[Perl pipeline] Do not duplicate violation entry if it already exists

docs/scripts_md/MRI.md

@@ -94,7 +94,7 @@ Inserts scans that do not correspond to any of the defined protocol from the
 database.
 
 INPUTS:
-  - $dbhr           : database handle reference
+  - $db             : database object
   - $series\_desc    : series description of the scan
   - $minc\_location  : location of the MINC file
   - $patient\_name   : patient name of the scan

docs/scripts_md/MRIProcessingUtility.md

@@ -284,6 +284,7 @@ INPUTS:
   - $visit\_label : visit label associated with the scan
   - $file        : information about the scan
   - $data\_dir    : path to the LORIS MRI data directory
+  - $scan\_type   : scan type associated to the file
 
 ### loadAndCreateObjectFile($minc, $upload\_id)
 

docs/scripts_md/MriCandidateErrorsOB.md

@@ -0,0 +1,106 @@
+# NAME
+
+NeuroDB::objectBroker::MriCandidateErrorsOB -- An object broker for `MriCandidateErrors` records
+
+# SYNOPSIS
+
+    use NeuroDB::Database;
+    use NeuroDB::objectBroker::MriCandidateErrorsOB;
+    use TryCatch;
+
+    my $db = NeuroDB::Database->new(
+        userName     => 'user',
+        databaseName => 'my_db',
+        hostName     => 'my_hostname',
+        password     => 'pwd'
+    );
+
+    try {
+        $db->connect();
+    } catch(NeuroDB::DatabaseException $e) {
+        die sprintf(
+            "User %s failed to connect to %s on %s: %s (error code %d)\n",
+            'user',
+            'my_db',
+            'my_hostname',
+            $e->errorMessage,
+            $e->errorCode
+        );
+    }
+
+    .
+    .
+    .
+
+    my $mriCandidateErrorsOB = NeuroDB::objectBroker::MriCandidateErrorsOB->new(db => $db);
+    my $mriCandidateErrorsRef;
+    try {
+        $mriCandidateErrorsRef = $mriCandidateErrorsOB->getByTarchiveID(
+            [ 'TarchiveID' ], 12
+        );
+    } catch(NeuroDB::objectBroker::ObjectBrokerException $e) {
+        die sprintf(
+            "Failed to retrieve MriCandidateErrors records: %s",
+            $e->errorMessage
+        );
+    }
+
+# DESCRIPTION
+
+This class provides a set of methods to either fetch records from the `MRICandidateErrors`
+table, insert new entries in it or update existing ones. If an operation cannot
+be executed successfully, a `NeuroDB::objectBroker::ObjectBrokerException` is thrown.
+
+## Methods
+
+### new(db => $db) >> (constructor)
+
+Create a new instance of this class. The only parameter to provide is the
+`Database` object used to access the database.
+
+INPUT: the database object used to read/modify the `MRICandidateErrors` table.
+
+RETURN: new instance of this class.
+
+### getWithTarchiveID($tarchiveID)
+
+Fetches the records from the `MRICandidateErrors` table that have a specific `TarchiveID`.
+
+INPUTS:
+    - ID of the tarchive used during the search.
+
+RETURN: a reference to an array of hash references. Every hash contains the values for a given
+        row returned by the function call: the key/value pairs contain the name of a column
+        (listed in `@MRICANDIDATEERRORS_FIELDS`) and the value it holds, respectively.
+        As an example, suppose array `$r` contains the result of a call to this method with
+        `@$fieldsRef` set to `('TarchiveID', 'MincFile'` one would fetch the `MincFile`
+        of the 4th record returned using `$r-`\[3\]->{'MincFile'}>.
+
+### insert($valuesRef)
+
+Inserts a new record in the `MRICandidateErrors` table with the specified column values.
+This method throws a `NeuroDB::objectBroker::ObjectBrokerException` if the operation
+could not be completed successfully.
+
+INPUT: a reference to a hash of the values to insert. The hash contains the column
+       names and associated record values used during insertion. All the keys of
+       `%$valuesRef` must exist in `@MRICANDIDATEERRORS_FIELDS` or an exception will be thrown.
+
+RETURNS: the index of the MRI upload record inserted.
+
+# TO DO
+
+Nothing planned.
+
+# BUGS
+
+None reported.
+
+# COPYRIGHT AND LICENSE
+
+License: GPLv3
+
+# AUTHORS
+
+LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative
+Neuroscience

