Merge tag 'v20.0.0' into HEAD

README.md

@@ -1,7 +1,7 @@
-This Readme covers release 19.0 of the LORIS Imaging Insertion Pipeline for Ubuntu or CentOS systems
+This Readme covers release 20.0 of the LORIS Imaging Insertion Pipeline for Ubuntu or CentOS systems
 
-This repo accompanies the [LORIS neuroimaging data platform main repo](https://github.com/aces/Loris/releases)</b>, release 19.0.*.<br>
-For documentation and detailed setup information, please see the [LORIS wiki](https://github.com/aces/Loris/wiki/Imaging-Database)</b>.
+This repo accompanies the [LORIS neuroimaging data platform main repo](https://github.com/aces/Loris/releases)</b>, release 20.0.*.<br>
+For documentation and detailed setup information, please see the [LORIS-MRI documentation](docs/) for your installed version</b>.
 
 This repo can be installed on the same VM as the main LORIS codebase, or on a different machine such as a designated fileserver where large imaging filesets are to be stored. 
 
@@ -66,10 +66,6 @@ Download the pre-compiled package for your operating system.  Install required d
   Note: The installer will allow Apache to write to the /data/ directories by adding user lorisadmin to the Apache linux group.  To ensure this change takes effect, log out and log back into your terminal session before running the imaging pipeline.
 The installer will also set Apache group ownership of certain /data/ subdirectories.
 
-  After having run the install script, it is possible to verify that certain
-    fields were correctly populated by `imaging_install.sh` (see
-    [section 2.4](02-Install.md#2.4-post-installation-checks)).
-
 #### 4. Configure paths and environment
 
    Ensure that /home/lorisadmin/.bashrc includes the statement:
@@ -78,8 +74,12 @@ The installer will also set Apache group ownership of certain /data/ subdirector
 
    Then source the .bashrc file.   
 
-<br>
-Installation complete.
+**INSTALLATION COMPLETE!**
+
+Please refer to the [Install](docs/02-Install.md) section in the 
+[LORIS-MRI documentation](docs/) for your installed version for:
+- customizations and protocol configurations ([Section 2.2](docs/02-Install.md#configuration)).
+- verifying that certain fields were correctly populated by `imaging_install.sh`
+([Section 2.3](docs/02-Install.md#post-installation-checks)).
 
-For customizations and protocol configurations, see LORIS Imaging Setup Guide : https://github.com/aces/Loris/wiki/Imaging-Database 
 

VERSION

@@ -1 +1 @@
-19.0.0
+20.0.0

batch_uploads_imageuploader

@@ -4,19 +4,18 @@
 
 =head1 NAME
 
-batch_uploads_imageuploader -- a script that runs imaging_upload_file.pl in
+batch_uploads_imageuploader -- a script that runs C<imaging_upload_file.pl> in
 batch mode
 
 =head1 SYNOPSIS
 
-./batch_uploads_imageuploader -profile prod < list_of_scans.txt > log_batch_imageuploader.txt 2>&1 `[options]`
+./batch_uploads_imageuploader -profile prod < list_of_scans.txt > log_batch_imageuploader.txt 2>&1 C[options]>
 
 Available options are:
 
--profile      : name of the config file in
-                C<../dicom-archive/.loris_mri>
+-profile: name of the config file in C<../dicom-archive/.loris_mri>
 
--verbose      : if set, be verbose
+-verbose: if set, be verbose
 
 
 =head1 DESCRIPTION
@@ -274,9 +273,9 @@ close MAIL;
 
 Function that inserts into the C<mri_upload> table entries for data coming from
 the list of scans in the text file provided when calling
-batch_upload_imageuploader
+C<batch_upload_imageuploader>
 
-INPUTS  :
+INPUTS:
     - $patientname  : The patient name
     - $phantom      : 'Y' if the entry is for a phantom,
                       'N' otherwise
@@ -320,14 +319,6 @@ __END__
 
 =pod
 
-=head1 TO DO
-
-Nothing planned.
-
-=head1 BUGS
-
-None reported.
-
 =head1 LICENSING
 
 License: GPLv3

batch_uploads_tarchive

@@ -4,46 +4,48 @@
 
 =head1 NAME
 
-batch_uploads_tarchive - upload a batch of tarchives using script tarchiveLoader
+batch_uploads_tarchive - upload a batch of DICOM archives using script
+C<tarchiveLoader>
 
 =head1 SYNOPSIS
 
 ./batch_uploads_tarchive
 
 =head1 DESCRIPTION
 
-This script uploads a list of tarchive files to the database by calling script 
+This script uploads a list of DICOM archives to the database by calling script
 C<tarchiveLoader> on each file in succession. The list of files to process is read 
-from STDIN, one file name per line. Each file name is assumed to be a path relative 
-to C<tarchiveLibraryDir> (see below).
+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<$ENV{LORIS_CONFIG}/.loris-mri/prod> affect the 
-behvavior of batch_uploads_tarchive (where C<$ENV{LORIS_CONFIG}> is the value of
-the Unix environment variable LORIS_CONFIG):
+behvaviour of C<batch_uploads_tarchive> (where C<$ENV{LORIS_CONFIG}> is the
+value of the Unix environment variable C<LORIS_CONFIG>):
 
 =over 4
 
 =item *
-B<dataDirBasepath> : controls where the STDOUT and STDERR of each qsub command
-  (see below) will go, namely in 
+B<dataDirBasepath> : controls where the C<STDOUT> and C<STDERR> of each qsub
+command (see below) will go, namely in
   F<< $dataDirBasepath/batch_output/tarstdout.log<index> >> and
   F<< $dataDirBasepath/batch_output/tarstderr.log<index> >>
-  (where C<< <index> >> is the index of the tarchive file processed, the first file having
-   index 1).
+  (where C<< <index> >> is the index of the DICOM archive processed, the
+  first file having index 1).
    
