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Tidied up the vignette prose.
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LTLA committed Apr 24, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: gobbler
Version: 0.3.3
Date: 2024-04-15
Version: 0.3.4
Date: 2024-04-24
Title: Interface to the gobbler service
Description:
Friendly interface to the gobbler service.
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17 changes: 12 additions & 5 deletions vignettes/userguide.Rmd
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Expand Up @@ -4,7 +4,7 @@ author:
- name: Aaron Lun
email: infinite.monkeys.with.keyboards@gmail.com
package: gobbler
date: "Revised: February 15, 2024"
date: "Revised: April 24, 2024"
output:
BiocStyle::html_document
vignette: >
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# Introduction

The `r self` package implements an R client for the [service of the same name](https://github.com/ArtifactDB/gobbler).
This allows Bioconductor packages to easily store and read data on a managed registry in a shared filesystem.
This allows users to easily store and read data on a managed registry in a shared filesystem, e.g., on high-performance computing (HPC) clusters.
It also provides mechanisms for project maintainers to easily manage upload authorizations and third-party contributions.
Readers are referred to [Gobbler documentation](https://github.com/ArtifactDB/gobbler?tab=readme-ov-file#gobbling-data-on-shared-filesystems) for a description of the concepts;
this guide will strictly focus on the usage of the `r self` package.

# Demonstration setup

The rest of this vignette assumes that a Gobbler service is actually running on a shared filesystem,
with known locations for the staging directory and registry.
Most of this vignette assumes that a Gobbler service is running on the same filesystem as the users of the `r self` package.
This is typically done with service managers like `systemctl` with fixed locations for the staging directory and registry.
For demonstration purposes, we'll set up a test instance of the service with some temporary paths for the staging directory and registry.
Real applications should run the service outside of R, e.g., via `systemctl`.

```{r}
library(gobbler)
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fetchLatest("test", "simple", registry=REGISTRY)
```

The functions in this section of the vignette can also be executed remotely (i.e., outside of the shared filesystem) if the `url=` argument is supplied.
This provides read-only access to the registry for a wider range of applications, e.g., on the cloud or in the browser.

```{r}
# Forcing remote access to stop it from using the filesystem.
fetchLatest('test', 'simple', registry=REGISTRY, url=URL, forceRemote=TRUE)
```

# Uploading files

## Basic usage
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