages in a pipeline priority:medium A medium priority issue.
#194 opened Aug 30, 2024 by mmcdermott
1
Metadata extraction should log a warning if code-part column names are not uniformly either extracted or not extracted across metadata sources. documentation Improvements or additions to documentation Logging MEDS-Extract Metadata Extraction priority:low A low priority issue.
#186 opened Aug 28, 2024 by mmcdermott
Should pull the generic hydra resolvers (e.g., get_script_docstring) into a separate package Code Cleanliness For code style, cleanliness, reduction of technical debt, etc. priority:low A low priority issue.
#180 opened Aug 27, 2024 by mmcdermott
We need a more robust interface for ways of (a) processing numerical and categorical values and (b) normalizing output data in light of those modes. Blocking External Tools For issues actively blocking external tools, such as ACES, MEDS-torch, MEDS-tab, etc. MEDS-Transform Issues for the data pre-processing transformations in MEDS_transforms Needs Clarification This issue needs further clarification before it can be operationalized New Transformation Requests for a new transformation function that can be used in MEDS pipelines priority:high A high priority issue. Release Blocking
#177 opened Aug 25, 2024 by mmcdermott
1 of 3 tasks
5
Error message when aggregate_code_metadata.py gets an aggregation that should be an object but is just a string should be clearer. Code aggregations Issues about building new aggregations over codes and values. MEDS-Transform Issues for the data pre-processing transformations in MEDS_transforms priority:medium A medium priority issue. Usability / Interface
#164 opened Aug 14, 2024 by mmcdermott
Pipeline Configuration Improvements MEDS-Extract MEDS-Transform Issues for the data pre-processing transformations in MEDS_transforms Needs Clarification This issue needs further clarification before it can be operationalized Pipeline Configuration and Stage Management Issues relating to proper definition and usability of different stages in a pipeline priority:low A low priority issue. Usability / Interface
#155 opened Aug 13, 2024 by mmcdermott
2 tasks
1
reshard_to_split should (in a configurable manner) sub-shard the input rather than re-shard the input where possible. Computational Performance Issues relating to efficient computational performance of MEDS_transforms pipelines MEDS-Transform Issues for the data pre-processing transformations in MEDS_transforms Needs Clarification This issue needs further clarification before it can be operationalized priority:medium A medium priority issue.
#153 opened Aug 13, 2024 by mmcdermott
The dropping of nulls and making the dataframe unique could be done once and shared across all time dependent fntrs. Code Cleanliness For code style, cleanliness, reduction of technical debt, etc. MEDS-Transform Issues for the data pre-processing transformations in MEDS_transforms priority:low A low priority issue.
#152 opened Aug 13, 2024 by mmcdermott
We need to be able to support joining on metadata based on partial code matches (e.g., no valueuom). Blocking External Tools For issues actively blocking external tools, such as ACES, MEDS-torch, MEDS-tab, etc. MEDS-Extract Metadata Extraction Needs Clarification This issue needs further clarification before it can be operationalized priority:low A low priority issue.
#148 opened Aug 12, 2024 by mmcdermott
2
reshard stage code is very messy and really stretches the limits of this "MR" library's API. Code Cleanliness For code style, cleanliness, reduction of technical debt, etc. priority:low A low priority issue.
#145 opened Aug 11, 2024 by mmcdermott
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