Merge pull request #284 from Open-Systems-Pharmacology/develop

Version 7.2.0

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "scripts"]
 	path = scripts
 	url = https://github.com/Open-Systems-Pharmacology/build-scripts.git
+[submodule "src/OSPSuite.SimModel.Schema"]
+	path = src/OSPSuite.SimModel.Schema
+	url = https://github.com/Open-Systems-Pharmacology/OSPSuite.SimModel.Schema.git

OSPSuite.Core.sln

@@ -1,8 +1,8 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio 14
-VisualStudioVersion = 14.0.25123.0
-MinimumVisualStudioVersion = 14.0.24720.0
+# Visual Studio 15
+VisualStudioVersion = 15.0.26430.4
+MinimumVisualStudioVersion = 10.0.40219.1
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{9ED8AA66-5E2F-4900-846B-4D2758832061}"
 	ProjectSection(SolutionItems) = preProject
 		appveyor-coverage.yml = appveyor-coverage.yml

README.md

@@ -4,14 +4,14 @@ Core functionalities of the Open Systems Pharmacology Suite.
 
 ## Code Status
 [![NuGet version](https://img.shields.io/nuget/v/OSPSuite.Core.svg?style=flat)](https://www.nuget.org/packages/OSPSuite.Core)
-[![Build status](https://ci.appveyor.com/api/projects/status/w3ecxmp3grryc5ts/branch/develop?svg=true)](https://ci.appveyor.com/project/open-systems-pharmacology-ci/ospsuite-core/branch/develop)
+[![Build status](https://ci.appveyor.com/api/projects/status/skw2giv5jxy3pvo0/branch/develop?svg=true)](https://ci.appveyor.com/project/open-systems-pharmacology-ci/ospsuite-core/branch/develop)
 [![Coverage status](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite.Core/branch/develop/graph/badge.svg)](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite.Core)
 
 ## Code of conduct
 Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc...) is expected to follow the Open Systems Pharmacology [code of conduct](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODE_OF_CONDUCT.md).
 
 ## Contribution
-We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the [contribution guidelines](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CONTRIBUTING.md). If you are contributing code, please be familiar with the [coding standard](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODING_STANDARD.md).
+We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the [contribution guidelines](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CONTRIBUTING.md). If you are contributing code, please be familiar with the [coding standards](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODING_STANDARDS.md).
 
 ## License
 OSPSuite.Core is released under the [GPLv2 License](LICENSE).

SolutionInfo.cs

@@ -7,5 +7,6 @@
 [assembly: ComVisible(false)]
 [assembly: AssemblyVersion("1.0.0.0")]
 [assembly: AssemblyFileVersion("1.0.0.0")]
+[assembly: AssemblyInformationalVersion("")]
 [assembly: InternalsVisibleTo("OSPSuite.Core.Tests")]
 [assembly: InternalsVisibleTo("OSPSuite.UI.Tests")]

appveyor-coverage.yml

@@ -1,7 +1,8 @@
 configuration: Debug
+image: Visual Studio 2017
 
 environment:
-  app_version: '7.1.0'
+  app_version: '7.2.0'
 
 version: '%app_version%.{build}'
 
@@ -37,8 +38,4 @@ test_script:
 install:  
  - set PATH=C:\Ruby22\bin;C:\\Python34;C:\\Python34\\Scripts;%PATH%"
  - pip install codecov
- - git submodule update --init --recursive
- - ps: >-
-    (new-object net.webclient).DownloadFile('https://download.microsoft.com/download/A/2/D/A2D8587D-0027-4217-9DAD-38AFDB0A177E/msxml.msi', 'C:\\msxml.msi')
-
-    Start-Process msiexec.exe -ArgumentList /i, C:\msxml.msi, /quiet, /qn, /norestart -Wait
+ - git submodule update --init --recursive

appveyor.yml

@@ -1,7 +1,8 @@
 configuration: Debug
+image: Visual Studio 2017
 
 environment:
-  app_version: '7.1.0'
+  app_version: '7.2.0'
 
 version: '%app_version%.{build}'
 
