VIFF (XML) Version History

The objects that we write to [wiki:VIFF] embed a version string so that when we need to change the VIFF format, our code can tell the difference between the new and old formats. Note that the version string is associated with individual elements (e.g. experiments, pulse projects, etc.); there is not one monolithic VIFF version. The version numbers for one object's format can change indepdendently of the others.

Once a VIFF version is released "into the wild", we have to support it forever.

This document describes the differences from one VIFF version to another. As of this writing (July 2011), only experiments and simulations have changed from their original version (1.0.0).

Experiments and Simulations

VIFF Version 1.0.0

Used in Vespa < 0.2.4.

Vespa < 0.1.6 didn't write version info on anything but the root element (vespa_export).

Here's an example of [browser:/trunk/common/resources/experiments.xml?rev=2000 experiments.xml with versions on the subelements] and [browser:/trunk/common/resources/experiments.xml?rev=1739 one without (as used in Vespa < 0.1.6).]

VIFF Version 1.1.0

Used in Vespa >= 0.2.4.

In VIFF 1.1.0, simulations are much more compact.

In VIFF 1.0.0, the following is true –

1. Each simulation element is a direct child of the experiment element.
2. Each simulation element has a version attribute so the string version="1.0.0" repeats for each simulation (which is just a waste of space).
3. Each simulation element has a spectrum element that contains 0 or more line elements. Each line contains a ppm, area and phase element each of which in turn contains a single float.

In 1.1.0, here's how those change.

1. We added a layer between the experiments element and the simulations in the form of a simulations element. Contrast –

   Version 1.0.0 —

    <experiment version="1.0.0">
        <simulation version="1.0.0">
            ...
        </simulation>
        <simulation version="1.0.0">
            ...
        </simulation>
        <simulation version="1.0.0">
            ...
        </simulation>
   

   Version 1.1.0 –

    <experiment version="1.1.0">
        <simulations version="1.1.0">
            <simulation>
                ...
            </simulation>
            <simulation>
                ...
            </simulation>
            <simulation>
                ...
            </simulation>
        </simulations>
   

   The simulations element serves two purposes. First, it gives us a place to store the VIFF version without repeating it on every simulation. Second, gives XML text editors a tag they can fold to hide the simulations.

2. As shown above, the XML version moved from the simulation elements to the simulations element.

3. We did away with the spectrum element entirely by representing the ppm, area and phase info as encoded arrays and making them subelements of the spectrum element.

   Version 1.0.0 —

    <experiment version="1.1.0">
        <simulation version="1.0.0">
            <started>2011-01-24T11:00:00</started>
            <completed>2011-01-24T11:00:00</completed>
            <metabolite_id>f03efaa3-d686-41db-8df2-8a2e450f596b</metabolite_id>
            <dim>0.0</dim>
            <dim>0.0</dim>
            <dim>0.0</dim>
            <spectrum version="1.0.0">
                <line>
                    <ppm>3.185</ppm>
                    <area>3.0</area>
                    <phase>0.0</phase>
                </line>
            </spectrum>
        </simulation>
   

   Version 1.1.0 —

    <experiment>
        <simulations version="1.1.0">
            <simulation>
                <started>2011-01-24T11:00:00</started>
                <completed>2011-01-24T11:00:00</completed>
                <metabolite_id>f03efaa3-d686-41db-8df2-8a2e450f596b</metabolite_id>
                <dim>0.0</dim>
                <dim>0.0</dim>
                <dim>0.0</dim>
                <ppms data_type="float64" encoding="xdr zlib base64" shape="1">eNpz4Kx66L5OpBoADVEDKQ==</ppms>
                <areas data_type="float64" encoding="xdr zlib base64" shape="1">eNpz4GAAAwACQABJ</areas>
                <phases data_type="float64" encoding="xdr zlib base64" shape="1">eNpjYIAAAAAIAAE=</phases>
            </simulation>
        </simulations>
    </experiment>