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I ran into this same issue when trying to use charts in Workspaces. I found that some queries made charts with the Group By attribute set in the query via the console without fuss. However, I would create another query try to create another chart and without reason, the designer not only did not use the Group By set in the original query, but it only allowed a small set of attributes to use to group the query. I believe I have found a work around.
In the Dashboard Designer, create the query as a chart, if you run into this issue, select the gadget type as a Data Grid. Uncheck "Group Query Results", you should see that the designer is now picking up the original Group By attribute set in the console. Select Gadget Type again, Select your chart as you did before, but now you should notice that the designer no longer gives the option to select a Group By attribute and instead will be using the original Group By attribute set in the console.
This is obviously a bug related to the designer no picking up the original Group By attribute under certain conditions and assuming you are trying to make a chart from a query without a Group By attribute set. Why it gives a only a small subset of attributes to group by I have no idea, but this work around seems to be enough to get around it in the meantime.
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