aces · cmadjar · Nov 6, 2025 · Oct 30, 2025 · Oct 30, 2025 · Oct 30, 2025
diff --git a/.github/actions/setup-python/action.yml b/.github/actions/setup-python/action.yml
@@ -15,7 +15,7 @@ runs:
       cache: 'pip'
 
   - name: Install Python dependencies
-    run: pip install -r install/requirements/requirements.txt
+    run: pip install .[dev]
     shell: bash
 
   - name: Set up environment variables

diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,6 @@
 **/__pycache__/*
 *.pyc
-.loris_mri/
+config/
 python_virtualenvs/
 environment
 **/.DS_Store
diff --git a/DTIPrep/DTIPrepRegister.pl b/DTIPrep/DTIPrepRegister.pl
@@ -12,7 +12,7 @@ =head1 SYNOPSIS
 
 Available options are:
 
--profile        : name of the config file in C<../dicom-archive/.loris-mri>
+-profile        : name of the config file in C<../config>
 
 -DTIPrep_subdir : C<DTIPrep> subdirectory storing the processed files to
                    be registered
@@ -114,7 +114,7 @@ =head2 Methods
 
 # Define the table describing the command-line options
 my  @args_table = (
-    ["-profile",              "string", 1,  \$profile,          "name of the config file in ../dicom-archive/.loris_mri."],
+    ["-profile",              "string", 1,  \$profile,          "name of the config file in ../config."],
     ["-DTIPrep_subdir",       "string", 1,  \$DTIPrep_subdir,   "DTIPrep subdirectory storing the processed files to be registered"],
     ["-DTIPrepProtocol",      "string", 1,  \$DTIPrepProtocol,  "DTIPrep protocol used to obtain the output files"],
     ["-DTI_file",             "string", 1,  \$dti_file,         "Native DWI dataset used to obtain the output files"],
@@ -132,10 +132,10 @@ =head2 Methods
     print STDERR "$Usage\n\tERROR: missing -profile argument\n\n";
     exit $NeuroDB::ExitCodes::PROFILE_FAILURE;
 }
-{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/$profile" }
+{ package Settings; do "$ENV{LORIS_CONFIG}/$profile" }
 if  ( !@Settings::db ) {
     print STDERR "\n\tERROR: You don't have a \@db setting in the file "
-                 . "$ENV{LORIS_CONFIG}/.loris_mri/$profile \n\n";
+                 . "$ENV{LORIS_CONFIG}/$profile \n\n";
     exit $NeuroDB::ExitCodes::DB_SETTINGS_FAILURE;
 }
 if (!$DTIPrep_subdir) {

diff --git a/DTIPrep/DTIPrep_pipeline.pl b/DTIPrep/DTIPrep_pipeline.pl
diff --git a/LICENSE b/LICENSE
diff --git a/batch_uploads_imageuploader.pl b/batch_uploads_imageuploader.pl
@@ -13,7 +13,7 @@ =head1 SYNOPSIS
 
 Available options are:
 
--profile: name of the config file in C<../dicom-archive/.loris_mri>
+-profile: name of the config file in C<../config>
 
 -verbose: if set, be verbose
 
@@ -63,7 +63,7 @@ =head2 Methods
 
 
 my $profile   = '';
-my $upload_id = undef; 
+my $upload_id = undef;
 my ($debug, $verbose) = (0,1);
 my $stdout = '';
 my $stderr = '';
@@ -72,7 +72,7 @@ =head2 Methods
     [ "Basic options", "section" ],
     [
         "-profile", "string", 1, \$profile,
-        "name of config file in ../dicom-archive/.loris_mri"
+        "name of config file in ../config"
     ],
     ["-verbose", "boolean", 1,   \$verbose, "Be verbose."]
 );
@@ -119,10 +119,10 @@ =head2 Methods
     print STDERR "$Usage\n\tERROR: missing -profile argument\n\n";
     exit $NeuroDB::ExitCodes::PROFILE_FAILURE;
 }
-{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/$profile" }
+{ package Settings; do "$ENV{LORIS_CONFIG}/$profile" }
 if ( !@Settings::db ) {
     print STDERR "\n\tERROR: You don't have a \@db setting in the file "
-                 . "$ENV{LORIS_CONFIG}/.loris_mri/$profile \n\n";
+                 . "$ENV{LORIS_CONFIG}/$profile \n\n";
     exit $NeuroDB::ExitCodes::DB_SETTINGS_FAILURE;
 }
 
