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git annex special remote for Globus

Project description

git-annex special remote for Globus

git-annex-remote-globus adds to git-annex the ability to retrieve files present in Globus.org.

Requirements

  • Datalad
  • Git annex

How to use

  1. Initialize a virtual environment

  2. Install the repository with pip install git-annex-remote-globus

  3. Install the dataset to be retrieved via the remote datalad install -r <dataset>and cd <dataset>.

  4. If it is the first time a user uses globus remote, authentication to Globus.ors must take place to continue Thus run git-annex-remote-globus setup anf follow the steps. Gmail and ORCHID are supported

  5. If the dataset was previously registered, which is expected, it is enough to enable the globus remote by running:

    git annex enableremote globus

  6. Try to download the desired file with

    datalad get path/to/file

If every step was followed correctly, it will get successfully downloaded !

Procedure for testing changes in the globus remote

This procedure is only for testing purposes:

  1. git clone this repository: git clone https://github.com/CONP-PCNO/git-annex-remote-globus.git and checkout the branch you want to test with git checkout -a <branch>. Using a virtual environment is suggested
  2. In a different folder, install the following dataset: datalad install -r <dataset>and cd <dataset>. From now on we are going to work from the dataset repo location where you cd'ed
  3. Add the path of your git-annex-remote-globus location to your current dataset PATH
  4. In the repository, run git-annex-remote-globus setup and follow the instructions to authenticate. Gmail and ORCHID are supported If may you need in a fresh virtual env, install dependencies specified. It will work after that
  5. Run git annex enableremote globus. This command should initialize the remote successfully if everything went all right
  6. Try to download any file with git annex get path/to/file

Manually registering a dataset with globus remote (internals)

Note: this procedure is a demonstration of how a dataset file present in Globus.org can be retrieved by git-annex. The following steps can be performed manually or can be automated as described in globus tools. The latter repo provides dataset administrators with an automated and efficient way to register globus datasets with git annex so that git annex can retrieve their content from Globus.org. Once a dataset is registered for the first time, users will be able to access the dataset files via git annex or datalad following the 'How to use' procedure above.

In order to understand how the globus remote works internally and how to register a globus file with git-annex, we can use an example dataset file currently present in Globus.org. The content of the dataset file is not available to us because the file on github consists in a symlink generated by annex. The symlink was generated once the file dataset was added to CONP following thi [procedure] () First the globus remote must be initialized to start the process. Then the file (whose content is in Globus) can be registered with git annex which will then be able to get access to its Globus location to retrieve the file content and send it to us. Therefore we can access the file content!

The following steps are usually performed when datasets files get registered with a git annex remote for the first time. Dedicated tools, i.e. globus tools automate this process, but the point of this section is to explain in details what happens when datasets are registered in the first place. So initialization first. We use this repository as an example and install it with datalad

cd FRDR-multimodal
git annex initremote globus type=external externaltype=globus encryption=none endpoint=FRDR_Prod_2 fileprefix=/5/published/publication_170/submitted_data/

To debug git-annex initremote --debug.

The endpoint and prefix are obtained from the globus location of the file available in Globus.org

Run the following to find the file symlink, which includes the file hash

ll 2015_11_18_cortex/mask/mask.mat

The last command will allow you to visualize the symlink which contains the MD6 hash of the file content. At this point, globus does not know anything about this file and its symlink, as you can see running the following command

git annex whereis 2015_11_18_cortex/mask/mask.mat

Globus is not listed indeed. We now need to tell globus of the existence of the file based on its hash, which we call key. When initialized, globus was given a location ID by annex which distributes one to every remote it communicates with. We can find Globus location ID by running the following command from the dataset root location:

cat .git/config

This file shows the remote "globus" which we just initialized, and the globus remote location ID given by annex. Therefore we need to make this location know about the file we want to retrieve.

To do that, run:

git annex setpresentkey <file_hash> <annex-uuid> 1

For example, for the file we are working with 2015_11_18_cortex/mask/mask.mat we would run:

git annex setpresentkey MD5E-s572--1e5e0b0c5896d16ac14170c8f546d4e1.mat 056ae102-61ce-4417-9180-b45eecc45082 1

The 1 at the end tells globus about the existence of this file with its given key. A 0 would remove knowledge of the file

Now, to make sure globus knows about this file, we can run the command below.

git annex whereis 2015_11_18_cortex/mask/mask.mat

At this point we can go ahead and register a url to be associated with the given file key. In this way, we will connect the points and tell annex where in globus the file is located, so it can reach it. Therefore we will add a globus url which will contain the endpoint name and fileprefix:

git annex registerurl MD5E-s572--1e5e0b0c5896d16ac14170c8f546d4e1.mat globus://frdr_prod_2/5/published/publication_170/submitted_data/2015_11_18_cortex/mask/mask.mat

At this point we can finally obtain the file running the command below

git annex get 2015_11_18_cortex/mask/mask.mat

This is the point where the file becomes available on your machine

You can run whereis again to check that

git annex whereis 2015_11_18_cortex/mask/mask.mat

Moreover you can always run the following command if you want to mack sure the file has not been modified in globus compared to your previously downloaded version by using the annex-uuid again

git annex checkpresentkey MD5E-s572--1e5e0b0c5896d16ac14170c8f546d4e1.mat 056ae102-61ce-4417-9180-b45eecc45082

It will return Success if the file in Globus has not change

Issues, Contributing

If you run into any problems, please check for issues on GitHub. Please submit a pull request or create a new issue for problems or potential improvements.

License

MIT

Project details


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