diff --git a/docs/first-steps.qmd b/docs/first-steps.qmd index 1cb3299..33f6dff 100644 --- a/docs/first-steps.qmd +++ b/docs/first-steps.qmd @@ -44,7 +44,7 @@ A workspace can also be called a 'Virtual Machine' or a 'Server'. It is a tempor See [here](manuals/creating.qmd) for detailed information on how to create a workspace. ## Pausing, Resuming, Deleting a workspace -You always need a wallet to create a workspace, by default a workspace can only be paused, resumed and deleted by the one that has created it. You can use SRAM to give persons permission to PAUSE, RESUME and DELETE a workspace that is created by someone else. It is also possible to share a wallet with a member of your CO in SRAM. See [Add collaborators to existing project](https://servicedesk.surf.nl/wiki/display/WIKI/Invite+admins+and+members+to+a+collaboration). +You always need a wallet to create a workspace, by default a workspace can only be paused, resumed and deleted by the one that has created it. You can use SRAM to give persons permission to PAUSE, RESUME and DELETE a workspace that is created by someone else. It is also possible to share a wallet with a member of your CO in SRAM. See [Add collaborators to existing project](https://servicedesk.surf.nl/wiki/display/IAM/Invite+admins+and+members+to+a+collaboration). ## Getting access to your workspace diff --git a/docs/imgs/ibridges.png b/docs/imgs/ibridges.png new file mode 100644 index 0000000..bbb3a65 Binary files /dev/null and b/docs/imgs/ibridges.png differ diff --git a/docs/manuals/ibridges.qmd b/docs/manuals/ibridges.qmd index 73bcaff..0af19b6 100644 --- a/docs/manuals/ibridges.qmd +++ b/docs/manuals/ibridges.qmd @@ -2,24 +2,105 @@ title: Using iBridges on SURF Research Cloud --- -The instructions below describe the process of data transfer between SURF Research Cloud and Yoda using iBridges. iBridges is a command-line tool for transfering data to and from Yoda (and other iRODS servers), focused on user-friendliness. It is developed and supported by the Utrecht University Research Engineering team. Like the [iCommands suite](icommands.qmd), it is suitable for transferring large amounts of data, but it is easier to use. +The instructions below describe the how to setup iBridges to transfer data between SURF Research Cloud and Yoda or any other iRODS instance. It is possible to use iBridges in three different ways: -Note: a graphical desktop version of iBridges is currently under development, but not yet supported on ResearchCloud. +- as a python package +- via the command line interface (CLI) +- via the graphical user interface (GUI) + + + +Using any of the three methods you can safely and easily transfer large amounts of data between Yoda and your Research cloud workspace. + +The python package and the command line interface are available (or can be made available) on all workspaces while the graphical user interface will only work on 'Desktop' workspaces, i.e. workspaces where you will have a Windows or Linux (e.g. Ubuntu) Desktop. + +![ibridges](../imgs/ibridges.png) ### Prerequisites -You will need some basic Linux (commandline) skills to be able to use iBridges. +Access to Yoda or another iRODS instance which hosts your data. + +iBridges needs to be installed on your workspace. Many SURF ResearchCloud workspaces developed by Utrecht University (such as Python and R workbenches) have iBridges preinstalled. + +- If you are working on a Desktop workspace, you can check by logging in to your workspace, clicking 'applications' in the top left corner, and clicking 'Development'. +- On non-desktop workspaces check if iBridges is installed by typing: `ibridges` in the terminal. If iBridges is installed, this should show you the program's help menu. On Jupyter or Rstudio workspaces, you need to open a terminal first: In Jupyter, click the + button in the file browser and select the terminal in the new Launcher tab ([find a short video here](https://jupyterlab.readthedocs.io/en/stable/user/terminal.html)). +In Rstudio, In the bottom left panel, click the ‘terminal’ tab. + +### Configure iBridges + +To connect to a Yoda or any other iRODS instance you will need a so-called `irods_environment.json` which needs to be stored in a specific location. You can create this file by hand or use the iBridges GUI or CLI to create it for you. + +#### Configuration through the GUI + +1. Open the GUI + - Windows: Go to the Main Menu and search for or click on the tile `ibridges` + - Linux: Go to Applications --> Development --> iBridges + +2. From the main menu click 'Configure' --> `Add Configuration`. Click on the template