add cdisc information into JoinKeys #132

mhallal1 · 2023-01-23T15:13:57Z

closes #120

removed CDISCTealData and replaced its functionality with TealData.
removed join_keys mentions in TealDataset and TealDatasetConnector.
updated wrappers cdisc_data and teal_data to set up join_keys by calling JoinKeys functionalities. They check if
join_keys are passed otherwise they create them according to primary keys.
deprecated cdisc_data_file
Added tests to test-joinKeys.R
Updated and added tests of test-TealData, test-TealDataAbstract, test-cdisc_data and test-teal_data.
updated teal.slice::init_filtered_data to remove CDISCTealData S3 method and to account for cdisc status in the TealData S3 method: update init_filtered_data teal.slice#169

github-actions · 2023-01-23T16:37:33Z

Unit Tests Summary

      1 files     27 suites 34s ⏱️
  366 tests   366 ✔️ 0 💤 0 ❌
1 020 runs 1 020 ✔️ 0 💤 0 ❌

Results for commit 2fa79ad.

♻️ This comment has been updated with latest results.

github-actions · 2023-01-24T17:36:50Z

Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/as_cdisc.R                                39       4  89.74%   107-110
R/Callable.R                                45       0  100.00%
R/CallableCode.R                            36       2  94.44%   26, 63
R/CallableFunction.R                        88       3  96.59%   160-162
R/CallablePythonCode.R                      58      58  0.00%    21-223
R/cdisc_data.R                              45       1  97.78%   79
R/CDISCTealDataConnector.R                  20       3  85.00%   31, 36, 49
R/CDISCTealDataset.R                        46      11  76.09%   108-115, 208-210
R/CDISCTealDatasetConnector.R               26       1  96.15%   116
R/CodeClass.R                              111       1  99.10%   157
R/data_label.R                              36      13  63.89%   35-39, 58-65, 105
R/deep_clone_r6.R                            9       0  100.00%
R/get_attrs.R                                2       2  0.00%    12-47
R/get_code.R                               173      19  89.02%   87, 140-143, 196-197, 207-208, 266, 297, 333, 337, 372, 381-385
R/get_dataname.R                             4       0  100.00%
R/get_dataset_label.R                        3       0  100.00%
R/get_dataset.R                             13       8  38.46%   41, 58, 85-91
R/get_datasets.R                            10       2  80.00%   86, 110
R/get_key_duplicates.R                      37       7  81.08%   42-48, 55-56
R/get_keys.R                                15       7  53.33%   72-73, 130-150
R/get_raw_data.R                            24      11  54.17%   161-174
R/include_css_js.R                           9       1  88.89%   20
R/is_pulled.R                                4       0  100.00%
R/JoinKeys.R                               181       7  96.13%   134, 230, 324, 327, 385-424
R/load_dataset.R                            25      18  28.00%   60-65, 89-222
R/MAETealDataset.R                         138      57  58.70%   53, 115, 153-208, 224-229, 236-245, 282, 323-339
R/mutate_dataset.R                          18       0  100.00%
R/set_args.R                                10       5  50.00%   42-46
R/teal_data.R                               31       2  93.55%   44, 52
R/TealData.R                               228     113  50.44%   207, 219-288, 331-338, 371-376, 378, 380-385, 387, 404-449
R/TealDataAbstract.R                       232      24  89.66%   72, 85-88, 97-106, 215-218, 429, 454-458, 480, 486
R/TealDataConnection.R                     297     180  39.39%   58-59, 64, 67, 70, 106-163, 183, 186-188, 194-200, 205-207, 233, 238, 254-277, 287, 300, 321, 325-330, 333-336, 358-360, 364-371, 374-377, 392-406, 425-426, 446-517, 535-543, 545, 549-564, 567-570, 602, 608-612, 626, 661-663, 672-674
R/TealDataConnector.R                      196     102  47.96%   167, 179, 183, 196, 199-208, 210, 218-227, 310-314, 372-477
R/TealDataset.R                            367      23  93.73%   141-151, 383-387, 443-452, 504
R/TealDatasetConnector_constructors.R      300      53  82.33%   176-212, 262, 830-835, 1033-1109
R/TealDatasetConnector.R                   326      90  72.39%   169, 237, 251, 256, 270, 433, 456-495, 525, 540-570, 660, 670, 679-686, 699, 714-741
R/to_relational_data.R                      54       7  87.04%   35-36, 40, 99, 106, 112, 127
R/topological_sort.R                        32       0  100.00%
R/utils.R                                   56       9  83.93%   22-23, 27, 76-83
R/validate_data_args.R                      32       0  100.00%
R/zzz.R                                      6       6  0.00%    4-12
TOTAL                                     3382     850  74.87%

Diff against main

Filename                    Stmts    Miss  Cover
------------------------  -------  ------  -------
R/cdisc_data.R                +45      +1  +97.78%
R/get_code.R                    0      -2  +1.16%
R/get_datasets.R                0      -3  +30.00%
R/JoinKeys.R                  +53      +3  -0.74%
R/teal_data.R                 +10      -1  +7.83%
R/TealData.R                  -45      -4  -6.70%
R/TealDataAbstract.R           +1     +11  -4.72%
R/TealDataset.R               -17       0  -0.28%
R/TealDatasetConnector.R      -16      -1  -1.00%
R/topological_sort.R            0      -4  +12.50%
TOTAL                         +31       0  -0.00%

