Fixes #2532 #2636

msevestre · 2023-05-24T19:23:25Z

msevestre · 2023-06-14T21:29:00Z

@ALL: This is a work in progress but this needs to be reviewed continuously here as I have to change quite a few things

msevestre · 2023-06-14T21:30:07Z

src/Db/Diff/PKSimDB_diff.txt

@@ -9,14 +27,25 @@ This parameterization does not differentiate the etiology of hepatic impairment.
 INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Child-Pugh score','Child-Pugh score','Child-Pugh score: A (5,6 points)
 Child-Pugh score: B (7-9 points)
 Child-Pugh score: C (10-15 points) ',NULL,NULL);
+INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Ontogeny factor GI table','Ontogeny factor GI table','Ontogeny factor GI table','Dimensionless',NULL);
+INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Ontogeny factor table','Ontogeny factor table','Ontogeny factor table','Dimensionless',NULL);
+INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Post menstrual age','Post menstrual age','Post menstrual age','Age in years',NULL);


@Yuri05 @rwmcintosh
I needed to add this parameter since the ontogeny table we load from the DB are not using Age but PMA in years. We have a weird estimated GA which is in fact PMA but the unit is in WEEKS?!?!?

msevestre · 2023-06-14T21:30:13Z

src/PKSim.Assets/PKSim.Assets.csproj

-    <PackageReference Include="OSPSuite.Assets" Version="12.0.191" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.191" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-rfeaf" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.0-rfeaf" />


msevestre · 2023-06-14T21:30:45Z

src/PKSim.Core/Mappers/ExpressionProfileToExpressionProfileBuildingBlockMapper.cs

-         //for expression profile, all formula are in the calculation method EXPRESSION_PARAMETERS
+         var formula = parameter.Formula;
+         //for expression profile, all formula are in the calculation method EXPRESSION_PARAMETERS unless they are distributed table
+         if (formula is TableFormula tableFormula)


we have two parameters with a table formula. I am returning it as is for now. Wonder if this is a problem?

Don't see a problem. (Does not mean there isn't one, though 😆)

msevestre · 2023-06-14T21:31:28Z

src/PKSim.Core/Services/IndividualMoleculeFactory.cs

-      public void AddOntogenyParameterTo(IndividualMolecule molecule)
+      public void AddAgeDependentOntogenyParametersTo(IndividualMolecule molecule)
+      {
+         AddGlobalExpression(molecule,


Adding TWO parameters that are referencing the table formula

msevestre · 2023-06-14T21:32:05Z

src/PKSim.Infrastructure/ORM/Repositories/OntogenyRepository.cs

@@ -99,6 +118,56 @@ public double OntogenyFactorFor(Ontogeny ontogeny, string containerName, double?
         return _interpolation.Interpolate(allOntogenies.Select(x => new Sample(x.PostmenstrualAge, factorRetriever(x))), postmenstrualAgeInYearsFor(age, gestationalAge));
      }

+      public DistributedTableFormula DataRepositoryToDistributedTableFormula(DataRepository ontogenyDataRepository)


This is existing code that I moved from presenter here so that I could reuse. In short, it helps creating a table from an ontogeny selection

msevestre · 2023-06-14T21:32:38Z

src/PKSim.Presentation/Presenters/Individuals/ShowOntogenyDataPresenter.cs

-         std.Values = values(allOntogenies, x => x.Deviation);
-         return dataRepository;
+         chart.AxisBy(AxisTypes.Y).GridLines = true;
+         _simpleChartPresenter.Refresh();


this was missing. Gridlines and caption were never updated!!

msevestre · 2023-06-14T21:33:25Z

src/PKSim.Presentation/UICommands/ExportBuildingBlockToPKMLCommand.cs

+
+      protected override void PerformExecute()
+      {
+         var file = _dialogCreator.AskForFileToSave(_caption, Constants.Filter.PKML_FILE_FILTER, Constants.DirectoryKey.MODEL_PART, Subject.Name);


this was renamed. Took me a while to figure out why the default name was never set properly. It's because a parameter was missing and therefor, the suject.name was never used! /cc @rwmcintosh

msevestre · 2023-06-14T21:33:52Z

src/PKSim.Presentation/UICommands/PkmlExportCommandForBuildingBlock.cs

-
-      protected override void PerformExecute()
-      {
-         var file = _dialogCreator.AskForFileToSave(DialogCaption(), Constants.Filter.PKML_FILE_FILTER, Subject.Name);


@rwmcintosh see here, the 3 parameters is not the right one

rwmcintosh · 2023-06-21T14:05:35Z

src/PKSim.Core/Model/DiscreteDistributionFormulaSpecificationFactory.cs

@@ -41,6 +41,6 @@ public DistributionFormula CreateFor(IDistributionMetaData distribution, IDistri

      public bool IsSatisfiedBy(IEnumerable<ParameterDistributionMetaData> distributions) => distributions.All(IsSatisfiedBy);