docs/scripts_md/MriProtocolViolatedScansOB.md

@@ -0,0 +1,106 @@
+# NAME
+
+NeuroDB::objectBroker::MriProtocolViolatedScansOB -- An object broker for `mri_protocol_violated_scans` records
+
+# SYNOPSIS
+
+    use NeuroDB::Database;
+    use NeuroDB::objectBroker::MriProtocolViolatedScansOB;
+    use TryCatch;
+
+    my $db = NeuroDB::Database->new(
+        userName     => 'user',
+        databaseName => 'my_db',
+        hostName     => 'my_hostname',
+        password     => 'pwd'
+    );
+
+    try {
+        $db->connect();
+    } catch(NeuroDB::DatabaseException $e) {
+        die sprintf(
+            "User %s failed to connect to %s on %s: %s (error code %d)\n",
+            'user',
+            'my_db',
+            'my_hostname',
+            $e->errorMessage,
+            $e->errorCode
+        );
+    }
+
+    .
+    .
+    .
+
+    my $mriProtocolViolatedScansOB = NeuroDB::objectBroker::MriProtocolViolatedScansOB->new(db => $db);
+    my $mriProtocolViolatedScansOBRef;
+    try {
+        $mriProtocolViolatedScansOBRef = $mriProtocolViolatedScansOB->getByTarchiveID(
+            [ 'TarchiveID' ], 12
+        );
+    } catch(NeuroDB::objectBroker::ObjectBrokerException $e) {
+        die sprintf(
+            "Failed to retrieve mri_protocol_violated_scans records: %s",
+            $e->errorMessage
+        );
+    }
+
+# DESCRIPTION
+
+This class provides a set of methods to either fetch records from the `mri_protocol_violated_scans`
+table, insert new entries in it or update existing ones. If an operation cannot
+be executed successfully, a `NeuroDB::objectBroker::ObjectBrokerException` is thrown.
+
+## Methods
+
+### new(db => $db) >> (constructor)
+
+Create a new instance of this class. The only parameter to provide is the
+`Database` object used to access the database.
+
+INPUT: the database object used to read/modify the `mri_protocol_violated_scans` table.
+
+RETURN: new instance of this class.
+
+### getWithTarchiveID($tarchiveID)
+
+Fetches the records from the `mri_protocol_violated_scans` table that have a specific `TarchiveID`.
+
+INPUTS:
+    - ID of the tarchive used during the search.
+
+RETURN: a reference to an array of hash references. Every hash contains the values for a given
+        row returned by the function call: the key/value pairs contain the name of a column
+        (listed in `@MRIPROTOCOLVIOLATEDSCANS_FIELDS`) and the value it holds, respectively.
+        As an example, suppose array `$r` contains the result of a call to this method with
+        `@$fieldsRef` set to `('TarchiveID', 'minc_location'` one would fetch the `minc_location`
+        of the 4th record returned using `$r-`\[3\]->{'minc\_location'}>.
+
+### insert($valuesRef)
+
+Inserts a new record in the `mri_protocol_violated_scans` table with the specified column values.
+This method throws a `NeuroDB::objectBroker::ObjectBrokerException` if the operation
+could not be completed successfully.
+
+INPUT: a reference to a hash of the values to insert. The hash contains the column
+       names and associated record values used during insertion. All the keys of
+       `%$valuesRef` must exist in `@MRIPROTOCOLVIOLATEDSCANS_FIELDS` or an exception will be thrown.
+
+RETURNS: the index of the MRI upload record inserted.
+
+# TO DO
+
+Nothing planned.
+
+# BUGS
+
+None reported.
+
+# COPYRIGHT AND LICENSE
+
+License: GPLv3
+
+# AUTHORS
+
+LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative
+Neuroscience

