SCIPROD-432 SCIPROD-499 SCIPROD-540 SCIPROD-560: CAWFR dataset utilities#786

Merged

kpjensen merged 86 commits intomasterfrom SCIPROD-432_CAWFR_dataset_utilities

Jul 8, 2022

+791-1

Commits on Apr 6, 2022

SCIPROD-432 dataset_utilities for CAWFR initial commit
npandeshwar-f
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Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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Commits on Apr 8, 2022

Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
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SCIPROD-432 dataset_utilities object structure for DxDatasetDiscriptor class
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Commits on Apr 11, 2022

SCIPROD-432 CAWFR dataset_utilities updated with load_entity_dictionary
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Commits on Apr 14, 2022

SCIPROD-432 CAWFR dataset_utilities added logic for coding dictionary
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Commits on Apr 15, 2022

SCIPROD-432 CAWFR dataset_utilities, basic write function. Additonal features in write function to be added
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Commits on Apr 18, 2022

SCIPROD-432 CAWFR dataset_utilities.py -added a part of data_dictionary function
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SCIPROD-432 CAWFR, dataset_utilities.py updated with more datadictionary logic
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Commits on Apr 20, 2022

SCIPROD-432 CAWFR dataset_utilities.py minor cosmetic changes
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SCIPROD-432 CAWFR dataset_utilities.py, updated column order in write function
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Commits on Apr 25, 2022

Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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SCIPROD-432 CAWFR, dataset_utilities.py updated with data_dictionary logic
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Commits on Apr 27, 2022

SCIPROD-432 CAWFR, dataset_utilities.py updated with docstrings, error handling, minor modifications in code structure
npandeshwar-f
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Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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SCIPROD-432 CAWFR, dataset_utilities.py updated with more docstrings
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Commits on May 2, 2022

SCIOROD-432 CAWFR, dataset_utilities.py updated with unique database name creation logic
npandeshwar-f
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Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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Commits on May 3, 2022

SCIPROD-432 CAWFR, dataset_utilities.py and dx.py updated to add --ddd and --output parameters
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SCIPROD-432 CAWFR, dataset_utilities.py updated to create csv files with dataset_name_prefix
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SCIPROD-432 CAWFR, requirement.txt updated with pandas version lockdown
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SCIRPOD-432 CAWFR, dataset_utilities.py updated with Directory not found exception logic
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Commits on May 4, 2022

Commits on May 10, 2022

SCIPROD-432 CAWFR, -ddd multiple small updates. Visualisation calls, input validations
npandeshwar-f
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Commits on May 12, 2022

SCIPROD-432 CAWFR, dataset_utilities.py import changes.
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Commits on May 18, 2022

SCIPROD-499 CAWFR, added initial logic for --fields
npandeshwar-f
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Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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SCIPROD-499 CAWFR, updated entity.field validations in dataset_utilities.py
npandeshwar-f
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Commits on May 20, 2022

SCIPROD-499 CAWFR: Updated dataset_utilities.py with correct output routing for --fields
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Commits on May 23, 2022

SCIPROD-499 CAWFR: dataset_utilities updated with --sql codes.
npandeshwar-f
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Commits on May 24, 2022

SCIPROD-499 CAWFR, dataset_utilities.py updated with more error handling blocks
npandeshwar-f
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Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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Commits on May 25, 2022

SCIPROD-499 CAWFR, dataset_utilities.py updated with file already exists errors
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SCIPROD-499 CAWFR: Updated e2e test for -ddd
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SCIPROD-499 CAWFR dx.py updated with help messages for extract_dataset
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Commits on May 26, 2022

Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
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SCIPROD-540 CAWFR Code review updates
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SCIPROD-540 CAWFR Code review updates - added back version check logic
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SCIPROD-540 CAWFR pandas import changes and --delim const and nargs changes
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SCIPROD-540 CAWFR dataset_utilities.py: changed writer to Dictwriter for csv writing
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Commits on May 27, 2022

SCIPROD-540 CAWFR check dataset_version instead of version - dataset_utilities.py
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Commits on May 31, 2022

