added telemetry to kinfitr #33

bendhouseart · 2025-01-16T20:45:58Z

I don' think this will be as easy as I would like, e.g. I think it's going to require adding in this to each file in the R folder:

MH02276145MLI:kinfitr galassiae$ tree R
R
├── kinfitr_1tcm.R
├── kinfitr_2tcm.R
├── kinfitr_2tcm1k.R
├── kinfitr_2tcm_irr.R
├── kinfitr_2tcm_macro.R
├── kinfitr_SIME.R
├── kinfitr_SUV.R
├── kinfitr_bids.R
├── kinfitr_blooddata.R
├── kinfitr_bloodfuncs.R
├── kinfitr_bloodmodels.R
├── kinfitr_bloodstream.R
├── kinfitr_data_oldbids_json.R
├── kinfitr_data_pbr28.R
├── kinfitr_data_simrefdata.R
├── kinfitr_feng_1tc_ref.R
├── kinfitr_frtm.R
├── kinfitr_lin2tcm.R
├── kinfitr_loganplot.R
├── kinfitr_ma1.R
├── kinfitr_ma2.R
├── kinfitr_methods.R
├── kinfitr_miscfuncs.R
├── kinfitr_mlloganplot.R
├── kinfitr_mrtm1.R
├── kinfitr_mrtm2.R
├── kinfitr_patlakplot.R
├── kinfitr_pfmodels.R
├── kinfitr_refPatlak.R
├── kinfitr_reflogan.R
├── kinfitr_refmllogan.R
├── kinfitr_srtm.R
├── kinfitr_srtm2.R
├── kinfitr_srtm_v.R
├── kinfitr_telemetry.R
├── kinfitr_weights.R
├── kiniftr.R
└── utils-pipe.R

0 directories, 38 files

But I could be wrong on that.

mathesong · 2025-01-16T20:55:59Z

These look great. I'll help to tidy up the code a little and make it a bit more R-y next week, but in principle having it as a couple of generic functions is perfect.

There's no need to define the telemetry in every function, especially because these can sometimes be run 500 times in a row, and we might overload people's internet connections and your server. I think the way to go will be to execute it on load of the package. Info here: https://stackoverflow.com/questions/20223601/r-how-to-run-some-code-on-load-of-package

mathesong · 2025-01-16T20:58:12Z

And more here. This is the definitive R package book: https://r-pkgs.org/code.html

bendhouseart · 2025-01-17T15:19:55Z

These look great. I'll help to tidy up the code a little and make it a bit more R-y next week, but in principle having it as a couple of generic functions is perfect.

There's no need to define the telemetry in every function, especially because these can sometimes be run 500 times in a row, and we might overload people's internet connections and your server. I think the way to go will be to execute it on load of the package. Info here: https://stackoverflow.com/questions/20223601/r-how-to-run-some-code-on-load-of-package

That seems much more manageable!

bendhouseart · 2025-01-24T22:18:44Z

Okay, it's nearly there. only issue I see is that on build it seems to post 3 times to it's endpoint. I think it should only do this once and after that's the case we just need to switch the url endpoints to our actual tracking server. See outputs here -> http://54.144.240.214/check/kinfitr/

Right now it's posting to dev.

We also might want to come up with a more clever way to silence the message about tracking.

── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/home/anthony/Projects/kinfitr/DESCRIPTION’ ...
─  preparing ‘kinfitr’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in
     serialize/load version 3 cannot be read in older versions of R.
     File(s) containing such objects:
       ‘kinfitr/data/oldbids_json.RData’ ‘kinfitr/data/pbr28.RData’
       ‘kinfitr/data/simref.RData’
─  building ‘kinfitr_0.8.0.tar.gz’
   
Running /usr/lib/R/bin/R CMD INSTALL /tmp/RtmpFNlekp/kinfitr_0.8.0.tar.gz \
  --install-tests 
* installing to library ‘/home/anthony/.local/lib/R’
* installing *source* package ‘kinfitr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Loading kinfitr
new debug message
Opt-out of sending tracking information to the KinFitR developers. This information provides an indicator of real world usage crucial for obtaining funding. To disable tracking set options(kinfitr.no_track = TRUE) or the environment variable KINFITR_NO_TRACK to TRUE), to hide this message set options(kinfitr.no_track = FALSE) or the environment variable KINFITR_NO_TRACK to FALSE
Sending telemetry
Debug: Starting send_telemetry
Debug: Telemetry data: package_loaded
Debug: KINFITR_NO_TRACK value: 
Debug: Attempting to send telemetry
Debug: Sending to URL: http://54.144.240.214/kinfitr/
Debug: Response status: 200
** testing if installed package can be loaded from final location
Loading kinfitr
new debug message
Opt-out of sending tracking information to the KinFitR developers. This information provides an indicator of real world usage crucial for obtaining funding. To disable tracking set options(kinfitr.no_track = TRUE) or the environment variable KINFITR_NO_TRACK to TRUE), to hide this message set options(kinfitr.no_track = FALSE) or the environment variable KINFITR_NO_TRACK to FALSE
Sending telemetry
Debug: Starting send_telemetry
Debug: Telemetry data: package_loaded
Debug: KINFITR_NO_TRACK value: 
Debug: Attempting to send telemetry
Debug: Sending to URL: http://54.144.240.214/kinfitr/
Debug: Response status: 200
** testing if installed package keeps a record of temporary installation path
* DONE (kinfitr)
Loading kinfitr
new debug message
Opt-out of sending tracking information to the KinFitR developers. This information provides an indicator of real world usage crucial for obtaining funding. To disable tracking set options(kinfitr.no_track = TRUE) or the environment variable KINFITR_NO_TRACK to TRUE), to hide this message set options(kinfitr.no_track = FALSE) or the environment variable KINFITR_NO_TRACK to FALSE
Sending telemetry
Debug: Starting send_telemetry
Debug: Telemetry data: package_loaded
Debug: KINFITR_NO_TRACK value: 
Debug: Attempting to send telemetry
Debug: Sending to URL: http://54.144.240.214/kinfitr/
Debug: Response status: 200
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mathesong · 2025-01-24T23:29:41Z

