pwiz: Fixed four vendor readers failing from an installer-based install

pwiz-sharp/build.bat

@@ -8,7 +8,7 @@ REM #
 REM # Usage:
 REM #   build.bat [Debug|Release] [--i-agree-to-the-vendor-licenses]
 REM #             [--require-vendor-support] [--without-mascot]
-REM #             [--automated] [--coverage]
+REM #             [--automated] [--coverage] [--with-vendor-sdks]
 REM #
 REM # Flags:
 REM #   --i-agree-to-the-vendor-licenses
@@ -23,6 +23,16 @@ REM #       Fail the build if vendor support isn't enabled. Use in CI to make
 REM #       sure --i-agree was passed, instead of silently building a stripped
 REM #       artifact.
 REM #
+REM #   --with-vendor-sdks
+REM #       Also produce ProteoWizard-WithVendorSdks-Setup-<ver>.exe: the
+REM #       bundled-runtime installer plus every Windows vendor SDK, extracted
+REM #       into VendorSdkLoader's cache. That build needs no network at run
+REM #       time (it carries the .NET runtime too), which is what the wine
+REM #       container needs. Costs ~30 s and ~26 MB over the default variants,
+REM #       so it is opt-in here and passed by tcbuild.bat on CI. No effect
+REM #       without --i-agree-to-the-vendor-licenses: the whole installer step
+REM #       is skipped in that case.
+REM #
 REM #   --without-mascot
 REM #       Disable Mascot (.dat) support in BiblioSpec. msparser is bundled
 REM #       under libraries\msparser_3_1_0_x86_win64\, so Mascot support is ON
@@ -60,6 +70,7 @@ set REQUIRE_VENDOR=0
 set AUTOMATED=0
 set COVERAGE=0
 set WITHOUT_MASCOT=0
+set WITH_VENDOR_SDKS=0
 set ERROR_TEXT=
 
 REM # Parse args. First non-flag arg is the configuration (Debug|Release).
@@ -68,6 +79,7 @@ if "%~1"=="" goto endparse
 if /i "%~1"=="--i-agree-to-the-vendor-licenses" (set IAGREE=1) else ^
 if /i "%~1"=="--require-vendor-support" (set REQUIRE_VENDOR=1) else ^
 if /i "%~1"=="--without-mascot" (set WITHOUT_MASCOT=1) else ^
+if /i "%~1"=="--with-vendor-sdks" (set WITH_VENDOR_SDKS=1) else ^
 if /i "%~1"=="--automated" (set AUTOMATED=1) else ^
 if /i "%~1"=="--coverage" (set COVERAGE=1) else ^
 if /i "%~1"=="Debug" (set CONFIG=Debug) else ^
@@ -136,10 +148,20 @@ if %IAGREE%==1 (
     if exist "%ProgramFiles%\Inno Setup 6\ISCC.exe"          set HAVE_ISCC=1
     if exist "%ProgramFiles(x86)%\Inno Setup 6\ISCC.exe"     set HAVE_ISCC=1
     if !HAVE_ISCC!==1 (
-        echo ##teamcity[progressMessage 'installer/build.ps1 -SkipBuild ^(uses Release artifacts^)']
-        pwsh -NoProfile -ExecutionPolicy Bypass -File "%SCRIPT_DIR%\installer\build.ps1" -SkipBuild
+        set INSTALLER_ARGS=-SkipBuild
+        if !WITH_VENDOR_SDKS!==1 set INSTALLER_ARGS=!INSTALLER_ARGS! -WithVendorSdks
+        echo ##teamcity[progressMessage 'installer/build.ps1 !INSTALLER_ARGS! ^(uses Release artifacts^)']
+        pwsh -NoProfile -ExecutionPolicy Bypass -File "%SCRIPT_DIR%\installer\build.ps1" !INSTALLER_ARGS!
+        REM # Fatal, not a warning. Reaching here means ISCC IS present -- the machine
+        REM # that lacks it took the else branch below -- so a failure is a real one.
+        REM # Downgrading it produced a false green: the installer never got built,
+        REM # Installer.Tests then went Inconclusive on "no ProteoWizard-Setup-*.exe
+        REM # found" and reported "Test Run Successful ... Skipped: 2", and the build
+        REM # went green with the vendor-resolution coverage silently not run.
         if !ERRORLEVEL! NEQ 0 (
-            echo ##teamcity[message text='installer build failed; Installer.Tests will skip' status='WARNING']
+            set EXIT=!ERRORLEVEL!
+            set ERROR_TEXT=installer/build.ps1 failed; Installer.Tests cannot run
+            goto error
         )
     ) else (
         echo ##teamcity[message text='Inno Setup ^(ISCC.exe^) not found; skipping installer build and Installer.Tests will skip' status='WARNING']