Commits on Jun 1, 2022

SCIPROD-540 CAWFR, updated delimiter validation logic
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SCIPROD-540 CAWFR updated license details
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SCIPROD-540 CAWFR updated docstrings for extract_dataset
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SCIPROD-540 CAWFR updated error messages in dataset_utilities.py
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Commits on Jun 2, 2022

SCIPROD-540 CAWFR. Updated dataset_utilities: Added logic to populate codes_to_concept, Fixed local key population logic in data dictionary
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Commits on Jun 3, 2022

SCIPROD-540 CAWFR added display_order logic for codings dictionary in dataset_utilities.py
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SCIPROD-540 CAWFR Removed debug logics in dataset_utilities.py
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SCIPROD-540 CAWFR: Added permission check validation logic in dataset_utilities.py
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SCIPROD-540 CAWFR: Updated tests with new dataset and cohort
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SCIPROD-540 CAWFR: Revert back pandas import to make it global. Delete an unwanted import
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Commits on Jun 8, 2022

SCIPROD-540 CAWFR: updated output file extensions. Added try catch block around API calls. Updated error messages
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SCIPROD-540 CAWFR Updated codes_to_concept logic to fix values. Updated tests
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SCIPROD-540 CAWFR, deleted a commented import statement from test_extract_dataset.py
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Commits on Jun 9, 2022

SCIPROD-540 CAWFR: Updated dataset_utilities.py; Replaced f-string with repr for python 2.7 compatibility.
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Commits on Jun 10, 2022

SCIPROD-560 CAWFR, dataset_utilities.py updated with cleaner exception handling blocks
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SCIPROD-560 CAWFR: Added test for file not found error
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Commits on Jun 16, 2022

SCIPROD-560 CAWFR updates to dataset_utilities.py
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Commits on Jun 21, 2022

SCIPROD-560 CAWFR minor code updates.
npandeshwar-f
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Commits on Jun 22, 2022

SCIPROD-560 CAWFR updated docstrings for extract_dataset function
npandeshwar-f
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Commits on Jun 24, 2022

SCIPROD-560 CAWFR, modified dx.py with updated help strings
npandeshwar-f
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Commits on Jun 29, 2022

Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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SCIPROD-560 CAWFR, updated error handling for double quotation character
npandeshwar-f
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Commits on Jun 30, 2022

SCIPROD-560 CAWFR: dataset_utilities.py updates for error handling
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Commits on Jul 1, 2022

SCIPROD-560 CAWFR Updated error message for invalid input record ID
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SCIPROD-560 CAWFR Updated error message when workspace_id not set
npandeshwar-f
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Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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SCIPROD-560 CAWFR Remove print statement
npandeshwar-f
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Commits on Jul 4, 2022

SCIPROD-560 CAWFR: dataset_utilities.py
npandeshwar-f
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Commits on Jul 5, 2022

SCIPROD-560 CAWFR: Updated tests to replace project-xx:record-xx with path to file
npandeshwar-f
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Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into SCIPROD-432_CAWFR_dataset_utilities
npandeshwar-f
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Commits on Jul 7, 2022

Select dataset project before running test suite

kpjensen
authored and
npandeshwar-f
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SCIPROD-560 CAWFR test script updates for python2 compatibility
npandeshwar-f
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SCIPROD-560 CAWFR dx.py helpstring updates

Niranjanpandeshwar
and
commandlinegirl
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SCIPROD-560 CAWFR dx.py helpstring updates

Niranjanpandeshwar
and
commandlinegirl
authored
SCIPROD-560 CAWFR dx.py helpstring updates

Niranjanpandeshwar
and
commandlinegirl
authored
SCIPROD-560 CAWFR dx.py helpstring updates

Niranjanpandeshwar
and
commandlinegirl
authored
SCIPROD-560 CAWFR dx.py helpstring updates

Niranjanpandeshwar
and
commandlinegirl
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SCIPROD-560 CAWFR remove preview monicker from helpstring and docstring
npandeshwar-f
committed