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Reintegrate changes in develop (#2668)
* 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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