I took a little look now, but I can try to find some time to merge and edit on Monday.

Firstly, regarding the running three times, I think it's because it's installing. With just attaching it with library(kinfitr), it won't do the testing the installation paths. So then I think it will only run once.

Secondly, to get it to work properly on installation too, I think we could borrow some code from here: there seems to be a session flag that we can take advantage of, or even set our own.

Third: I'm not happy with having to change to LazyLoad: no in the DESCRIPTION file. I think there's an issue someplace that's causing it not to work without that. I'll see if I can get rid of the issue. Some clues here: https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/lazyLoad . I think this might have something to do with the very prescribed nature of R packages (and devtools and usethis have functions to simplify this): I've just not bumped into this issue before because I usually use those packages for building packages.

Fourth: I guess the makefile is there for testing? Or was the idea to leave it?

NAMESPACE

mathesong · 2025-01-27T13:34:58Z

R/kinfitr_telemetry.R

+get_telemetry <- function(url = get_url, number_of_records = 0) {
+  # checks to see what's been posted to the url endpoint, should return location,
+  # and any other data that gets put there with send_telemetry
+  req <- request(paste(url, as.character(number_of_records), sep = ""))


Is there a reason you didn't chain these together? I've not used httr2 before, but usually these kinds of things would be chained together.

I think it's because I'm writing things like C or Python functions and not R functions. I'm also wrapping them into line by line b/c my R linter is screaming at me if I go over 80 characters.

R/kinfitr_telemetry.R

mathesong · 2025-01-27T13:37:52Z

DESCRIPTION

 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
+LazyLoad: no


I'm not 100% on what LazyLoad is, but I'm really hesitant for it to be altered...

I'm not sure what it does either, but I'm planning on reverting this before we merge.

R/zzz.R

R/kinfitr_telemetry.R

DESCRIPTION

NAMESPACE

R/kinfitr_telemetry.R

Switch import() to specific httr2:: syntax

NAMESPACE

R/kinfitr_telemetry.R

…esong/kinfitr into 32-adding-telemetry-kinfitr

bendhouseart · 2025-02-07T16:56:19Z

R/kinfitr_telemetry.R

@@ -0,0 +1,42 @@
+# set url_base to http://openneuropet.org for deployment
+url_base <- "http://54.144.240.214"


Suggested change

url_base <- "http://54.144.240.214"

url_base <- "http://openneuropet.org"

Apply this suggestion before merge!

mathesong · 2025-02-19T14:11:44Z

I looked this through and made some changes for readability and style. I'm just a little bit particular about a few things.

However, when I make this, there appear to be 6 new entries at the URL endpoint each time, which seems like a lot... I don't think I've added any issues. I tried backtracking on some of the things I was a little concerned about (I don't like the %>% as.logical() syntax ), but it's still doing the same thing. So maybe let's look at this together.

bendhouseart · 2025-02-19T15:35:04Z

Check to see if this crashes when writing the json file to a root owned folder, when run as non-root user.

added telemetry functions

b0e621c

bendhouseart linked an issue Jan 16, 2025 that may be closed by this pull request

Adding telemetry KinFitR #32

Open

bendhouseart changed the base branch from master to Development January 17, 2025 15:18

Anthony Galassi added 3 commits January 21, 2025 16:48

add send telemetry to import

952f2ac

sends a request on library load

bf530b9

add makefile and update DESCRIPTION

66982f8

bendhouseart marked this pull request as ready for review January 24, 2025 22:17

bendhouseart requested a review from mathesong January 24, 2025 22:17

mathesong reviewed Jan 27, 2025

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mathesong reviewed Jan 27, 2025

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mathesong reviewed Jan 27, 2025

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gave up on fancy tricks, writing things to a json inside the library

b3ddd09