you want to use, fill in your user name and save the file as `irods_environment.json` in the suggested `.irods` folder. + +If there are no templates in the drop-down menu of the configuration window, you will need to install the plugin. To this end you will need python and git and execute in power shell, git bash or Anaconda terminal: + +``` +pip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git +``` + +#### Configuration through the CLI + +If you want to connect to a server hosted by Utrecht University please check whether this information is already present for ibridges. + +``` +ibridges setup --list +``` + +From that list simply choose the server you want to connect to with `ibridges setup uu-` and follow the instructions. +In case you get the message `No server information was found.` please install: -iBridges is already installed on many SURF ResearchCloud workspaces developed by Utrecht University. You can check if it is present by simply typing the following command on your terminal: `ibridges`. If iBridges is installed, this should show you the program's help menu. +``` +pip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git +``` -If you need to install iBridges, you can execute: `pip install ibridges`. +#### What shall I do if iBridges is not on my workspace? -### Creating an iRODS environment file +If your workspace has python installed, you can install the packages using the command line (or aka terminal): + +- GUI: `pip install ibridgesgui` +- CLI/API: `pip install ibridges` + +To start the GUI application you would then need to open a terminal and type in `ibridges-gui`. (Note: this will only work on Desktop workspaces). + +Please contact us if you need help with installing iBridges or if you want to have iBridges preinstalled on your workspace. + + +#### How to connect to a Yoda or iRODS instance not provided by Yoda? + +In this case you will have to create your irods_environment.json by hand: {{< include partials/_irods_env.qmd >}} -For a more extensive tutorial, see [here](https://github.com/UtrechtUniversity/iBridges/blob/develop/tutorials/01-Setup-and-connect.ipynb). +For a more extensive tutorial, see + +- [Setup by GUI](https://chstaiger.github.io/iBridges-Gui/docs/getting-started.html) + +- [Setup](https://github.com/UtrechtUniversity/iBridges/blob/develop/tutorials/01-Setup-and-connect.ipynb) ### Using iBridges -For instructions on how to use the `ibridges` command please see the [iBridges documentation](https://github.com/UtrechtUniversity/iBridges?tab=readme-ov-file#commandline-interface). \ No newline at end of file +To use iBridges on Yoda hosted by Utrecht University you will need a [data access password](https://www.uu.nl/en/research/yoda/using-data-access-passwords). + +#### Graphical user interface + +Once you have an `irods_environment.json`, click on `Connect` --> `Connect to iRODS`, choose your `irods_environment.json` and provide your data access password + +In the [iBridges GUI documentation](https://chstaiger.github.io/iBridges-Gui/docs/userdoc.html) + +#### Command line interface + +Simply try `ibridges --help` or `ibridges --help` to get examples and help for the usage. + +For instructions on how to use the `ibridges` command please see the [iBridges documentation](https://ibridges.readthedocs.io/en/stable/cli.html). + +#### Using the python package + +We offer [tutorials in form of Jupyter notebooks](https://github.com/UtrechtUniversity/iBridges/tree/main/tutorials) to show you the capabilities of the ibridges python package. + +For more information please see the [iBridges documentation](https://ibridges.readthedocs.io/en/stable/) diff --git a/docs/onboarding.qmd b/docs/onboarding.qmd index b3697b6..060c973 100644 --- a/docs/onboarding.qmd +++ b/docs/onboarding.qmd @@ -58,7 +58,7 @@ This will be done for you by the UU support team after intake meeting (step 1). ::: {.callout-note collapse="true"} ## What is SRAM? -SRAM (SURF Research Access Management) is a service to manage access to research resources, intended for Dutch led research collaborations. [More information](https://servicedesk.surf.nl/wiki/display/WIKI/SURF+Research+Access+Management). +SRAM (SURF Research Access Management) is a service to manage access to research resources, intended for Dutch led research collaborations. [More information](https://servicedesk.surf.nl/wiki/display/IAM/SURF+Research+Access+Management). ::: ::: {.callout-note collapse="true"} @@ -115,7 +115,7 @@ Perform step 1, 2(optional), and 3 ### 1. Invite a new collaborator -SRAM is used for access management for SURF Research Cloud. It is possible