Updating DERIVA catalog annotations via the DERIVA-Workbench

The DERIVA-Workbench is a desktop application with a graphical user interface for browsing and updating DERIVA catalog annotations.

1. Initial Setup

The first time you launch deriva-workbench, the application will ask you if you want to add a server configuration.

Add Connection Message

Click “yes” to bring up the “Configuration Options” dialog (you can also do this at any time by clicking the “Options” button at the top of the page).

Configuration Options Dialog

Click “Add” to bring up the “Server Configuration” form and enter the values provided by the DERIVA administrator.

Server Configuration Dialog

Enter the host name, a memorable description, and a catalog number. Select a directory location for dumping and restoring annotations. Optionally, check the box to “Set as Default” if you want to connect to this server and catalog by default on restart of the workbench. After clicking “OK” on the Server Configuration dialog, you must click “OK” again on the Configuration Options dialog to actually connect to the server.

2. Connect and Log In

At any time, you may return to the Options in order to add a new server + catalog configuration or to change the currently selected server from the drop down.

Toolbar Buttons Left

On normal startup or after changing the server through the Options dialog, the workbench will attempt to connect to the default server. If no authentication credential is available, you must login.

Toolbar Buttons Right

The login sequence will follow the usual flow that you experience through the DERIVA web application (e.g., Chaise) and other DERIVA desktop applications. You may also use the workbench in combination with the DERIVA-Authentication agent to maintain a persistent user credential to skip the login step in the DERIVA-Workbench.

3. Browsing a Schema

When connected and authenticated to a server, the left panel of the application will display a tree view of the catalog schema.

Schema Browser (Collapsed)

You may then navigate through the model by expanding each model element either by double-clicking on the label or on the chevron icon to the left of the label.

Schema Browser (Expanded)

4. Editing Annotations (Text-based)

Any annotation in the schema may be edited using an integrated JSON text editor. Double-clicking on the “annotations” label will open the JSON text editor with the full annotations document for the selected model object.

Annotation Editor (JSON)

At present, malformed JSON will simply be ignored. The editor will only change the underlying annotation if the text entered can be parsed without errors. While editing, the annotations document you may add an annotation by adding the appropriate key and body or remove an annotation by removing its key and body from the document.

5. Editing Annotations (Graphically)

The workbench currently provides enhanced support for several key annotations, including visible-columns, visible-foreign-keys, source-definitions, table-display, citation, display, foreign-key, asset, key-display, and column-display. For all other annotations, the workbench will fall back to the JSON editor.

a. Editing visible-columns

You will find a tab for each known context in the annotation. Each tab contains a table of the configured columns. The X next to the context name in the tab allows you to delete the context, but you will be asked for confirmation before it proceeds. In order to create a new context, switch to the <create> tab, enter a unique name, and click Add.

Visible-Columns Contexts

Click on a row in the table, and use the - button to remove the visible column, use the up button to move it up in the order, down to move it down in the order, or use copy to make a duplicate of the visible column.

To add a visible column click the + button beneath the table of visible columns. This will open the “Add Visible Source Entry” dialog. From this dialog you may select the type of visible column from Column, Constraint, or Pseudo-Column. The values for the Constraint type entries include primary keys and outbound foreign keys for the containing table for the annotation. Shown in the dialog is a hypothetical visible column based on a source entry that follows a foreign key path and terminates in a column name.

Add Visible Column

To edit a visible column, double click on a row in the table and the “Edit Visible Source” dialog will be opened.

b. Editing visible-foreign-keys

The primary difference from visible-columns is that visible-foreign-keys entries (a) do not allow Column type entries, and (b) the Constraint type entries are of inbound foreign keys to the present table.

Add Visible FKey

c. Editing source-definitions

The source-definitions editor allows you to define new “sources” that can be used by referencing their respective source key in other annotations like visible-columns or in templating environments used in various other annotations such as citation.

You may add All or a select subset of columns (Columns) or foreign keys (FKeys) to be made available in templating environments, along with the sources (Sources).


In the middle “Sources” section, you may define new sources. The Source Definition dialog differs subtly from the add/edit visible sources dialog. A source definition requires that you enter a unique Source Key. Sources may be added (+), removed (-), and duplicated (copy) with the respective buttons below the Sources table.


(Note: some of the fields in the dialog are not useful for defining a new source and will be removed in subsequent development previews.)

Finally, the special search-box source may be defined by adding columns. The search columns may be added (+) or (-) removed using the respecitve buttons below the Search Box table.

d. Editing table-display

The table-display annotation makes use of display contexts like the visible- sources annotations. Each context allows definition of its Row Order as an ordered sequence of columns with optional ‘descending’ modifier. The Markdown Patterns may be Page or some combination of Row, row Separator, Prefix, and Suffix. For a complete description, see the annotation guide.

Table Display

e. Editing citation

The citation editor allows entry of markdown patterns, selection of template engine, and the optional sources to “Wait For” at bottom.


f. Editing display

The display editor allows entry of display names, display modifiers, comments, null handling directives, and foriegn key presentation instructions.


g. Editing foreign-key

The foreign-key annotation editor allows entry of to and from direction names and comments, the domain_filter property, and the contextualized display property that allows modiviation of the sorting and link display behavior. The editor will update the deprecated domain_filter_pattern property to the current format.

Foreign Key Annotation Editor

6. Adding or Removing Annotations (Graphically)

You may also add or remove annotations in the Schema Browser window using each annotation item’s context menu (typically, right-clicking on the item).

To add an annotation, go to the context menu for the annotations item for any model object (i.e., schema, table, column, key, foreign key). Select the “Add …” menu item for the desired annotation. Note that not all available annotations are applicable to all model objects. Please review the DERIVA Annotation Guide.

Add Annotation

To remove an annotation, open the context menu for the specific annotation by its tag:... item label in the schema browser. You will be asked to confirm before removing.

Remove Annotation

7. Updating Server-side Annotations

You may make any number of changes to annotations using the graphical editors or the JSON editor. Changes will only be updated on the server by pressing the Update toolbar button found in the upper left hand side of the workbench.

Update Button

Confirmation or errors will be reported in the log display panel at the bottom of the window.

8. Validating Catalog Annotations

You may validate annotations of any model object in the catalog. First, you must select a model object that contains an annotation resource (don’t select the annotations themselves but the schema, table, column, foreign key, etc. that contains them). Then click the “Validate” button in the toolbar.

Validate Summary Response

An initial dialog will indicate the count of errors found (above). To see the complete details, see the log display at the bottom of the application window (below). You can drag the log panel for better viewing.

Validate Detailed Output

9. Refresh From Server and Discard Local Changes

At any time, you may refresh the local copy of the catalog model, and potentially discard any changes that have not been updated on the remote server. To do so, use the “Refresh” button toward the left in the toolbar.

10. Dump and Restore Annotations To/From Files

You may dump and restore annotations to and from the local file system for any model object in the catalog. First, you must select a model object that contains an annotation resource.

Dump and Restore Actions

Then click on “Dump” to dump the annotations recursively to the “Dump and Restore Directory” configured for the server connection. Click on “Restore” to restore the annotations recursively from the configured directory. If a dump file is not found for a given model object in the hierarchy, that object will simply be skipped and an error message logged to the log window.

The directory hierarchy will resemble the structure seen in the Schema Browser window. Even if you select a single table, column, etc., the annotations will be saved in a directory structure according to the schema structure. Also, any non-word characters (aside from a-zA-Z0-9_) in the model element names will be replaced with _ characters. For example, % This Name! will be converted to __This_Name_. (Limitation: currently, name collisions are possible if you have model elements that only differ in non-word characters.)