Querying the Version Tree¶
VisTrails is designed for manipulating collections of workflows, and an integral part of this design is the ability to quickly search through these collections. VisTrails provides two methods for querying vistrails and workflows. The first is a Query by Example interface which allows you to build query workflows and search for those with similar structures and parameters. The second is a textual interface with a straightforward syntax. For each interface, the results are visual: each matching version is highlighted in the History view, and if the query involves specific workflow characteristics, any matching entities are also highlighted in the Pipeline view for the current version.
Query By Example¶
Example pipeline in Query mode.
One of the problems faced when trying to query a collection of workflows is the fact that structure is important. Suppose that you want to find only workflows where two modules are used in sequence. Instead of trying to translate this into a text-based syntax, it is easier to construct this relationship visually. VisTrails provides such an interface which mirrors the Pipeline view, allowing you to construct a (partial) workflow to serve as the search criteria.
To use the Query by Example interface, click on the Query button on the toolbar. This view is extremely similar to the Pipeline view and pipelines can be built in a similar manner. Just like the Pipeline view, modules are added by dragging them from the list on the left side of the window, connections are added by clicking and dragging from a port on one module to a corresponding port on another module. Figure Example pipeline in Query mode. shows an example pipeline that has been built in the query builder.
Query results in the History view.
The results in the Pipeline view.
After constructing a pipeline, click the Execute button to begin the query. This button will be available as long as the query window is not empty. Executing the query will bring you back to the History view where the matching versions are displayed. Section Query Results provides information on interacting with query results.
Try it now!
Let’s practice making a simple query. Open the “offscreen.vt” example vistrail. Click on the Query button to enter Query mode. Create a query like the one shown in Figure Example pipeline in Query mode. by dragging the modules SheetReference, CellLocation, and RichTextCell onto the Query canvas. (These modules can be found under the “VisTrails Spreadsheet” header in the Modules panel.) Connect the input and output ports of the modules as shown, then click the Execute button to perform the query. VisTrails will automatically switch to the History view, with all matching versions highlighted (Figure Query results in the History view.).
Note that Query by Example provides the capability to iteratively refine searches by adding more criteria. For example, if you were interested in workflows that contain a certain module, you may find that such a query returns too many results. You could then refine the query to find only those workflows where the given module has a parameter setting that falls within a given range. This is done by specifying parameter values in the Methods panel on the right side of the window. One major difference between the Pipeline view and the Query view is that you can use comparison operations, such as ‘<’ and ‘>’, in parameter values. The following example illustrates this.
Try it now!
Open the “terminator.vt” example file, and enter Query mode. Drag the vtkActor module from the Modules panel onto the Query canvas. Execute the query, and see which versions of the workflow contain a vtkActor modules. Return to the Query view, select the vtkActor icon, then drag the RotateZ method from the Methods panel to the Set Methods panel. In the RotateZ text field, type '> 90'. When you Execute the query this time, you will notice that the results are different. This is because we are searching for versions that not only contain a vtkActor module, but that also use a value greater than 90 in this module’s RotateZ method. Your results should resemble those in Figure Query result showing all workflows in the “terminator.vt” example that contain the module vtkActor..
Query result showing all workflows in the “terminator.vt” example that contain the module vtkActor.
The same query refined to show only those workflows whose RotateZ value is greater than 90.
Textual Queries¶
There are many ways to search for versions in the version tree using textual queries, but they all rely on a simple text box for input. Begin a search by activating the History view. The search box is in the Properties panel, and can be identified by the magnifying glass icon next to it. If you enter query text, VisTrails will attempt to match logical categories, but if your query is more specific, VisTrails has special syntax to markup the query. To execute a query, simply press the ‘Enter’ key after typing your query.
| Search Type | Syntax |
|---|---|
| User name | user: user name |
| Annotation | notes: phrase |
| Tag | name: version tag |
| Date | before: date | relative time |
| after: date | relative time |
Note
Since we allow regular expressions in our search box, question marks are treated as meta-characters. Thus, searching for ”?” returns everything and “abc?” will return everything containing “abc”. You need to use “\?” instead to search for ”?”. So the search for ”??” would be “\?\?”.
Table Syntax for querying specific information using textual queries. lists the different ways to markup a query. Note that you can search by user name to see which changes a particular user has made, and also by date to see which changes were made in a specific time frame. When searching by date, you can search for all changes before or after a given date or an amount of time relative to the present. If searching for changes before or after a specific date, the date can be entered in a variety of formats. The simplest is ‘day month year,’ but if the year is omitted, the current year is used. The month may be specified by either its full name or an abbreviation. For example, 'before: 18 November 2004' and 'after: 20 Dec' are both valid queries. If searching by relative time, you can prepend the amount of time relative to the present including the units to ‘ago’. An example of this type of query is 'after: 30 minutes ago'. The available units are seconds, minutes, hours, days, months, or years.
You can concatenate simple search statements to create a compound query to search across different criteria or for a specific range. For example, to search for workflows whose tag includes 'brain' and were created by the user 'johnsmith', the query would be 'name: brain user: johnsmith'. To search for all workflows created between April 1 and June 1, the query would be 'after: April 1 before: June 1'.
Try it now!
Open the “terminator.vt” example file, and enter History mode. Let’s look for all workflows that were created after July 1, 2007. In the search box in the Properties panel, type 'after: 1 july 2007' and press ‘Enter’. The expected result is shown in Figure Results of a query to find any changes made after July 1, 2007..
Results of a query to find any changes made after July 1, 2007.
Query Results¶
After executing either a query by example or a textual query, the matching versions are highlighted in the version tree. In addition, there is a button named Reset Query in the lower-left of the version tree that allows you to reset the query, returning the view to normal. For queries by example, if you click on a specific matching version and change to the Pipeline view, the matching structure will also be highlighted. Figure Query results in the History view. shows the results of the query by example in Figure Example pipeline in Query mode. in both the History and Pipeline views.
While in the History view, you can select two different ways of viewing search results. The magnifying glass icon to the left of the textual search box contains andropdown menu with two options: “Search” and “Refine” (Figure Clicking the button to the left of the query text box accesses a dropdown menu.). The first displays results by simply highlighting the matching nodes while the second condenses the tree to show only the versions that match. For large vistrails, this second method can help you determine relationships between the matching versions more easily.
Clicking the button to the left of the query text box accesses a dropdown menu.
In addition, VisTrails keeps track of the most recent textual queries, and repeating these queries can be accomplished by selecting the recent query from the dropdown menu attached to the search box. You can also clear recent searches using this menu. Finally, the ‘X’ button next to the search box will reset the query and restore the normal view of the version tree.