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Observer added in MoBi not available when simulation is exported to PK-Sim #2485

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Yuri05 opened this issue Dec 16, 2022 · 5 comments
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@Yuri05
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Yuri05 commented Dec 16, 2022

01_ObserverPKSim.zip

Simulation created in PK-Sim was sent to MoBi. In MoBi, new Container Observer IsActive was added:

grafik

In the simulation, this observer is created under Applications/Application_i:

grafik

Then the new observed IsActive together with the standard PK-Sim obswerver Fraction dissolved was plotted

grafik

Simulation was exported to pkml and imported in PK-Sim.
Now in PK-Sim when selecting the curves to plot: the new IsActive observer is not available in the selection dialog and cannot be plotted:

grafik

@Yuri05 Yuri05 changed the title Observer added in MoBi not available in PK-Sim Observer added in MoBi not available when simulation is exported to in PK-Sim Dec 16, 2022
@Yuri05 Yuri05 changed the title Observer added in MoBi not available when simulation is exported to in PK-Sim Observer added in MoBi not available when simulation is exported to PK-Sim Dec 16, 2022
@Yuri05
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Yuri05 commented Dec 16, 2022

@msevestre FYI

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Yuri05 commented Dec 16, 2022

P.S. If I define the new observer in MoBi not under Applications but under Organism: it works. I can plot the new observer in PK-Sim.

grafik

So seems PK-Sim restricts displayed quantities only to those stored under Organism?
If so: this should be changed.
grafik

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Interesting

@msevestre msevestre self-assigned this Dec 17, 2022
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@Yuri05 This is by design

image

https://github.com/Open-Systems-Pharmacology/PK-Sim/blob/develop/src/PKSim.Core/Services/SimulationPersistableUpdater.cs#L87

We are hiding all observers under application except a few that are predefined. Maybe we should instead only hide the one we do not want to show.Like the the Concentration of the C1 under APP etc..

Not sure what should be the rule? Alternatively, we can just not hide anything.... Thoughts?

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Yuri05 commented Dec 18, 2022

We are hiding all observers under application except a few that are predefined. Maybe we should instead only hide the one we do not want to show.Like the the Concentration of the C1 under APP etc..

Yep, exactly this. I think we should show all application observers except Concentration

msevestre added a commit that referenced this issue Jan 2, 2023
@Yuri05 Yuri05 closed this as completed in 670a4fc Jan 2, 2023
msevestre added a commit that referenced this issue Mar 20, 2023
* Fixes #2439 Misleading info in global POP PK Analysis if no parameter… (#2459)

* Fixes #2439 Misleading info in global POP PK Analysis if no parameters can be calculated

* PR feedback

* Fixes #2469 show hidden entities (#2488)

* Fixes buil failing (#2489)

* Fixes #2495 failing tests (#2499)

* Fixes #2485 observed added mobi (#2500)

* Fixes #2484 bug when exporting pop simulation (#2503)

* Fixes #2275 #2279 #2277 by updating OSPSuite.Core (#2506)

* Fixes #2405 mapping lost after configure (#2507)

* Fixes #2255 resetting concentration issue (#2512)

* Fixes #2255 resetting concentration issue

* Small update to stay symetrical

* Update MoleculeExpressionTask.cs

* Modify the comment to reflect population

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>

* update core (#2514)

* Prepare for v11_1 (#2515)

* Fixes #2516 Cannot run population simulations imported from pkml (#2517)

* Fixes #2516 Cannot run population simulations imported from pkml

* PR feedback

* Fixes #2518 11.1 Cannot show PK-Analysis in a population simulations … (#2520)

* Fixes #2518 11.1 Cannot show PK-Analysis in a population simulations imported from pkml

* PR feedback

* PR feedback

* Updated OSPSuite.Core and OSPSuite.BuildingBlockTemplates (#2524)

* Updated OSPSuite.Core and OSPSuite.BuildingBlockTemplates

* Updated OSPSuite.Core again

Co-authored-by: Yuri05 <Yuri05@github.com>

* Update documentation v11.1

* Fixes #2553 pksim changes molecule name (#2561)

* Fixes #2536 loading project from snapshot observed data (#2560)

* Fixes #2536 loading project from snapshot observed data

* Fixes #2536 loading project from snapshot observed data

* Fixes #2536 loading project from snapshot observed data

* Fixes #2558 project created with v10< do not export properly (#2559)