docs/scripts_md/MriViolationsLogOB.md

@@ -0,0 +1,106 @@
+# NAME
+
+NeuroDB::objectBroker::MriViolationsLogOB -- An object broker for `mri_violations_log` records
+
+# SYNOPSIS
+
+    use NeuroDB::Database;
+    use NeuroDB::objectBroker::MriViolationsLogOB;
+    use TryCatch;
+
+    my $db = NeuroDB::Database->new(
+        userName     => 'user',
+        databaseName => 'my_db',
+        hostName     => 'my_hostname',
+        password     => 'pwd'
+    );
+
+    try {
+        $db->connect();
+    } catch(NeuroDB::DatabaseException $e) {
+        die sprintf(
+            "User %s failed to connect to %s on %s: %s (error code %d)\n",
+            'user',
+            'my_db',
+            'my_hostname',
+            $e->errorMessage,
+            $e->errorCode
+        );
+    }
+
+    .
+    .
+    .
+
+    my $mriViolationsLogOB = NeuroDB::objectBroker::MriViolationsLogOB->new(db => $db);
+    my $mriProtocolViolatedScansOBRef;
+    try {
+        $mriViolationsLogOBRef = $mriViolationsLogOB->getByTarchiveID(
+            [ 'TarchiveID' ], 12
+        );
+    } catch(NeuroDB::objectBroker::ObjectBrokerException $e) {
+        die sprintf(
+            "Failed to retrieve mri_violations_log records: %s",
+            $e->errorMessage
+        );
+    }
+
+# DESCRIPTION
+
+This class provides a set of methods to either fetch records from the `mri_violations_log`
+table, insert new entries in it or update existing ones. If an operation cannot
+be executed successfully, a `NeuroDB::objectBroker::ObjectBrokerException` is thrown.
+
+## Methods
+
+### new(db => $db) >> (constructor)
+
+Create a new instance of this class. The only parameter to provide is the
+`Database` object used to access the database.
+
+INPUT: the database object used to read/modify the `mri_violations_log` table.
+
+RETURN: new instance of this class.
+
+### getWithTarchiveID($tarchiveID)
+
+Fetches the records from the `mri_violations_log` table that have a specific `TarchiveID`.
+
+INPUTS:
+    - ID of the tarchive used during the search.
+
+RETURN: a reference to an array of hash references. Every hash contains the values for a given
+        row returned by the function call: the key/value pairs contain the name of a column
+        (listed in `@MRIVIOLATIONSLOG_FIELDS`) and the value it holds, respectively.
+        As an example, suppose array `$r` contains the result of a call to this method with
+        `@$fieldsRef` set to `('TarchiveID', 'MincFile'` one would fetch the `MincFile`
+        of the 4th record returned using `$r-`\[3\]->{'MincFile'}>.
+
+### insert($valuesRef)
+
+Inserts a new record in the `mri_violations_log` table with the specified column values.
+This method throws a `NeuroDB::objectBroker::ObjectBrokerException` if the operation
+could not be completed successfully.
+
+INPUT: a reference to a hash of the values to insert. The hash contains the column
+       names and associated record values used during insertion. All the keys of
+       `%$valuesRef` must exist in `@MRIVIOLATIONSLOG_FIELDS` or an exception will be thrown.
+
+RETURNS: the index of the MRI upload record inserted.
+
+# TO DO
+
+Nothing planned.
+
+# BUGS
+
+None reported.
+
+# COPYRIGHT AND LICENSE
+
+License: GPLv3
+
+# AUTHORS
+
+LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative
+Neuroscience