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Refactoring snapshots #1483
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@boriskovar-m2ms has started to review the time/steps needed for this refcatoring excercise and estimates update next Tuesday. |
SnapshotsRework-Estimations.xlsx |
Thanks for the estimate @boriskovar-m2ms. @Waztom and I discussed the refactor and we think you should go ahead on this. |
@boriskovar-m2ms has been thinking about the approach to the state-based snapshot resolution, and will begin work imminently. An update on the time estimate: 18 working days would resolve to 6 weeks as Boris is working 3 days per week on Fragalysis. |
@boriskovar-m2ms has completed the state-based rendering of ligands, and is working ligand removal. The rest of the rendering elements are pending. This would round off the NGL changes necessary for the rest of the refactor. |
@boriskovar-m2ms hit a roadblock with rendering densities, that only occurs when rendering locally, but it has been fixed. Once this is done, Boris will move on to the RHS, after which the groundwork for the snapshot refactor itself will complete. |
Last week @boriskovar-m2ms fixed the electron density and atom quality rendering, and will work on RHS rendering ligands, complexes, surfaces and interactions. |
@boriskovar-m2ms confirms that state based rendering is complete for the RHS. Now Boris can workshop sending state to the backend |
@boriskovar-m2ms says he can upload the state to the b/e but there is outstanding work (being skipped for now) regarding the copying the state (have to work around hard limit of 2GB RAM usage e.g. in Chrome), Boris wants to have the end-to-end functionality first and then will craft a copy algorithm that works within the memory limits. Estimate is three weeks of work required including this week |
@boriskovar-m2ms reports that restoring orientations has been more challenging. Some of the effects for opening modals happen in a random order, and some effects require data to be loaded which is not generally true. Currently, Boris is dealing with a too large request header error - hopefully a fresh Docker install will resolve the discrepancy between working Tibor stack and Boris' local build (especially as the Tibor stack header is larger than the local one). |
@matej-vavrek reports that @boriskovar-m2ms is almost done, working on restoring scroll functionality, and switching between snapshots. Optimistically, could be all done next week @phraenquex asks that the NGL view should smoothly interpolate between the two orientations when switching between snapshots |
@boriskovar-m2ms says that scrolling is working, and he is working on restoring the saving the project functionality (which is very similar to saving snapshots). Boris will also work on restoring the interpolation between snapshots in the projects. There may be another optimisation to complete but otherwise Boris hopes to be done this week. |
@boriskovar-m2ms is working on saving and restoring projects, and will move on to interpolating between snapshots within a project With @boriskovar-m2ms managing his time on other projects he is anticipating the implementation, testing and release can be finished around October 17th/18th. Almost all files from the f/e have been changed but the b/e is untouched |
@boriskovar-m2ms is unwell but he will finish switching between the snapshots and then the refactor is complete (pending a large merge with all the other f/e changes) |
@boriskovar-m2ms is back to working on changing between snapshots, after which we will be feature complete and will implement the optimisation which is necessary to allow for states larger than 1GB ETA is pushed back around 7 days |
Bugs spotted by @phraenquex:
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@boriskovar-m2ms is working on @phraenquex's bugs @boriskovar-m2ms also needs to squash bugs from QA @phraenquex asks that larger bug fixes be moved to separate tickets and placed into
2024-11-21 snapshots
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@boriskovar-m2ms is finalising the work today, and will create a PR to merge to staging |
* - #1483 - removed old code * - #1483 - state based rendering is now done * #1483 - checkpoint * - #1483 - removed old code * - #1483 - state based rendering is now done * rebase checkpoint * - #1483 - before dirty snapshot detection * - storing middleware approach before pivoting to compare states approach * - #1483 - implemented last features * - #1483 - removed old code * - #1483 - state based rendering is now done * merging * - #1483 - before dirty snapshot detection * - storing middleware approach before pivoting to compare states approach * - #1483 - implemented last features * #1483 - first round of bugfixes * #1483 - final fixes
All known bugs are resolved now and PR is waiting here xchem#461 which can be merged after stuff from staging is merged to production |
Merged to staging |
Unfortunately all the snapshots I made occasionally crash:
Additionally, wireframe density (sigmaa) maps are not rendered here: |
First one is crashing because there are datasets on RHS with no molecules? Should I fix it? Because I think such datasets shouldn't even be served to the frontend because they're clearly broken. Second one works for me (tried like 10 times). Third one - I can confirm that density is not rendered. |
Thanks for confirming @boriskovar-m2ms Weirdly all three of them crashed occasionally for me but I'm just going to ignore that fact as reloading seemed to help. No need to support empty compound sets |
@mwinokan I know what's the problem with densities and why they worked for me before. I think now I know how to fix it but I don't think that's something I'll finish today. |
@boriskovar-m2ms No problem. I'll make another ticket |
The issue is that for our convenience we at some places extending data downloaded from backend with some operational data and when saving snapshot we are striping the state of all downloaded data so this operational data will get lost so know I need to move this information somewhere else and with it also chunk of the code. But I think there might be more of this kind of stinkers (maybe two or three other cases and I'm trying to remember). |
See spinout ticket #1603 |
Based on #1419
If we want to switch current action based snapshots for state based snapshots, this is how it should work.
Saving snapshot:
Snapshot restoration:
PROS:
CONS:
Not quite sure how long it would take me to implement this but we are definitely talking about several weeks but most likely we are not talking about multiple months.
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