<commit_before><?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">

  <!--Shorthand way of getting the install directory-->
  <?define GUI_TargetDir=$(var.GUI.TargetDir)?>

  <!--Product compiles into an msi file. Only one can be present.-->
  <!--Version needs to be replaced automatically-->
  <Product Id="*" Name="MetaMorpheus" Language="1033" Version="!(bind.FileVersion.MetaMorpheusGUI.exe)" Manufacturer="Smith Group" UpgradeCode="438ad6ff-f027-423a-ab0b-c73384c0e2e5">

    <!--Properties about the package to be placed in the Summary Information Stream.-->
    <!--These are visible from COM through the IStream interface, and these properties can be seen on the package in Explorer.-->
    <Package Id="*" InstallerVersion="500" Compressed="yes" InstallScope="perMachine" Platform="x64"/>
    <MajorUpgrade AllowSameVersionUpgrades="yes" Schedule="afterInstallValidate" DowngradeErrorMessage="A newer version of MetaMorpheus is already installed."/>

    <Condition Message="This application is only supported on Windows 7 or higher.">
      <![CDATA[Installed OR (VersionNT >= 601)]]>
    </Condition>

    <Condition Message="This application requires 64-bit windows">
      <![CDATA[Installed OR VersionNT64]]>
    </Condition>

    <MediaTemplate EmbedCab="yes"/>



    <!--A feature for the Feature table. Features are the smallest installable unit.-->
    <Feature Id="ProductFeature" Level="1">

      <!-- ComponentGroupRef creates a reference to a ComponentGroup in another Fragment-->
      <ComponentGroupRef Id="ExecutablesAndLibrariesComponentGroup" />
      <!--ComponentRef creates a reference to a Component element in another Fragment-->
      <ComponentRef Id="MetaMorpheusProgramMenuFolderComponent"/>
      <!--App Data Section-->

      <ComponentGroupRef Id="Appsrc_Mods_files"/>
      <ComponentGroupRef Id="Appsrc_Data_files"/>
      <ComponentGroupRef Id="Appsrc_ProteolyticDigestion_files" />
      <!--<ComponentGroupRef Id="ExcelDefaults"/>-->
      <ComponentRef Id="MetaAppsettings.toml"/>
      <ComponentRef Id="MetaAppGUIsettings.toml"/>
      <ComponentRef Id="RemoveApp"/>
      <ComponentRef Id="DesktopShortcut"/>
      
    </Feature>

    <Directory Id="TARGETDIR" Name="SourceDir">
      <!--Desktop Shortcut Installation-->
      <Directory Id="DesktopFolder" Name="Desktop">
        <Component Id="DesktopShortcut" Guid="ef1fd292-b162-4990-80cb-cd2a0c839d4b">
          <Condition>INSTALLDESKTOPSHORTCUT</Condition>
          <RegistryKey Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Action="createAndRemoveOnUninstall">
            <RegistryValue Name="MetaMorpheusDeskTop" Value="1" Type="integer" KeyPath="yes"/>
          </RegistryKey>
          <Shortcut Id="AppDeskTopSC" Name="MetaMorpheus" Description="Shortcut to App" Target="[#MetaMorpheusGUI.exe]" WorkingDirectory="MetaMorpheusInstallFolder" />
        </Component>
      </Directory>

      <Directory Id="ProgramFiles64Folder">
        <Directory Id="MetaMorpheusInstallFolder" Name="MetaMorpheus">
          <Directory Id="DataFolder" Name="Data" />
          <Directory Id="ModsFolder" Name="Mods" />
          <Directory Id="ProteolyticDigestionFolder" Name="ProteolyticDigestion" />
        </Directory>
      </Directory>
      <Directory Id="ProgramMenuFolder">
        <Directory Id="MetaMorpheusProgramMenuFolder" Name="MetaMorpheus">

