Advanced Features and Troubleshooting
=========================
<a id="advanced_features"> </a>

## URL Query Parameters
<a id="url_parameters"></a>

Cytoscape Web's ```import``` URL parameter provides an easy way for web applications and third-party tools to use Cytoscape Web to inspect and process the result from their workflows as long as the result can be served on a REST endpoint in CX2 format. 

For example, if my Jupyter notebook generates a CX2 network and the file is available at

```
http://localhost:8080/xyz/mytempresult.cx2
```

using the following URL

```
https://web.cytoscape.org/?import=http://localhost:8080/xyz/mytempresult.cx2
```

will open the CX2 network in Cytoscape Web in the user's default web browser.

Additional URL parameters allow to specify the behavior of some of the interface components. These parameters let users customize the way a network is displayed in Cytoscape Web prior to sharing it with collaborators, such as a collapsed or expanded table panel, the active table panel’s tab and the node/edge selection in the network’s graphic rendering.

The resulting URL not only allows immediate interactive access to the network in the recipient’s Cytoscape Web workspace, but also preserves some of the interface settings that the sender defined. 

For example, pasting the following URL in a web browser

```
https://web.cytoscape.org/0/networks/9a8f5326-aa6e-11ea-aaef-0ac135e8bacf?selectednodes=41536+41580+41605+41606+41719&selectededges=e42257+e42161+e42160+e42117&left=open&right=closed&bottom=open&activeTableBrowserTab=2
```

will open a network in Cytoscape Web that has 5 nodes and 4 edges selected in the "Homologous Recombination" cluster on the left side of the graphic rendering, an expanded table panel and the active table panel tab set to "Network". 

Below is the list of all additional query parameters available:

```selectednodes``` >> Defines the selected nodes

```selectededges``` >> Defines the selected edges

```left``` >> Defines the state of Workspace Panel (open or closed)

```right``` >> Defines the state of Sub Network View Panel (open or closed)

```bottom``` >> Defines the state of Table Panel (open or closed)

```activeTableBrowserTab``` >> Defines the active tab in the table panel (0= Nodes, 1= Edges or 2= Network)


## Troubleshooting Cytoscape Web
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Web applications are complex software, sometimes they can get in an abnormal state that prevents normal operation and Cytoscape Web is no exception. Should Cytoscape Web get in a state that prevents it from operating normally, users can take measures to try resolve the issue.

The first measure consists in performing a **hard reload** of the Cytoscape Web application. This can be achieved by holding down  the **Shift** key on your keyboard and clicking the browser's reload icon ![](_static/images/Advanced/reload_icon.png). A hard reload bypasses the browser's cache and can help restoring a web application's normal state by refreshing outdated files in the cache.

The second measure consists in **clearing the browser's cache** entirely and then reloading Cytoscape Web. [THIS PAGE](https://www.wikihow.com/Clear-Your-Browser%27s-Cache) describes how to clear the cache in different web browsers and platforms.

The third and last measure involves **clearing the local database**. This fetaure is available in the Cytoscape web main menu under **Data → Clear Local Database** and should only be used as a last resort. You can think about this as a "factory reset", that will completely erase and restore Cytoscape Web to a clean slate.

Finally, we remind you that Cytoscape Web is still in active development and may contain unidentified bugs. Should you find one, please make sure to report it by choosing **Help → Report a Bug** in the Cytoscape Web main menu.