thermos

thermos provides a simple way to interact with ThermoFisher’s IonReporter API from within R.

Installation

You can install the development version of thermos from GitHub with:

# install.packages("devtools")
# devtools::install_github("KaiAragaki/thermos")
install.packages("thermos", repos = c('https://kaiaragaki.r-universe.dev', 'https://cloud.r-project.org'))

Philosophy

API endpoint names have been translated to function names by converting camelCase to snake_case, even when the original names were not so good. I’m not particularly fond of some of the names, so I might add some aliases later.

Here’s a decoder ring:

API	thermos	Possible Alias
`isAnalysisRunning`	`is_analysis_running`
`isSampleExists`	`is_sample_exists`	`sample_exists`
`downloadBam`	`download_bam`
`download`	`download`
`analysis`	`analysis`	`get_analysis`
`getAssociatedBamfiles`	`get_associated_bamfiles`
`getAvailableCancerType`	`get_available_cancer_type`
`getAvailableStorageSpace`	`get_available_storage_space`
`currentResultsTsv`	`current_results_tsv`
`getDataUploadPathWithAuth`	`get_data_upload_path_with_auth`
`finalreport`	`finalreport`	`get_final_report`
`qcreport`	`qcreport`	`get_qc_report`
`getUserDetails`	`get_user_details`
`getUserDetailsWithAuth`	`get_user_details_with_auth`
`getvcf`	`getvcf`	`get_vcf`
`genomeView`	`genome_view`
`getWorkflowNamesWithApplicationTypeWithAuth`	`get_workflow_names_with_application_type_with_auth`	`get_workflow_names`
`startAnalysis`	`start_analysis`
`unsharedAnalyses`	`unshared_analyses`	`unshare_analyses`[1]

Whenever possible, I’ve tried to maintain similar behavior between the API and the package, so hopefully you only have to learn one thing. In particular, default arguments should be the same as in the API.

I will try my best to make the documentation a bit more detailed than the documentation provided by ThermoFisher.

Sometimes request query parameters are exposed that only have one options (mainly ‘format’, which only has the ‘json’ option). I won’t expose these arguments.

This package will attempt coerce responses into sensible types, such as converting the response string "true" into the boolean TRUE

The documentation is conflicted about the naming of this function, with the title saying ‘unshare’, the endpoint saying ‘unshared’, and the description saying ‘unshares’. The intent implies it is a verb - ‘to unshare’ - so this function name makes more sense.