 =item * 
-B<tarchiveLibraryDir>: directory that contains the tarchive files to process. The path
-  of the files listed on STDIN should be relative to this directory.
+B<tarchiveLibraryDir>: directory that contains the DICOM archives to process.
+The path of the files listed on C<STDIN> should be relative to this directory.
   
 =item *
-B<is_qsub>: whether the output (STDOUT) of each tarchiveLoader command should be
-  processed by the qsub Unix command (allows batch execution of jobs on the 
-  Sun Grid Engine, if available). If set, then the qsub command will send its STDOUT
-  and STDERR according to the value of dataDirBasepath (see above). 
+B<is_qsub>: whether the output (STDOUT) of each C<tarchiveLoader> command
+should be processed by the C<qsub> Unix command (allows batch execution of jobs
+on the Sun Grid Engine, if available). If set, then the C<qsub> command will
+send its C<STDOUT> and C<STDERR> according to the value of C<dataDirBasepath>
+(see above).
   
 =item *
 B<mail_use>: upon completion of the script, an email will be sent to email address
-  $mail_user cointaining the list of files processed by batch_upload_tarchive
+  $mail_user containing the list of files processed by C<batch_uploads_tarchive>
   
 =back
 
@@ -70,10 +72,6 @@ The database hostname
 
 Code cleanup: remove unused C<-D> and C<-v> program arguments
 
-=head1 BUGS
-
-None reported.
-
 =head1 LICENSING
 
 License: GPLv3

dicom-archive/DICOM/DCMSUM.pm

@@ -35,9 +35,11 @@ use NeuroDB::ExitCodes;
 
 Creates a new instance of this class.
 
-INPUTS: DICOM directory, target location
+INPUTS:
+  - $dcm_dir: DICOM directory
+  - $tmp_dir: target location
 
-RETURNS: a DICOM::DCMSUM object
+RETURNS: a C<DICOM::DCMSUM> object
 
 =cut
 
@@ -86,18 +88,18 @@ sub new {
 
 =pod 
 
-=head3 database($dbh, $meta, $update, $tarType, $tarLog, $DCMmd5, ...)
+=head3 database($dbh, $meta, $update, $tarType, $tarLog, $DCMmd5, $Archivemd5, $Archive, $neurodbCenterName)
 
-Inserts or updates the tarchive tables.
+Inserts or updates the C<tarchive> tables.
 
 INPUTS:
   - $dbh              : database handle
   - $meta             : name of the .meta file
-  - $update           : set to 1 to update tarchive entry, 0 otherwise
+  - $update           : set to 1 to update C<tarchive> entry, 0 otherwise
   - $tarType          : tar type version
   - $tarLog           : name of the .log file
   - $DCMmd5           : DICOM MD5SUM
-  - $Archivemd5       : tarchive MD5SUM
+  - $Archivemd5       : DICOM archive MD5 sum
   - $Archive          : archive location
   - $neurodbCenterName: center name
 
@@ -431,7 +433,7 @@ QUERY
 
 =head3 read_file($file)
 
-Reads the content of a file (typically .meta file in the tarchive).
+Reads the content of a file (typically .meta file in the DICOM archive).
 
 INPUT: the file to be read
 
@@ -782,10 +784,10 @@ sub fill_header {
 =head3 confirm_single_study()
 
 Confirms that only one DICOM study is in the DICOM directory to be archived.
-Returns False if there is more than one StudyUID, otherwise it returns that
-StudyUID.
+Returns C<False> if there is more than one C<StudyUID>, otherwise it returns
+that C<StudyUID>.
 
-RETURNS: StudyUID found in the DICOM directory, or false if more than one
+RETURNS: C<StudyUID> found in the DICOM directory, or C<false> if more than one
 study was found
 
 =cut
@@ -1149,9 +1151,10 @@ sub date_format {
 
 =head3 md5sum($filename)
 
-Computes the MD5 sum of a file and outputs a format similar to md5sum on Linux.
+Computes the MD5 sum of a file and outputs a format similar to C<md5sum> on
+Linux.
 
-INPUT: file name to use to computer MD5 sum
+INPUT: file name to use to compute MD5 sum
 
 RETURNS: MD5 sum of the file
 
@@ -1172,10 +1175,6 @@ sub md5sum {
 
 Fix comments written as #fixme in the code.
 
-=head1 BUGS
-
-None reported.
-
 =head1 LICENSING
 
 Copyright (c) 2006 by J-Sebastian Muehlboeck, McConnell Brain Imaging Centre,