git remote add origin git @data . neuro . polymtl . ca : datasets / my - new - repo
-git branch - M master
-# initialize remote and upload metadata
-git push - u origin master
-# initialize remote annex
-git annex sync - a -- no - content
-# upload images to remote annex
-git annex copy -- to origin
-# verify your .nii.gz files were annexed and uploaded
-git annex whereis
+
+Connecting from wifi or off-campus
+If you want to use the web interface:
+
+If you’re off-campus: first connect to the VPN
Next, set up port forwarding for the duration of your task, by running the following command in a terminal window. You should replace "$USER" GRAMES / GE
+ -N -L 3000 :localhost:3000 " $USER " @data.neuro.polymtl.ca
This command won’t produce any output while it’s running. Once you’re done using the web interface, you should terminate the SSH command with ctrl-C.
+In your web browser, go to http://localhost:3000/ .
+Note that this is an HTTP (not HTTPS) address, but your connection to the server is protected by SSH. This also means that you won’t have to accept the server’s self-signed HTTPS certificate.
+Click “Sign In” at the top right of the page.
The username and password is the same as your GRAMES / GE account
If it’s your first time using the web interface, you may want to start by changing some of your settings .
Remember to terminate the SSH command with ctrl-C when you’re done using the web interface.
-
-Releases
-To make a release, use an annotated git tag . Use the tag name for the name of the release, and the annotation for the release notes. Our naming convention for datasets is “rYYYYMMDD”.
-For example, if today is September 8th, 2019, then to create a release do:
-
-To view available releases, first download a dataset, then run
-git tag - l
+
+Initial setup
+While you’re logged in to the web interface:
+
+(Optional) You may want to change the default language between French and English.
+
+Click your user icon at the top right of any page.
Select “Configuration” or “Settings ” in the menu that unrolls.
Select “Apparence” or “Appearance ” in the left menu bar.
Update the “Langue” or “Language” selection.
Click “Modifier la langue” or “Update Language”.
+(Optional) You may want to change your user icon, instead of using the auto-generated abstract art.
+
+Click your user icon at the top right of any page.
Select “Settings ” in the menu that unrolls.
Select “Profile ” in the left menu bar.
Next to “Choose new avatar”, click the “Browse…” button.
Select the user image file you want to upload.
Click “Update Avatar”.
+(Recommended) Set up command-line access with an SSH key.
+(This needs to be done once for each computer you use.)
+
+Get your SSH key from the terminal:
+
+Check whether you already have an SSH key:
+
-To see the release notes for a specific release, use
-git show r20190908
+
+If the above file doesn’t exist, create it with this command:
+
-To use a specific release, either download the dataset and then
-git checkout r20190908
+
+Display the public part of your SSH key:
+ ~/.ssh/id_ed25519.pub
or , for example in a reproducible processing script, you can use clone -b
-git clone -- depth 1 - b r20190908 git @data . neuro . polymtl . ca : datasets / example . git
+It should be a single line of text that looks something like this:
+ssh - ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIEWpqMuw5ifj87tdl12x5 + LJ3uqHdfFQmoVQKsDLjKYG your . user . name @some . computer . name
-Permissions
-You can grant others permissions to your repositories with perms
-ssh git @data . neuro . polymtl . ca perms datasets / my - new - repo + WRITERS someone # grant someone upload rights
-ssh git @data . neuro . polymtl . ca perms datasets / my - new - repo - WRITERS someone # revoke someone's upload rights
-ssh git @data . neuro . polymtl . ca perms datasets / my - new - repo + OWNERS researcher2 # grant someone rights to add (and remove) others and to merge to master
-ssh git @data . neuro . polymtl . ca perms datasets / my - new - repo - l # view users
-ssh git @data . neuro . polymtl . ca perms datasets / my - new - repo - lr # view access rules
+
+
+
+Put the SSH key in the web interface:
+
+Click your user icon at the top right of any page.
Select “Settings ” in the menu that unrolls.
Select “SSH / GPG Keys ” in the left menu bar.
To the right of the heading “Manage SSH Keys”, click “Add Key”.
Paste the contents of the file ~/.ssh/id_ed25519.pub
Click “Add Key” below.
