553 introduce internal `log_shiny_input_changes` function #84

m7pr · 2024-06-18T14:00:39Z

Part of https://github.com/insightsengineering/coredev-tasks/issues/553 and https://github.com/insightsengineering/coredev-tasks/issues/568

Function is an extended copy of logger::log_shiny_input_changes but curated to our needs.

Currently features comparison to what's included in logger

we do not provide an initialization message with the list of input values at start
created excluded_patterns parameter that allows to exclude inputs from logging based on grep patterns - we are excluding plot resizing by default
usage of session object to detect that the session is a mocked session
extension of logs with a namespace name

…gger

github-actions · 2024-06-18T14:01:01Z

CLA Assistant Lite bot ✅ All contributors have signed the CLA

m7pr · 2024-06-18T14:03:23Z

I have read the CLA Document and I hereby sign the CLA

m7pr · 2024-06-18T14:03:28Z

recheck

github-actions · 2024-06-18T14:04:35Z

Code Coverage Summary

Filename                       Stmts    Miss  Cover    Missing
---------------------------  -------  ------  -------  ---------
R/log_shiny_input_changes.R       24      24  0.00%    41-69
R/register_handlers.R             39       0  100.00%
R/register_logger.R               56       1  98.21%   115
R/supress_logs.R                   5       5  0.00%    17-21
R/utils.R                         20       0  100.00%
TOTAL                            144      30  79.17%

Diff against main

Filename                       Stmts    Miss  Cover
---------------------------  -------  ------  --------
R/log_shiny_input_changes.R      +24     +24  +100.00%
TOTAL                            +24     +24  -15.83%

Results for commit: 049e630

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2024-06-18T14:04:44Z

Unit Tests Summary

1 files 3 suites 0s ⏱️
25 tests 25 ✅ 0 💤 0 ❌
37 runs 37 ✅ 0 💤 0 ❌

Results for commit 049e630.

♻️ This comment has been updated with latest results.

R/log_shiny_input_changes.R

DESCRIPTION

m7pr · 2024-06-18T14:54:01Z

@pawelru if we want to have our own implementation of log_input_shiny_changes that has nothing to do with the logger version then there is a lot of places where this function can get improved just to fit our needs

R/log_shiny_input_changes.R

Merge branch '553_log_shiny_input_changes@main' of https://github.com/insightsengineering/teal.logger into 553_log_shiny_input_changes@main # Conflicts: # R/log_shiny_input_changes.R

R/log_shiny_input_changes.R

Co-authored-by: Pawel Rucki <[email protected]> Signed-off-by: Marcin <[email protected]>

DESCRIPTION

R/log_shiny_input_changes.R

Co-authored-by: Pawel Rucki <[email protected]> Signed-off-by: Marcin <[email protected]>

…/insightsengineering/teal.logger into 553_log_shiny_input_changes@main

m7pr · 2024-06-19T07:58:55Z

For a simple input change in UI I see 5 logs displayed in the console

[TRACE] 2024-06-19 09:55:27.7176 pid:24656 token:[31ad1df8] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select_open: NULL -> TRUE
[TRACE] 2024-06-19 09:55:35.0600 pid:24656 token:[31ad1df8] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select: SEX -> ACTARM
[TRACE] 2024-06-19 09:55:35.0645 pid:24656 token:[31ad1df8] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select_open: NULL -> TRUE
[TRACE] 2024-06-19 09:55:35.0780 pid:24656 token:[31ad1df8] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select: SEX -> ACTARM
[TRACE] 2024-06-19 09:55:35.0830 pid:24656 token:[31ad1df8] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select_open: NULL -> FALSE

Where first two and another two are the same, which made me think we have some duplicates. This was not the case while this feature was using utils::assignInMyNamespace() and utils::assignInNamespace(). I think this is due how the shiny_input_values is treated in the shiny::observer. Will try to bring utils::assignInMyNamespace() and utils::assignInNamespace() back to see if this removed duplicated logs.

m7pr · 2024-06-19T08:09:02Z

When I brought back the usage of utils::assignInMyNamespace() and utils::assignInNamespace() I do no longer see duplicated logs, and we only see 3 logs for one single input change

[TRACE] 2024-06-19 10:06:20.3276 pid:17336 token:[37e75bcf] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select_open: NULL -> TRUE
[TRACE] 2024-06-19 10:06:23.9033 pid:17336 token:[37e75bcf] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select: SEX -> RACE
[TRACE] 2024-06-19 10:06:24.3814 pid:17336 token:[37e75bcf] teal.modules.clinical teal-main_ui-root-adae_analysis-module Shiny input change detected in fill-dataset_ADSL_singleextract-select_open: TRUE -> FALSE