to [invite collaborators to your collaboration (project)](https://servicedesk.surf.nl/wiki/display/WIKI/Invite+admins+and+members+to+a+collaboration) +SRAM is used for access management for SURF Research Cloud. It is possible to [invite collaborators to your collaboration (project)](https://servicedesk.surf.nl/wiki/display/IAM/Invite+admins+and+members+to+a+collaboration) ::: {.callout-note collapse="true"} ## Who can I invite? @@ -124,10 +124,10 @@ It is possible to invite anyone who has an email address to join your project. S ::: ### 2. Workspace admins -In SRAM there are [groups](https://servicedesk.surf.nl/wiki/display/WIKI/Manage+groups+of+collaboration+members) that can be used to grant members of your collaboration to the right to [pause, resume and delete workspaces](https://servicedesk.surf.nl/wiki/display/WIKI/Sharing+control%3A+workspace+admin) +In SRAM there are [groups](https://servicedesk.surf.nl/wiki/display/IAM/Manage+groups+of+collaboration+members) that can be used to grant members of your collaboration to the right to [pause, resume and delete workspaces](https://servicedesk.surf.nl/wiki/display/WIKI/Sharing+control%3A+workspace+admin) ### 3. Share your wallet -In SRAM there are [groups](https://servicedesk.surf.nl/wiki/display/WIKI/Manage+groups+of+collaboration+members) that can be used to grant members of your collaboration to the right to [create new workspaces using the wallet of your project](https://servicedesk.surf.nl/wiki/display/WIKI/Access+to+project+wallet) +In SRAM there are [groups](https://servicedesk.surf.nl/wiki/display/IAM/Manage+groups+of+collaboration+members) that can be used to grant members of your collaboration to the right to [create new workspaces using the wallet of your project](https://servicedesk.surf.nl/wiki/display/WIKI/Access+to+project+wallet) ## Next When your collaboration and wallet is ready, see this page for [first steps](first-steps.qmd). diff --git a/docs/privacy.qmd b/docs/privacy.qmd index 2db7115..b401bf2 100644 --- a/docs/privacy.qmd +++ b/docs/privacy.qmd @@ -10,7 +10,7 @@ The Utrecht University Privacy Statement is applicable: In addition to the UU Privacy Statement, the following privacy policies at SURF are applicable: - [SURF Research Cloud Privacy Policy](https://servicedesk.surf.nl/wiki/display/WIKI/SRC+Acceptable+Use+Policy#SRCAcceptableUsePolicy-4-Personaldataandprivacy) -- [SURF SRAM Privacy Policy](https://servicedesk.surf.nl/wiki/display/WIKI/Privacy+Policy) +- [SURF SRAM Privacy Policy](https://servicedesk.surf.nl/wiki/display/IAM/Privacy+Policy) By accepting this invitation, users agree to adhere to the terms and conditions in the documents listed above. diff --git a/docs/research-cloud-intro.qmd b/docs/research-cloud-intro.qmd index ca79966..089e1ae 100644 --- a/docs/research-cloud-intro.qmd +++ b/docs/research-cloud-intro.qmd @@ -56,7 +56,7 @@ SURF Research Cloud uses the concept of a 'collaboration' to facilitate working A collaboration may be viewed as a *virtual* organization, with members that can originate from different research institutes, or from the private sector. A collaboration can accommodate a virtual organization the size of a European research project consortium. In contrast, it might also consist of a single member, e.g. a researcher in need of compute power or a private workspace. -Managing memberships of the collaboration is done via a self-service portal (called [SRAM](https://servicedesk.surf.nl/wiki/display/WIKI/SURF+Research+Access+Management), +Managing memberships of the collaboration is done via a self-service portal (called [SRAM](https://servicedesk.surf.nl/wiki/display/IAM/SURF+Research+Access+Management)), short for SURF Research Access Management. For example, a researcher can give (temporary) access to PhDs or students. It is important to understand that SRC assumes all members of the collaboration to be diff --git a/docs/terms-of-use.qmd b/docs/terms-of-use.qmd index 6158dfa..07c509f 100644 --- a/docs/terms-of-use.qmd +++ b/docs/terms-of-use.qmd @@ -11,7 +11,7 @@ The Virtual Research Environment (VRE) service of Utrecht University is based on In addition to the UU terms of use, the following Acceptable Use policies at SURF are applicable: - [SURF Research Cloud Acceptable Use Policy](https://servicedesk.surf.nl/wiki/display/WIKI/SRC+Acceptable+Use+Policy) -- [SURF SRAM Acceptable Use Policy](https://servicedesk.surf.nl/wiki/display/WIKI/Acceptable+Use+Policy) +- [SURF SRAM Acceptable Use Policy](https://servicedesk.surf.nl/wiki/display/IAM/Acceptable+Use+Policy) The [VRE Privacy Policy](privacy.qmd) is also applicable.