Add lbt07 #366

ayogasekaram · 2023-01-19T02:29:33Z

lbt07 template.

closes insightsengineering/chevron-tasks#27

github-actions · 2023-01-19T02:48:46Z

🧪 $Test coverage: 89.50%$

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  ------------------------------------------------------------------------
R/aet01_aesi.R                 188       8  95.74%   39, 41-45, 272, 285
R/aet01.R                      330       6  98.18%   38, 240, 253, 316, 322, 554
R/aet02.R                      222       2  99.10%   136, 489
R/aet03.R                       85       0  100.00%
R/aet04.R                      104       6  94.23%   81-86
R/assertions.R                  36       0  100.00%
R/checks.R                      14       0  100.00%
R/chevron_tlg-S4class.R         21       0  100.00%
R/chevron_tlg-S4methods.R       42      16  61.90%   47-55, 90-98, 218-290
R/cmt01a.R                     191       0  100.00%
R/cmt02_pt.R                    52       0  100.00%
R/dmt01.R                       40       0  100.00%
R/dst01.R                      287       0  100.00%
R/dtht01.R                     104       0  100.00%
R/egt01.R                       46       0  100.00%
R/egt02.R                       60       0  100.00%
R/egt03.R                      129      85  34.11%   32-52, 111, 125-232, 291, 305-339
R/ext01.R                       81       8  90.12%   238-241, 245-248
R/gen_args.R                     1       1  0.00%    27
R/lbt01.R                       95       0  100.00%
R/lbt04.R                       52       1  98.08%   127
R/lbt05.R                       70       2  97.14%   121, 149
R/lbt07.R                       81       2  97.53%   34, 164
R/lbt14.R                      196      28  85.71%   57, 59, 107-110, 112-117, 147, 178, 265, 267, 315-318, 320-325, 355, 386
R/mht01.R                       72       2  97.22%   33-34
R/mng01.R                       93      12  87.10%   113, 117-120, 129-137, 182
R/pdt01.R                       61      38  37.70%   35-52, 108-150
R/pdt02.R                       68       0  100.00%
R/utils.R                      163     109  33.13%   70, 83-212
R/vst01.R                       48       0  100.00%
R/vst02.R                      102       3  97.06%   42, 120, 257
TOTAL                         3134     329  89.50%

Results for commit: ea0290e0026458621290aadce0c760463f03a486

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-01-19T02:51:35Z

Unit Tests Summary

    1 files   25 suites 1m 18s ⏱️
112 tests   77 ✔️ 35 💤 0 ❌
241 runs 152 ✔️ 89 💤 0 ❌

Results for commit 37274e5.

♻️ This comment has been updated with latest results.

R/lbt07.R

clarkliming · 2023-01-20T02:34:46Z

R/lbt07.R

+#'
+#' @inheritParams gen_args
+#' @param lbl_param (`character`) label of the `PARAM` variable.
+#' @param lbl_gradedir (`character`) label of the `GRADE_DIR` variable.


this can cause confusion: what is GRADE_DIR variable? though we are going to have changes to the preprocessing part, it is necessary to add more information on the derived variables for now

R/lbt07.R

barnett11

Thanks @ayogasekaram ,
I get the below error on my data, do we need to ensure we're converting PARAM to factor if it is required?
Error: Error applying analysis function (var - GRADE_ANL): Assertion on 'df[[variables$param]]' failed: Must be of type 'factor' (or 'NULL'), not 'character'.

npaszty · 2023-01-25T19:28:44Z

@ayogasekaram

chatted with Joe last week and thought it would be helpful for me to review some PRs. Looking at the chevron readme and following the directions to install staged dependencies etc., I get errors that I can address by using chevron:::<function_name> but I can't get around the following error. I'm running this in an R 4.1.3 container.

Error in force(.formats) :
object 'format_count_fraction_fixed_dp' not found

I assume I'm doing something wrong but only find one reference to this object and it's on the right hand side of an assignment statement.