        </Directory>
      </Directory>
      <Directory Id="LocalAppDataFolder">
        <Directory Id="MetaMorpheusAppFolder" Name="MetaMorpheus">
          <Component Id="MetaAppsettings.toml" Guid="1d8da0c2-5b44-4fe4-a581-1fc526346313">
            <Condition>OVERWRITEAPPDATA</Condition>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            <File Id="settings.toml" Name="settings.toml" Source="$(var.GUI_TargetDir)settings.toml" />
          </Component>
          <Component Id="MetaAppGUIsettings.toml" Guid="9b60d7a4-a764-4ba1-8903-1733fc70618a">
            <Condition>OVERWRITEAPPDATA</Condition>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            <File Id="GUIsettings.toml" Name="GUIsettings.toml" Source="$(var.GUI_TargetDir)GUIsettings.toml" />
          </Component>
          <Component Id="RemoveApp" Guid="a5443b89-65b0-4855-b521-e7bcc9c5a85c">
            <RemoveFolder Id="MetaMorpheusAppFolder" On="uninstall"/>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
          </Component>
          <Directory Id="MetaAppDataFolder" Name="Data" />
          <Directory Id="MetaAppModsFolder" Name="Mods" />
          <Directory Id="MetaAppProteolyticDigestionFolder" Name="ProteolyticDigestion" />
        </Directory>
      </Directory>
    </Directory>

    <UI>
      <UIRef Id="WixUI_Mondo"/>
      <UIRef Id="newDlg"/>
      <UIRef Id="MyMaintenance"/>
      <Publish Dialog="WelcomeDlg" Control="Next" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Back" Event="NewDialog" Value="WelcomeDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Next" Event="NewDialog" Value="VerifyReadyDlg" Order="1">1</Publish>

      <Publish Dialog="VerifyReadyDlg" Control="Back" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MaintenanceWelcomeDlg" Control="Next" Event="NewDialog" Value="MyMaintenanceTypeDlg">1</Publish>
      <Publish Dialog="MyMaintenanceTypeDlg" Control="Back" Event="NewDialog" Value="MaintenanceWelcomeDlg" Order="1">1</Publish>
      <!--<Publish Dialog="MyMaintenanceTypeDlg" Control="Next" Event="NewDialog" Value="ExitDialog" Order="1">1</Publish>-->

      <Publish Dialog="ExitDialog"<commit_msg>fix installer contaminants db (#1365)<commit_after><?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">

  <!--Shorthand way of getting the install directory-->
  <?define GUI_TargetDir=$(var.GUI.TargetDir)?>

  <!--Product compiles into an msi file. Only one can be present.-->
  <!--Version needs to be replaced automatically-->
  <Product Id="*" Name="MetaMorpheus" Language="1033" Version="!(bind.FileVersion.MetaMorpheusGUI.exe)" Manufacturer="Smith Group" UpgradeCode="438ad6ff-f027-423a-ab0b-c73384c0e2e5">

    <!--Properties about the package to be placed in the Summary Information Stream.-->
    <!--These are visible from COM through the IStream interface, and these properties can be seen on the package in Explorer.-->
    <Package Id="*" InstallerVersion="500" Compressed="yes" InstallScope="perMachine" Platform="x64"/>
    <MajorUpgrade AllowSameVersionUpgrades="yes" Schedule="afterInstallValidate" DowngradeErrorMessage="A newer version of MetaMorpheus is already installed."/>

    <Condition Message="This application is only supported on Windows 7 or higher.">
      <![CDATA[Installed OR (VersionNT >= 601)]]>
    </Condition>

    <Condition Message="This application requires 64-bit windows">
      <![CDATA[Installed OR VersionNT64]]>
    </Condition>

    <MediaTemplate EmbedCab="yes"/>



    <!--A feature for the Feature table. Features are the smallest installable unit.-->
    <Feature Id="ProductFeature" Level="1">

      <!-- ComponentGroupRef creates a reference to a ComponentGroup in another Fragment-->
      <ComponentGroupRef Id="ExecutablesAndLibrariesComponentGroup" />
      <!--ComponentRef creates a reference to a Component element in another Fragment-->
      <ComponentRef Id="MetaMorpheusProgramMenuFolderComponent"/>
      <!--App Data Section-->

      <ComponentGroupRef Id="Appsrc_Mods_files"/>
      <ComponentGroupRef Id="Appsrc_Data_files"/>
      <ComponentGroupRef Id="Appsrc_ProteolyticDigestion_files" />
      <ComponentGroupRef Id="Appsrc_Contaminants_files"/>
      <!--<ComponentGroupRef Id="ExcelDefaults"/>-->
      <ComponentRef Id="MetaAppsettings.toml"/>
      <ComponentRef Id="MetaAppGUIsettings.toml"/>
      <ComponentRef Id="RemoveApp"/>
      <ComponentRef Id="DesktopShortcut"/>
      