pwiz-sharp/build/vendor-sdk-pins.json

@@ -24,10 +24,18 @@
         "copy instead of pwiz_aux/msrc/utility/vendor_api_Bruker.7z: the upstream archive is",
         "shared with the C++ build, which still wants CompassXtract in the same archive."
       ],
+      "$comment2": [
+        "BaseCommon / BaseDataAccess / BaseError / BaseTof are deliberately NOT here. They are",
+        "Agilent MHDAC assemblies and this archive holds none of them (it ships exactly two",
+        "DLLs: baf2sql_c and timsdata). Listing them here broke Agilent from every",
+        "installer-based install: FindPin returns the FIRST pin whose prefix matches, Bruker",
+        "precedes Agilent, so a BaseCommon bind resolved to this archive and failed with",
+        "'extracted cleanly but contains no BaseCommon.dll'. Dev and CI builds never saw it",
+        "because they keep the vendor DLLs app-local, which the resolver prefers over the cache."
+      ],
       "path": "pwiz-sharp/vendor-archives/vendor_api_Bruker.7z",
       "prefixes": [
-        "Bruker.", "BaseDataAccess", "ProtocolBuffers", "BaseError", "BaseCommon", "BaseTof",
-        "timsdata", "baf2sql", "mcd_lib"
+        "Bruker.", "ProtocolBuffers", "timsdata", "baf2sql", "mcd_lib"
       ]
     },
     {
@@ -76,10 +84,16 @@
     },
     {
       "name": "Agilent",
+      "$comment": [
+        "MIDAC has no trailing dot on purpose. Prefixes are matched with StartsWith against the",
+        "assembly simple name, and this archive's assembly is plain 'MIDAC', which never starts",
+        "with 'MIDAC.' - so the dotted form silently matched nothing and Agilent failed one",
+        "assembly later than the BaseCommon collision, with 'Could not load MIDAC'."
+      ],
       "path": "pwiz_aux/msrc/utility/vendor_api_Agilent.7z",
       "prefixes": [
-        "Agilent.", "BaseDataAccess", "MIDAC.", "Mhdac.", "MassHunter.", "MassSpecDataReader",
-        "agtsampleinforw"
+        "Agilent.", "BaseCommon", "BaseDataAccess", "BaseError", "BaseTof", "MIDAC", "Mhdac.",
+        "MassHunter.", "MassSpecDataReader", "agtsampleinforw"
       ]
     },
     {
@@ -102,8 +116,15 @@
     },
     {
       "name": "Mobilion",
+      "$comment": [
+        "MobilionShim is deliberately NOT a prefix here. It is pwiz-sharp's own shim assembly,",
+        "built from src/Vendor/Mobilion, not something this archive carries (the archive holds",
+        "MBI_SDK.dll and its headers). Listing it made the installer's staging filter strip a",
+        "binary nothing could then supply, so Mobilion failed from every installer-based install",
+        "with 'archive contains no library matching MobilionShim.dll'."
+      ],
       "path": "pwiz_aux/msrc/utility/vendor_api_Mobilion.7z",
-      "prefixes": [ "Mobilion.", "MBISDK", "MBI_SDK", "MobilionShim" ]
+      "prefixes": [ "Mobilion.", "MBISDK", "MBI_SDK" ]
     }
   ]
 }

