If you just followed the steps in Development Environment for the first time, you will need to get set up to deploy code to Glassfish. Below you’ll find other tips as well.
Contents:
When you followed the steps in the Development Environment section, the war file was deployed to Glassfish by the install 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 Glassfish.
It’s certainly possible to manage deployment and undeployment of the war file via the command line using the asadmin command that ships with Glassfish (that’s what the install script uses and the steps are documented below), but we recommend getting set up with and IDE such as Netbeans to manage deployment for you.
install Script¶Because the initial deployment of the war file was done outside of Netbeans by the install script, it’s a good idea to undeploy that war file to give Netbeans a clean slate to work with.
Assuming you installed Glassfish in /usr/local/glassfish4, run the following asadmin command to see the version of Dataverse that the install script deployed:
/usr/local/glassfish4/bin/asadmin list-applications
You will probably see something like dataverse-4.8.5 <ejb, web> as the output. To undeploy, use whichever version you see like this:
/usr/local/glassfish4/bin/asadmin undeploy dataverse-4.8.5
Now that Glassfish doesn’t have anything deployed, we can proceed with getting Netbeans set up to deploy the code.
Dataverse only works with a specific version of Glassfish (see https://github.com/IQSS/dataverse/issues/2628 ) so you need to make sure Netbeans is deploying to that version rather than a newer version of Glassfish that may have come bundled with Netbeans.
Launch Netbeans and click “Tools” and then “Servers”. Click “Add Server” and select “Glassfish Server” and set the installation location to /usr/local/glassfish4. The default are fine so you can click “Next” and “Finish”. If you are running Netbeans 8.2 and there is already a bundled version of Glassfish, you should probably remove it because (again) you need a specific version of Glassfish (4.1 as of this writing).
Please note that if you are on a Mac, Netbeans may be unable to start Glassfish 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 Glassfish using Netbeans. Click “Window” and then “Services”. Expand “Servers” and right-click Glassfish to stop and then start it so that it appears in the Output window. Note that you can expand “Glassfish” 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 Glassfish 4.1. 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):
scripts/installer/custom-build-number hello
This should update or place a file at src/main/java/BuildNumber.properties.
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:
curl http://localhost:8080/api/info/version
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 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.)
Back in the Development Environment section, we had you install pgAdmin, which can help you explore the tables and execute SQL commands. It’s also listed in the Tools 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 scripts/deploy/phoenix.dataverse.org/post
To read more about the phoenix server, see the Testing section.
asadmin¶Sometimes you want to deploy code without using Netbeans or from the command line on a server you have ssh’ed into.
For the asadmin commands below, we assume you have already changed directories to /usr/local/glassfish4/glassfish/bin or wherever you have installed Glassfish.
There are four steps to this process:
mvn package./asadmin list-applications./asadmin undeploy dataverse-VERSION./asadmin deploy /path/to/dataverse-VERSION.warinstall Script in Non-Interactive Mode¶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.
Once some dataverses, 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 .git/hooks/post-checkout and .git/hooks/post-commit to scripts/installer/custom-build-number-hook
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 installation(s) of Dataverse with sample data. You have a couple options:
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