+
+
Test your SSH key from the terminal with the command:
+ git@data.neuro.polymtl.ca
Use
-ssh git @data . neuro . polymtl . ca perms - h
+It might ask for the passphrase for your key ~/.ssh/id_ed25519.pub
+and see https://gitolite.com/gitolite/user#setget-additional-permissions-for-repos-you-created for full details.
-
-
-
-Deletion
-If you created or own a repo and decide it is no longer necessary:
-ssh git @data . neuro . polymtl . ca D trash repo
+If it asks for a password for git@data.neuro.polymtl.ca ask for help :
+...
+git @data . neuro . polymtl . ca : Permission denied ( publickey , password ) .
The “trash” is cleaned out after a week. Except it’s not, yet: https://github.com/neuropoly/data-management/issues/54
-
-Deleting a branch
-If you no longer are working on a specific, make sure that it is deleted (in order to save space and avoid maintaining unnecessary commit history). The relevant commands can be found under Clean up a branch here .
-
-
-
+
+Listing the available datasets
+To view the existing repositories, connect to the web interface and use the “Explore ” tab, which is linked from the top of every page. Keep in mind that there are multiple pages, so either use the search box or click “Next” if you’re looking for a specific repository or username.
-
-Admin Guide
-We are using Gitolite git-annex datalad
-Datasets are stored as git repositories on the server, with the bulk of their data also stored on the server in each repo’s “annex” folder. Using git-annex git-annex ssh remotes .
-gitolite data.neuro.polymtl.ca:datasets/* datasets/*
-The VM is monitored here (requires VPN to connect to the dashboard monitor).
-
-List users
-ssh git @data . neuro . polymtl . ca keys list
+
+Connecting from the command-line (cloning a repo)
+If you just want to run git clone pull push
+
+If you’re off-campus: first connect to the VPN
+Note that there’s no need to do SSH port forwarding.
+To make a local clone, replace "$REPO"
+ clone git@data.neuro.polymtl.ca:datasets/" $REPO "
+cd " $REPO "
+git annex dead here
+git annex get
If the clone initial setup .
+All other git
-
-Add users
-To grant access to a lab member, as above , ask the lab member to generate an ssh key using ssh-keygen public key . Save it to a file firstnamelastname.pub
-cat firstnamelastname . pub | ssh git @data . neuro . polymtl . ca keys add firstnamelastname
-
-
You can also paste the key in, followed by ctrl-d
-ssh git @data . neuro . polymtl . ca keys add firstnamelastname
-
-
The output looks like:
-Enter passphrase for key '/home/kousu/.ssh/id_rsa.github' :
-please supply the new key on STDIN ( e . g . cat you . pub | ssh gitolite @git . example . com keys add @laptop ) .
-ssh - ed25519 AAAAC3NzaC1lZDI1NTE5AAAAID11N3hQpJP4Okivd5xO3N0CuO24ioMwXYv + l / 1 PM /+ z firstname . lastname @polymtl . ca
-Added SHA256 : hwil2tmaw / prgIBX5odO8vOAj2i38gPrUGjGZnnkVvo : firstnamelastname . pub
+
+Getting changes from the server
+If you have already cloned a repository and would like to get the latest version:
+
+Make sure you’re on the right branch, and all your changes are saved, and you have a clean worktree. The command git status
+On branch "$BRANCH"
+...
+nothing to commit , working tree clean
You should use the person’s full name as their username, in the form firstnamelastname info perms like to use the format firstname.lastname@polymtl.ca, but there is a bug , so just use firstnamelastname
-
-
-Permissions
-As admin, you can add or revoke any permissions to any repo using perms .
-There is unfortunately no way to view permissions as another user so you will need to rely on people sending you screenshots if they are having problems
-but you can at least inspect the active sets of permissions on a repo with
-ssh git @data . neuro . polymtl . ca perms < repo > - l
+
+Run the command:
+
-If you need to add new namespaces or finer grained permissions, first, reconsider if the extra complexity and the risk of locking yourself out is worth it. Everything you should need to manage the lab should be doable via ssh git@data.neuro.polymtl.ca help gitolite’s permissions model and official docs for this use case , then:
-git clone git @data . neuro . polymtl . ca : gitolite - admin
-cd gitolite - admin
-vi conf / gitolite . conf # optional: investigate/change the repo definitions
-ls - R keydir / # optional: investigate/change who has access; this *should* be unnecessary, use `keys` as above instead.