* Fixes #2563 notification weird column no image data (#2564)

* Try update core

* Update to latest core

* More work to make sure we can still load indiviudals

* Remove creation of PSV for simulation

* Fixes test project"

* Fixes test project"

* No more psv

---------

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>
Co-authored-by: Juri Solodenko <Yuri05@users.noreply.github.com>
Co-authored-by: Yuri05 <Yuri05@github.com>
rwmcintosh added a commit that referenced this issue Apr 3, 2023
* Fixes #2439 Misleading info in global POP PK Analysis if no parameter… (#2459)

* Fixes #2439 Misleading info in global POP PK Analysis if no parameters can be calculated

* PR feedback

* Fixes #2469 show hidden entities (#2488)

* Fixes buil failing (#2489)

* Fixes #2495 failing tests (#2499)

* Fixes #2485 observed added mobi (#2500)

* Fixes #2484 bug when exporting pop simulation (#2503)

* Fixes #2275 #2279 #2277 by updating OSPSuite.Core (#2506)

* Fixes #2405 mapping lost after configure (#2507)

* Fixes #2255 resetting concentration issue (#2512)

* Fixes #2255 resetting concentration issue

* Small update to stay symetrical

* Update MoleculeExpressionTask.cs

* Modify the comment to reflect population

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>

* update core (#2514)

* Prepare for v11_1 (#2515)

* Fixes #2516 Cannot run population simulations imported from pkml (#2517)

* Fixes #2516 Cannot run population simulations imported from pkml

* PR feedback

* Fixes #2518 11.1 Cannot show PK-Analysis in a population simulations … (#2520)

* Fixes #2518 11.1 Cannot show PK-Analysis in a population simulations imported from pkml

* PR feedback

* PR feedback

* Updated OSPSuite.Core and OSPSuite.BuildingBlockTemplates (#2524)

* Updated OSPSuite.Core and OSPSuite.BuildingBlockTemplates

* Updated OSPSuite.Core again

Co-authored-by: Yuri05 <Yuri05@github.com>

* Update documentation v11.1

* Fixes #2553 pksim changes molecule name (#2561)

* Fixes #2536 loading project from snapshot observed data (#2560)

* Fixes #2536 loading project from snapshot observed data

* Fixes #2536 loading project from snapshot observed data

* Fixes #2536 loading project from snapshot observed data

* Fixes #2558 project created with v10< do not export properly (#2559)

* Fixes #2563 notification weird column no image data (#2564)

* Try update core

* Update to latest core

* More work to make sure we can still load indiviudals

* Remove creation of PSV for simulation

* Fixes test project"

* Fixes test project"

* No more psv

---------

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>
Co-authored-by: Juri Solodenko <Yuri05@users.noreply.github.com>
Co-authored-by: Yuri05 <Yuri05@github.com>
msevestre added a commit that referenced this issue Jun 23, 2023
* Fixes #2344 Implement "Parameter Value Export" for Expression Profiles BB in PK-Sim (#2442)

* use GetAllChildren of Individual (#2445)

* 2438 outptu mappings not cleared (#2444)

* waiting for Core PR to be accepted

* nugets updated

* updating nuget

* 2364 export expression profile domain object  (#2461)

* initial try

* temp nuget update

* adjusting mapper

* Fixes #2344 Implement "Parameter Value Export" for Expression Profiles BB in PK-Sim (#2442)

* use GetAllChildren of Individual (#2445)

* 2438 outptu mappings not cleared (#2444)

* waiting for Core PR to be accepted

* nugets updated

* updating nuget

* temp nuget update

* working export

* spacing

* updating packages

* do not map object path for  'ROOT'

* do not repeat formulae in the formula cache

* adding tests

* fixing test

* correction

* consolidate assets

* correcting nugets

* code review changes

* code review

* PR feedback

* update core version

* Appveyor builds turned on

* PR feedback

* pr feedback

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>

* Fixes #2470 Refactor StartValues vs PathWithValueEntity (#2473)

* 2475 expression profile from pksim (#2476)

* #784_expression_profile_from_pksim

* updating with mapper

* Fixes #2475 Create expression profile from PK-sim

* add dimensions as resource for tests

* Add pkparameters for test project

* add sqlite db

* PR feedback

* Fixes #2480 individual serialization (#2494)

