Tutorial on using CellML with Auckland Physiome Repository¶
About this tutorial¶
The Auckland Physiome Repository provides extensive support for CellML model and related files. Previously it was called the CellML Model Repository, this has since been merged completely along with the FieldML Model Repository into the unified repository. The underlying software is PMR2, which in turn relies on the distributed version control system Git, which allows the repository to maintain a complete history of all changes made to every file it contains. This tutorial demonstrates how to work with the repository using TortoiseGit, which provides a Windows explorer integrated system for working with Git repositories.
Brief mention of the equivalent command line versions of the TortoiseGit actions will also be mentioned, so that these ideas can also be used without a graphical client, and on Linux and similar systems. These will be denoted by boxes like this.
This tutorial requires you to have:
The Auckland Physiome Repository use a certain amount of jargon - some is specific to the repository software, and some is related to distributed version control systems (DVCSs). Below are basic explanations of some of these terms as they apply to the repository.
A container (much like a folder or directory on your computer) to hold the files that make up a model, as well as any other files such as documentation or metadata, etc. In practical terms, each workspace is a Git repository.
An exposure is a publicly viewable presentation of a particular revision of a model. An exposure can present one or many files from your workspace, along with documentation and other information about your model.
The Git DVCS has a range of terms that are useful to know, and definitions of these terms can be found in the Git Reference http://git-scm.com/docs.
Working with the repository web interface¶
This part of the tutorial will teach you how to find models in the Auckland Physiome Repository https://models.physiomeproject.org, how to view a range of information about those models, and how to download models. The first page in the repository consists of basic navigation, a link to the main model listing, a search box at the top right, and a list of model category links as shown below.
Clicking on the main model listing or any of the category listings will take you to a page displaying a list of exposed models in that category. Click on electrophysiology for example, and a list of over 100 exposed models in that category will be displayed, as shown here.
Clicking on an item in the list will take you to the exposure page for that model.
Searching the repository¶
You can search for the model that you wish to work on by entering a search term in the box at the top right of the page. Many of the models in the repository are named by the first author and publication date of the paper, so a good search query might be something like goldbeter 1991. A list of the results of your search will probably contain both workspaces and exposures - you will need to click on the workspace of the model you wish to work on. Workspaces can be identified by where they are located, as they will be located inside Workspaces. In the following screenshot, the first two results are workspaces, and the remainder are exposures. Note that red links are exposures that are marked as expired.
Click on an exposure result to view information about the model and to get links for downloading or simulating the model. Click on workspaces to see the contents of the model workspace and the revision history of the model.
Working with the repository using Git¶
This part of the tutorial will teach you how to clone a workspace from the model repository using a Git client, create your own workspace, and then push the cloned workspace into your new workspace in the repository. We will be using a fork of an existing workspace, which provides you with a personal copy of a workspace that you can edit and push changes to.
Registering an account and logging in¶
The teaching instance of the repository is a mirror of the main repository site found at https://teaching.physiomeproject.org/, running the latest development version of PMR2. User accounts are periodicly synchronised from the main repository, but if you recently created an account on the main site you might need to also create a new account on the teaching instance.
Any changes you make to the contents of the teaching instance are not permanent, and will be overwritten with the contents of the main repository whenever the teaching instance is upgraded to a new release of PMR2. For this reason, you can feel free to experiment and make mistakes when pushing to the teaching instance. Please subscribe to the cellml-discussion mailing list to receive notifications of when the teaching instance will be refreshed.
See the section Migrating content to the main repository for instructions on how to migrate any content from the teaching instance to the main (permanent) Auckland Physiome Repository.
In order to make changes to models in the CellML repository, you must first register for an account. Your account will have the appropriate access privileges so that you can push any changes you have made to a model back into the repository.
To register an account, access the Log in link and access the registration form from there. Enter your desired username and password. After completing the email validation step, you can now log in to the repository.
This username and password are also the credentials you use to interact with the repository via Git.
Once logged in to the repository, you will notice that there is a new link in the navigation bar, My Workspaces. This is where all the workspaces you create later on will be listed. The Log in link is also replaced by your username and a Log out link.
Git username configuration¶
Username setup for Git
Since you are about to make changes, your name and email address must be recorded as part of the workspace revision history. When commit your changes using Git, they exist independently from the Auckland Physiome Repository. This means that you have to set-up your username for the Git client software, even though you have registered a username on Auckland Physiome Repository.
You only need to do this once.
Steps for TortoiseGit:
- From the right-click menu in Windows Explorer (which is accessible by right-clicking anywhere on the file selection area) you can select the Settings by .
- On the settings screen, under the Git section, enter your details into the respective sections.
Steps for command line:
The configurations are saved in the
.gitconfigfile in the user’s home directory, and the recommended way to do so is:$ git config --global user.name "<Your Name>" $ git config --global user.email "<Your Email address>"
Forking an existing workspace¶
It is essential to use a Git client to obtain models from the repository for editing. The Git client is not only able to keep track of all the changes you make (allowing you to back-track if you make any errors), but using a Git client is the only way to add any changes you have made back into the repository.
For this tutorial we will fork an existing workspace. This creates new workspace owned by you, containing a copy of all the files in the workspace you forked including their complete history. This is equivalent to cloning the workspace, creating a new workspace for yourself, and then pushing the contents of the cloned workspace into your new workspace.