Surprisingly I see many more logs that poped-up during this input change

[TRACE] 2024-06-19 10:06:22.0966 pid:17336 token:[37e75bcf] teal.transform data_extract_read_srv@2 dataname: ADSL; select: RACE.
[TRACE] 2024-06-19 10:06:22.1528 pid:17336 token:[37e75bcf] teal.transform merge_datasets called with: ADSL, ADAE datasets; x, fill, x_facet, y_facet selectors; dplyr::full_join merge function.
[TRACE] 2024-06-19 10:06:22.1560 pid:17336 token:[37e75bcf] teal.transform merge_selectors called with: x, fill, x_facet, y_facet selectors.
[TRACE] 2024-06-19 10:06:22.1596 pid:17336 token:[37e75bcf] teal.transform get_dplyr_call_data called with: x, x_facet selectors.
[TRACE] 2024-06-19 10:06:22.1628 pid:17336 token:[37e75bcf] teal.transform get_merge_key_grid called with: x, x_facet selectors.
[TRACE] 2024-06-19 10:06:22.1808 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair called with: x, x selectors; STUDYID, USUBJID keys.
[TRACE] 2024-06-19 10:06:22.1838 pid:17336 token:[37e75bcf] teal.transform get_dropped_filters called with x selector.
[TRACE] 2024-06-19 10:06:22.1863 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair returns STUDYID, USUBJID merge keys.
[TRACE] 2024-06-19 10:06:22.1973 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair called with: x, x_facet selectors; STUDYID, USUBJID keys.
[TRACE] 2024-06-19 10:06:22.2010 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair returns STUDYID, USUBJID merge keys.
[TRACE] 2024-06-19 10:06:22.2109 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair called with: x_facet, x selectors; STUDYID, USUBJID keys.
[TRACE] 2024-06-19 10:06:22.2159 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair returns STUDYID, USUBJID merge keys.
[TRACE] 2024-06-19 10:06:22.2251 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair called with: x_facet, x_facet selectors; STUDYID, USUBJID, ASTDTM, AETERM, AESEQ keys.
[TRACE] 2024-06-19 10:06:22.2287 pid:17336 token:[37e75bcf] teal.transform get_dropped_filters called with x_facet selector.
[TRACE] 2024-06-19 10:06:22.2311 pid:17336 token:[37e75bcf] teal.transform get_merge_key_pair returns STUDYID, USUBJID, ASTDTM, AETERM, AESEQ merge keys.
[TRACE] 2024-06-19 10:06:22.2406 pid:17336 token:[37e75bcf] teal.transform get_dplyr_call called with: ADSL, ADAE datasets; x, x_facet selectors.
[TRACE] 2024-06-19 10:06:22.2463 pid:17336 token:[37e75bcf] teal.transform get_filter_call called with: ADSL dataset;  filters.
[TRACE] 2024-06-19 10:06:22.2496 pid:17336 token:[37e75bcf] teal.transform get_select_call called with: STUDYID, USUBJID, ACTARM, RACE columns.
[TRACE] 2024-06-19 10:06:22.2521 pid:17336 token:[37e75bcf] teal.transform get_rename_call called with: x selector; ACTARM, RACE renamed columns.
[TRACE] 2024-06-19 10:06:22.2551 pid:17336 token:[37e75bcf] teal.transform get_dplyr_call called with: ADSL, ADAE datasets; x, x_facet selectors.
[TRACE] 2024-06-19 10:06:22.2595 pid:17336 token:[37e75bcf] teal.transform get_filter_call called with: ADAE dataset;  filters.
[TRACE] 2024-06-19 10:06:22.2635 pid:17336 token:[37e75bcf] teal.transform get_select_call called with: STUDYID, USUBJID, AETOXGR, AESEV columns.
[TRACE] 2024-06-19 10:06:22.2658 pid:17336 token:[37e75bcf] teal.transform get_rename_call called with: x_facet selector; AETOXGR, AESEV renamed columns.
[TRACE] 2024-06-19 10:06:22.2681 pid:17336 token:[37e75bcf] teal.transform get_merge_call called with: x, x_facet selectors; dplyr::full_join merge function.
[TRACE] 2024-06-19 10:06:22.2707 pid:17336 token:[37e75bcf] teal.transform get_merge_key_i called with x, x_facet selectors; idx = 2.
[TRACE] 2024-06-19 10:06:22.2738 pid:17336 token:[37e75bcf] teal.transform get_merge_key_i returns STUDYID USUBJID unique keys.
[TRACE] 2024-06-19 10:06:22.2793 pid:17336 token:[37e75bcf] teal.transform parse_merge_key_i called with STUDYID USUBJID keys.
[TRACE] 2024-06-19 10:06:22.2835 pid:17336 token:[37e75bcf] teal.transform get_relabel_cols called with: x, fill, x_facet, y_facet columns_source.
[TRACE] 2024-06-19 10:06:22.2857 pid:17336 token:[37e75bcf] teal.transform get_anl_relabel_call called with: x, fill, x_facet, y_facet columns_source; ANL merged dataset.
[TRACE] 2024-06-19 10:06:22.2934 pid:17336 token:[37e75bcf] teal.transform get_relabel_call called with: Description of Actual Arm Race Analysis Toxicity Grade Severity/Intensity labels.
[TRACE] 2024-06-19 10:06:22.2973 pid:17336 token:[37e75bcf] teal.transform merge_datasets merge code executed resulting in ANL dataset.
[TRACE] 2024-06-19 10:06:22.3974 pid:17336 token:[37e75bcf] teal.transform get_anl_relabel_call called with: x, fill, x_facet, y_facet columns_source; counts merged dataset.
[TRACE] 2024-06-19 10:06:22.4046 pid:17336 token:[37e75bcf] teal.transform get_relabel_call called with: Description of Actual Arm Race Analysis Toxicity Grade Severity/Intensity labels.