Might need a walkthrough to get me started...

shajoezhu · 2023-01-26T02:38:44Z

hi @npaszty , I was wondering if you are using the latest tern?

npaszty · 2023-01-26T20:50:11Z

@shajoezhu
yes, I verified the installed version and what's in the description file.
0.1.1.9031

I updated the ref = from main to this branch for staged.dependencies and after I run build for chevron, the version changes to 0.1.1.9028. so something definitely up there. looking further into this.

this works to produce the AET02 table
db <- syn_test_data()
run(aet02_1, db)

but this doesn't, see error below
run(lbt07_1, db)

similar initial errors and now another error once addressed previous in same way.

Error in h(simpleError(msg, call)) :
error in evaluating the argument 'obj' in selecting a method for function 'last_rowsplit': error in evaluating the argument 'obj' in selecting a method for function 'next_rpos': error in evaluating the argument 'lyt' in selecting a method for function '.add_row_summary': error in evaluating the argument 'obj' in selecting a method for function 'next_rpos': error in evaluating the argument 'obj' in selecting a method for function 'next_cpos': could not find function "basic_table_deco"

best to have walkthrough so I'm not wasting developer time. I can't imagine my environment is properly set up but it's been a while since I did this for NEST so must be missing something or maybe readme needs update. let's circle back next Tuesday at our checkin

barnett11

The preprcoessing has filtering that is not described in the specification - can the redundant parts be removed please (eg. ANL01FL=Y)

Signed-off-by: Abinaya Yogasekaram <[email protected]>

edelarua · 2023-02-02T15:03:37Z

@ayogasekaram FYI the egt01_1 failure is known and is being fixed by Davide here so that error can be ignored.

tests/testthat/test-default_tlg.R

github-actions · 2023-02-03T06:20:28Z

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 132_lbt07@main as a PR comment.

clarkliming

looks good to me!

barnett11

I don't think the below is doing anything, as the values for missing are just "" rather than <Missing>
filter(.data$ATOXGR != "<Missing>"

clarkliming · 2023-02-03T11:44:47Z

@shajoezhu maybe you can just add a explicit_na for ATOXGR just like other templates so that the missing values will be explicit missing and then remove those rows? And after this is completed we just merge this PR; @barnett11 If there are further comments, we can create another issue as this PR is getting large

ayogasekaram added 3 commits January 18, 2023 21:35

Add lbt07 template.

63ebc65

Adding tests.

0767cdd

fix label description.

7ced5da

ayogasekaram added the sme label Jan 19, 2023

Resolving lintr issues.

675dd3f

ayogasekaram requested review from barnett11 and clarkliming January 19, 2023 15:55

ayogasekaram changed the title ~~132 lbt07@main~~ Add lbt07 Jan 19, 2023

clarkliming self-assigned this Jan 20, 2023

clarkliming reviewed Jan 20, 2023

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ayogasekaram added 2 commits January 20, 2023 18:42

Exposin "GRADE_DIR" and "GRADE_ANL". Updating percentage format.

dc8c251

update for lintr.

c933d71

barnett11 requested changes Jan 23, 2023

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adding conversion of param to factor.

ef4dc54

Merge branch 'main' into 132_lbt07@main

7dfc06d

shajoezhu requested review from barnett11 and clarkliming January 30, 2023 03:36

barnett11 requested changes Jan 31, 2023

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ayogasekaram and others added 2 commits January 31, 2023 18:15

Removing unspecified filtering.

74764e8

Merge branch 'main' into 132_lbt07@main

51aecb3

Signed-off-by: Abinaya Yogasekaram <[email protected]>

clarkliming reviewed Feb 3, 2023

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update test snap

37274e5

shajoezhu requested review from barnett11 and clarkliming February 3, 2023 06:23

clarkliming approved these changes Feb 3, 2023

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barnett11 requested changes Feb 3, 2023

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barnett11 self-requested a review February 3, 2023 13:46

barnett11 approved these changes Feb 3, 2023

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clarkliming merged commit 0f1306f into main Feb 3, 2023

clarkliming deleted the 132_lbt07@main branch February 3, 2023 13:49

clarkliming mentioned this pull request Feb 3, 2023

lbt07 preprocessing is not working as expected #382

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Add lbt07 #366

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Add lbt07 #366

Add lbt07 #366

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