    </Feature>

    <Directory Id="TARGETDIR" Name="SourceDir">
      <!--Desktop Shortcut Installation-->
      <Directory Id="DesktopFolder" Name="Desktop">
        <Component Id="DesktopShortcut" Guid="ef1fd292-b162-4990-80cb-cd2a0c839d4b">
          <Condition>INSTALLDESKTOPSHORTCUT</Condition>
          <RegistryKey Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Action="createAndRemoveOnUninstall">
            <RegistryValue Name="MetaMorpheusDeskTop" Value="1" Type="integer" KeyPath="yes"/>
          </RegistryKey>
          <Shortcut Id="AppDeskTopSC" Name="MetaMorpheus" Description="Shortcut to App" Target="[#MetaMorpheusGUI.exe]" WorkingDirectory="MetaMorpheusInstallFolder" />
        </Component>
      </Directory>

      <Directory Id="ProgramFiles64Folder">
        <Directory Id="MetaMorpheusInstallFolder" Name="MetaMorpheus">
          <Directory Id="DataFolder" Name="Data" />
          <Directory Id="ModsFolder" Name="Mods" />
          <Directory Id="ProteolyticDigestionFolder" Name="ProteolyticDigestion" />
        </Directory>
      </Directory>
      <Directory Id="ProgramMenuFolder">
        <Directory Id="MetaMorpheusProgramMenuFolder" Name="MetaMorpheus">

        </Directory>
      </Directory>
      <Directory Id="LocalAppDataFolder">
        <Directory Id="MetaMorpheusAppFolder" Name="MetaMorpheus">
          <Component Id="MetaAppsettings.toml" Guid="1d8da0c2-5b44-4fe4-a581-1fc526346313">
            <Condition>OVERWRITEAPPDATA</Condition>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            <File Id="settings.toml" Name="settings.toml" Source="$(var.GUI_TargetDir)settings.toml" />
          </Component>
          <Component Id="MetaAppGUIsettings.toml" Guid="9b60d7a4-a764-4ba1-8903-1733fc70618a">
            <Condition>OVERWRITEAPPDATA</Condition>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            <File Id="GUIsettings.toml" Name="GUIsettings.toml" Source="$(var.GUI_TargetDir)GUIsettings.toml" />
          </Component>
          <Component Id="RemoveApp" Guid="a5443b89-65b0-4855-b521-e7bcc9c5a85c">
            <RemoveFolder Id="MetaMorpheusAppFolder" On="uninstall"/>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
          </Component>
          <Directory Id="MetaAppDataFolder" Name="Data" />
          <Directory Id="MetaAppModsFolder" Name="Mods" />
          <Directory Id="MetaAppProteolyticDigestionFolder" Name="ProteolyticDigestion" />
          <Directory Id="MetaAppContaminantsFolder" Name="Contaminants" />
        </Directory>
      </Directory>
    </Directory>

    <UI>
      <UIRef Id="WixUI_Mondo"/>
      <UIRef Id="newDlg"/>
      <UIRef Id="MyMaintenance"/>
      <Publish Dialog="WelcomeDlg" Control="Next" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Back" Event="NewDialog" Value="WelcomeDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Next" Event="NewDialog" Value="VerifyReadyDlg" Order="1">1</Publish>

      <Publish Dialog="VerifyReadyDlg" Control="Back" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MaintenanceWelcomeDlg" Control="Next" Event="NewDialog" Value="MyMaintenanceTypeDlg">1</Publish>
      <Publish Dialog="MyMaintenanceTypeDlg" Control="Back" Event="NewDialog" Value="MaintenanceWelcomeDlg" Order="1">1</Publish>
      <!--<Publish Dialog="MyMaintenanceTypeDlg" Control="Next" Event="NewDialog" Value="ExitDialog" Order="1">1</Publish>-->

      <Publish Dialog="ExitDialog"
{'fraction_non_alphanumeric': 0.14248855597170204, 'fraction_numerical': 0.024968789013732832, 'mean_word_length': 4.111016588685666, 'pattern_counts': {'":': 0, '<': 209, '<?xml version=': 2, '>': 209, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '334474', 'n_tokens_mistral': 3779, 'n_tokens_neox': 3499, 'n_words': 698}