extend verifications

Author: ammarcsj

release/macos/build_package_macos.sh

@@ -97,11 +97,41 @@ rm "$TEMP_ZIP2"
 
 # Verify the downloads and extraction
 echo "Verifying extracted resources..."
-if [ ! -d "${CONTENTS_FOLDER}/MacOS/_internal/alphaquant/resources/" ]; then
+RESOURCES_DIR="${CONTENTS_FOLDER}/MacOS/_internal/alphaquant/resources"
+if [ ! -d "$RESOURCES_DIR" ]; then
     echo "Error: Resources directory not found after extraction"
     exit 1
 fi
+
+# Verify that specific database subdirectories exist
+REFERENCE_DB_DIR="$RESOURCES_DIR/reference_databases"
+PHOSPHOPRED_DB_DIR="$RESOURCES_DIR/phosphopred_databases"
+
+echo "Checking for reference_databases directory..."
+if [ ! -d "$REFERENCE_DB_DIR" ]; then
+    echo "Error: reference_databases directory not found at $REFERENCE_DB_DIR"
+    exit 1
+fi
+
+echo "Checking for phosphopred_databases directory..."
+if [ ! -d "$PHOSPHOPRED_DB_DIR" ]; then
+    echo "Error: phosphopred_databases directory not found at $PHOSPHOPRED_DB_DIR"
+    exit 1
+fi
+
+# Verify that the phosphopred database contains the expected file
+HUMAN_PHOSPHO_FILE="$PHOSPHOPRED_DB_DIR/human_uniprot_reviewed_phos_prob.tsv"
+if [ ! -f "$HUMAN_PHOSPHO_FILE" ]; then
+    echo "Error: Expected phosphopred database file not found at $HUMAN_PHOSPHO_FILE"
+    echo "Contents of phosphopred_databases directory:"
+    ls -la "$PHOSPHOPRED_DB_DIR"
+    exit 1
+fi
+
 echo "Resources successfully downloaded and extracted"
+echo "  - reference_databases: OK"
+echo "  - phosphopred_databases: OK"
+echo "  - human_uniprot_reviewed_phos_prob.tsv: OK"
 
 ###Download section complete
 

release/windows/alphaquant_innoinstaller.iss

@@ -45,6 +45,10 @@ Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{
 [Dirs]
 ; Create the alphamap (no typo!) data directory and ensure users can modify it. This is where AlphaMap (which is imported by AlphaQuant) stores downloaded data, such as fasta files.
 Name: "{app}\_internal\alphamap\data"; Permissions: users-modify
+; Ensure alphaquant resources directories exist and are readable
+Name: "{app}\_internal\alphaquant\resources"; Permissions: users-read
+Name: "{app}\_internal\alphaquant\resources\reference_databases"; Permissions: users-read
+Name: "{app}\_internal\alphaquant\resources\phosphopred_databases"; Permissions: users-read
 
 [Files]
 Source: "..\..\dist_pyinstaller\alphaquant_gui\{#MyAppExeName}"; DestDir: "{app}"; Flags: ignoreversion

release/windows/build_package_windows.ps1

@@ -81,7 +81,36 @@ if (-not (Test-Path -Path $resourcesDir)) {
     Write-Host "Error: Resources directory not found after extraction"
     exit 1
 }
+
+# Verify that specific database subdirectories exist
+$referenceDbDir = Join-Path $resourcesDir "reference_databases"
+$phosphopredDbDir = Join-Path $resourcesDir "phosphopred_databases"
+
+Write-Host "Checking for reference_databases directory..."
+if (-not (Test-Path -Path $referenceDbDir)) {
+    Write-Host "Error: reference_databases directory not found at $referenceDbDir"
+    exit 1
+}
+
+Write-Host "Checking for phosphopred_databases directory..."
+if (-not (Test-Path -Path $phosphopredDbDir)) {
+    Write-Host "Error: phosphopred_databases directory not found at $phosphopredDbDir"
+    exit 1
+}
+
+# Verify that the phosphopred database contains the expected file
+$humanPhosphoFile = Join-Path $phosphopredDbDir "human_uniprot_reviewed_phos_prob.tsv"
+if (-not (Test-Path -Path $humanPhosphoFile)) {
+    Write-Host "Error: Expected phosphopred database file not found at $humanPhosphoFile"
+    Write-Host "Contents of phosphopred_databases directory:"
+    Get-ChildItem -Path $phosphopredDbDir -Recurse | Format-Table Name, FullName
+    exit 1
+}
+
 Write-Host "Resources successfully downloaded and extracted"
+Write-Host "  - reference_databases: OK"
+Write-Host "  - phosphopred_databases: OK"
+Write-Host "  - human_uniprot_reviewed_phos_prob.tsv: OK"
 
 # Wrapping the pyinstaller folder in a .exe package
 &  "C:\Program Files (x86)\Inno Setup 6\ISCC.exe" .\release\windows\alphaquant_innoinstaller.iss