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molgenis-r-armadillo

Client to manage shared files in the MOLGENIS Armadillo suite from R

https://github.com/molgenis/molgenis-r-armadillo

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 12 committers (8.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.1%) to scientific vocabulary

Keywords

hacktoberfest
Last synced: 11 months ago · JSON representation

Repository

Client to manage shared files in the MOLGENIS Armadillo suite from R

Basic Info
Statistics
  • Stars: 3
  • Watchers: 9
  • Forks: 6
  • Open Issues: 3
  • Releases: 40
Topics
hacktoberfest
Created about 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing

README.Rmd 

---
title: "MolgenisArmadillo"
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```


[![Build Status](https://api.travis-ci.com/molgenis/molgenis-r-armadillo.svg?branch=master)](https://api.travis-ci.com/molgenis/molgenis-r-armadillo.svg?branch=master)
[![CRAN status](https://www.r-pkg.org/badges/version/MolgenisArmadillo)](https://CRAN.R-project.org/package=MolgenisArmadillo)
[![codecov](https://codecov.io/gh/molgenis/molgenis-r-armadillo/branch/master/graph/badge.svg?token=ITPMERAWYI)](https://app.codecov.io/gh/molgenis/molgenis-r-armadillo)


Client to share data in a [MOLGENIS Armadillo DataSHIELD Service](https://github.com/molgenis/molgenis-service-armadillo/).

## Purpose
This library can be used by data managers to share datasets on a
MOLGENIS Armadillo server.

## Overview
The datasets are stored in shared folders on a MinIO file store. The MOLGENIS
Armadillo server has access to the file store and can load the data sets into
a shielded RServe environment so that researchers can call DataSHIELD analysis
methods on the data.

## Usage
Login to the service.
``` R
library('MolgenisArmadillo')
armadillo.login("https://armadillo-url-example.org")
```

Now you can create a project and upload tables to the project to share them for
analysis.
``` R
library(datasets)
armadillo.create_project("project")
armadillo.upload_table("project", "folder", iris)
```

Listing the tables.
``` R
armadillo.list_tables("project")
```

Removing the data from the storage. First you need to remove the content of a project before you can delete the project.
``` R
armadillo.delete_table("project", "folder", "iris")
armadillo.delete_project("project")
```

## Documentation
For more in depth documentation please check the [howto](https://molgenis.github.io/molgenis-r-armadillo/articles/MolgenisArmadillo.html).

## Armadillo 2
The newest version (2.x) of MolgenisArmadillo will be only compatible with Armadillo version 3. If you still use Armadillo 2, you should use the 1.1.13 version of MolgenisArmadillo. You can install this specific version using
the following commands:

For windows:
``` R
packageurl <- "https://cran.rstudio.com/bin/windows/contrib/4.2/MolgenisArmadillo_1.1.3.zip"
install.packages(packageurl, repos=NULL, type="source")
```

For Mac:
``` R
packageurl <- "https://cran.rstudio.com/bin/macosx/contrib/4.2/MolgenisArmadillo_1.1.3.tgz"
install.packages(packageurl, repos=NULL, type="source")
```

For Linux:
``` R
packageurl <- "https://cran.rstudio.com/src/contrib/MolgenisArmadillo_1.1.3.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
```

## For developers

- To build documentation, do `devtools::document()`
- To run all unit tests, do `devtools::test()`
- While writing code (or tests), you can use `devtools::load_all()` to quickly "install" the package.
- To run a single test file, open it in Rstudio and do `devtools::test_active_file()`
- To run the linter, do `devtools::lint()`. Tip: run it often :)
- To create new README from Rmd: run `devtools::build_readme()`

Owner

  • Name: MOLGENIS - open source solutions for scientific data
  • Login: molgenis
  • Kind: organization
  • Location: The Netherlands, Europe

GitHub Events

Total
  • Create event: 11
  • Release event: 3
  • Issues event: 14
  • Delete event: 8
  • Issue comment event: 16
  • Push event: 83
  • Pull request review event: 8
  • Pull request event: 19
Last Year
  • Create event: 11
  • Release event: 3
  • Issues event: 14
  • Delete event: 8
  • Issue comment event: 16
  • Push event: 83
  • Pull request review event: 8
  • Pull request event: 19

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 344
  • Total Committers: 12
  • Avg Commits per committer: 28.667
  • Development Distribution Score (DDS): 0.77
Past Year
  • Commits: 43
  • Committers: 6
  • Avg Commits per committer: 7.167
  • Development Distribution Score (DDS): 0.465
Top Committers
Name Email Commits
Fleur Kelpin f****n@u****l 79
MOLGENIS Jenkins m****i@g****m 73
Sido Haakma s****o@h****g 67
tommy t****4@g****m 50
mkslofstra m****a@h****m 45
Fleur Kelpin f****r@k****l 12
Tim Cadman 4****n 11
Morris Swertz m****z@r****l 2
BrendaH b****s@g****m 2
timcadman t****n@g****m 1
Tommy de boer t****r 1
erikzwart e****t@u****l 1
Committer Domains (Top 20 + Academic)
umcg.nl: 2 rug.nl: 1 kelpin.nl: 1 haakma.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 31
  • Total pull requests: 148
  • Average time to close issues: 4 months
  • Average time to close pull requests: 13 days
  • Total issue authors: 8
  • Total pull request authors: 9
  • Average comments per issue: 0.65
  • Average comments per pull request: 1.17
  • Merged pull requests: 123
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 28
  • Average time to close issues: 23 days
  • Average time to close pull requests: 2 days
  • Issue authors: 4
  • Pull request authors: 2
  • Average comments per issue: 0.56
  • Average comments per pull request: 0.89
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • marikaris (11)
  • timcadman (10)
  • nakikkertumcg (3)
  • fdlk (2)
  • hadley (2)
  • clemens-tolboom (1)
  • sidohaakma (1)
  • ESCRI11 (1)
Pull Request Authors
  • marikaris (44)
  • timcadman (42)
  • fdlk (23)
  • sidohaakma (14)
  • tommydeboer (9)
  • mswertz (5)
  • clemens-tolboom (5)
  • BrendaHijmans (3)
  • SietsmaRJ (3)
Top Labels
Issue Labels
bug (7) enhancement (3) molgenis-r-armadillo (1) good first issue (1)
Pull Request Labels
hacktoberfest-accepted (4)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 496 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 11
  • Total maintainers: 1
cran.r-project.org: MolgenisArmadillo

Armadillo Client for the Armadillo Service

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 496 Last month
Rankings
Forks count: 10.9%
Downloads: 23.0%
Average: 23.4%
Dependent repos count: 24.3%
Dependent packages count: 27.8%
Stargazers count: 31.0%
Maintainers (1)
m.k.slofstra@umcg.nl
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • MolgenisAuth * imports
  • arrow * imports
  • aws.iam * imports
  • aws.s3 * imports
  • httr * imports
  • urltools * imports
  • xml2 * imports
  • DSMolgenisArmadillo * suggests
  • datasets * suggests
  • knitr * suggests
  • mockery * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tibble * suggests