Upload package assessments outside of app

[Jeff-Thompson12]

Addresses #691

[codecov]

Codecov Report

Attention: Patch coverage is 76.14679% with 26 lines in your changes are missing coverage. Please review.

Project coverage is 79.20%. Comparing base (c08b273) to head (68e699e).

Files	Patch %	Lines
R/utils_insert_db.R	78.26%	20 Missing ⚠️
R/mod_decision_automation_utils.R	0.00%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #730      +/-   ##
==========================================
- Coverage   79.34%   79.20%   -0.14%     
==========================================
  Files          33       33              
  Lines        5063     5112      +49     
==========================================
+ Hits         4017     4049      +32     
- Misses       1046     1063      +17     

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[Jeff-Thompson12]

I believe this PR does enough to justify merging. Inside the application itself there is not much of a change from a user experience point of view. I did update the shiny notification so that the details are on a separate line. Current functionality will allow an app deployer to pre-seed the database before server deployment. A test has also been included.

[Robert-Krajcik]

Hi @Jeff-Thompson12
I switched to the branch and did a build/install.
Then tried uploading three packages: glue, stringr, forcats
Getting an error:

[Jeff-Thompson12]

I can't replicate the issue but I can add in a try-catch for the tarball downloading.

[Robert-Krajcik]

Hi @Jeff-Thompson12
I am not seeing the tarball downloading errors this morning.
package upload is working fine.

upload_pkg_lst function working

> pkg_list <- c("Tplyr", "pkglite", "dplyr", "forcats")
> riskassessment::upload_pkg_lst(pkg_list)
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
# A tibble: 4 × 4
  package version status    score
  <chr>   <chr>   <chr>     <dbl>
1 Tplyr   1.1.0   new        0.37
2 pkglite 0.2.1   new        0.32
3 dplyr   1.1.4   duplicate NA   
4 forcats 1.0.0   new        0.24

[Robert-Krajcik]

Looks good to me!

[AARON-CLARK]

Per discussion today:

# Don't export for now while these issues persist:
# Adding a vignette example, showing how to use
# Add check to make sure db is actually there
# Note: there will be no startup initializing Credential DB using QWERTY
# User should probably supply a username and password
initialize_raa(assess_db = "database.sqlite",
              cred_db =,
              configuration = # tied to env
              )

upload_pkg_lst("Tplyr")

[AARON-CLARK]

Per discussion on 2/27, ready for another review.

[AARON-CLARK]

Hey @Jeff-Thompson12! Can you make sure you open new issue(s) to tackle/ address the items identified below?

• Don't export for now while these issues persist:
• Adding a vignette example, showing how to use
• Note: there will be no startup initializing Credential DB using QWERTY; User should probably supply a username and password

[AARON-CLARK]

Hi @Jeff-Thompson12, sorry it's taken me so long to re-look at this PR. In total, it's great! But one thing I noticed is that the local (external to the app) score is different than the app-derived score. So, see if you can reproduce the following:

Notice the score was 0.33. Then I launched the app, deleted the tidyr package from the db, then loaded it on the package uploads tab. Notice the new score below is 0.25.

Let me know what you find. Keep in mind that I'm on a new laptop and just installed hundreds of packages to my machine... but they should all fall in line with the renv lock file.

[AARON-CLARK]

@Jeff-Thompson12, this might help... I noticed that when tidyr was loaded locally (before deleting & re-uploading it in the app), I got the following error message on the Package Dependencies tab. However, when I loaded tidyr after launching the app, there was no error here.

[Jeff-Thompson12]

@AARON-CLARK I will take a look. I will note that we moved external uploading to a different PR. So if we believe it is functioning correctly within the application, technically we don't have a problem (yet).

[Jeff-Thompson12]

@AARON-CLARK I cannot duplicate this issue. Can you verify this is still a problem on your end?

[aclark02-arcus]

Looks amazing! The problem (previously referenced) doesn't exist any more. Apologies if it was user error. Merging!

stale - issues fixed.