A View is a type of Synapse Table that queries across metadata (Annotations) for particular items (projects, files or submissions) with a particular “scope”. A File View lists all Files or Tables within one or more Folders or Projects. A Project View lists all Projects you’ve added to the view. A Submission View lists all Submissions within one or multiple Evaluation Queues. Views can:

• Allow Projects, Files, Submissions, and Tables to be easily searched and queried

• Allow view/editing metadata attributes in bulk

• Provide a way of isolating or linking data based on similarities

• Provide the ability to link Projects, Files, Submissions, and Tables together by their annotations

Create a File View

To create a File View, select the Project in which you would like to create the View. The Project you choose does not have to contain the files you are including in your view. In order to create the File View, navigate to the Tables tab and select “Add File View” in the Tables Tools menu. You will select the files of interest by defining the scope, which is the Project(s) and Folders that contain your files. File Views can also contain Tables or Folders; you can choose which kinds of items you would like to include during this process.

Instructions for creating Views using the clients can be found in the Python docs and in the R docs.

Create a Project View

To create a Project View, select the Project in which you would like to create the view. You will select the projects of interest by defining the scope as above. The only notable difference between creating a Project View and a File View is that for project views, there is a 1:1 relationship between the projects you select in your scope and the projects that are shown in the view.

Create a Submission View

To create a Submission View, select the Project in which you would like to create the view. The Project you choose does not have to contain the submissions or the evaluation queues that are included in the view. Navigate to the Tables tab and select “Add Submission View” in the Tables Tools menu. The submissions that are included in the view are defined by its scope, which is the list of Evaluation Queues containing the submissions. For more information, read about how to use Submission Views with Evaluation Queues.

Instructions for creating Views using the clients can be found in the Python docs and in the R docs.

Updating the Scope or Content-Type of a View

Views can be edited to change the scope of the view (e.g. the Project or Folder the view is showing) or which types of content is shown. Both of these options are found by navigating to “Show Scope of View” in the Tools menu; from there you may View and Edit the scope and the content-type of the view.

Note that it may take a few moments for the updated View to rebuild as it queries across the system.

Query a View

A view can be queried exactly the same as any other Table in Synapse. Please see Tables for more examples. See the Using Simple Search and Using Advanced Search sections below.

For example, to query for everything in syn123:

Command Line

synapse query 'SELECT * FROM syn123'

Python

query = syn.tableQuery('SELECT * FROM syn123')

R

query <- synTableQuery('SELECT * FROM syn123')

Update Annotations in Bulk

Views can be used to update annotations in bulk. To add new annotations, see the Annotations article. To update other metadata in bulk, such as provenance, see the Bulk Processing article.

For example, if you would like to use the Python client to update the annotation “dogSays:bark” to “dogSays:woof” in every file in a File View with the synId syn456, you can use:

from synapseclient import Table

foo = syn.tableQuery('select * from syn456')

bar = foo.asDataFrame()

# add in annotation as a column
bar['dogSays'] = 'woof'

# store the fileview with the new annotation in Synapse
fv = syn.store(synapseclient.Table(foo.tableId, bar))

Using Simple Search

Views are in Simple Search mode by default. You can filter out Projects or Files of interest by selecting what characteristics you like using the facet menu on the left. You can toggle between simple and advanced search using the Show advanced search/Show simple search link.

Using Advanced Search

In advanced search, you can use a SQL-like query to search for items in that view. In the example below, we’re selecting for all files that have a Cell Type of “PSC”.

Insert a View into a Wiki

Views can also be placed inside a Wiki once they have been created. You can embed the entire view or a subset of a query on it.

To insert a file view with a synId of syn456:

In the Edit Project Wiki window, select Table: Query on a Synapse Table/View under the Insert dropdown. To embed the entire file view into the wiki enter “SELECT * FROM syn456” in the resulting pop-up.

To embed a subset of the file view, like the advanced search query in the previous example, enter “SELECT * FROM syn456 WHERE Cell_Type = ‘PSC’”.

Save the query and the edits to the Wiki to embed the view.

See Also

Annotations and Queries, Tables, Wikis