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earnaud committed Sep 7, 2021
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# V1.6.1

## Features

* Fixed navigation error when clicking 'previous' in EAL.

* Added a counter for the number of users, outputting in the logs.

## Work in progress

* Tests: write a complete set of tests.

* Annotations: continue `dev-metafin` branch.

# v1.6.0

## Features
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62 changes: 27 additions & 35 deletions README.md
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4297467.svg)](https://doi.org/10.5281/zenodo.4297467)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5376278.svg)](https://doi.org/10.5281/zenodo.5376278)

[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-orange.svg)](https://www.tidyverse.org/lifecycle/#maturing)
[![docker](https://img.shields.io/docker/cloud/build/eliearnaud/metashark)](https://hub.docker.com/r/eliearnaud/metashark)

<img src="./inst/media/logo.png" alt="" width="50%">

**Stable Server address:**
http://metashark.pndb.fr/ ![Maintenance](https://placehold.it/15/FF0000/000000?text=+) `Maintenance`
http://metashark.pndb.fr/ <b style="color:red"> Maintenance </b>

**Stable Test Server address:**
https://metashark.test.pndb.fr/ ![Active](https://placehold.it/15/c5f015/000000?text=+)`Active`
https://metashark.test.pndb.fr/ <b style="color:green"> Active </b>

<!-- ![Active](https://placehold.it/15/c5f015/000000?text=+)`Active` -->
<!-- ![Maintenance](https://placehold.it/15/FF0000/000000?text=+) `Maintenance` -->

Metadata Shiny-Automated Resources & Knowledge
Metadata Shiny Application for Resources & Knowledge
_First released on 15-04-2019_

The aim of the MetaShARK app is to allow any user a bit familiar with ecology to fill in data packages to provide as many information as possible on any dataset used in a publication, communication, etc. in ecology. The challenge of this work is to produce a user-friendly tool to a science community which is not familiar to heavy metadata standards and their informatic specification. Consequently, the choice has been made to work only with R as it is the currentest programming language in this community and it can be easily accessible as an open source application, despite of its low performances.
This project has the ambition to offer the user a user-friendly alternative to existing tools (such as the hardcore Morpho ;) ) but also to address an other issue which is the EML is not always fully considered.
The aim of **MetaShARK** is to allow any user a bit familiar with ecology to fill in data packages to provide as many information as possible on any dataset used in a publication, communication, etc. in ecology. The challenge of this work is to produce a user-friendly tool to a science community which is not familiar to heavy metadata standards and their informatic specification. Consequently, the choice has been made to work only with R as it is the current programming language in this community and it can be easily accessible as an open source application, despite of its low performances.
This project has the ambition to offer the public a user-friendly alternative to existing tools (such as the hardcore Morpho ;) ) but also to address an other issue which is the EML is not always fully considered.

This MetaShARK git is called "v2" because it is the evolution with {golem} package of the previous [MetaShARK git](https://github.com/earnaud/MetaShARK)

MetaShARK has a dedicated [dockerhub](https://hub.docker.com/r/eliearnaud/metashark/dockerfile). You can also deploy MetaShARK in a local version: for this, check the `local installation` section.

## Legal disclaimers

By using MetaShARK on a machine, you can get to make the app write files on your machine (see `local installation` and docker items for more details). It is discouraged to launch MetaShARK outside of a docker container.
By using MetaShARK on a personal machine, you can get to make the app write files on your machine (see `local installation` and docker items for more details). It is discouraged to launch MetaShARK outside of a docker container.

**Any suggestion is welcome, feel free to contact the dev !**

Expand All @@ -38,11 +39,11 @@ Once "docker Desktop" is installed, you have to run it so Docker is activated, t

### Local installation

It is now possible to deploy a local container for MetaShARK.
It is now possible to deploy a local container for MetaShARK. Check for the whole repository [here](https://hub.docker.com/r/eliearnaud/metashark).

