removed mincPath, data and imagePath from the ConfigSettings

removed mincPath and imagePath from get_file.php replaced all instances of imagePath and mincPath by dataDirBasepath in the code missed one instance of mincPath Melanie's feedback reintegrated imagePath to have one path for apache and one for the LORIS-MRI server if ever the paths are different forgot to add again the imagePath to the Config SQL default schema...
aces · Feb 27, 2019 · def9351 · def9351
1 parent fa29b10
commit def9351
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Showing 7 changed files with 25 additions and 20 deletions.
diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql
@@ -74,9 +74,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('paths', 'Specify directories where LORIS-related files are stored or created. Take care when editing these fields as changing them incorrectly can cause certain modules to lose functionality.', 1, 0, 'Paths', 2);
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'imagePath', 'Path to images for display in Imaging Browser (e.g. /data/$project/data/) ', 1, 0, 'text', ID, 'Images', 9 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'base', 'The base filesystem path where LORIS is installed', 1, 0, 'text', ID, 'Base', 1 FROM ConfigSettings WHERE Name="paths";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'data', 'Path to main imaging data directory (e.g. /data/$project/data/) ', 1, 0, 'text', ID, 'Imaging data', 5 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'extLibs', 'Path to external libraries', 1, 0, 'text', ID, 'External libraries', 3 FROM ConfigSettings WHERE Name="paths";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mincPath', 'Path to MINC files (e.g. /data/$project/data/)', 1, 0, 'text', ID, 'MINC files', 8 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DownloadPath', 'Where files are downloaded', 1, 0, 'text', ID, 'Downloads', 4 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'log', 'Path to logs (relative path starting from /var/www/$projectname)', 1, 0, 'text', ID, 'Logs', 2 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MRICodePath', 'Path to directory where Loris-MRI (git) code is installed', 1, 0, 'text', ID, 'LORIS-MRI code', 6 FROM ConfigSettings WHERE Name="paths";
@@ -187,9 +185,7 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "YMd" FROM ConfigSettings WHERE
 
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/data/" FROM ConfigSettings WHERE Name="imagePath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "%LORISROOT%" FROM ConfigSettings WHERE Name="base";
-INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/data/" FROM ConfigSettings WHERE Name="data";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/EXTERNAL/LIBRARY/" FROM ConfigSettings WHERE Name="extLibs";
-INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/data/" FROM ConfigSettings WHERE Name="mincPath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "%LORISROOT%" FROM ConfigSettings WHERE Name="DownloadPath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "tools/logs/" FROM ConfigSettings WHERE Name="log";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/bin/mri/" FROM ConfigSettings WHERE Name="MRICodePath";
@@ -230,7 +226,7 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "Produced by LorisDB" FROM Confi
 INSERT INTO Config (ConfigID, Value) SELECT ID, "S3cret" FROM ConfigSettings WHERE Name="JWTKey";
 
 
-INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/DATA/location" FROM ConfigSettings cs WHERE cs.Name="Loris-MRI Data Directory";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/data/" FROM ConfigSettings cs WHERE cs.Name="dataDirBasepath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info";

diff --git a/SQL/New_patches/2019-02-08_cleanup_duplicated_data_path_in_Config.sql b/SQL/New_patches/2019-02-08_cleanup_duplicated_data_path_in_Config.sql
@@ -0,0 +1,13 @@
+-- Remove entries for mincPath and data from the Config table
+DELETE
+FROM Config
+WHERE ConfigID IN (
+  SELECT ID
+  FROM ConfigSettings
+  WHERE Name IN ('mincPath', 'data')
+);
+
+-- Remove entries for mincPath and data from the ConfigSettings table
+DELETE
+FROM ConfigSettings
+WHERE Name IN ('mincPath', 'data');
diff --git a/htdocs/api/v0.0.2/candidates/visits/images/Image.php b/htdocs/api/v0.0.2/candidates/visits/images/Image.php
@@ -168,7 +168,7 @@ protected function getAssemblyRoot()
     {
         $factory = \NDB_Factory::singleton();
         $config  = $factory->Config();
-        return $config->getSetting("mincPath");
+        return $config->getSetting("imagePath");
     }
 
