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fix get_code_dependency for empty input #197

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Merged
m7pr merged 4 commits into from
Nov 22, 2023
Merged

fix get_code_dependency for empty input #197

m7pr merged 4 commits into from
Nov 22, 2023

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@m7pr m7pr commented Nov 22, 2023 •
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Close insightsengineering/teal#972

data("miniACC", package = "MultiAssayExperiment")
acc <- miniACC

app <- teal::init(
  data = teal_data(
    MAE = acc
  ),
  modules = list(
    example_module()
  )
) %>% 
  shiny::runApp()
Capture

@m7pr m7pr added the core label Nov 22, 2023
@m7pr m7pr enabled auto-merge (squash) November 22, 2023 15:38
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github-actions bot commented Nov 22, 2023 •
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Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/as_cdisc.R                                39       4  89.74%   99-102
R/Callable.R                                45       0  100.00%
R/CallableCode.R                            36       2  94.44%   26, 63
R/CallableFunction.R                        88       3  96.59%   159-161
R/CallablePythonCode.R                      58      58  0.00%    21-227
R/cdisc_data.R                              41       1  97.56%   55
R/cdisc_join_keys.R                         11      11  0.00%    17-35
R/CDISCTealDataConnector.R                  20       3  85.00%   31, 36, 49
R/CDISCTealDataset.R                        46      11  76.09%   108-115, 204-206
R/CDISCTealDatasetConnector.R               26       1  96.15%   116
R/CodeClass.R                              111       1  99.10%   157
R/data_label.R                              36      13  63.89%   33-37, 56-63, 103
R/datanames.R                               11       0  100.00%
R/deep_clone_r6.R                            9       0  100.00%
R/dummy_function.R                           5       1  80.00%   23
R/formatters_var_labels.R                   49      21  57.14%   30, 38, 43-44, 46, 53, 99, 129-151
R/get_attrs.R                                2       2  0.00%    12-45
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                             5       1  80.00%   39
R/get_dataset_label.R                        3       0  100.00%
R/get_dataset.R                             13       8  38.46%   39, 55, 80-86
R/get_datasets.R                            11       3  72.73%   96, 116, 140
R/get_join_keys.R                           10       0  100.00%
R/get_key_duplicates.R                      37       7  81.08%   41-47, 54-55
R/get_keys.R                                15       7  53.33%   68-69, 126-146
R/get_raw_data.R                            24      11  54.17%   168-181
R/include_css_js.R                           9       1  88.89%   20
R/is_pulled.R                                4       0  100.00%
R/join_key.R                                32       0  100.00%
R/join_keys-c.R                             26       0  100.00%
R/join_keys-extract.R                      122       0  100.00%
R/join_keys-names.R                         15       0  100.00%
R/join_keys-parents.R                       28       0  100.00%
R/join_keys-print.R                         47       0  100.00%
R/join_keys-utils.R                         87       1  98.85%   130
R/join_keys.R                               23       0  100.00%
R/load_dataset.R                            25      18  28.00%   58-63, 87-186
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%   34-38
R/teal_data-class.R                         23       1  95.65%   68
R/teal_data.R                               39       2  94.87%   32, 59
R/TealData.R                               233     114  51.07%   183, 210, 222-291, 335-342, 375-380, 382, 384-389, 391, 408-453
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%   178, 190, 194, 207, 210-219, 221, 229-238, 321-325, 383-488
R/TealDataset.R                            367      23  93.73%   141-151, 382-386, 442-451, 503
R/TealDatasetConnector_constructors.R      270      52  80.74%   177-214, 727-732, 930-1006
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/testhat-helpers.R                         54       0  100.00%
R/to_relational_data.R                      57       8  85.96%   34-35, 39, 98, 105, 111, 122-123
R/topological_sort.R                        32       0  100.00%
R/utils-code_dependency.R                  192       7  96.35%   37, 42, 252-253, 321-324
R/utils.R                                   56       9  83.93%   22-23, 27, 76-83
R/validate_data_args.R                      32       0  100.00%
R/zzz.R                                     11      11  0.00%    4-19
TOTAL                                     3925     893  77.25%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  -------
R/utils-code_dependency.R       +2       0  +0.04%
TOTAL                           +2       0  +0.01%

Results for commit: 4181e53

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Nov 22, 2023 •
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Unit Test Performance Difference

Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
code_dependency 👶 $+0.01$ get_code_dependency_does_not_brake_for_empty_input

Results for commit 5e44482

♻️ This comment has been updated with latest results.

averissimo
averissimo approved these changes Nov 22, 2023
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Works well with the set of examples that were used to detect this issue 👍

R/utils-code_dependency.R
checkmate::assert_multi_class(code, classes = c("character", "expression"))
checkmate::assert_character(names)

if (identical(code, character(0)) || identical(code, "")) {
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Small suggestion to treat string that only has whitespace as an empty string

Suggested change
if (identical(code, character(0)) || identical(code, "")) {
if (identical(code, character(0)) || identical(trimws(code), "")) {

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github-actions bot commented Nov 22, 2023

Unit Tests Summary

       1 files       37 suites   15s ⏱️
   470 tests    469 ✔️ 1 💤 0 ❌
1 089 runs  1 088 ✔️ 1 💤 0 ❌

Results for commit 4181e53.

@m7pr m7pr merged commit 8bd3e03 into main Nov 22, 2023
@m7pr m7pr deleted the fix_empty_code_at_get_code_dependency@main branch November 22, 2023 15:54
@m7pr m7pr mentioned this pull request Nov 22, 2023
Merged
gogonzo pushed a commit that referenced this pull request Nov 23, 2023
@m7pr
trimws to code at "" if (#199)
22a2a48 
Have had an automerge on
#197 and could not
apply suggestions

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
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@averissimo averissimo averissimo approved these changes

@gogonzo gogonzo Awaiting requested review from gogonzo

@chlebowa chlebowa Awaiting requested review from chlebowa

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[Bug]: teal fails if the teal_data has no code

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