bd2kccd / ccd-annotations

Annotations API

CCD Annotations

CCD Annotations API

Building

Dependencies

• CCD DB v0.6.3
• CCD OAuth2 v1.3.4

All commands shown use the included Gradle wrapper executable. If you want to run a command with your system's Gradle installation, replace ./gradlew with gradle. This option requires Gradle version 3.1 or greater.

If you are using Windows, there is a Gradle batch script included (gradlew.bat). You may also use your system's Gradle installation following the requirement(s) as stated above.

Build
To build CCD Annotations: ./gradlew clean build.
To update documentation: ./gradlew asciidoctor.

Install
To install CCD Annotations to your your local maven repository: ./gradlew install

Customizing

You may edit the application.properties file in src/main/resources/ to change the server settings and select a database (HSQLDB or MySQL). Additionally, edit the appropriate properties file to change database settings.

Running

To start the server with documentation, ./gradlew start. This is a custom command that is identical to the following: ./gradlew build asciidoctor; java -jar build/libs/ccd-annotations-0.8.0.jar.

Other

To view a list of all available Gradle tasks with descriptions: ./gradlew tasks.

ccd-annotations's Issues

Remove security

Remove security and replace with Causal-Web's AppUser. Secured endpoints should use Causal-Web's secured/ path.

Incorrect db column size

@marksilvis I noticed an error when testing the updated annotation against changes that @kvb2univpitt made in causal web.

I couldn't add text with more than 255 characters.

According to @kvb2univpitt, in the ccd-db v0.6.3 branch, it needs to specify the size of the string field as text, otherwise it uses varchar(255) in MySQL.

https://github.com/bd2kccd/ccd-db/blob/v0.6.3/src/main/java/edu/pitt/dbmi/ccd/db/entity/AnnotationData.java#L58

Annotation error caused by file name

@marksilvis there's a small bug I noticed when testing the annotation service on ccd4. I uploaded a dataset file named "data_%20.txt" and after adding a new annotation, I had to refresh the page to see it being added. And my debugger says a 500 error as well. It must be caused by the file name since there's a percentage sign. I discovered similar issue with Causal Web and @kvb2univpitt has fixed that by encoding the file name in the request and decode it later.

Click the screenshot to view full size version.

Update developer documentation

The API documentation is lacking. It will be added to the ccd-docs project.

JWT authentication

Switch the REST API from OAuth2.0 to JWT for user authentication.

Base/REST controller separation

Add base controllers that return a view/template. REST controllers return JSON to update views.

Annotation size limit

There should be an error response when an annotation is created that is too large (> 1000 characters).

Add to Causal-Web 2.0

This should be moved to Causal-Web 2.0. Ideally, ccd-annotations will remain a separate dependency, however, this might not be possible due to requiring shiro authentication and Causal-Web's AppUser class for authorization.