Forking a workspace can be done using the Physiome Model Repository web interface. The first step is to find the workspace you wish to fork. We will use the Beeler, Reuter 1977 workspace which can be found at: https://teaching.physiomeproject.org/workspace/beeler_reuter_1977.
Now click on the fork option in the toolbar, as shown below.
You will be asked to confirm the fork action by clicking the Fork button. You will then be shown the page for your forked workspace.
Cloning your forked workspace¶
In order to make changes to your workspace, you have to clone it to your own computer. In order to do this, copy the URI for Git clone/pull/push as shown below:
In Windows explorer, navigate the folder where you want to create the clone of the workspace. Then use the right-click menu and selectas shown below:
Paste the copied URL into the Source: area and then click the Clone
button. This will create a folder called
contains all the files and history of your forked workspace. The folder
will be created inside the folder in which you instigated the clone
Command line equivalent
git clone [URI]
You will need to enter your username and password to clone the workspace, as the fork will be set to private when it is created.
The repository will be cloned within the current directory of your command line window.
Making changes to workspace contents¶
Your cloned workspace is now ready for you to edit the model file and make a commit each time you want to save the changes you have made. As an example, open the model file in your text editor and remove the paragraph which describes validation errors from the documentation section, as shown below:
Save the file. If you are using TortoiseGit, you will notice that the icon overlay has changed to a red exclamation mark. This indicates that the file now has uncommitted changes.
If you are using TortoiseGit, bring up the shell menu for the altered file and select. A window will appear showing details of the changes you are about to commit, and prompting for a commit message. Every time you commit changes, you should enter a useful commit message with information about what changes have been made. In this instance, something like “Removed the paragraph about validation errors from the documentation” is appropriate.
Click on the Commit button at the far left of the toolbar. The icon overlay for the file will now change to a green tick, indicating that changes to the file have been committed.
Command line equivalent
git commit -m "Removed the paragraph about validation errors from the documentation"
Pushing changes to the repository¶
Your cloned workspace on your local machine now has a small history of changes which you wish to push into the repository.
Right click on your workspace folder in Windows explorer, and selectfrom the shell menu. This will bring up a window from which you can manage changes to the workspace in the repository. Click on the Push button in the toolbar, and enter your username and password when prompted.
Command line equivalent
Now navigate to your workspace and click on the history toolbar button. This will show entries under the Most recent changes, complete with the commit messages you entered for each commit, as shown below:
Create an exposure¶
As explained earlier, an exposure aims to bring a particular revision to the attention of users who are browsing and searching the repository.
There are two ways of making an exposure - creating a new exposure from scratch, or “Rolling over” an exposure. Rolling over is used when a workspace already has an existing exposure, and the updates to the workspace have not fundamentally changed the structure of the workspace. This means that all the information used in making the previous exposure is still valid for making a new exposure of a more recent revision of the workspace. Strictly speaking, an exposure can be rolled over to an older revision as well, but this is not the usual usage.
As you are working in a forked repository, you will need to create a new exposure from scratch. To learn how to create exposures, please refer to Creating CellML exposures.
Migrating content to the main repository¶
As noted above, the teaching instance used in this tutorial is not suitable for permanent storage of your work. One of the advantages of using a distributed version control system to manage workspaces is that it is straightforward to move the entire workspace, including the full history and provenance record, from one location to another. PMR2 also provides a feature that exports exposures so that they can then be imported into another PMR2 instance.
For example: if you would like to move your work from any publicly accessible Git repository (such as a published workspace on the teaching repository or a public repository on GitHub.com) to a new workspace on the Auckland Physiome Repository, you should follow these steps:
- Ensure that you have pushed all your commits to the source instance;
- Create the new workspace in the destination repository;
- Navigate to the workspace created and choose the synchronize action from the workspace toolbar, as shown below.
- Fill in the URI of your workspace on the source instance (e.g., https://teaching.physiomeproject.org/w/andre/cortassa-ECME-2006)
- Click the Synchronize button.
If you would like to move your work from a private workspace on the teaching instance (or any non-publicly accessible Git repository), you will need to use your Git client to directly push your repository up to the newly created workspace. This is because you will need to make use of the relevant authentication to access the private workspace or repository.
In a similar manner, you are able to copy exposures you might have made on the teaching instance over to the main repository, or from the main to the teaching instance if you want to test things out. Follow these steps to migrate an exposure from one repository to another.
- Navigate to the exposure you would like to migrate in the source repository.
- Choose the wizard item from the toolbar as shown below.
- In the destination repository, navigate to the desired revision of the (published) workspace and choose the Create exposure action as described in the directions for creating an exposure from scratch
- Rather than building a new exposure, choose the Exposure Import via URI tab in the exposure creation wizard, as shown below.
- Copy and paste the URI from the source exposure wizard, highlighted above, into the Exposure Export URI field in the exposure creation wizard shown above.
- Click the Add button. This will take you back to the standard exposure build page, but now with all the fields pre-populated from the source exposure.
- Navigate to the bottom of the page and click the Build button to actually build the exposure pages. You are free to reconfigure the exposure if desired, some help is available for this if needed.