     /**

diff --git a/htdocs/api/v0.0.3-dev/candidates/visits/images/Image.php b/htdocs/api/v0.0.3-dev/candidates/visits/images/Image.php
@@ -168,7 +168,7 @@ protected function getAssemblyRoot()
     {
         $factory = \NDB_Factory::singleton();
         $config  = $factory->Config();
-        return $config->getSetting("mincPath");
+        return $config->getSetting("imagePath");
     }
 
     /**

diff --git a/htdocs/mri/jiv/get_file.php b/htdocs/mri/jiv/get_file.php
@@ -39,14 +39,12 @@
 
 $imagePath    = $paths['imagePath'];
 $DownloadPath = $paths['DownloadPath'];
-$mincPath     = $paths['mincPath'];
 $tarchivePath = $pipeline['tarchiveLibraryDir'];
 // Basic config validation
 if (!validConfigPaths(
     array(
      $imagePath,
      $DownloadPath,
-     $mincPath,
      $tarchivePath,
     )
 )) {
@@ -90,17 +88,17 @@
 $DownloadFilename = '';
 switch($FileExt) {
 case 'mnc':
-    $FullPath         = $mincPath . '/' . $File;
+    $FullPath         = $imagePath . '/' . $File;
     $MimeType         = "application/x-minc";
     $DownloadFilename = basename($File);
     break;
 case 'nii':
-    $FullPath         = $mincPath . '/' . $File;
+    $FullPath         = $imagePath . '/' . $File;
     $MimeType         = "application/x-nifti";
     $DownloadFilename = basename($File);
     break;
 case 'nii.gz':
-    $FullPath         = $mincPath . '/' . $File;
+    $FullPath         = $imagePath . '/' . $File;
     $MimeType         = "application/x-nifti-gz";
     $DownloadFilename = basename($File);
     break;
@@ -190,17 +188,16 @@ function validConfigPaths(array $paths): bool
     foreach ($paths as $p) {
         if (empty($p)) {
             throw new \LorisException(
-                'Config paths are not initialized. Please ensure that valid ' .
-                'paths are set for imagePath, downloadPath, mincPath and ' .
-                'tarchiveLibraryDir'
+                'Config paths are not initialized. Please ensure that valid paths ' .
+                'are set for imagePath, downloadPath and tarchiveLibraryDir'
             );
             return false;
         }
         if ($p === '/') {
             throw new \LorisException(
                 'Config path invalid. Paths cannot be set to root, i.e., `/`' .
                 ' Please verify your path settings for imagePath, ' .
-                'downloadPath, mincPath and tarchiveLibraryDir.'
+                'downloadPath and tarchiveLibraryDir.'
             );
             return false;
         }
@@ -226,8 +223,8 @@ function validDownloadPath($path): bool
     }
     // Make sure that the user isn't trying to break out of the $path by
     // using a relative filename.
-    // No need to check for '/' since all downloads are relative to $imagePath,
-    // $DownloadPath or $mincPath
+    // No need to check for '/' since all downloads are relative to $imagePath or
+    // $DownloadPath
     if (strpos($path, "..") !== false) {
         error_log(
             'ERROR: Invalid filename. Contains path traversal characters'

diff --git a/modules/brainbrowser/ajax/image.php b/modules/brainbrowser/ajax/image.php
@@ -84,7 +84,7 @@ function getFileLocation()
 {
     $config     = & NDB_Config::singleton();
     $paths      = $config->getSetting('paths');
-    $image_path = $paths['mincPath'];
+    $image_path = $paths['imagePath'];
     return $image_path;
 }
 

diff --git a/php/installer/Installer.class.inc b/php/installer/Installer.class.inc
@@ -324,7 +324,6 @@ class Installer
 
         $this->_updateConfig($DB, "imagePath", $datadir);
         $this->_updateConfig($DB, "data", $datadir);
-        $this->_updateConfig($DB, "mincPath", $datadir);
         $this->_updateConfig($DB, "MRICodePath", $datadir);
 
         // Update the host based and URL based on the location that