Protocol Model in Beta-4

The way that the Beta-4 OMERO.editor models protocols has changed since the Beta-3 release.

"Common Protocol Exchange" format (.cpe.xml file)

The Beta-4 OMERO.editor uses a file format (called CPE) that has been designed in collaboration with developers of other  protocol-editing software, allowing protocol files to be exchanged between users of the two tools. In the Beta-3 OMERO.editor, a protocol was described as a hierarchy of "Fields" and each field stored a single variable. In Beta-4, Fields are now termed "Steps" and Steps can contain multiple "parameters". When a Beta-3 file (".pro.xml") is opened in the Beta-4 Editor, it's Fields are represented as Steps with a single parameter each. Parameters can also be 'in context' with the step's description, as described here. Example CPE files can be viewed and downloaded on the  demo files page. These files will be formatted by the browser for display, so you will see a "pretty" version of the file, and not the "raw" XML. To see the XML of the files in your browser, go to View > Source.

The Beta-4 Editor software was completely re-written to become part of Insight. This has meant that some features in the Beta-3 editor have not yet been rebuilt in the Beta-4 Editor, but will be in due course. Other, more experimental, features have been removed with no plans to re-introduce them unless there is reasonable demand/justification.

Beta-3 Features not yet in Beta-4

These are features that have not yet made the transition to the Beta-4.0 Editor, but we intend to support this functionality again in the future.

• Locking steps. The ability to prevent someone from editing parts of the "Protocol", while still allowing editing of "Experimental values".
• 'Required' parameters. This is currently supported in the data model, so any 'required' fields from Beta-3 files will be stored and displayed, but you can't yet edit this in Beta-4.
• 'Find' function, to search for particular words in a currently opened file.

Beta-3 Features changed

In some cases, the data will be preserved but presented in a slightly different way.

• "Table" fields. Tabular data is now represented by creating a table from a number of parameters. Each parameter defines one column of the table. This allows you to present Text, "Drop-down menu" and "Check-box" parameters in tables. Table data from Beta-3 files is converted into this new format in the Beta-4 Editor.
• Links to files, urls and images. In the CPE file format, these are considered "Data Links", that link to some data generated by a particular step in the protocol. You can add a data-link using the "Add Parameter" button in the RIGHT panel of the Editor.

Beta-3 Features removed

• Background colour.
• Timer field. No "countdown" feature.
• Calendar. The web client has a calendar powered by events from the OMERO server, and it's possible that the Editor/Insight client will get a calendar at some point, but this wasn't considered a priority for Beta-4.
• 'Relative' dates. As with the Timer field, these are now represented as "Number Parameters" eg 4 days.
• 'Search' function, for a Google-like search of Editor files in you file system. This functionality is being developed in the OMERO server, so it will not be replicated in the Beta-4 Editor, including the standalone Editor.