m7pr · 2024-06-19T08:12:54Z

But this is the regular amount of logs that we have on TRACE level, when log_shiny_input_changes is commented out and not used.

App for testing:

options(teal.log_level = "TRACE", teal.show_js_log = TRUE)

library(nestcolor)
library(dplyr)
#library(teal.modules.clinical)
devtools::load_all("../teal.logger/")
devtools::load_all(".")

ADSL <- tmc_ex_adsl %>%
  mutate(ITTFL = factor("Y") %>%
           with_label("Intent-To-Treat Population Flag"))
ADAE <- tmc_ex_adae %>%
  filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADAE = ADAE,
    code = "ADSL <- tmc_ex_adsl %>%
              mutate(ITTFL = factor(\"Y\") %>%
              with_label(\"Intent-To-Treat Population Flag\"))
            ADAE <- tmc_ex_adae %>%
              filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))"
  ),
  modules = modules(
    tm_g_barchart_simple(
      label = "ADAE Analysis",
      x = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = variable_choices(
            ADSL,
            c(
              "ARM", "ACTARM", "SEX",
              "RACE", "ITTFL", "SAFFL", "STRATA2"
            )
          ),
          selected = "ACTARM",
          multiple = FALSE
        )
      ),
      fill = list(
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = "SEX",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      x_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AETOXGR",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      y_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AESEV",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

m7pr · 2024-06-19T08:15:50Z

@pawelru I needed to bring back utils:: solution. This is a work-around to get the shiny::observer be executed only once, not twice. You can test on the app provided in here #84 (comment).

If this PR is fine, then I'll start merging PRs in module packages and in teal.slice but this one is first to be merged

revert logger::log_shiny_input_changes teal.slice#597
553 change level in log_shiny_input_changes and exclude plot sizes in logging teal.modules.clinical#1191
553 change level in log_shiny_input_changes and exclude plot sizes in logging teal.osprey#270
553 change level in log_shiny_input_changes and exclude plot sizes in logging teal.goshawk#281
553 change level in log_shiny_input_changes and exclude plot sizes in logging teal.modules.hermes#386
553 change level in log_shiny_input_changes and exclude plot sizes in logging teal.modules.general#760

R/log_shiny_input_changes.R

…/insightsengineering/teal.logger into 553_log_shiny_input_changes@main

pawelru

I believe that this is good to go 👍

m7pr added 8 commits August 30, 2023 12:57

#51 unify page version to /latest-tag/

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Merge branch 'main' of https://github.com/insightsengineering/teal.lo…

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…gger

Merge branch 'main' of https://github.com/insightsengineering/teal.lo…

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Merge branch 'main' of https://github.com/insightsengineering/teal.lo…

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Merge branch 'main' of https://github.com/insightsengineering/teal.lo…

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Merge branch 'main' of https://github.com/insightsengineering/teal.lo…

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…gger

log_shiny_input_changes

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session should be defined first

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m7pr added the core label Jun 18, 2024

[skip style] [skip vbump] Restyle files

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release the kraken

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session

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Merge branch '553_log_shiny_input_changes@main' of https://github.com/insightsengineering/teal.logger into 553_log_shiny_input_changes@main # Conflicts: # R/log_shiny_input_changes.R

export log_shiny_input_changes

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Update R/log_shiny_input_changes.R

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Co-authored-by: Pawel Rucki <[email protected]> Signed-off-by: Marcin <[email protected]>

m7pr added 3 commits June 18, 2024 18:00

extend pkgdown

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remove jsonlite dependency

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lintr and spellcheck

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Update DESCRIPTION

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Co-authored-by: Pawel Rucki <[email protected]> Signed-off-by: Marcin <[email protected]>

Update R/log_shiny_input_changes.R

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Co-authored-by: Pawel Rucki <[email protected]> Signed-off-by: Marcin <[email protected]>

[skip style] [skip vbump] Restyle files

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use ns as glue syntax

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Merge branch '553_log_shiny_input_changes@main' of https://github.com…

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bring back utils solution

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excluded_pattern as singular word

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m7pr requested a review from pawelru June 19, 2024 09:37

typo in example

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553 introduce internal `log_shiny_input_changes` function #84

553 introduce internal `log_shiny_input_changes` function #84

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553 introduce internal `log_shiny_input_changes` function #84

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