Upload package assessments outside of app

pharmaR / riskassessment

Collaborative Deployment: https://app.pharmar.org/riskassessment/ Risk Assessment Demo App: https://rinpharma.shinyapps.io/riskassessment

https://pharmar.github.io/riskassessment/

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Upload package assessments outside of app #730

Closed Jeff-Thompson12 closed 6 months ago

Jeff-Thompson12 commented 9 months ago

Addresses #691

codecov[bot] commented 9 months ago

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

```diff @@ 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 commented 9 months ago

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.

Jeff-Thompson12 commented 9 months ago

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

Robert-Krajcik commented 8 months ago

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

AARON-CLARK commented 7 months ago

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

AARON-CLARK commented 6 months ago

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 commented 6 months ago

@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 commented 6 months ago

@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 commented 6 months ago

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

pharmaR / riskassessment

Upload package assessments outside of app #730

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