If you just followed the steps in Development Environment for the first time, you will need to get set up to deploy code to your app server. Below you’ll find other tips as well.
When you followed the steps in the Development Environment section, the war file was deployed to Payara by the Dataverse Software installation script. That’s fine but once you’re ready to make a change to the code you will need to get comfortable with undeploying and redeploying code (a war file) to Payara.
It’s certainly possible to manage deployment and undeployment of the war file via the command line using the
asadmin command that ships with Payara (that’s what the Dataverse Software installation script uses and the steps are documented below), but we recommend getting set up with an IDE such as Netbeans to manage deployment for you.
Because the initial deployment of the war file was done outside of Netbeans by the Dataverse Software installation script, it’s a good idea to undeploy that war file to give Netbeans a clean slate to work with.
Assuming you installed Payara in
/usr/local/payara5, run the following
asadmin command to see the version of the Dataverse Software that the Dataverse Software installation script deployed:
You will probably see something like
dataverse-5.0 <ejb, web> as the output. To undeploy, use whichever version you see like this:
/usr/local/payara5/bin/asadmin undeploy dataverse-5.0
Now that Payara doesn’t have anything deployed, we can proceed with getting Netbeans set up to deploy the code.
Launch Netbeans and click “Tools” and then “Servers”. Click “Add Server” and select “Payara Server” and set the installation location to
/usr/local/payara5. The defaults are fine so you can click “Next” and “Finish”.
Please note that if you are on a Mac, Netbeans may be unable to start Payara due to proxy settings in Netbeans. Go to the “General” tab in Netbeans preferences and click “Test connection” to see if you are affected. If you get a green checkmark, you’re all set. If you get a red exclamation mark, change “Proxy Settings” to “No Proxy” and retest. A more complicated answer having to do with changing network settings is available at https://discussions.apple.com/thread/7680039?answerId=30715103022#30715103022 and the bug is also described at https://netbeans.org/bugzilla/show_bug.cgi?id=268076
At this point you can manage Payara using Netbeans. Click “Window” and then “Services”. Expand “Servers” and right-click Payara to stop and then start it so that it appears in the Output window. Note that you can expand “Payara” and “Applications” to see if any applications are deployed.
Click “Window” and then “Projects”. Click “File” and then “Project Properties (dataverse)”. Click “Run” and change “Server” from “No Server Selected” to your installation of Payara. Click OK.
Let’s make a tiny change to the code, compile the war file, deploy it, and verify that that we can see the change.
One of the smallest changes we can make is adjusting the build number that appears in the lower right of every page.
From the root of the git repo, run the following command to set the build number to the word “hello” (or whatever you want):
This should update or place a file at
Then, from Netbeans, click “Run” and then “Clean and Build Project (dataverse)”. After this completes successfully, click “Run” and then “Run Project (dataverse)”
After deployment, check the build number in the lower right to make sure it has been customized. You can also check the build number by running the following command:
If you can see the change, great! Please go fix a bug or work on a feature! :)
Actually, before you start changing any code, you should create a branch as explained in the Version Control section.
While it’s fresh in your mind, if you have any suggestions on how to make the setup of a development environment easier, please get in touch!
For faster iteration while working on JSF pages, it is highly recommended that you install the Netbeans Connector Chrome Extension listed in the Tools section. When you save XHTML or CSS files, you will see the changes immediately. Hipsters call this “hot reloading”. :)
With over 100 tables, the Dataverse Software PostgreSQL database (“dvndb”) can be somewhat daunting for newcomers. Here are some tips for coming up to speed. (See also the SQL Upgrade Scripts section.)
SchemaSpy is a tool that creates a website of entity-relationship diagrams based on your database.
As part of our build process for running integration tests against the latest code in the “develop” branch, we drop the database on the “phoenix” server, recreate the database by deploying the latest war file, and run SchemaSpy to create the following site: http://phoenix.dataverse.org/schemaspy/latest/relationships.html
To run this command on your laptop, download SchemaSpy and take a look at the syntax in
To read more about the phoenix server, see the Testing section.
Sometimes you want to deploy code without using Netbeans or from the command line on a server you have ssh’ed into.
asadmin commands below, we assume you have already changed directories to
/usr/local/payara5/glassfish/bin or wherever you have installed Payara.
There are four steps to this process:
Build the war file:
Check which version of the Dataverse Software is deployed:
Undeploy the Dataverse Software (if necessary):
./asadmin undeploy dataverse-VERSION
Copy the war file to the server (if necessary)
Deploy the new code:
./asadmin deploy /path/to/dataverse-VERSION.war
Rather than running the installer in “interactive” mode, it’s possible to put the values in a file. See “non-interactive mode” in the Installation section of the Installation Guide.
By default, Glassfish reports analytics information. The administration guide suggests this can be disabled with
./asadmin create-jvm-options -Dcom.sun.enterprise.tools.admingui.NO_NETWORK=true, should this be found to be undesirable for development purposes. It is unknown if Payara phones home or not.
Once some Dataverse collections, datasets, and files have been created and indexed, you can experiment with searches directly from Solr at http://localhost:8983/solr/#/collection1/query and look at the JSON output of searches, such as this wildcard search: http://localhost:8983/solr/collection1/select?q=*%3A*&wt=json&indent=true . You can also get JSON output of static fields Solr knows about: http://localhost:8983/solr/collection1/schema/fields
You can simply double-click “start.jar” rather that running
java -jar start.jar from the command line. Figuring out how to stop Solr after double-clicking it is an exercise for the reader.
You can use git with passwords over HTTPS, but it’s much nicer to set up SSH keys. https://github.com/settings/ssh is the place to manage the ssh keys GitHub knows about for you. That page also links to a nice howto: https://help.github.com/articles/generating-ssh-keys
From the terminal,
ssh-keygen will create new ssh keys for you:
~/.ssh/id_rsa- It is very important to protect your private key. If someone else acquires it, they can access private repositories on GitHub and make commits as you! Ideally, you’ll store your ssh keys on an encrypted volume and protect your private key with a password when prompted for one by
ssh-keygen. See also “Why do passphrases matter” at https://help.github.com/articles/generating-ssh-keys
~/.ssh/id_rsa.pub- After you’ve created your ssh keys, add the public key to your GitHub account.
On a Mac, you won’t have git installed unless you have “Command Line Developer Tools” installed but running
git clone for the first time will prompt you to install them.
You can create symbolic links from
to let Git automatically update
src/main/java/BuildNumber.properties for you. This will result in showing branch name and
commit id in your test deployment webpages on the bottom right corner next to the version.
When you prefer manual updates, there is another script, see above: Make a Small Change to the Code.
You may want to populate your non-production Dataverse installations with sample data. You have a couple options:
Code in https://github.com/IQSS/dataverse-sample-data (recommended). This set of sample data includes several common data types, data subsetted from production datasets in dataverse.harvard.edu, datasets with file hierarchy, and more.
Scripts called from