Convert PD to AF using service

[ugurdogrusoz]

We should implement a conversion operation of PD maps to AF maps and open the AF maps constructed in a new Newt tab. Let's do this in a separate branch or as a PR for now.

[ugurdogrusoz]

After testing the deployment here, below are some issues.

UI improvements on PD2AF conversion facility:

• [x] 1. Rename menu item "Convert PD2AF" to "Convert PD map to AF map"
• [x] 2. Rename root context menu item as "Convert PD map to AF map" as well
• [x] 3. Name the AF map constructed as the same as the original one with " AF" appended to the name
• [x] 4. Name the file for the AF map constructed as the same as the original file name with "_af" appended before the extension
• [x] 5. Rename "AF graph " prepended to the description as "AF map "
• [x] 6. Sometimes conversion takes a long time (e.g. mammalian_cholesterol.nwt sample takes 15 secs in my case). It would be good to check whether there is any performance problem on our side or it is totally because of the conversion service. In addition, users should know that the conversion is in progress especially for these long cases, so when users click on the conversion button we can show the spinner as we do in Pathway Commons queries or during layout.
• [x] 7. Display appropriate warning/error messages when the operation is not completed properly
• [x] 8. Let's apply the color scheme in the original PD map to the AF map before displaying as well.

Issues/bugs:

• [x] 10. When the AF is displayed in a new tab, it should fit into the window properly.
• [x] 11. After conversion, while loading converted file, we can set inferNestingOnLoad to true temporarily, because otherwise we lose nesting relation in the loaded map. For example, we change this attribute temporarily while loading results of Pathway Commons queries like here.
• [x] 12. Convert only the visible (ignore hidden map content) part of the map
• [x] 13. Let's make sure we timeout in 1 minute and display an appropriate warning
• [x] 14. Collapsed nodes still converted and expanded in the AF map
• [x] 15. After conversion, some hidden node's compartments are displayed

Tasks:

• [x] 20. Document how to deploy the PD2AF service on our public server in this document (see highlighted ToDo)

[acanalpay]

For UI improvements, commit 8f40f2ba356a9dfc24398644f73299a72df7de31 addresses the problem 1 and 2

[acanalpay]

There was a bug when adding map description to the new AF map, PD map description also changed and become AF map's description. Commit 1667d9697dc5cf7c0bb6a31e87526d7e0bfa8781 fixed that bug

[ugurdogrusoz]

11. infer nesting on load should be set back to its original value (default false) after the conversion (it stays true even if the original value is false)