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Convert PD to AF using service #680

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ugurdogrusoz opened this issue Jul 5, 2021 · 4 comments
Closed

Convert PD to AF using service #680

ugurdogrusoz opened this issue Jul 5, 2021 · 4 comments
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@ugurdogrusoz @hasanbalci @acanalpay
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feature New feature or request

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@ugurdogrusoz
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ugurdogrusoz commented Jul 5, 2021 •
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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 ugurdogrusoz added the feature New feature or request label Jul 5, 2021
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ugurdogrusoz commented Jul 5, 2021 •
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After testing the deployment here, below are some issues.

UI improvements on PD2AF conversion facility:

  • 1. Rename menu item "Convert PD2AF" to "Convert PD map to AF map"
  • 2. Rename root context menu item as "Convert PD map to AF map" as well
  • 3. Name the AF map constructed as the same as the original one with " AF" appended to the name
  • 4. Name the file for the AF map constructed as the same as the original file name with "_af" appended before the extension
  • 5. Rename "AF graph " prepended to the description as "AF map "
  • 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.
  • 7. Display appropriate warning/error messages when the operation is not completed properly
  • 8. Let's apply the color scheme in the original PD map to the AF map before displaying as well.

Issues/bugs:

  • 10. When the AF is displayed in a new tab, it should fit into the window properly.
    Screenshot 2021-07-06 135809
  • 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.
  • 12. Convert only the visible (ignore hidden map content) part of the map
  • 13. Let's make sure we timeout in 1 minute and display an appropriate warning
  • 14. Collapsed nodes still converted and expanded in the AF map
  • 15. After conversion, some hidden node's compartments are displayed

Tasks:

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

acanalpay added a commit that referenced this issue Jul 5, 2021
@acanalpay
Modified the UI #680
8f40f2b
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acanalpay commented Jul 5, 2021 •
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For UI improvements, commit 8f40f2b addresses the problem 1 and 2

@ugurdogrusoz ugurdogrusoz removed their assignment Jul 6, 2021
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 6, 2021
@acanalpay
Description changed AF graph to AF map iVis-at-Bilkent#680
4bce457
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 6, 2021
@acanalpay
Description changed AF graph to AF map iVis-at-Bilkent#680
5645c80
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 6, 2021
@acanalpay
Possible fix to the window fit problem iVis-at-Bilkent#680
46f3278
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 7, 2021
@acanalpay
Map description bug fixed iVis-at-Bilkent#680
1667d96
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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 1667d96 fixed that bug

@iVis-at-Bilkent iVis-at-Bilkent deleted a comment from hasanbalci Jul 7, 2021
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 8, 2021
@acanalpay
Added spinner and temporarly set inferNestingOnLoad to true iVis-at-B…
4873512 
…ilkent#680
@ugurdogrusoz ugurdogrusoz removed their assignment Jul 8, 2021
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 8, 2021
@acanalpay
Modified the map string so that only the visible map will be converte…
d761d36 
…d. Error display messages mmodified iVis-at-Bilkent#680
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 14, 2021
@acanalpay
Fixed hidden compartment issue and used setTimeout for fitting the ma…
6a308bc 
…p after conversion iVis-at-Bilkent#680
@ugurdogrusoz
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  1. 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)

acanalpay added a commit to acanalpay/newt that referenced this issue Jul 16, 2021
@acanalpay
Color scheme added and inferNestingOnLoad value set to original value…
a4c7c8a 
… (Issue 8-11) iVis-at-Bilkent#680
acanalpay added a commit to acanalpay/newt that referenced this issue Jul 16, 2021
@acanalpay
Fixed inferNestingOnLoad is not true while loading iVis-at-Bilkent#680
5ad7e8d
hasanbalci pushed a commit that referenced this issue Jul 16, 2021
@acanalpay
Implementation of PD map to AF map conversion feature (#682)
6c501f0 
* Fixed

* Update

* body-parser

* heroku upload problem fix

* added node_modules

* add engine

* add engine

* express

* Delete node_modules directory

* port

* Update server.js

* Update server.js

* process.env.port => process.env.PORT

* changed the post url

* AF map name specified

* Added map description to converted AF graph

* Description changed AF graph to AF map #680

* Description changed AF graph to AF map #680

* Possible fix to the window fit problem #680

* Added comments

* Assigned port 80

* Map description bug fixed #680

* Added spinner and temporarly set inferNestingOnLoad to true #680

* Modified the map string so that only the visible map will be converted. Error display messages mmodified  #680

* PR changes except Heroku files #682

* Resolved some additional styling issues. (not Heroku yet) #682

* Resolved requested changes including Heroku #682

* URL updated for public server #682

* Resolved the loading from url issue

* Create Procfile

* For Heroku update

* Deleted Heroku files

* Changed public server url #682

* Fixed hidden compartment issue and used setTimeout for fitting the map after conversion #680

* Heroku deployment

* Heroku dependicies deleted

* Heroku sbgnviz update

* Heroku upload dependicies deleted

* Color scheme added and inferNestingOnLoad value set to original value (Issue 8-11) #680

* Reduced the timeout and made smooth transaction while loading the map

* Fixed inferNestingOnLoad is not true while loading #680

* Deleted spinner which is not centered

* Heroku deployment

* Heroku deleted

* Deleted Procfile
acanalpay added a commit that referenced this issue Jul 22, 2021
@acanalpay
inferNestingOnLoad's original value restored for the converted map #680
e5d3b2f
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