pwiz-sharp/installer/Setup.iss

@@ -1,24 +1,31 @@
 ; -----------------------------------------------------------------------------
-; Inno Setup script for ProteoWizard-Sharp.
+; Inno Setup script for ProteoWizard.
 ;
-; build.ps1 invokes ISCC twice from this one script to produce two variants:
+; build.ps1 invokes ISCC from this one script to produce up to three variants:
 ;
-;   ProteoWizard-Sharp-Setup.exe (~62 MB)
+;   ProteoWizard-Setup.exe (~78 MB)
 ;     Bundles the .NET 10 Desktop Runtime installer. On install, checks for
 ;     .NET 10; if missing, silently invokes the bundled runtime installer
 ;     (which triggers UAC for its per-machine install).
 ;
-;   ProteoWizard-Sharp-NoNetRuntime-Setup.exe (~5 MB)
+;   ProteoWizard-NoNetRuntime-Setup.exe (~22 MB)
 ;     Same payload minus the bundled runtime. On install, aborts with a
 ;     dialog + download link if .NET 10 isn't already present. For users
 ;     who manage their own runtime install (corp deployments, dev boxes
 ;     that already have it, etc.).
 ;
+;   ProteoWizard-WithVendorSdks-Setup.exe (~104 MB, opt-in: build.ps1 -WithVendorSdks)
+;     The bundled-runtime variant PLUS every Windows vendor SDK, pre-extracted
+;     into VendorSdkLoader's cache. Carries the .NET runtime too -- the name
+;     says only what it adds over the default variant, not what it inherits.
+;     Nothing it needs is fetched at run time, so it is the one to use where
+;     there is no network: an offline site install, or the wine container.
+;
 ;   Both variants:
 ;     - Ask the user to pick "for me" (per-user, no admin) or "for everyone"
 ;       (per-machine, admin) at install time
-;     - Install to %LOCALAPPDATA%\Programs\ProteoWizard-Sharp\ or
-;       %ProgramFiles%\ProteoWizard-Sharp\ accordingly
+;     - Install to %LOCALAPPDATA%\Programs\ProteoWizard\ or
+;       %ProgramFiles%\ProteoWizard\ accordingly
 ;     - Create Start Menu shortcuts for MSConvertGUI and SeeMS
 ;     - Register Windows Explorer right-click verbs
 ;     - Standard uninstall via Programs and Features
@@ -35,7 +42,7 @@
 ; `winget install JRSoftware.InnoSetup`).
 ; -----------------------------------------------------------------------------
 
-#define MyAppName "ProteoWizard-Sharp"
+#define MyAppName "ProteoWizard"
 ; Version comes in from build.ps1 via /DMyAppVersion=4.0.YYDOY-gitsha. The
 ; fallback below keeps direct ISCC invocations buildable for local debugging.
 #ifndef MyAppVersion
@@ -53,7 +60,13 @@
   #define OutputDir "build"
 #endif
 #ifndef OutputBaseFilename
-  #define OutputBaseFilename "ProteoWizard-Sharp-Setup"
+  #define OutputBaseFilename "ProteoWizard-Setup"
+#endif
+; WithVendorSdks: bundle the vendor SDKs and pre-populate VendorSdkLoader's cache, so the
+; installed app never reaches raw.githubusercontent.com. build.ps1 -WithVendorSdks sets this
+; and points VendorCacheDir at a tree it extracted into the runtime's own cache layout.
+#ifndef VendorCacheDir
+  #define VendorCacheDir "build\vendor-cache"
 #endif
 
 [Setup]
@@ -64,7 +77,7 @@
 ; own uninstaller log. Same-version reinstalls still upgrade in place.
 ;
 ; The base GUID stays stable so future migration code (or scripts iterating
-; "all ProteoWizard-Sharp installs") can match on the prefix.
+; "all ProteoWizard installs") can match on the prefix.
 ;
 ; Shared resources policy (last-installed-wins, no automatic cleanup):
 ;   - Explorer context-menu verbs are SHARED across versions: each install
@@ -138,6 +151,24 @@ Source: "cache\windowsdesktop-runtime-10.0-win-x64.exe"; DestDir: "{tmp}"; \
     Flags: deleteafterinstall; Check: not IsDotNetDesktopInstalled
 #endif
 
+#ifdef WithVendorSdks
+; Vendor SDKs, pre-extracted by build.ps1 into exactly the layout
+; VendorSdkLoader.EnsureExtracted would have produced on first use — one
+; <Vendor>-<ShortSha> directory per pin, flattened, each holding a .ok marker.
+; The marker is the whole point: with it present the loader neither downloads
+; nor extracts, so the app works offline and needs no write access to the cache.
+;
+; Destination is {commonappdata}, not {localappdata}: one copy shared by every
+; user on the machine, which is what the cache-root override below is for.
+;
+; uninsneveruninstall because the cache is keyed by SDK version, not by app
+; version, so side-by-side pwiz-sharp installs share these directories — the
+; same last-installed-wins / leave-it-alone policy the Explorer verbs use.
+; Removing every version therefore leaves the cache behind on purpose.
+Source: "{#VendorCacheDir}\*"; DestDir: "{commonappdata}\ProteoWizard\vendor"; \
+    Flags: ignoreversion recursesubdirs createallsubdirs uninsneveruninstall
+#endif
+
 [Icons]
 Name: "{group}\MSConvertGUI"; Filename: "{app}\MSConvertGUI-sharp.exe"; \
     WorkingDir: "{app}"; Tasks: startmenu_msconvertgui; \
@@ -285,6 +316,37 @@ begin
   end;
 end;
 
