esqlabs / shinyscenarioeditor Goto Github PK

All try-catch must return the error (show it as pop-up)

Code exists.

If the excel file is on SharePoint and opened in excel.

Opening excel files should be in try-catch and errors forwarded to the user.

• Snapshot
• pksim project
• related excel files
• autofill script

esqLABS/esqlabsR#554

Code for converting output intervals to a common unit:

Eaxample JSON file:

Tables should be editable. Would be great to have some sorting, filtering etc.

• https://clarewest.github.io/blog/post/making-tables-shiny/
• https://rfortherestofus.com/2019/11/how-to-make-beautiful-tables-in-r/ (rhandsontable looks neat)

Function to add a new output interval (or delete an existing one) to the list of output intervals of a scenario.

Start, end, and resolution and select units.

The r$data data structure contains:

• a generic key for each excel file (scenarios for Scenarios.xlsx)
• For each key:
  • file_path path to the file
  • sheets: vector of sheet names
  • [Sheet]: a daframe containing the data loaded from a sheet of the excel file
  • [Sheet]_modified: a dataframe intialised as [Sheet] but where modified dataframe will be stored when changed.

Example:

r$data
  $Scenarios
    $file_path
    $sheets
    $Scenarios
    $Scenarios_modified
    $OutputPaths
    $OutputPaths_modified
  $Individuals
    $file_path
    $sheets
    ...

When trying to restore renv packages, I get an error for the httpuv package, last lines:

nce to `FOLDERID_LocalAppData'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'httpuv'
* removing 'D:/Work/OSPS/Repos/shinyScenarioEditor/renv/profiles/dev/renv/staging/1/httpuv'
install of package 'httpuv' failed [error code 1]

When manually installing httpuv from CRAN, an updated version is intalled (1.6.15, lockfile has 1.6.12). Maybe update your package locally and commit updated lockfile?

Load a PK-Sim snapshots and add all simulations as scenarios

datamods uses the reactable package.

readxl function assumes that empty columns are logical with NA values. This makes {datamods} crash when editing value because logical cannot be NA. To solve this, all columns are read as characters.

However, for making the editing UI more convenient to the users, the data should be correctly typed.

1. Open app
2. Click on "Export"
3. Screen is gray.

Add (first design?) and esqlabs app logo to the app.

An option to create a new scenario from a pkml.

• Scenario_name: simulation$name
• IndividualId: empty
• PopulationId: empty
• ModelParameterSheets: empty
• ApplicationProtocol: simulation$name, create additional sheet with application parameters? Only non-formula or formula overwritten
• SimulationTime: parse.
  • In case the output time schema contains fixed time points, show a warning that they will be discarded.
  • ModelFile: name of the selected pkml
  • OutputPathsIds: parse outputs from pkml. Do not create an additional entry in OutputPaths sheet if such a path is already defined.

Checks:

• A scenario with the same is already present
• An application protocol sheet with the name is already present

The edit_data with passable reactable options currently lives in this branch: https://github.com/dreamRs/datamods/tree/dev-2

V1 supports loading projects via project configuration.
V2 should support setting up the whole project structure from the app.

Empty cells in the columns

• ApplicationProtocol,
• SimulationTime
• SimulationTimeUnit
• OutputPathsIds

denote that the original values from the pkml will be taken. Can we show something like <unchanged> (grey color?) for these cells, so it is clear to the user that he does not have to fill those cells out?

to be changed/added:

• "plots" element in the data_structure()
• assign file_path with corresponding projectConfiguration() item in mod_import.R (~line 60)
• new module called tab_plots for example
• add tab_plots in mod_main_panel
• tab_plots should contain calls to mod_table_tab_server and mod_table_tab_ui

Since the app will be used to modify all esqlabsR excel sheets, it should not be called shinyScenarioEditor anymore.

• Script to highlight invalid rows with the red

Scenarios

Scenarios Table

• Scenario_name - text type; text input; no predefined values; no validation
• IndividualId - text type; dropdown multiple selection input; options come from Individuals$IndividualBiometrics sheet
• PopulationId - text type; dropdown selection input; options come from Populations$PopulationName sheet;
• ReadPopulationFromCSV - text type; text input; no predefined values; no validation
• ModelParameterSheets - text type; text input; no predefined values; no validation
• ApplicationProtocol - text type; text input; no predefined values; no validation
• SimulationTime - text type with the integer numeric values split by ";", modal window input with the only integer values allowed
• SimulationTimeUnit - text type; dropdown selection input; options come from ospsuite::ospUnits
• SteadyState - boolean type; checkbox input; strict validation -> allowed values: true/false
• SteadyStateTime - text type; text input; no predefined values; no validation
• SteadyStateTimeUnit - text type; dropdown selection input; options come from ospsuite::ospUnits
• ModelFile - text type; text input; no predefined values; no validation
• OutputPathsIds - text type; text input; no predefined values; no validation