-git add - u . && git push
+If your version of git-annex
+ annex sync --content --no-push
-Renaming
-As an admin, you can rename a repo by connecting to the server directly:
-
-
-Deletion
-You can also delete any repo using D .
-You can also get rid of a dataset immediately by:
-ssh git @data . neuro . polymtl . ca D unlock datasets /< dataset >
-ssh git @data . neuro . polymtl . ca D rm datasets /< dataset >
-
-
+Opening an issue
+If you’re working with a dataset, and you notice that something is wrong, or something could be better, consider opening an issue!
+
+If it’s your first issue or pull request for the repository, ask for write access .
In the web interface, go to the repository page.
Click on the “Issues” tab.
Click “New Issue”.
Fill in the title and describe the issue in as little or as much detail as you want.
Click “Create Issue”.
-
-Backups
-Encrypted backups are sent daily to s3+https://s3.ca-central-1.amazonaws.com/data.neuro.polymtl.ca.restic sftp://narval.computecanada.ca:projects/def-jcohen/data.neuro.polymtl.ca.restic
-We use a backup tool called restic review its full recovery documentation to use it safely, but the quick version is that you need to provide backup credentials, one set for either location. It is your responsibility as a data server admin to ensure you have generated and can protect these credentials.
-# AWS
-export RESTIC_REPOSITORY = s3 : s3 . ca - central - 1. amazonaws . com / data . neuro . polymtl . ca . restic
-export RESTIC_PASSWORD = "...."
-export AWS_ACCESS_KEY_ID = "...."
-export AWS_SECRET_ACCESS_KEY = "....."
-
-
# ComputeCanada
-export RESTIC_REPOSITORY = sftp : narval . computecanada . ca : projects / def - jcohen / data . neuro . polymtl . ca . restic
-export RESTIC_PASSWORD = "...."
-# you also implicitly need an account that can `ssh narval.computecanada.ca`
+
+Making a pull request
+If you want to modify a dataset, you should make a pull request, which can then be reviewed and merged into the master branch.
+
+First make sure you have a local clone up to date .
Create a new branch for your work, starting from the current master xyz some-topic xyz/some-topic
+ checkout -b xyz/some-topic master
Once credentialed, the easiest way to recover files is restic mount
-mkdir data - backups
-restic mount backups &
-# datasets are now in backups/snapshots/*/repositories/datasets/
-ls - l backups / snapshots / latest / repositories / datasets /
+
+Make the changes you want to the files in the repo, then save the changes in a commit (or several commits). You can use the commands:
+
-Then you can use git clone rsync
-For example
-You can examine any old version of any git repo
-For the previous steps, only read access was needed. For the following steps, you will need write access .
+
To push the changes to the server (both the changes in your branch xyz/some-topic git-annex
+
-
-
-Recovery Shortcut
-If you are in a pinch, and the server is still running , you can use its credentials instead of loading your own.
-ssh root @data . neuro . polymtl . ca
-su - l git - s / bin / bash
-set - a && . . config / restic / s3
-mkdir - p backups
-restic mount backups &
-# datasets are now in backups/snapshots/*/repositories/datasets/
+If your version of git-annex
+ annex sync --all --content
On the web interface https://data.neuro.polymtl/ca/ , open a pull request:
+
+Go the the repository’s page.
Click on the “Pull Requests” tab.
Click the “New Pull Request” button.
Leave the dropdown menu that says “merge into: datasets:master” as it is.
Select your branch datasets:xyz/some-topic
Click the “New Pull Request” button that appeared below.
Enter a title and a description of your changes, along with any relevant context, in the text boxes that appeared.
Click “Create Pull Request”.
+
+
-
-
-Troubleshooting
-If you are having a problem, please open an issue here . Please don’t be shy, if you don’t report the issue, we won’t know about it and it will never be solved 😉
-If the server is doing something strange, contact someone with sysadmin-access to the server.
-These people can investigate by following the gitolote guide in the sysadmin docs .