@@ -37,20 +38,16 @@ skip_branch_with_pr: true
 
 branches:
   only:
-    - master
     - develop
-
 test:
   assemblies:
     - OSPSuite.Core.Tests.dll
     - OSPSuite.UI.Tests.dll
 
 install:
  - git submodule update --init --recursive
- - ps: >-
-    (new-object net.webclient).DownloadFile('https://download.microsoft.com/download/A/2/D/A2D8587D-0027-4217-9DAD-38AFDB0A177E/msxml.msi', 'C:\\msxml.msi')
 
-    Start-Process msiexec.exe -ArgumentList /i, C:\msxml.msi, /quiet, /qn, /norestart -Wait
+skip_tags: true
 
 skip_commits:
   files:

rakefile.rb

@@ -28,7 +28,7 @@
 
 def copy_to_app(app_target_relative_path)
   app_target_path = File.join(solution_dir, app_target_relative_path)
-  source_dir = File.join(src_dir, 'OSPSuite.UI', 'bin', 'Debug')
+  source_dir = File.join(tests_dir, 'OSPSuite.Starter', 'bin', 'Debug')
 
   copy_depdencies source_dir,  app_target_path do
     copy_file 'OSPSuite.*.dll'
@@ -41,7 +41,7 @@ def solution_dir
 	File.dirname(__FILE__)
 end
 
-def src_dir
-	File.join(solution_dir, 'src')
+def tests_dir
+	File.join(solution_dir, 'tests')
 end
 

src/OSPSuite.Assets/OSPSuite.Assets.csproj

@@ -34,9 +34,8 @@
     <WarningLevel>4</WarningLevel>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="OSPSuite.Utility, Version=2.0.0.5, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\packages\OSPSuite.Utility.2.0.0.5\lib\net45\OSPSuite.Utility.dll</HintPath>
-      <Private>True</Private>
+    <Reference Include="OSPSuite.Utility, Version=2.0.1.4, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\OSPSuite.Utility.2.0.1.4\lib\net452\OSPSuite.Utility.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />

src/OSPSuite.Assets/UIConstants.cs

@@ -179,6 +179,16 @@ public static class Captions
       public static readonly string Exception = "Exception";
       public static readonly string StackTrace = "Stack Trace";
 
+      public static string ShouldWatermarkBeUsedForChartExportToClipboard(string applicationName, string optionLocation)
+      {
+         var sb = new StringBuilder();
+         sb.AppendLine("The watermark feature was introduced to clearly identify draft versions of plots.");
+         sb.AppendLine();
+         sb.AppendLine($"Do you want this installation of {applicationName} to use this feature? If yes, a watermark will be used when copying charts to clipboard.");
+         sb.AppendLine($"This setting, as well as the watermark text, can be changed anytime under '{optionLocation}'.");
+         return sb.ToString();
+      }
+
       public static string IssueTrackerLinkFor(string application) => $"Go to {application} Issue Tracker";
 
       public static string ReallyDeleteAllObservedData(IEnumerable<string> anythingNotDeleted)
@@ -188,7 +198,7 @@ public static string ReallyDeleteAllObservedData(IEnumerable<string> anythingNot
          if (notDeleted.Count == 0)
             return prompt;
 
-         return $"{prompt}\n\nWarning:\n\n{notDeleted.ToString("\n\n")}\n\nand will not be removed.";
+         return $"{prompt}\n\nWarning: Following observed data are still in use and will not be deleted: \n\n{notDeleted.ToString("\n\n")}";
       }
 
       public static string CloneObjectBase(string entityType, string name)
@@ -241,31 +251,53 @@ public static string DoYouWantToDeleteDirectory(string newDirectoryName)
          return $"Do you want to delete the directory '{newDirectoryName}' and continue?";
       }
 
