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

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

Merged
merged 86 commits into from
Jul 8, 2022
Merged

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

Show file tree
Hide file tree
Changes from 62 commits
Commits
Show all changes
86 commits
Select commit Hold shift + click to select a range
7880a47
SCIPROD-432 dataset_utilities for CAWFR initial commit
Apr 6, 2022
680009f
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
Apr 6, 2022
e90897c
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
Apr 8, 2022
ced142b
SCIPROD-432 dataset_utilities object structure for DxDatasetDiscripto…
Apr 8, 2022
b6b103a
SCIPROD-432 CAWFR dataset_utilities updated with load_entity_dictionary
Apr 11, 2022
2d4c52f
SCIPROD-432 CAWFR dataset_utilities added logic for coding dictionary
Apr 14, 2022
cb41e8b
SCIPROD-432 CAWFR dataset_utilities, basic write function. Additonal …
Apr 15, 2022
d9abfd6
SCIPROD-432 CAWFR dataset_utilities.py -added a part of data_dictiona…
Apr 18, 2022
ee4a8ed
SCIPROD-432 CAWFR, dataset_utilities.py updated with more datadiction…
Apr 18, 2022
21dcb63
SCIPROD-432 CAWFR dataset_utilities.py minor cosmetic changes
Apr 20, 2022
aed4101
SCIPROD-432 CAWFR dataset_utilities.py, updated column order in write…
Apr 20, 2022
955f245
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
Apr 25, 2022
8dad5f6
SCIPROD-432 CAWFR, dataset_utilities.py updated with data_dictionary …
Apr 25, 2022
2a96856
SCIPROD-432 CAWFR, dataset_utilities.py updated with docstrings, erro…
Apr 27, 2022
f7a9834
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
Apr 27, 2022
2239930
SCIPROD-432 CAWFR, dataset_utilities.py updated with more docstrings
Apr 27, 2022
2e6a2e4
SCIOROD-432 CAWFR, dataset_utilities.py updated with unique database …
May 2, 2022
ff58ecb
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
May 2, 2022
639a944
SCIPROD-432 CAWFR, dataset_utilities.py and dx.py updated to add --dd…
May 3, 2022
7914d46
SCIPROD-432 CAWFR, dataset_utilities.py updated to create csv files w…
May 3, 2022
7f7f66a
SCIPROD-432 CAWFR, requirement.txt updated with pandas version lockdown
May 3, 2022
9deb08e
SCIRPOD-432 CAWFR, dataset_utilities.py updated with Directory not fo…
May 3, 2022
302483a
SCIPROD-432 CAWFR, dataset_utilities.py updates. Added type conversio…
May 4, 2022
37a9533
SCIPROD-432 CAWFR, added E2E tests for DXDataset class
May 4, 2022
cb06c4a
SCIPROD-432 CAWFR, -ddd multiple small updates. Visualisation calls, …
May 10, 2022
2b30df7
SCIPROD-432 CAWFR, dataset_utilities.py import changes.
May 12, 2022
869fd53
SCIPROD-499 CAWFR, added initial logic for --fields
May 18, 2022
63b1f2e
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
May 18, 2022
24084c9
SCIPROD-499 CAWFR, updated entity.field validations in dataset_utilit…
May 18, 2022
5c17afe
SCIPROD-499 CAWFR: Updated dataset_utilities.py with correct output r…
May 20, 2022
44e01d2
SCIPROD-499 CAWFR: dataset_utilities updated with --sql codes.
May 23, 2022
40fe6ba
SCIPROD-499 CAWFR, dataset_utilities.py updated with more error handl…
May 24, 2022
79df259
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
May 24, 2022
ab8a9de
SCIPROD-499 CAWFR, dataset_utilities.py updated with file already exi…
May 25, 2022
4768957
SCIPROD-499 CAWFR: Updated e2e test for -ddd
May 25, 2022
fa68929
SCIPROD-499 CAWFR dx.py updated with help messages for extract_dataset
May 25, 2022
c773000
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
May 26, 2022
6f18887
SCIPROD-540 CAWFR Code review updates
May 26, 2022
f1357cc
SCIPROD-540 CAWFR Code review updates - added back version check logic
May 26, 2022
4e3312f
SCIPROD-540 CAWFR pandas import changes and --delim const and nargs c…
May 26, 2022
a533c7e
SCIPROD-540 CAWFR dataset_utilities.py: changed writer to Dictwriter …
