[tools] 20.0 tools and SQL moved to proper directory (aces#3855)

This moves

the Normalize_protocol_split_rows.php to the proper directory and updates its relative references
the SQL output on Normalize_Consent_Data.php to the archive directory directly to avoid uncommitted code in the production environment's Cleanup_patches directory.

.gitignore

@@ -25,4 +25,7 @@ htdocs/js/components/.module-cache/
 node_modules/
 modules/*/js/*.map
 htdocs/js/components/*.map
-npm-debug.log*
+npm-debug.log*
+SQL/Archive/autogenerated/reversion/*.sql
+SQL/Archive/autogenerated/single_use/*.sql
+SQL/Archive/autogenerated/*.sql

SQL/Archive/autogenerated/README.md

@@ -0,0 +1,5 @@
+This directory contains SQL patches automatically generated from scripts in the 
+tools directory. 
+
+**Note:** SQL patches should not be generated directly into this directory;
+they should be added to one of the subdirectories it contains.

SQL/Archive/autogenerated/reversion/README.md

@@ -0,0 +1,9 @@
+This directory contains SQL patches automatically generated to revert database changes 
+applied in a tool script. Patches in this directory are designed to roll-back the 
+database into a previous state and should only be run by project administrators after 
+thorough testing.  
+
+**Notes:** 
+ - It is left to the author of the tool script to decide if a 
+roll-back behaviour is required. 
+ - Files in this directory are not tracked by github.

SQL/Archive/autogenerated/single_use/README.md

@@ -0,0 +1,5 @@
+This directory contains SQL patches automatically generated by tool scripts and 
+designed to be applied on the database only once; running these scripts more 
+than once might result in an SQL failure.
+
+**Note:** Files in this directory are not tracked by github.

tools/single_use/Normalise_Consent_Data.php → tools/single_use/Normalize_Consent_Data.php

@@ -4,7 +4,7 @@
  * 
  * This script imports existing consent data from `participant_status` and `consent_info_history` into new normalized tables.
  * 
- * A SQL file is exported to path: loris_root/SQL/Cleanup_patches/delete_old_consent_tables.sql
+ * A SQL file is exported to path: loris_root/SQL/Archive/autogenerated/single_use/delete_old_consent_tables.sql
  * after running this script. Source this file to delete the now deprecated tables and columns.
  * 
  * affected tables:
@@ -144,7 +144,7 @@
 $configID    = $db->pselectOne("SELECT ID FROM ConfigSettings WHERE Name='useConsent'", array());
 if (empty($configID)) {
     array_push($errors, "useConsent missing from ConfigSettings table.
-               Run SQL/New_patches/2018-03-01_normalise_consent.sql");
+               Run SQL/Release_patches/19.1_To_20.0_upgrade.sql");
     print_r($errors);
     echo "\nResolve errors and run script again.\n";
     die();
@@ -154,12 +154,12 @@
                    array('configid'=>$configID));
 if (empty($configValue)) {
     array_push($errors, "useConsent's Config value missing from Config table.
-               Run SQL/New_patches/2018-03-01_normalise_consent.sql");
+               Run SQL/Release_patches/19.1_To_20.0_upgrade.sql");
 }
 // Check new consent tables exist
 if (!$db->tableExists('consent') || !$db->tableExists('candidate_consent_rel') || !$db->tableExists('candidate_consent_history')) {
     array_push($errors, "New, normalized consent tables do not exist.
-               Run SQL/New_patches/2018-03-01_normalise_consent.sql");
+               Run SQL/Release_patches/19.1_To_20.0_upgrade.sql");
 }
 // Check rel and history tables are empty
 $consentRelResult     = $db->pselect("SELECT * FROM candidate_consent_rel", array());
@@ -300,6 +300,12 @@
                 'EntryDate'     => $entryDate,
                 ];
                 //Populate candidate_consent_history table
+                //Nullifying empty field to avoid data truncation
+                foreach ($formattedHistory as $k=>$v) {
+                    if ($v === '') {
+                        Utility::nullifyEmpty($formattedHistory,$k);
+                    }
+                }
                 $db->insert('candidate_consent_history', $formattedHistory);
             }
         }
@@ -316,8 +322,8 @@
     $columnName = $column['Column_name'];
     $output .= "ALTER TABLE participant_status DROP COLUMN " . $columnName . ";\n";
 }
-$filename = __DIR__ . "/../../SQL/Cleanup_patches/delete_old_consent_tables.sql";
+
+$filename = __DIR__ . "/../../SQL/Archive/autogenerated/single_use/delete_old_consent_tables.sql";
 $fp       = fopen($filename, "w");
 fwrite($fp, $output);
 fclose($fp);
-?>

tools/normalize_protocol_split_rows.php → tools/single_use/Normalize_protocol_split_rows.php

@@ -13,7 +13,7 @@
  * @link     https://www.github.com/aces/Loris
  */
 
-require_once 'generic_includes.php';
+require_once __DIR__ . '/../generic_includes.php';
 require_once 'Database.class.inc';
 require_once 'Utility.class.inc';
 
@@ -80,6 +80,4 @@ function split_commas($table_name) {
 $tables_to_normalize = array("mri_protocol", "mri_protocol_checks");
 foreach ($tables_to_normalize as $table) {
     split_commas($table);
-}
-
-?>
+}