Results for commit: 3cbb1d7

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

nikolas-burkoff

Looking good a few comments to address then we'll take another look

R/CDISCTealData.R

tests/testthat/test-CDISCTealData.R

R/JoinKeys.R

R/cdisc_data.R

nikolas-burkoff · 2023-01-25T10:44:36Z

R/cdisc_data.R

+      recursive = FALSE
+    )
+
+    names(new_parents) <- unlist(lapply(data_objects, function(x) {


Is there a way to create a named list without having to do it separately for new_parents and parents?

R/cdisc_data.R

github-actions · 2023-02-02T09:24:16Z

JUnit report for branch main doesn't exist on _junit_xml_reports branch yet.
Once this workflow runs on main branch, you'll see comparison of tests performance between main and join_keys@main as a PR comment.

nikolas-burkoff

All looks good, a few minor comments and one in teal.slice then I suggest the team run some example apps (might be worth adding ones you've been using to the PR description if you haven't already) and then this can be merged

R/cdisc_data.R

tests/testthat/test-TealDataAbstract.R

tests/testthat/test-data_label.R

tests/testthat/test-cdisc_data.R

tests/testthat/test-TealData.R

Adds a few tests for TealData class. I didn't really see anything else to change. Should be final step for #133 --------- Co-authored-by: Dawid Kałędkowski <[email protected]>

R/JoinKeys.R

R/cdisc_data.R

NAMESPACE

gogonzo

👍 Thanks for a huge simplification here

mhallal1 added 8 commits January 20, 2023 18:32

remove CDISCTealData

2392eb7

remove join_keys from TealDataset and TealDatasetConnector

f9a74bc

wrappers

8471096

TealData

a0f6157

JoinKeys

703e39b

docs

8bb61b9

update to accept TealDataConnector

d5e7e38

docs

e57ea2f

mhallal1 added the core label Jan 23, 2023

mhallal1 and others added 3 commits January 23, 2023 17:18

teal_data

57e5239

vignette

f7546e1

Merge branch 'main' into join_keys@main

5a8d77d

mhallal1 added 5 commits January 24, 2023 17:31

update cdisc_/teal_data

2b89a1b

remove CDISCTealData tests

040a41b

tests

d7abf1e

remove cdisc_data_file

40a204e

test

15b0697

mhallal1 added 5 commits January 25, 2023 07:55

fixes

1c37dbd

pkgdown

3cd627f

lintr

479c947

example cdisc_data

a497b8f

example cdisc_data

30f427e

mhallal1 requested a review from nikolas-burkoff January 25, 2023 08:52

pkgdown

00de8d5

nikolas-burkoff assigned nikolas-burkoff and chlebowa Jan 25, 2023

nikolas-burkoff reviewed Jan 25, 2023

View reviewed changes

review Nik

2da4deb

mhallal1 added 8 commits January 25, 2023 16:47

add check

f7bb26d

remove tealData$get_datanames

66f2b6d

tests 1

ab7a0c7

lintr

e199319

test-TealDataAbstract

1947eb7

remove comment

186081e

test-TealData

08960d9

test-teal_data

0fa2683

mhallal1 added 4 commits February 2, 2023 11:42

test-cdisc_data

44c428f

tests

ffc0226

NEWS

f9f8b89

test-TealDataAbstract

33a3f73

nikolas-burkoff reviewed Feb 3, 2023

View reviewed changes

mhallal1 and others added 5 commits February 3, 2023 16:52

review

d1c83a6

[skip actions] Roxygen Man Pages Auto Update

bf6673d

Empty-Commit

1600df5

Add TealData tests (#134)

06024d0

Adds a few tests for TealData class. I didn't really see anything else to change. Should be final step for #133 --------- Co-authored-by: Dawid Kałędkowski <[email protected]>

review

84cc992

gogonzo reviewed Feb 7, 2023

View reviewed changes

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[skip actions] Roxygen Man Pages Auto Update

5078b78

gogonzo reviewed Feb 7, 2023

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R/cdisc_data.R Show resolved Hide resolved

mhallal1 added 2 commits February 7, 2023 14:52

docs

08f5804

Merge remote-tracking branch 'origin/join_keys@main' into join_keys@main

1eda648

gogonzo reviewed Feb 8, 2023

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NAMESPACE Outdated Show resolved Hide resolved

revert mutate_join_keys.JoinKeys

2fa79ad

gogonzo approved these changes Feb 8, 2023

View reviewed changes

mhallal1 merged commit 36090d2 into main Feb 8, 2023

mhallal1 deleted the join_keys@main branch February 8, 2023 13:22

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add cdisc information into JoinKeys #132

add cdisc information into JoinKeys #132

mhallal1 commented Jan 23, 2023 •

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add cdisc information into JoinKeys #132

add cdisc information into JoinKeys #132

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