May 26, 2022
f7533ed
SCIPROD-540 CAWFR check dataset_version instead of version - dataset_…
May 27, 2022
cfb5b86
SCIPROD-540 CAWFR: added tests for SQL. Fixed printing error while ru…
May 31, 2022
9ef5938
SCIPROD-540 CAWFR added tests for --fields
May 31, 2022
8f2d496
SCIPROD-540 CAWFR: Updated dataset_utilities.py with more doctrings
May 31, 2022
7927947
SCIPROD-540 CAWFR, dataset_utilities.py output refactoring
May 31, 2022
dde5ddb
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
May 31, 2022
43cb400
SCIPROD-540 CAWFR, dataset_utilities.py updated. Python2 considered d…
May 31, 2022
05db269
SCIPROD-540 CAWFR, updated delimiter validation logic
Jun 1, 2022
f2fb496
SCIPROD-540 CAWFR updated license details
Jun 1, 2022
46d7e63
SCIPROD-540 CAWFR updated docstrings for extract_dataset
Jun 1, 2022
34cd2ee
SCIPROD-540 CAWFR updated error messages in dataset_utilities.py
Jun 1, 2022
10b9fa2
SCIPROD-540 CAWFR. Updated dataset_utilities: Added logic to populate…
Jun 2, 2022
085a0f0
SCIPROD-540 CAWFR added display_order logic for codings dictionary in…
Jun 3, 2022
ea50a20
SCIPROD-540 CAWFR Removed debug logics in dataset_utilities.py
Jun 3, 2022
b1cc072
SCIPROD-540 CAWFR: Added permission check validation logic in dataset…
Jun 3, 2022
5b02b9a
SCIPROD-540 CAWFR: Updated tests with new dataset and cohort
Jun 3, 2022
f7bc1f1
SCIPROD-540 CAWFR: Revert back pandas import to make it global. Delet…
Jun 3, 2022
6264a4c
SCIPROD-540 CAWFR: updated output file extensions. Added try catch bl…
Jun 8, 2022
6d75100
SCIPROD-540 CAWFR Updated codes_to_concept logic to fix values. Upda…
Jun 8, 2022
a9636da
SCIPROD-540 CAWFR, deleted a commented import statement from test_ext…
Jun 8, 2022
db80409
SCIPROD-540 CAWFR: Updated dataset_utilities.py; Replaced f-string wi…
Jun 9, 2022
cb9f3b9
SCIPROD-560 CAWFR, dataset_utilities.py updated with cleaner exceptio…
Jun 10, 2022
9f78dab
SCIPROD-560 CAWFR: Added test for file not found error
Jun 10, 2022
701497d
SCIPROD-560 CAWFR updates to dataset_utilities.py
Jun 16, 2022
51292c4
SCIPROD-560 CAWFR minor code updates.
Jun 21, 2022
8807050
SCIPROD-560 CAWFR updated docstrings for extract_dataset function
Jun 22, 2022
2f54bce
SCIPROD-560 CAWFR, modified dx.py with updated help strings
Jun 24, 2022
c273bf4
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
Jun 29, 2022
74346ed
SCIPROD-560 CAWFR, updated error handling for double quotation character
Jun 29, 2022
f589022
SCIPROD-560 CAWFR: dataset_utilities.py updates for error handling
Jun 30, 2022
61f3204
SCIPROD-560 CAWFR Updated error message for invalid input record ID
Jul 1, 2022
626b74f
SCIPROD-560 CAWFR Updated error message when workspace_id not set
Jul 1, 2022
96aaca0
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
Jul 1, 2022
1da3a87
SCIPROD-560 CAWFR Remove print statement
Jul 1, 2022
7dfcf52
SCIPROD-560 CAWFR: dataset_utilities.py
Jul 4, 2022
683eda3
SCIPROD-560 CAWFR: Updated tests to replace project-xx:record-xx with…
Jul 5, 2022
39e0194
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit into …
Jul 5, 2022
e922acf
Select dataset project before running test suite
kpjensen Jul 7, 2022
aa77f11
SCIPROD-560 CAWFR test script updates for python2 compatibility
Jul 7, 2022
092bcee
SCIPROD-560 CAWFR dx.py helpstring updates
Niranjanpandeshwar Jul 7, 2022
f83eebf
SCIPROD-560 CAWFR dx.py helpstring updates
Niranjanpandeshwar Jul 7, 2022
91e6972
SCIPROD-560 CAWFR dx.py helpstring updates
Niranjanpandeshwar Jul 7, 2022
52add6d
SCIPROD-560 CAWFR dx.py helpstring updates
Niranjanpandeshwar Jul 7, 2022
b2add8f
SCIPROD-560 CAWFR dx.py helpstring updates
Niranjanpandeshwar Jul 7, 2022
8d9a249
SCIPROD-560 CAWFR remove preview monicker from helpstring and docstring
Jul 7, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Loading