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"blog" build action/CI is broken #887

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melange396 opened this issue Nov 8, 2023 · 0 comments · Fixed by #891
Closed

"blog" build action/CI is broken #887

melange396 opened this issue Nov 8, 2023 · 0 comments · Fixed by #891
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blog bug github_actions Pull requests that update Github_actions code

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@melange396
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The "blog" building CI workflow has been failing (see run history here) since quidel protections went into place (which happened with delphi-epidata releases 4.1.8 and 4.1.9 in mid/late August). The offending call happens in a request for data with a source of "quidel":

covidcast_signal(
data_source = "quidel",

Possible fix options include:

  • Use the repository's secret API key like some of the other blog pages do.
    • Caveat: that also means we need to give that key access to quidel data.
  • Rewrite that code to use a signal that is not protected like quidel.
    • This option might mean that we should also make edits to other parts of the blog post to make sure it is congruent (and then re-render the post).
  • Comment out the call that causes the error.
  • Somehow exclude the file from the blog github action workflow.
  • Remove the (markdown) file.

None of those listed fixes would entail (by themselves) removing the blog post from the website or altering it in any way; its content is already rendered in the associated html file and the post is still on the live site even though we have done two releases from this repo (v3.2.6 and v3.2.7) since the quidel signals went private. Also FWIW, we previously added R code to the markdown files to use the secret repo key in #819 and #843, but never rendered that code to actually show up on the live site.

error/failure output text is as follows (taken from https://github.com/cmu-delphi/www-main/actions/runs/6789159996/job/18455738035 ) :

Run npm run build:blog
  npm run build:blog
  shell: /usr/bin/bash -l {0}
  env:
    MSYS: winsymlinks:nativestrict
    MAMBA_ROOT_PREFIX: /home/runner/micromamba-root
    MAMBA_EXE: /home/runner/micromamba-bin/micromamba
    API_KEY: ***

> www-main@3.[2](https://github.com/cmu-delphi/www-main/actions/runs/6789159996/job/18455738035#step:9:2).7 build:blog
> Rscript -e "blogdown::build_site(local=FALSE, run_hugo=FALSE, build_rmd='md5sum')"

Rendering content/blog/2015-07-2[3](https://github.com/cmu-delphi/www-main/actions/runs/6789159996/job/18455738035#step:9:3)-template-post.Rmd... Done.
Rendering content/blog/2020-08-10-hello-world.Rmd... Done.
Rendering content/blog/2020-08-26-fb-survey.Rmd... Done.
Rendering content/blog/2020-08-28-api.Rmd... 
Quitting from lines 286-302 [q-versioning] (2020-08-28-api.Rmd)
Error in `select()`:
! Can't subset columns that don't exist.
✖ Column `time_value` doesn't exist.
Backtrace:
 1. ... %>% ...
 [5](https://github.com/cmu-delphi/www-main/actions/runs/6789159996/job/18455738035#step:9:5). dplyr:::select.data.frame(., time_value, value, sample_size, issue, lag)
Execution halted
Error: Failed to render content/blog/2020-0[8](https://github.com/cmu-delphi/www-main/actions/runs/6789159996/job/18455738035#step:9:8)-28-api.Rmd
Execution halted
Error: Process completed with exit code 1.
@melange396 melange396 added bug blog github_actions Pull requests that update Github_actions code labels Nov 8, 2023
@minhkhul minhkhul self-assigned this Nov 8, 2023
melange396 added a commit that referenced this issue Dec 5, 2023
* add instruction to build blog locally with personal api key

* fix quidel #887 by removing r chunk result + warn readers

* upgrade python covidcast version + add api key to python chunk in blog

* more api key visibility + instruction link

* every R chunk that import library(covidcast) will have an associated API key + instruction link code line in that chunk

* fix visuals not showing up due to warning messages

* workaround render python chunk plot

* generated files from rmd with changes

* remove warning in blog 2021-01-15-causal-effect-mobility

* remove warning 2020-12-10-masks-public

---------

Co-authored-by: melange396 <george.haff@gmail.com>
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