[BUG] [R] Code generated not immediately useable

[eddelbuettel]

Bug Report Checklist

• Have you provided a full/minimal spec to reproduce the issue?
• Have you validated the input using an OpenAPI validator (example)?
• What's the version of OpenAPI Generator used?
• Have you search for related issues/PRs?
• What's the actual output vs expected output?
• [Optional] Bounty to sponsor the fix (example)

Description

Using the (Docker-based) openapi-generator-cli on a yaml template used otherwise, I end up with an R package that is not installable as a portion of the files are not parseable by R.

To reproduce:

edd@rob:~$ mkdir /tmp/openapi-generator-issue; cd /tmp/openapi-generator-issue
edd@rob:/tmp/openapi-generator-issue/$ curl https://raw.githubusercontent.com/TileDB-Inc/TileDB-Cloud-API-Spec/master/openapi-v1.yaml -o openapi-v1.yaml
edd@rob:/tmp/openapi-generator-issue/$ docker run --rm -u 1000:1000 -v ${PWD}:/local openapitools/openapi-generator-cli generate -i /local/openapi-v1.yaml -g r -o /local/r-pkg/
edd@rob:/tmp/openapi-generator-issue/$ cd r-pkg
edd@rob:/tmp/openapi-generator-issue/r-pkg$ R CMD build .                                          # standard step of building R package
edd@rob:/tmp/openapi-generator-issue/r-pkg$ R CMD INSTALL openapi_1.0.0.tar.gz

which fails on

edd@rob:/tmp/openapi-generator-issue/r-pkg$ R CMD INSTALL openapi_1.0.0.tar.gz 
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘openapi’ ...
** using staged installation
** R
Error in parse(outFile) : bad value
ERROR: unable to collate and parse R files for package ‘openapi’
* removing ‘/usr/local/lib/R/site-library/openapi’
* restoring previous ‘/usr/local/lib/R/site-library/openapi’
edd@rob:/tmp/openapi-generator-issue/r-pkg$ 

I am actually pretty experienced in R but find this hard to debug too. We can list the files that yield 'bad value' on sourcing though:

edd@rob:/tmp/openapi-generator-issue/r-pkg/R$ Rscript -e 'files <- dir("."); for (f in files) { res <- try(source(f), silent=TRUE); if (inherits(res, "try-error")) cat("Error processing file", f, "\n") }'
Error processing file activity_event_type.R 
Error processing file array_actions.R 
Error processing file array_task_status.R 
Error processing file array_task_type.R 
Error processing file array_type.R 
Error processing file datatype.R 
Error processing file filter_option.R 
Error processing file filter_type.R 
Error processing file invitation_status.R 
Error processing file invitation_type.R 
Error processing file layout.R 
Error processing file namespace_actions.R 
Error processing file organization_roles.R 
Error processing file pricing_aggregate_usage.R 
Error processing file pricing_currency.R 
Error processing file pricing_interval.R 
Error processing file pricing_type.R 
Error processing file pricing_unit_label.R 
Error processing file public_share_filter.R 
Error processing file querystatus.R 
Error processing file querytype.R 
Error processing file sso_provider.R 
Error processing file udf_actions.R 
Error processing file udf_language.R 
Error processing file udf_result_type.R 
Error processing file udf_type.R 
edd@rob:/tmp/openapi-generator-issue/r-pkg/R$ 


##### openapi-generator version

```sh
edd@rob:/tmp/openapi-generator-issue/r-pkg/R$ docker run --rm openapitools/openapi-generator-cli --version
openapi-generator-cli 5.0.0-SNAPSHOT
  commit : 52b80e9
  built  : 2020-06-18T17:05:53Z
  source : https://github.com/openapitools/openapi-generator
  docs   : https://openapi-generator.tech/

edd@rob:/tmp/openapi-generator-issue/r-pkg/R$ 

OpenAPI declaration file content or url

The YAML file is given above in the snippet and from here: https://github.com/TileDB-Inc/TileDB-Cloud-API-Spec/blob/master/openapi-v1.yaml

Command line used for generation

See above. I used your Docker container, downloaded yesterday

Steps to reproduce

See above, I followed your recommended invocation.

Related issues/PRs

N/A

Suggest a fix

N/A

[wing328]

I've tested your spec with this PR: #5728, which provides better support for Enum in R.

I was able to install it after purging some incorrect test files generated for Enum type:

/tmp/R-test $ R CMD INSTALL openapi_1.0.0.tar.gz

* installing to library ‘/usr/local/lib/R/3.5/site-library’
* installing *source* package ‘openapi’ ...
** R
** byte-compile and prepare package for lazy loading
	** help
No man pages found in package  ‘openapi’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (openapi)

Can you please also give it a try by building the JAR locally?

git checkout -b LiNk-NY-enum master
git pull https://github.com/LiNk-NY/openapi-generator.git enum
mvn clean package -DskipTests
java -jar modules/openapi-generator-cli/target/openapi-generator-cli.jar generate -g r -i ~/Downloads/openapi-v1.txt -o /tmp/R-test

[eddelbuettel]

Thanks for the reply, and happy to try, but could you (if possible) provide a Docker-based setup? I have very little Java on my machine. What container with mvn could I start from?

[eddelbuettel]

I leaned on a colleague and we got it sorted out. Thumbs up for the PR #5728. Resulting package now builds, lacks some documentation (normal at this stage) and fails some unit tests (ditto). I can live with that.

So take this as my thumbs up for merging the PR!

[eddelbuettel]

(For completeness I updated the initial post with the new URL of the YAML file describing our service; we have done some work at our end and that repo is now public.)

[eddelbuettel]

There is one new bug. The generated code tries to deparse a content field on the returned JSON but does not notice that the chars are raw and need to converted from raw first. Shall I file a new issue for that?

[wing328]

Yes please open a new issue with the details for tracking

[eddelbuettel]

Done, #6767. Thanks in advance for your consideration, it is appreciated!

[wing328]

For the enum issue in auto-generated test files, I've filed #6936 to fix it.

[Bronson-Brown-deVost]

I am getting the same error as OP when I try to build my package: Error in parse(outFile) : bad value.

Steps to reproduce:

git clone https://github.com/Scripta-Qumranica-Electronica/SQE_API_Connectors.git
cd SQE_API_Connectors/libs/r
R CMD build .
R CMD check qumranicaApiConnector_0.7.2.tar.gz

Unfortunately I don't have enough experience with building R packages to debug much further than that, but perhaps there is some data type in my openapi spec that is giving some trouble.

The r client code can be generated from the project root SQE_API_Connectors folder with yarn generate-r-api (assuming you have the node dependencies installed by running yarn --pure-lockfile at the project root). I am using v2.0.3 of @openapitools/openapi-generator-cli.

Thanks for any help you can provide, this is a really cool project.

[chinsoon12]

Hi @eddelbuettel, understand that this is more than 1y ago but this might be useful for you:
https://stat.ethz.ch/pipermail/r-help/2014-May/374864.html

for my case, the offending line was initialize = function(, ...){ which is fixed by removing the comma

[eddelbuettel]

@chinsoon12 This is a by-now oldish bug report, and I don't think we have that issue anymore with the subsequent / current release.