@@ -158,7 +158,7 @@ =head2 Methods
 
 
 
-my ($stdoutbase, $stderrbase) = ("$data_dir/batch_output/imuploadstdout.log", 
+my ($stdoutbase, $stderrbase) = ("$data_dir/batch_output/imuploadstdout.log",
 				 "$data_dir/batch_output/imuploadstderr.log");
 
 while($_ = $ARGV[0] // '', /^-/) {
@@ -201,7 +201,7 @@ =head2 Methods
     my $phantom     = $phantomarray[$counter-1];
     my $patientname = $patientnamearray[$counter-1];
 
-    ## Ensure that 
+    ## Ensure that
     ## 1) the uploaded file is of type .tgz or .tar.gz or .zip
     ## 2) check that input file provides phantom details (Y for phantom, N for real candidates)
     ## 3) for non-phantoms, the patient name and path entries are identical; this mimics the imaging uploader in the front-end
@@ -235,7 +235,7 @@ =head2 Methods
 	}
     }
 
-    ## Populate the mri_upload table with necessary entries and get an upload_id 
+    ## Populate the mri_upload table with necessary entries and get an upload_id
 
     $upload_id = insertIntoMRIUpload(\$dbh,
 				     $patientname,

diff --git a/batch_uploads_tarchive.pl b/batch_uploads_tarchive.pl
@@ -18,7 +18,7 @@ =head1 DESCRIPTION
 from C<STDIN>, one file name per line. Each file name is assumed to be a path
 relative to C<tarchiveLibraryDir> (see below).
 
-The following settings of file F<$ENV{LORIS_CONFIG}/.loris-mri/prod> affect the
+The following settings of file F<$ENV{LORIS_CONFIG}/prod> affect the
 behvaviour of C<batch_uploads_tarchive> (where C<$ENV{LORIS_CONFIG}> is the
 value of the Unix environment variable C<LORIS_CONFIG>):
 
@@ -100,7 +100,7 @@ =head1 AUTHORS
 
 my $profile = undef;
 my $verbose = 0;
-my $profile_desc = "name of the config file in ../dicom-archive/.loris_mri";
+my $profile_desc = "name of the config file in ../config";
 
 my @opt_table = (
   [ "Basic options", "section" ],
@@ -148,10 +148,10 @@ =head1 AUTHORS
     exit 3;
 }
 
-{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/$profile" }
+{ package Settings; do "$ENV{LORIS_CONFIG}/$profile" }
 if ($profile && !@Settings::db) {
     print "\n\tERROR: You don't have a configuration file named ".
-        "'$profile' in:  $ENV{LORIS_CONFIG}/.loris_mri/ \n\n";
+        "'$profile' in:  $ENV{LORIS_CONFIG}/ \n\n";
     exit 2;
 }
 

diff --git a/dicom-archive/dicomSummary.pl b/dicom-archive/dicomSummary.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl 
+#!/usr/bin/perl
 # J-Sebastian Muehlboeck 2006
 # [email protected]
 # Perl tool based on DCMSUM.pm and DICOM.pm to create a summary report for a given dir containing dicoms
@@ -25,8 +25,7 @@ =head1 SYNOPSIS
 -dbreplace : use this option only if the DICOM data changed and need to be updated
              in the database
 
--profile   : specify the name of the config file residing in C<.loris_mri> of the
-             current directory
+-profile   : specify the name of the config file residing in the config directory
 
 -tmp       : to specify a temporary directory. It will contain the summaries if
              used with -noscreen option
@@ -94,9 +93,9 @@ =head2 METHODS
 - a tool for producing an informative summary for dicoms in a given directory
 - a quick way to get an idea on what there is for a given subject
 - a quick way to obtain information about the suject, scanner and acquisition parameters
-- a quick way of listing all acquisitions aquired for a given subject 
-- a convenient way to compare two directories in terms of the dicom data they contain... 
-  or the contents of a directory with a database repository 
+- a quick way of listing all acquisitions aquired for a given subject
+- a convenient way to compare two directories in terms of the dicom data they contain...
+  or the contents of a directory with a database repository
 