Two possibilities :

#### Using the public eliearnaud/metashark prebuilt Docker image
#### Using the public Docker image (recommended)

Typing this command line on a shell:

Expand All @@ -57,12 +58,13 @@ On windows computer (using Powershell on Windows 10 for example and if you are i
By downloading the git in locale following the described steps. Please refer to the `reload_docker.sh` script to get all necessary command lines.
**Disclaimer:** you can use docker volumes to access files outside of the container (steps 3 & 4a), but this will require to *write files to your computer*. Since you execute by yourself the given command lines, we consider this as a consent from the user.

1. Make sure to have built the package as an archive. To achieve this, in an RStudio console:
1. Make sure to have built the package as an archive. To achieve this, in an R or RStudio console:
```
# in the root of the package git
> devtools::build(path=".")
```
You shall get a file like `MetaShARK_0.0.0.9000.tar.gz`.

You shall get a file like `MetaShARK_*.tar.gz` (replace `*` with the current version number).

2. In a command shell, get to this git's root: `cd <path/to/MetaShARK/git>`.

Expand All @@ -71,27 +73,25 @@ You shall get a file like `MetaShARK_0.0.0.9000.tar.gz`.
mkdir ~/metashark_data
```

4. Execute the following command lines:
4. Execute the following command lines to set up the container:
a. If you use volumes:
```
# build the MetaShARK image
docker build -t metashark:local .
# run the app using the image
docker run -d --rm -p 3838:3838 --name MS -v ~/metashark_data:/root/dataPackagesOutput metashark:local
```

b. If you do not use volumes:
```
# build the MetaShARK image
docker build -t metashark:local .
# run the app using the image
docker run -d --rm -p 3838:3838 --name MS metashark:local
```

5. In a web browser, access the following URL: `127.0.0.1:3838`.


### Server installation

A dedicated [git](https://github.com/earnaud/MetaShARK_docker) shows the step for setting up an online instance of MetaShARK.
Online version of MetaShARK can be subject to some misfunctions due to incorrect handling of simultaneous multiple users (see issue #124).

## MetaShARK features

### Documentation
Expand All @@ -103,38 +103,30 @@ First feature developped in MetaShARK, it is possible to consult any documented
Two methods are being developped to fill in metadata:

* EML Assembly Line (EAL) : it is the EDI tool allowing the user to interact with a major part of the EML. MetaShARK is a user front-end solution to offer more automated and visual access to this tool.
* Metadata Fill-In (MetaFIN) : still not accessible, it is the PNDB specific tool exploring automatic inference to fill in metadata from datasets.
* Metadata Fill-In (MetaFIN) : in active development, it is a complementary tool to edit and annotate EML files.

### Data Package upload

It is possibe to upload data packages to metacats registered in MetaShARK. You will need to fetch your metacat token in the corresponding MetaCatUI. During development phase, this might not be fully operable as we are trying to properly set our MetaCat and MetaShARK linked together.
It is possible to upload data packages to metacats registered in MetaShARK. You will need to fetch your metacat token in the corresponding MetaCatUI. Refer to the `upload` part of the app to get guided into this.

### References

Some references are given that sustain the base principles of this work.
Given references were used as base principles of our work.

#### Features

MetaShARK/EAL supports:
* data package management (CC BY or CC 0 Licences)
* table files's description \*\* (and *only* those ones yet, badly. WIP on other file types)
* automated\* tables' attributes filling
* custom units' descriptions
* automated\* categorical variables description
* geographic, taxonomic and temporal coverages
* description of persons involved (possibly through ORCID)
* Metadata automated\* generation at EML format

\* automation still requires user's verification
\*\* see Known Bugs below
Features are emphasized into the NEWS.md file.

## Authors

* Elie Arnaud (developper) - [email protected]

## Contribute

### Code edit

Any contribution can be done and submitted. Care about documenting code chunks you want to edit, and also add motivations about these changes.

### Issues post
On posting issues, make sure your problem/idea has not been discussed before (beware of the "is closed" filter). Some issues are named with a "[XXX]" tag meaning this issue is a topic dedicated to "XXX": such issues are not meant to be closed before a long time.

On posting issues, make sure your problem/idea has not been discussed before (beware of the "is closed" filter).

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