-      public static void AppendListItem(string listItem, StringBuilder sb)
+      public static void AppendListItem(StringBuilder sb, bool html, string listItem, int index)
+      {
+         if(html)
+            sb.Append($"<li>{listItem}</li>");
+         else
+            sb.AppendLine($"   {index}: {listItem}");
+      }
+
+      public static void AppendLine(StringBuilder sb, bool html, string lineToAppend)
       {
-         sb.Append($"<li>{listItem}</li>");
+         if (html)
+            sb.Append($"<p>{lineToAppend}</p>");
+         else
+            sb.AppendLine(lineToAppend);
       }
 
-      public static void AppendLine(string lineToAppend, StringBuilder sb)
+
+      public static void AddOrderedList(StringBuilder sb, bool html, params string [] list)
       {
-         sb.Append($"<p>{lineToAppend}</p>");
+         if(html)
+            sb.Append("<ol>");
+
+         list.Each((item, i) =>
+         {
+            //index in list item should start at 1
+            AppendListItem(sb, html, item, i + 1);
+         });
+
+         if (html)
+            sb.Append("</ol>");
       }
 
-      public static string ExceptionViewDescription(string issueTrackerUrl)
+      public static string ExceptionViewDescription(string issueTrackerUrl, bool html=true)
       {
          var sb = new StringBuilder();
-         AppendLine("oops...something went terribly wrong.", sb);
-         AppendLine(string.Empty, sb);
-         AppendLine("To best address the error, please enter an issue in our issue tracker:", sb);
-         sb.Append("<ol>");
-         AppendListItem($"Visit <b>{issueTrackerUrl}</b> or click on the link below", sb);
-         AppendListItem("Click on the <b>New Issue</b> button", sb);
-         AppendListItem("Describe the steps you took prior to the problem emerging", sb);
-         AppendListItem($"Copy the information below by using the <b>{CopyToClipboard}</b> button and paste it in the issue description", sb);
-         AppendListItem("if possible, attach your project file to the issue (do not attach confidential information)", sb);
-         sb.Append("</ol>");
-         AppendLine(string.Empty, sb);
-         AppendLine("Note: A GitHub account is required to create an issue", sb);
+         AppendLine(sb, html, "oops...something went terribly wrong.");
+         AppendLine(sb, html, string.Empty);
+         AppendLine(sb, html, "To best address the error, please enter an issue in our issue tracker:");
+         AddOrderedList(sb, html, 
+            $"Visit <b>{issueTrackerUrl}</b> or click on the link below",
+            "Click on the <b>New Issue</b> button",
+            "Describe the steps you took prior to the problem emerging",
+            $"Copy the information below by using the <b>{CopyToClipboard}</b> button and paste it in the issue description",
+            "if possible, attach your project file to the issue (do not attach confidential information)"
+         );
+         AppendLine(sb, html, string.Empty);
+         AppendLine(sb, html, "Note: A GitHub account is required to create an issue");
          return sb.ToString();
       }
 
@@ -572,6 +604,7 @@ public static string FormulaComparisonModeDescription
          }
 
          public static readonly string OnlyComputeModelRelevantProperties = "Only compare properties relevant to simulation results";
+         public static readonly string CompareHiddenEntities = "Compare hidden entities (e.g. parameters)";
          public static readonly string FormulaComparisonValue = "Values";
          public static readonly string FormulaComparisonFormula = "Formulas";
          public static readonly string RunComparison = "Start";
@@ -638,6 +671,7 @@ public static class ParameterIdentification
          public static readonly string RunMessage = "Message";
          public static readonly string RunIndex = "Run #";
          public static readonly string UseAsFactor = "Use as Factor";
+         public static readonly string IsFixed = "Fixed";
          public static readonly string LLOQMode = "Transform data below LLOQ";
          public static readonly string RemoveLLOQMode = "Remove data below LLOQ";
          public static readonly string TimeProfileAnalysis = "Time Profile";
@@ -945,10 +979,6 @@ public static string ReallyDeleteObservedData(string observedDataName)
          return $"Really delete observed data '{observedDataName}' from project";
       }
 
