https://github.com/aces/cbrain-plugins-loris
CBRAIN extensions for supporting LORIS installations
https://github.com/aces/cbrain-plugins-loris
cbrain-plugin
Last synced: 10 months ago
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CBRAIN extensions for supporting LORIS installations
- Host: GitHub
- URL: https://github.com/aces/cbrain-plugins-loris
- Owner: aces
- Created: 2018-02-20T19:15:48.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2022-03-04T20:56:21.000Z (over 4 years ago)
- Last Synced: 2025-01-16T20:18:50.199Z (over 1 year ago)
- Topics: cbrain-plugin
- Language: Ruby
- Size: 18.6 KB
- Stars: 0
- Watchers: 9
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## Introduction
This repository is a package containing a set of plugins for the
[CBRAIN](https://github.com/aces/cbrain) platform.
## Contents of this package
This package provides some support models, tasks and data providers for interacting
with [LORIS](https://github.com/aces/loris) installations.
#### 1. Userfile models
| Name | Description |
|------------------------------|-------------------------------------------------------------------------------------------------|
| LorisBySubjectAndVisit | A FileCollection used to represent the mappings in LorisPhantomNativeSshDataProvider |
#### 2. CbrainTasks
| Name | Description |
|---------------|------------------------------------------------------------------------------------------------|
| TODO | TODO |
#### 3. DataProviders
All these DataProviders ruby models implement subclasses of the SshDataProvider, where
the target files are selectively chosen among the directory structure for the LORIS Assembly
file system tree.
| Name | Description |
|---------------|---------------------------------------------------------------------------------------------------------------------------------|
| LorisAssemblyNativeSshDataProvider | Maps only MINC files in \*/\*/mri/native/\*.mnc |
| LorisAssemblyProcessedSshDataProvider | Maps any files in \*/\*/mri/processed/\* |
| LorisCcnaPhantomAssemblyNativeSshDataProvider | Like LorisAssemblyNativeSshDataProvider except the path components are more strictly controlled |
| LorisPhantomNativeSshDataProvider | Maps Loris repository according to some convention regarding the Subject_id and the Visit_id |
## How to install this package
An existing CBRAIN installation is assumed to be operational before
proceeding.
This package must be installed once on the BrainPortal side of a
CBRAIN installation, and once more on each Bourreau side.
#### 1. Installation on the BrainPortal side:
* Go to the `cbrain_plugins` directory under BrainPortal:
```bash
cd /path/to/BrainPortal/cbrain_plugins
```
* Clone this repository. This will create a subdirectory called
`cbrain-plugins-neuro` with the content of this repository:
```bash
git clone git@github.com:aces/cbrain-plugins-loris.git
```
* Run the following rake task:
```bash
rake cbrain:plugins:install:all
```
* Restart all the instances of your BrainPortal Rails application.
#### 2. Installation on the Bourreau side:
**Note**: If you are using the Bourreau that is installed just
besides your BrainPortal application, you do not need to make
any other installation steps, as they share the content of
the directory `cbrain_plugins` through a symbolic link; you
only need to *restart your Bourreau server*.
* Go to the `cbrain_plugins` directory under BrainPortal
(yes, *BrainPortal*, because that's where files are installed; on
the Bourreau side `cbrain_plugins` is a symbolic link):
```bash
cd /path/to/BrainPortal/cbrain_plugins
```
* Clone this repository:
```bash
git clone git@github.com:aces/cbrain-plugins-loris.git
```
* Run the following rake task (which is not the same as for
the BrainPortal side):
```bash
rake cbrain:plugins:install:plugins
```
* Restart your execution server (with the interface, click stop, then start).
#### 3. In case of problems during installation
* Consider running the rake task that cleans all previous installations
of tools and userfiles, then trying again the rake tasks mentioned above.
```bash
rake cbrain:plugins:clean:all
```