* work in progress

* work in progress

* Revise to map origin data as strings instead of keeping a common OriginData class

* Update core and mapping of origin data

* Testing the mapper

* testing the mapper

* revert an unintentional change

* PR Feedback

* Update core (#2502)

* Fixes #2508 Do not export calculation methods with Individual when there is only one possible value (#2510)

* Fixes #2508 Do not export calculation methods with Individual when there is only one possible value

* PR feedback

* PR feedback and update core

* update core

* update core osmoses (#2513)

* update core (#2528)

* Fixes update latest core (#2541)

* 2525 creating individual from MoBi (PK-Sim code changes) (#2526)



---------

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>

* Fixes #2534 Imported expression profile is not populated from the PKS… (#2548)

* Fixes #2534 Imported expression profile is not populated from the PKSim Database

* PR Changes

* PR feedback

* update core

* Fixes #2552 Export of Expression profile to PKML - include initial conditions (#2554)

* Update PKSIm with latest changes (#2555)

* Fixes #2551 Use DevExpress skin to color grid cells (#2556)

* No more psv (#2567)

* Fixes #2439 Misleading info in global POP PK Analysis if no parameter… (#2459)

* Fixes #2439 Misleading info in global POP PK Analysis if no parameters can be calculated

* PR feedback

* Fixes #2469 show hidden entities (#2488)

* Fixes buil failing (#2489)

* Fixes #2495 failing tests (#2499)

* Fixes #2485 observed added mobi (#2500)

* Fixes #2484 bug when exporting pop simulation (#2503)

* Fixes #2275 #2279 #2277 by updating OSPSuite.Core (#2506)

* Fixes #2405 mapping lost after configure (#2507)

* Fixes #2255 resetting concentration issue (#2512)

* Fixes #2255 resetting concentration issue

* Small update to stay symetrical

* Update MoleculeExpressionTask.cs

* Modify the comment to reflect population

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>

* update core (#2514)

* Prepare for v11_1 (#2515)

* Fixes #2516 Cannot run population simulations imported from pkml (#2517)

* Fixes #2516 Cannot run population simulations imported from pkml

* PR feedback

* Fixes #2518 11.1 Cannot show PK-Analysis in a population simulations … (#2520)

* Fixes #2518 11.1 Cannot show PK-Analysis in a population simulations imported from pkml

* PR feedback

* PR feedback

* Updated OSPSuite.Core and OSPSuite.BuildingBlockTemplates (#2524)

* Updated OSPSuite.Core and OSPSuite.BuildingBlockTemplates

* Updated OSPSuite.Core again

Co-authored-by: Yuri05 <Yuri05@github.com>

* Update documentation v11.1

* Fixes #2553 pksim changes molecule name (#2561)

* Fixes #2536 loading project from snapshot observed data (#2560)

* Fixes #2536 loading project from snapshot observed data

* Fixes #2536 loading project from snapshot observed data

* Fixes #2536 loading project from snapshot observed data

* Fixes #2558 project created with v10< do not export properly (#2559)

* Fixes #2563 notification weird column no image data (#2564)

* Try update core

* Update to latest core

* More work to make sure we can still load indiviudals

* Remove creation of PSV for simulation

* Fixes test project"

* Fixes test project"

* No more psv

---------

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>
Co-authored-by: Juri Solodenko <Yuri05@users.noreply.github.com>
Co-authored-by: Yuri05 <Yuri05@github.com>

* Fixes #2570 Move IndividualToIndividualBuildingBlockMapper from presentation to core (#2572)

* 2569 use individualbuildingblock and module from core (#2571)

* WIP #2569 use Individual Building block and module from core

* Some local variable rename. Build configuration not used anymore

* Map also indiviudal and expression building block. Needs #2570 to compile

* More work on #2569 to make test pass again:

* Fixes #2569 use of individual building blocks

* Fixes #2569 use individual building block and module from core

* Fixes #2577 Exported expression profiles contains duplicate formulae (#2578)

* 2584 update to support moduleconfiguration (#2585)

* Fixes #2584 update to support module configuration

* Fixes #2584 update to support module configuration

* Make test pass again

* 2586 parameters not common for all species (#2587)

