Vignettes and tests

Tests and vignettes need an empty ElasticSearch (ES) instance to really test the core KibioR methods (e.g. push, pull, search). They can be conducted throught an ES instance run via Docker to easily select multiple versions. Unfortunately, interactive build has been removed since each build should test them on the spot (with the current machine they are tested on).

When linked to ES, you can run the full test suite and compile the interactive vignettes. Follow the rest of the file to make it happen.

Folder organization

After downloading the project sources, you can find all that is needed inside the “doc_env” folder:

Requirements

  1. An empty and accessible ES running instance. You can download the project from ES website or run a single instance via Docker. See the fixed vignette, section Deploying an Elasticsearch instance to set one with Docker.

  2. The Github version of the project. The packaged version has not some scripts that automatically load environment variables and prepare for tests. The scripts required are: inst/doc_env/kibior_build.R and inst/doc_env/tests_suite/helper.R.

Process

Install and check ES instance

Interactive vignettes generation

Full test suite

Be warned that there are lots of tests (> 1500), a 1/3 are pushing/pulling data which takes time. My laptop is running all tests on a Dell inspiron core i5-8250U CPU @ 1.60GHz, 4c/8t. It takes about 45min to run all tests, but can easily take more than an hour to run on older CPUs. You can regulate the number of tests by modifying the calls inside the “tests/testthat.R” file.

Data informations

samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455 -O bam > test.bam.bai
https://s3.amazonaws.com/bedtools-tutorials/web/cpg.bed
ftp://ftp.ensembl.org/pub/release-99/gff3/homo_sapiens/Homo_sapiens.GRCh38.99.chromosome.Y.gff3.gz
ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_rm.chromosome.Y.fa.gz
ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz
ftp://ftp.ensembl.org/pub/release-99/fasta/mus_spretus/pep/Mus_spretus.SPRET_EiJ_v1.pep.all.fa.gz