 Usage:\n\t $0 </PATH/TO/DICOM/DIR> [ -comparedir </PATH/TO/DICOM/COMPARE/DIR> ] [ -tmp </PATH/TO/TMP/DIR> ] [options]
 \n\n See $0 -help for more info\n\n";
@@ -108,17 +107,17 @@ =head2 METHODS
      ["-dbcompare","boolean",1, \$databasecomp, "Compare with database. Will only work if you actually archived your data using a database."],
      ["-database","boolean", 1, \$dbase, "Use a database if you have one set up for you. Just trying will fail miserably"],
      ["-dbreplace","boolean",1, \$dbreplace, "Use this option only if your dicom data changed and you want to re-insert the new summary"],
-     ["-profile","string",1, \$profile, "Specify the name of the config file which resides in .loris_mri in the current directory."],
+     ["-profile","string",1, \$profile, "Specify the name of the config file which resides in the config directory."],
+
 
-
      ["Output options", "section"],
      ["-screen","boolean",1,    \$screen, "Print output to the screen."],
      # fixme add more options based on the capabilities of the DCMSUM class
      # ["-produce","string",1,    \$produce, "Default is summary, other options are header, files, and acquisitions"],
      ["-tmp","string",1,        \$temp, "You may specify a tmp dir. It will contain the summaries, if you use -noscreen"],
      ["-xdiff","boolean",1,     \$xdiff, "You are comparing two folders or with the database and you want to see the result with sdiff."],
      ["-batch","boolean",1,     \$batch, "Run in batchmode. Will log differences to a /tmp/diff.log"],
-     
+
      ["General options", "section"],
      ["-verbose","boolean",1,  \$verbose, "Be verbose."],
      ["-version","boolean",1,  \$version, "Print version and revision number and exit"],
@@ -130,8 +129,8 @@ =head2 METHODS
 if ($version) { print "$versionInfo\n"; exit; }
 
 # checking for profile settings
-if($profile && -f "$ENV{LORIS_CONFIG}/.loris_mri/$profile") { { package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/$profile" } }    
-if ($profile && !@Settings::db) { print "\n\tERROR: You don't have a configuration file named '$profile' in:  $ENV{LORIS_CONFIG}/.loris_mri/ \n\n"; exit 33; }
+if($profile && -f "$ENV{LORIS_CONFIG}/$profile") { { package Settings; do "$ENV{LORIS_CONFIG}/$profile" } }
+if ($profile && !@Settings::db) { print "\n\tERROR: You don't have a configuration file named '$profile' in:  $ENV{LORIS_CONFIG}/ \n\n"; exit 33; }
 
 
 # basic error checking on dcm dir
@@ -148,7 +147,7 @@ =head2 METHODS
 if ($xdiff || $compare || $batch || $databasecomp || $dbase){ $screen = undef; } elsif (!$compare || !$databasecomp) { $xdiff = undef; }
 
 # you can't compare with db and a dir at the same time
-if (($compare || $databasecomp) && $dbase) { print $Usage; 
+if (($compare || $databasecomp) && $dbase) { print $Usage;
     print "\t Please consider that some option combinations do not make sense. \n\n"; exit 1;
 }
 
@@ -162,19 +161,19 @@ =head2 METHODS
 push @dcmDirs, $dcm_folder; if ($compare) { push @dcmDirs, $compare; } # if compare is set
 
 # This will make sure that a user specified tmp dir does exist and is writeable
-my $TmpDir = $temp || "/tmp";  if (! -e $TmpDir) { print "This is not a valid tmp dir choice: \n".$!; exit 2; } 
+my $TmpDir = $temp || "/tmp";  if (! -e $TmpDir) { print "This is not a valid tmp dir choice: \n".$!; exit 2; }
 elsif(! -w $TmpDir) { print "Sorry you have no permission to use $TmpDir as tmp dir\n"; exit 2; }
 
 # establish database connection if database option is set
 my $dbh;
 if ($dbase) { $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db); print "Testing for database connectivity. \n" if $verbose; $dbh->disconnect(); print "Database is available.\n\n" if $verbose; }
 
-####################### main ########################################### main ########################################### 
+####################### main ########################################### main ###########################################
 
 my $count = 0;
 my ($studyUnique, $metaname, @metaFiles, $dcmdir, $sumTypeVersion);
 
-# this silly header will only show, if you choose to send your output to the screen.    
+# this silly header will only show, if you choose to send your output to the screen.
 if ($screen){ &silly_head(); }
 
 foreach $dcmdir (@dcmDirs) {
@@ -197,8 +196,8 @@ =head2 METHODS
 
 # print the summary
     $summary->dcmsummary();
-    
-# If output went to a meta file, rename it and give it a count if -compare was specified.     
+
+# If output went to a meta file, rename it and give it a count if -compare was specified.
     if (!$screen) {
 	close META;
 	my $newName;
@@ -208,7 +207,7 @@ =head2 METHODS
 	push @metaFiles, $newName;
 	`$move`;
     }
-# Print to stout again          
+# Print to stout again
     select (STDOUT);
     print "Done with $metaname\n" if $verbose;
 