-      public static string IsUsedBy(string name, string typeNamesUsingObservedData)
-      {
-         return $"'{name}' is used by \n{typeNamesUsingObservedData}";
-      }
 
       public static class Chart
       {
@@ -1015,6 +1045,8 @@ public static class FontAndSizeSettings
             public static readonly string FontSizeTitle = "Font Size Title";
             public static readonly string FontSizeDescription = "Font Size Description";
             public static readonly string FontSizeOrigin = "Font Size Origin";
+            public static readonly string FontSizeWatermark = "Font Size Watermark";
+            public static readonly string IncludeOriginData = "Include Origin Data";
          }
       }
    }
@@ -1033,16 +1065,24 @@ public static class Error
       public static readonly string SessionDisposed = "Session was disposed";
       public static readonly string OutputMappingHasInconsistentDimension = "Output mapping has inconsistent dimension";
       public static readonly string WeightValueCannotBeNegative = "Weights cannot be negative";
-      public static readonly string CurveNameMissing = "Curve Name is missing";
       public static readonly string DifferentXAxisDimension = "Different from X axis dimension";
       public static readonly string DifferentYAxisDimension = "Different from Y axis dimension";
       public static readonly string CannotConvertYAxisUnits = "Cannot convert to Y axis unit";
 
       public static string LinkedParameterIsNotValidInIdentificationParameter(string identificationParameterName) => $"At least one linked parameter is invalid in identification paramter '{identificationParameterName}'";
 
-      public static string CannotDeleteBuildingBlockUsedBy(string buildingBlockType, string buildingBlockName, IReadOnlyList<string> typesNamed)
+      public static string CannotDeleteBuildingBlockUsedBy(string buildingBlockType, string buildingBlockName, IReadOnlyList<string> usersOfBuildingBlock)
+      {
+         var content = usersOfBuildingBlock.Count > 1 ? 
+            $"\n{usersOfBuildingBlock.ToString("\n", "  ")}\n" : 
+            $"{usersOfBuildingBlock.ToString(""," ")}"; 
+
+         return $"{buildingBlockType} '{buildingBlockName}' is used by{content}and cannot be deleted.";
+      }
+
+      public static string CannotDeleteObservedData(string observedDataName, IReadOnlyList<string> usersOfObservedData)
       {
-         return $"{buildingBlockType} '{buildingBlockName}' is used by\n\n{typesNamed.ToString("\n")}\n\nand cannot be deleted.";
+         return CannotDeleteBuildingBlockUsedBy(ObjectTypes.ObservedData, observedDataName, usersOfObservedData);
       }
 
       public static string OutputsDoNotAllHaveTheSameScaling(string outputName)
@@ -1231,6 +1271,8 @@ public static string CouldNotLoadTemplateFromFile(string templateFilePath)
          return $"Could not load chart template. Make sure that the file '{templateFilePath}' is a template file.";
       }
 
+      public static string CannotFindResource(string resourceFullPath) => $"Cannot find resource located at '{resourceFullPath}'";
+
       public static string IndividualIdDoesNotMatchTheValueLength(int indiviudalId, int count)
       {
          return $"Individual Id '{indiviudalId}' does not match the expected number of individual '{count}'. A reason could be that the results were imported starting with an id of 1 instead of 0.";
@@ -1261,6 +1303,8 @@ public static string FirstDataRowOutOfRange(int firstDataRow, int lastRow, strin
          return rowOutOfRange(firstDataRow, lastRow, "first data", sheetName);
       }
 
+      public static string RemoveHigherAxisTypeFirst(string type) => $"Please remove Y-Axis {type} first.";
+
       public static string LastDataRowLessThanFirstDataRow(int dataEndRow, int dataStartRow, string sheetName)
       {
          return $"Cannot import data from {sheetName} worksheet.{Environment.NewLine}The first data row index is greater than the last data row index";
@@ -1269,7 +1313,6 @@ public static string LastDataRowLessThanFirstDataRow(int dataEndRow, int dataSta
       public const string MESSAGE_ERROR_NAN = "Error information has been truncated because invalid values have been replaced by NaN.\n\n An arithmetic error must be at least 0.\n A geometric error must be at least 1.\n";
 