-      public bool IsSatisfiedBy(IDistributionMetaData distribution) => distribution.Distribution == DistributionTypes.Discrete;
+      public bool IsSatisfiedBy(IDistributionMetaData distribution) => distribution.Distribution == OSPSuite.Core.Domain.Formulas.DistributionType.Discrete;


Did that need to be expanded? Looks like the only change in the file.
It moved, but it can still be shorter I think.

msevestre · 2023-06-22T17:47:25Z

@Yuri05 Can you please review this. Some major changes. Any questions, and suggestions, please create an issue so that we can address them

Yuri05 · 2023-06-23T10:14:28Z

It's an older issue and has nothing to do with this PR, but I wonder if the ontogeny export can be also fixed now:
#2537

Yuri05 · 2023-06-23T10:17:16Z

src/PKSim.Infrastructure/ORM/Repositories/OntogenyRepository.cs

+         var mean = new DataColumn(dataRepository.Name, _dimensionRepository.Fraction, pma) {DisplayUnit = yUnit };
+         var std = new DataColumn(PKSimConstants.UI.StandardDeviation, _dimensionRepository.Fraction, pma) {DisplayUnit = yUnit};
+         mean.DataInfo.AuxiliaryType = AuxiliaryType.GeometricMeanPop;
+         std.AddRelatedColumn(mean);


Confused. Shouldn't it be mean.AddRelatedColumn(std) ??

Confused too. I swapped it to try and it crashes
In this case the goal is to display area. So the idea is that it's not like for oba data where mean is the main curve with some extra info
In this case, the area is the main curve and the mean is the extra stuff

Yuri05 · 2023-06-23T10:18:27Z

src/PKSim.Infrastructure/ORM/Repositories/OntogenyRepository.cs

+
+         var pma = new BaseGrid(PKSimConstants.UI.PostMenstrualAge, _dimensionRepository.AgeInWeeks) {DisplayUnit = xUnit };
+         var mean = new DataColumn(dataRepository.Name, _dimensionRepository.Fraction, pma) {DisplayUnit = yUnit };
+         var std = new DataColumn(PKSimConstants.UI.StandardDeviation, _dimensionRepository.Fraction, pma) {DisplayUnit = yUnit};


Should we name the STD column "Geometric standard deviation" instead of just "Standard Deviation" to become more clear?
#2666

src/PKSim.Infrastructure/ORM/Repositories/OntogenyRepository.cs

* 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Juri Solodenko <[email protected]> Co-authored-by: Yuri05 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: georgeDaskalakis <[email protected]> Co-authored-by: Juri Solodenko <[email protected]> Co-authored-by: Yuri05 <[email protected]>

msevestre force-pushed the 2532-ontogeny-factor-in-expression-profile branch from eb4303a to 898084f Compare June 2, 2023 14:46

msevestre added 5 commits June 14, 2023 10:14

WIP #2532

4d9c866

fix using the wrong assertion

07255f1

Add default parameters to all molecules

fe314fc

add parameter to actual proten

55049b0

Also add the parmaeter values

27b6082

msevestre force-pushed the 2532-ontogeny-factor-in-expression-profile branch from c56bd91 to 27b6082 Compare June 14, 2023 14:16

msevestre added 4 commits June 14, 2023 11:08

add reference to tablews

5131009

WIP #2532 ontogeny factor in expression profile

bcf1d6a

WIP #2532 ontogeny factor

f1e3456

WIP #2532 ontogeny factor

cb29b53

msevestre requested review from rwmcintosh and Yuri05 June 14, 2023 21:28

msevestre commented Jun 14, 2023

View reviewed changes

msevestre added 2 commits June 14, 2023 17:41

Rename db field

2805e37

Make PMA only human dependent

7de6d6d

rwmcintosh reviewed Jun 21, 2023

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rwmcintosh approved these changes Jun 21, 2023

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msevestre changed the title ~~WIP #2532~~ Fixes #2532 Jun 22, 2023

rwmcintosh merged commit 2748339 into OSMOSES Jun 22, 2023

rwmcintosh deleted the 2532-ontogeny-factor-in-expression-profile branch June 22, 2023 17:00

Yuri05 reviewed Jun 23, 2023

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Yuri05 mentioned this pull request Jun 23, 2023

Should we name the STD column "**Geometric standard deviation**" instead of just "Standard Deviation" to become more clear? #2666

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Yuri05 reviewed Jun 23, 2023

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Fixes #2532 #2636

Fixes #2532 #2636

msevestre commented May 24, 2023

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Fixes #2532 #2636

Fixes #2532 #2636

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