@@ -226,16 +225,16 @@ =head2 METHODS
 # END OF LOOP #######################################################################################
 
 my $returnVal = 0;
-    
+
 # if -databasecompare has been given look for an entry based on unique studyID
 if ($databasecomp) {
     my $conflict = &version_conflict($studyUnique);
     if ($conflict) { print "\n\n\tWARNING: You are using Version: $versionInfo but archived with Version : $conflict\n\n"; }
     $metaFiles[1] = &read_db_metadata($studyUnique);
     if (!$metaFiles[1]) { print "\nYou never archived this study or you are looking in the wrong database.\n\n"; exit; }
     if ($xdiff) { $diff = "sdiff $metaFiles[0] $metaFiles[1]"; system($diff); }
-    else { 
-	$diff = "diff -q $metaFiles[0] $metaFiles[1]"; 
+    else {
+	$diff = "diff -q $metaFiles[0] $metaFiles[1]";
 	my $Comp = `$diff`;
 	if ($Comp ne "") { print "There are differences\n" if $verbose; $returnVal = 99; }
 	else { print "Comparing $dcm_folder with the database returned no differences. Smile :)\n" if $verbose; }
@@ -282,7 +281,7 @@ sub read_db_metadata {
     $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db);
     print "Getting data from database.\n" if $verbose;
     (my $query = <<QUERY) =~ s/\n/ /gm;
-SELECT 
+SELECT
   AcquisitionMetadata
 FROM
   tarchive
@@ -296,7 +295,7 @@ sub read_db_metadata {
 	$dbmeta = $row[0];
 	$dbcomparefile = "$TmpDir/dbcompare.meta";
 	open(DBDATA,">$dbcomparefile") || die ("Cannot Open File");
-	print DBDATA "$dbmeta"; 
+	print DBDATA "$dbmeta";
 	close(DBDATA);
         return $dbcomparefile;
     }
@@ -350,10 +349,10 @@ =head3 silly_head()
 sub silly_head {
     print  <<HEAD;
 * * * * * * * * * * * * * *
-                      _   
- _|* _  _  _ _   * _ |_ _ 
+                      _
+ _|* _  _  _ _   * _ |_ _
 (_]|(_ (_)[ | )  |[ )| (_)
-                          
+
 HEAD
 }
 
@@ -371,14 +370,3 @@ =head1 AUTHORS
 Neuroscience
 
 =cut
-
-
-
-
-
-
-
-
-
-
-
diff --git a/dicom-archive/dicomTar.pl b/dicom-archive/dicomTar.pl
@@ -30,7 +30,7 @@ =head1 SYNOPSIS
                           resulting tarball!
 
 -profile                : Specify the name of the config file which resides in
-                          C<.loris_mri> in the current directory
+                          the config directory
 
 -centerName             : Specify the symbolic center name to be stored
                           alongside the DICOM institution
@@ -124,7 +124,7 @@ =head2 Methods
      ["-clobber", "boolean", 1,   \$clobber, "Use this option only if you want
      to replace the resulting tarball!"],
      ["-profile","string",1, \$profile, "Specify the name of the config file
-     which resides in .loris_mri in the current directory."],
+     which resides in the config directory."],
      ["-centerName","string",1, \$neurodbCenterName, "Specify the symbolic
      center name to be stored alongside the DICOM institution."],
      ["General options", "section"],
@@ -146,12 +146,12 @@ =head2 Methods
     print STDERR "$Usage\n\tERROR: missing -profile argument\n\n";
     exit $NeuroDB::ExitCodes::PROFILE_FAILURE;
 }
-if(-f "$ENV{LORIS_CONFIG}/.loris_mri/$profile") {
-	{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/$profile" }
+if(-f "$ENV{LORIS_CONFIG}/$profile") {
+	{ package Settings; do "$ENV{LORIS_CONFIG}/$profile" }
 }
 if ( !@Settings::db ) {
     print STDERR "\n\tERROR: You don't have a \@db setting in the file "
-                 . "$ENV{LORIS_CONFIG}/.loris_mri/$profile \n\n";
+                 . "$ENV{LORIS_CONFIG}/$profile \n\n";
     exit $NeuroDB::ExitCodes::DB_SETTINGS_FAILURE;
 }
 # The source and the target dir have to be present and must be directories.