+#ifdef WithVendorSdks
+{ ----- Point VendorSdkLoader at the bundled cache -----
+  The loader's default cache root is %LOCALAPPDATA%\ProteoWizard\vendor, but this
+  variant installs one shared copy under %PROGRAMDATA%. GetCacheRoot() reads a path
+  out of %PROGRAMDATA%\ProteoWizard\vendor-cache-root.txt when that file exists, so
+  writing it is what makes the bundled cache the one the app actually consults.
+  Without this the SDKs would sit on disk unused and the app would still try to
+  download them.
+
+  ProgramData is writable by standard users for new subdirectories, so this works
+  for a per-user install too; if it ever does not, failing loudly beats installing
+  a cache nothing reads. }
+procedure StampVendorCacheRoot();
+var
+  dir: String;
+begin
+  dir := ExpandConstant('{commonappdata}\ProteoWizard');
+  if not ForceDirectories(dir) then
+    RaiseException('Could not create ' + dir);
+  if not SaveStringToFile(dir + '\vendor-cache-root.txt',
+                          ExpandConstant('{commonappdata}\ProteoWizard\vendor'), False) then
+    RaiseException('Could not write vendor-cache-root.txt in ' + dir);
+end;
+
+procedure CurStepChanged(CurStep: TSetupStep);
+begin
+  if CurStep = ssPostInstall then
+    StampVendorCacheRoot();
+end;
+#endif
+
 { ----- Pre-flight check (NoNetRuntime variant only) -----
   When this installer was built without the bundled .NET runtime
   (build.ps1's second ISCC pass), we can't install .NET ourselves. Abort
@@ -302,9 +364,9 @@ begin
   if not IsDotNetDesktopInstalled() then
   begin
     rc := MsgBox(
-      'ProteoWizard-Sharp requires the .NET 10 Desktop Runtime (x64), which is not installed on this machine.' + #13#10#13#10 +
+      'ProteoWizard requires the .NET 10 Desktop Runtime (x64), which is not installed on this machine.' + #13#10#13#10 +
       'Click OK to open the Microsoft download page in your browser, then re-run this installer after installing the runtime.' + #13#10#13#10 +
-      'If you prefer an installer that bundles the runtime, use ProteoWizard-Sharp-Setup.exe instead.',
+      'If you prefer an installer that bundles the runtime, use ProteoWizard-Setup.exe instead.',
       mbError, MB_OKCANCEL);
     if rc = IDOK then
       ShellExec('', 'https://dotnet.microsoft.com/download/dotnet/10.0/runtime',

pwiz-sharp/installer/build-linux.sh

@@ -4,9 +4,9 @@
 # Mirrors the Windows pipeline and its two-variant split:
 #
 #   Windows                                         Linux
-#   ProteoWizard-Sharp-Setup-<ver>.exe              ProteoWizard-Sharp-linux-x64-<ver>.tar.gz
+#   ProteoWizard-Setup-<ver>.exe              ProteoWizard-linux-x64-<ver>.tar.gz
 #     bundles the .NET desktop runtime                self-contained: the runtime is IN the payload
-#   ProteoWizard-Sharp-NoNetRuntime-Setup-<ver>.exe ProteoWizard-Sharp-NoNetRuntime-linux-x64-<ver>.tar.gz
+#   ProteoWizard-NoNetRuntime-Setup-<ver>.exe ProteoWizard-NoNetRuntime-linux-x64-<ver>.tar.gz
 #     needs .NET 8 already installed                  framework-dependent: same requirement
 #
 # "Setup" is dropped for the runtime identifier because a tarball is not an installer; the
@@ -139,8 +139,8 @@ package() {
 }
 
 RC=0
-package self-contained      true  "ProteoWizard-Sharp-$RID-$APP_VERSION"              || RC=1
-package framework-dependent false "ProteoWizard-Sharp-NoNetRuntime-$RID-$APP_VERSION" || RC=1
+package self-contained      true  "ProteoWizard-$RID-$APP_VERSION"              || RC=1
+package framework-dependent false "ProteoWizard-NoNetRuntime-$RID-$APP_VERSION" || RC=1
 
 # Same side-car build.ps1 writes, so packaging tests can pin the version without re-deriving it
 # from a filename.