OutputPaths Table

• OutputPathId - text type; text input;
• OutputPath - text type; text input;

Individuals

IndividualBiometrics Table

• IndividualId - text type; text input; no predefined values; no validation
• Species - text type; dropdown selection input; options come from ospsuite::Species
• Population - text type; text input;
• Gender - text type; dropdown selection input; options come from ospsuite::Gender
• Weight - numeric (integer) type; text input; min/max value ???
• Height - numeric (integer) type; text input; min/max value ???
• Age - numeric (integer) type; text input; min/max value ???

Populations

Demographics Table

• PopulationName - text type; text input; no predefined values; no validation
• species - text type; dropdown selection input; options come from ospsuite::Species
• population - text type; text input;
• numberOfIndividuals - numeric (integer) type; text input; min/max value ???
• proportionOfFemale - numeric (integer) type; text input; min/max value ???
• weightMin - numeric (integer) type; text input
• weightMax - numeric (integer) type; text input
• weightUnit - text type; dropdown selection input; options come from ospsuite::ospUnits
• heightMin - numeric (integer) type; text input
• heightMax - numeric (integer) type; text input
• heightUnit - text type; dropdown selection input; options come from ospsuite::ospUnits
• ageMin - numeric (integer) type; text input
• ageMax - numeric (integer) type; text input
• BMIMin - numeric (integer) type; text input
• BMIMax - numeric (integer) type; text input
• BMIUnit - text type; dropdown selection input; options come from ospsuite::ospUnits

Plots

DataCombined Table

• DataCombinedName - text type; text input; no predefined values; no validation
• dataType - text type; dropdown selection input; options: ['simulated', 'observed'] ???
• label - text type; text input; no predefined values; no validation
• scenario - text type; text input; no predefined values; no validation
• path - text type; text input; no predefined values; no validation
• dataSet - text type; text input; no predefined values; no validation
• group - text type; text input; no predefined values; no validation
• xOffsets - numeric (integer) type; text input
• xOffsetsUnits - text type; dropdown selection input; options come from ospsuite::ospUnits ???
• yOffsets - numeric (integer) type; text input
• yOffsetsUnits - text type; dropdown selection input; options come from ospsuite::ospUnits ???
• xScaleFactors - numeric (integer) type; text input
• yScaleFactors - numeric (integer) type; text input

plotConfigurations Table

• plotID - text type; text input; no predefined values; no validation
• dataCombinedName - text type; text input; no predefined values; no validation
• plotType - text type; dropdown selection input; options: ['individual'] ???
• title - text type; dropdown selection input; options come from ospsuite::ospUnits ???
• xUnit - text type; dropdown selection input; options come from ospsuite::ospUnits ???
• yUnit - text type; dropdown selection input; options come from ospsuite::ospUnits ???
• xAxisScale - text type; dropdown selection input; options: ['lin', 'log'] ???
• yAxisScale - text type; dropdown selection input; options: ['lin', 'log'] ???
• xAxisLimits - numeric (integer) type; text input
• yAxisLimits - numeric (integer) type; text input
• quantiles - numeric type; text input
• foldDistance - numeric type; text input

plotGrids Table

• name - text type; text input; no predefined values; no validation
• plotIDs - text type; text input; no predefined values; no validation
• title - text type; text input; no predefined values; no validation

IndividualBiometrics -> Species -> Population

If some sheets cannot be parsed with current data importer configuration, nothing happens because by default all sheets are read. Provide a check-box selection of sheets present in the data file and "reload" button that triggers reading of data only from selected sheets.

Keyboard shortcuts do not work. Ctrl + z to undo would be the most useful one.

Configuration (and whole project structure) provided internally.

Error is:.

New names:
• `Bone` -> `Bone...1`
• `` -> `...2`
• `` -> `...3`
• `` -> `...4`
• `Bone` -> `Bone...5`
• `` -> `...6`
• `` -> `...7`
• `` -> `...8`
Warning: Error in [.data.frame: undefined columns selected
  4: runApp
  3: print.shiny.appobj
  1: source

How should inputs be organized ?

• table (datamods)
• Separate fields

For the future.

We could offer an option to load a pkml with the simulation and present all possible outputs as a tree view, where the user cal select which outputs to add.

Not reproducible @AKostiv8

Each time I make any change to the "Scenarios" table, the whole table is re-drawn (lost focus).