 
-
       public static class SensitivityAnalysis
       {
          public static readonly string NoSimulationDefined = "No simulation defined";
@@ -1415,6 +1458,20 @@ public static string CircularReferenceFoundInFormula(string entity, string entit
          var separator = "\n\t- ";
          return $"A circular reference was found in formula of {entityType.ToLower()} '{entity}' with path '{entityPath}'\nPlease check the direct or indirect references:{separator}{references.ToString(separator)}";
       }
+
+      public static string AxisMaxMustBeGreaterThanOrEqualToAxisMin(float? axisMinimumValue)
+      {
+         var preamble = "The axis maximum value should be greater than or equal to the axis minimum value";
+         return axisMinimumValue.HasValue ? $"{preamble} '{axisMinimumValue}'" : preamble;
+      }
+
+      public static string AxisMinMustBeLessThanOrEqualToAxisMax(float? axisMaximumValue)
+      {
+         var preamble = "The axis minimum value should be less than or equal to the axis maximum value";
+         return axisMaximumValue.HasValue ? $"{preamble} '{axisMaximumValue}'" : preamble;
+      }
+
+      public static readonly string LogAxisMaxMustBeGreaterThanZero = "Loagarithmic axis maximum must be greater than 0";
    }
 
    public static class Rules
@@ -1458,6 +1515,7 @@ public static class Warning
       public static readonly string OptimizedValueIsCloseToBoundary = "Identified value is close to boundary";
       public static readonly string ImportingParameterIdentificationValuesFromCancelledRun = "This parameter identification run was cancelled.\nDo you really want to import the identified parameters?";
       public static readonly string ImportingParameterIdentificationValuesFromCategorialRun = "Only the VALUES of the identified parameters will be transfered.\nPlease set the calculation methods manually.";
+      public static readonly string CurveNameIsMissing = "Curve name is missing";
    }
 
    public static class RibbonCategories
@@ -1559,7 +1617,7 @@ public static class MenuDescriptions
       public static readonly string CreateParameterIdentification = "Create a new parameter identification.";
       public static readonly string CreateSensitivityAnalysis = "Create a new sensitivity analysis.";
       public static readonly string RunParameterIdentification = "Run the active parameter identification.";
-      public static readonly string StopParameterIdentification = "Stop the current Parparameterameter identification.";
+      public static readonly string StopParameterIdentification = "Stop the current parameter identification.";
       public static readonly string UnlinkParameter = "Unlink the Parameter";
       public static readonly string TimeProfileAnalysisDescription = "Create a new chart displaying the optimized time profile in comparison to the observed data.";
       public static readonly string PredictedVsObservedAnalysisDescription = "Create a new chart displaying the optimized output vs. the observed data.";
@@ -1571,7 +1629,7 @@ public static class MenuDescriptions
       public static readonly string CovarianceMatrix = "Show the covariance matrix.";
       public static readonly string TimeProfilePredictionInterval = "Plot a pointwise linearization of the 95% prediction interval due to both the parameter uncertainty and the measurement error. This plot is only available for measured quantities.";
       public static readonly string TimeProfileConfidenceInterval = "Plot a pointwise linearization of the 95% confidence interval due to the parameter uncertainty.";
-      public static string TimeProfileVPCInterval = "Plot a pointwise linearization of the 95% visual predictive check interval due to the measurement error. This plot is only available for measured quantities.";
+      public static readonly string TimeProfileVPCInterval = "Plot a pointwise linearization of the 95% visual predictive check interval due to the measurement error. This plot is only available for measured quantities.";
       public static readonly string RunSensitivityAnalysis = "Run the active sensitivity analysis.";
       public static readonly string StopSensitivityanalysis = "Stop the current sensitivity analysis.";
    }