-
-
-References
+
+Getting help
+If you need help with anything related to https://data.neuro.polymtl.ca/ , your best bet is to post a question on the #database_mri Slack channel.
+The usual server admins are:
-Patel, Hiren - Wildrepos in Gitolite – detailing how a research lab manages their code and publications collaboratively through gitolite
mathieu.guay-paquet@polymtl.ca
emma.lichtenstein@polymtl.ca
+In case of emergency, these people also have admin access:
+
+eva.alonso-ortiz@polymtl.ca
jcohen@polymtl.ca
joshua.newton@polymtl.ca
mathieu.boudreau@polymtl.ca
nathan.gorvett@polymtl.ca
-
@@ -1032,47 +757,16 @@
References
diff --git a/data/index.html b/data/index.html
index bb4dec68..38fa7cb3 100644
--- a/data/index.html
+++ b/data/index.html
@@ -227,7 +227,7 @@
💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data💾 Data": [[24, "source-filename"]], "\u2601\ufe0f Microsoft 365": [[14, "microsoft-365"]], "\u2697\ufe0f Lab Manual": [[0, "lab-manual"]], "\u2708\ufe0f Conferences": [[20, "conferences"]], "\u270d\ufe0f Academic Writing": [[109, "academic-writing"]], "\ud83c\udde8\ud83c\udde6 Living in Montreal": [[96, "living-in-montreal"]], "\ud83c\udf0e VISAs and Work Permits": [[99, "visas-and-work-permits"]], "\ud83c\udf93 University Courses": [[22, "university-courses"]], "\ud83c\udfe5 Medical": [[97, "medical"]], "\ud83d\udc4b Onboarding": [[80, "onboarding"]], "\ud83d\udca1 Ideas for Cool Projects": [[74, "ideas-for-cool-projects"]], "\ud83d\udca1 Other configuration tips": [[83, "other-configuration-tips"]], "\ud83d\udcb0 Scholarships": [[108, "scholarships"]], "\ud83d\udcbb Shell Profile": [[86, "shell-profile"]], "\ud83d\udcbe Data": [[23, "data"]], "\ud83d\udcc5 Calendar & Meetings": [[1, "calendar-meetings"]], "\ud83d\udcce Practical Information": [[95, "practical-information"]], "\ud83d\udcd6 Comprehensive Exam": [[10, "comprehensive-exam"]], "\ud83d\udcda Bibliography": [[2, "bibliography"]], "\ud83d\udcde Contact": [[21, "contact"]], "\ud83d\udce7 Email": [[85, "email"]], "\ud83d\udcf6 Eduroam": [[84, "eduroam"]], "\ud83d\udd27 RF Lab": [[102, "rf-lab"]], "\ud83d\udda5 Compute Canada": [[13, "compute-canada"]], "\ud83d\udda5 Computers @CRIUGM": [[12, "computers-criugm"]], "\ud83d\udda5 Computers @NeuroPoly": [[15, "computers-neuropoly"]], "\ud83d\udda5 Computing Resources": [[11, "computing-resources"]], "\ud83d\udda8 Printer": [[18, "printer"]], "\ud83d\udde3 Slack": [[87, "slack"]], "\ud83d\udee0 Purchasing Supplies": [[98, "purchasing-supplies"]], "\ud83e\udd13 Geek tips": [[29, "geek-tips"]], "\ud83e\udde9 EDI": [[28, "edi"]], "\ud83e\uddf2 MRI Scanning": [[75, "mri-scanning"]], "AI and deep learning": [[94, "ai-and-deep-learning"]], "ANSI Escape Codes for Colours": [[31, "ansi-escape-codes-for-colours"]], "AWS": [[58, "aws"]], "Abstracts": [[20, "abstracts"]], "Access from stations": [[26, "access-from-stations"]], "Access to UNF": [[79, "access-to-unf"]], "Accessing Datasets (external volumes)": [[54, "accessing-datasets-external-volumes"]], "Account Creation": [[14, "account-creation"]], "Acknowledgements": [[109, "acknowledgements"]], "Acquisition": [[74, "acquisition"]], "Add LINUX machine to GRAMES ": [[39, 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