* Added views to DB

* DB - adjusted naming of view and columns

* Fixes #2586 Provide info which parameters are not common for all species

* Fixes #2586 Provide info which parameters are not common for all species

* review comments

* Add serializer for the new dummy type

---------

Co-authored-by: Yuri05 <Yuri05@github.com>

* Fixes #2589 only export species indepednent parameters to spatial str… (#2591)

* Fixes #2589 only export species indepednent parameters to spatial structure

* Update to real DLLs

* Fixes typo

* Remove unused action

* Fixes update core (#2593)

* Fixes update core

* Fixes weird definition

* Update latest core (#2594)

* update to core 12.0.170 (#2604)

* Fixes #2596 implement hepatic impairment disease state (#2597)

* WIP #2596 implement hepatic impairment disease state

* More work on #2596

* More work on #2596

* More work on #2592

* Fixes #2596 implement hepatic impairement disease sate

* Fixes #2596

* Fixes #2596

* Small update

* Fixes merge conflict

* 2615 overriding ref conc and applying hi should use the updated refconc (#2620)

* Some rename first

* Add test showing issue with #2615

* Update to algorithm to match specificaitons

* Move logic of disease state to own view

* Fixes #2615 overriding ref conc

* Update DiseaseStateDTO.cs

just a typo

* Fixes failing test

* Fixes #2615 overriding ref conc

---------

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>

* Core updates (#2625)

* Update to 12.0.178

* update to 12.0.178

* Update core

* update core (#2629)

* Fixes #2621. Fixes #2622 (#2630)

* Fixes #2621. Fixes #2622

* Fixes #2621. Fixes #2622

* Fixes #2621

* update core (#2633)

* Fixes #2624. Fixes #2623 (#2637)

* Fixes #2638 cannot export HI to snapshot (#2639)

* Fixes #2638 cannot export HI to snapshot

* Update DiseaseState.cs

make sure we use old way of namespacing

* Update DiseaseStateMapper.cs

* Update DiseaseStateMapper.cs

* Fixes #2638. Use file scoped namespace

* Fixes #2638 by reverting to namespace

* 2632 errorvalue cannot be null parameter name source (#2641)

* WIP #2632

* Fixes #2632 error value cannot be null

* Also null for protocol mapper

* Fixes #2643 when to show global pk analysis (#2644)

* Fixes #2643 when to show global pk analysis

* Fixes #2643 when to show global pk analysis

* Could not let it go

* 2627 no expression profiles created when exporting a simulation from pk sim to mobi (#2645)

* Fixes #2627 no expression profiles created

* Fixes #2627 no expression profiles created

* Fixes type

* Fixes update latest core (#2648)

* 2640 export initial conditions for expressions as part of the expression profile (#2649)

* Fixes #2640 Export initial conditions for expressions as part of the expression profile

* Update core

* separate MoleculeBuilders by their presence and definition in the individual

* rename

* refactor enumerable

* PR feedback

* remove dead starter tests project

* core updated to 12.0.191. No diffbuilders with Dimension specified (#2652)

* 2654 fix failing tests (#2655)

* Fixes #2654 by removing support for version <7.0

* Fixes #2654 by removing support for version <7.0

* Fixes #2658 differences in simulations created by pk sim and mobi molecule types (#2659)

* Too many molecules in molecules list for some observers

* Do not change container observer type to Drug

* Fixes #2532 (#2636)

* WIP #2532

* fix using the wrong assertion

* Add default parameters to all molecules

* add parameter to actual proten

* Also add the parmaeter values

* add reference to tablews

* WIP #2532 ontogeny factor in expression profile

* WIP #2532 ontogeny factor

* WIP #2532 ontogeny factor

* Rename db field

* Make PMA only human dependent

* 2657 ontogeny factor is it dimensionless or fraction (#2662)

* Fixes #2657 ontogeny factor dimensionless

* Fixes #2657

* Fixes #2661 exception when using 2 pore simulations (#2663)

* Fixes #2660 remove estimated ga and use PMA instead (#2664)

* Fixes #2660 remove estimated ga and use PMA instead

* Actual real formula

* Fixes #2617 export to snapshot (#2665)

* undo changes in appveryor

* undo changes in appveryor

* Update to latest core

---------

Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com>
Co-authored-by: georgeDaskalakis <37107428+georgeDaskalakis@users.noreply.github.com>
Co-authored-by: Juri Solodenko <Yuri05@users.noreply.github.com>
Co-authored-by: Yuri05 <Yuri05@github.com>
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