[biobank] bugfix: Update DB schema, and fix CandidateID references (#10037)

SQL/0000-00-06-BiobankTables.sql

@@ -182,7 +182,9 @@ CREATE TABLE `biobank_specimen_protocol_attribute_rel` (
   `SpecimenAttributeID` int(10) unsigned NOT NULL,
   `Required` tinyint(1) DEFAULT NULL,
   `showInDataTable` tinyint(1) DEFAULT NULL,
+  `OrderIndex` INT UNSIGNED NOT NULL,
   PRIMARY KEY (`SpecimenProtocolID`,`SpecimenAttributeID`),
+  UNIQUE KEY `UK_SpecimenProtocolId_OrderIndex` (`SpecimenProtocolID`, `OrderIndex`),
   KEY `FK_biobank_specimen_protocol_attribute_rel_SpecimenAttributeID` (`SpecimenAttributeID`),
   CONSTRAINT `FK_biobank_specimen_protocol_attribute__rel_SpecimenProtocolID` FOREIGN KEY (`SpecimenProtocolID`) REFERENCES `biobank_specimen_protocol` (`SpecimenProtocolID`),
   CONSTRAINT `FK_biobank_specimen_protocol_attribute_rel_SpecimenAttributeID` FOREIGN KEY (`SpecimenAttributeID`) REFERENCES `biobank_specimen_attribute` (`SpecimenAttributeID`)
@@ -399,6 +401,7 @@ VALUES (1,'Blood Collection',1,1),
 INSERT INTO `biobank_specimen_type_unit_rel` VALUES (1,1),(2,2);
 INSERT INTO `biobank_specimen_type_parent` VALUES (2,1);
 INSERT INTO `biobank_specimen_type_container_type_rel` VALUES (1,1),(2,1);
+INSERT INTO `shipment_type` VALUES (1, 'Gel Pack Container'),(2, 'Insulated Foam Box'),(3, 'Dry Shipper');
 
 -- Insert ConfigSettings for label printing endpoint
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('biobank', 'Settings related to the biobank module', 1, 0, 'Biobank', 16);

SQL/New_patches/2025-10-29_add-order-index-to-specimen-protocols.sql

@@ -0,0 +1,41 @@
+-- Step 1: Add the column allowing NULL (temporarily)
+-- This allows the operation to succeed on a table that already has existing rows.
+ALTER TABLE biobank_specimen_protocol_attribute_rel
+ADD COLUMN OrderIndex INT UNSIGNED NULL;
+
+-- Step 2: Populate the existing rows with unique, non-NULL OrderIndex values.
+-- This uses a variable-based method to assign a sequential number (0, 1, 2, ...)
+-- to each row within the same SpecimenProtocolID group.
+
+SET @r := -1;
+SET @g := 0;
+
+-- A temporary table/derived table is used to calculate the unique index for each group
+UPDATE biobank_specimen_protocol_attribute_rel AS t1
+INNER JOIN (
+    SELECT
+        t2.SpecimenProtocolID,
+        t2.SpecimenAttributeID,
+        @r := CASE WHEN @g = t2.SpecimenProtocolID THEN @r + 1 ELSE 0 END AS new_OrderIndex,
+        @g := t2.SpecimenProtocolID AS current_group
+    FROM
+        biobank_specimen_protocol_attribute_rel AS t2
+    ORDER BY
+        t2.SpecimenProtocolID, t2.SpecimenAttributeID
+
+) AS ranked_data
+ON t1.SpecimenProtocolID = ranked_data.SpecimenProtocolID
+AND t1.SpecimenAttributeID = ranked_data.SpecimenAttributeID
+SET t1.OrderIndex = ranked_data.new_OrderIndex;
+
+-- Step 3: Enforce the constraints (NOT NULL and UNIQUE).
+-- Now that every row has a valid, unique value, these operations will succeed.
+
+-- 3a. Add the UNIQUE Constraint
+ALTER TABLE biobank_specimen_protocol_attribute_rel
+ADD CONSTRAINT UK_SpecimenProtocolId_OrderIndex
+UNIQUE (SpecimenProtocolID, OrderIndex);
+
+-- 3b. Change the Column to NOT NULL
+ALTER TABLE biobank_specimen_protocol_attribute_rel
+MODIFY COLUMN OrderIndex INT UNSIGNED NOT NULL;

modules/biobank/php/optionsendpoint.class.inc

@@ -138,18 +138,25 @@ class OptionsEndpoint extends \NDB_Page implements RequestHandlerInterface
         // TODO: This should eventually be replaced by a call directly to a
         // Candidate endpoint or Candidate controller that will be able to
         // provide Candidate Objects.
-        $query      = "SELECT c.CandID as id,
-                            PSCID as pscid,
-                            Sex as sex,
-                            GROUP_CONCAT(DISTINCT DiagnosisID) as diagnosisIds,
-                            GROUP_CONCAT(DISTINCT s.ID) as sessionIds
-                       FROM candidate c
-                            LEFT JOIN session s USING (CandID)
-                            LEFT JOIN candidate_diagnosis_rel USING (CandID)
-                       WHERE s.CenterID IN ($userCenters)
-                            AND s.ProjectID IN ($userProjects)
-                       GROUP BY
-                          CandID";
+        $query      = "
+            SELECT
+                c.CandID as id,
+                PSCID as pscid,
+                Sex as sex,
+                GROUP_CONCAT(DISTINCT DxEvolutionID) as diagnosisIds,
+                GROUP_CONCAT(DISTINCT s.ID) as sessionIds
+            FROM
+                candidate c
+                LEFT JOIN session s
+                  ON s.CandidateID=c.ID
+                LEFT JOIN candidate_diagnosis_evolution_rel cder
+                  ON cder.CandidateID=c.ID
+            WHERE
+                s.CenterID IN ($userCenters)
+                AND s.ProjectID IN ($userProjects)
+            GROUP BY
+                CandID
+        ";
         $candidates = $db->pselectWithIndexKey($query, [], 'id');
         foreach ($candidates as $id => $candidate) {
             $candidates[$id]['diagnosisIds'] = $candidate['diagnosisIds']
@@ -163,7 +170,13 @@ class OptionsEndpoint extends \NDB_Page implements RequestHandlerInterface
         // XXX: This should eventually be replaced by a call directly to a
         // Candidate endpoint or Candidate controller that will be able to
         // provide Diagnosis Options.
-        $query     = 'SELECT DiagnosisID as id, Name as label FROM diagnosis';
+        $query     = '
+            SELECT
+                DxEvolutionID as id,
+                Name as label
+            FROM
+                diagnosis_evolution
+        ';
         $diagnoses = $db->pselectWithIndexKey($query, [], 'id');
 
         $sessionQuery = "SELECT

modules/biobank/php/specimendao.class.inc

@@ -115,7 +115,7 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
                         as ParentSpecimenIDs,
                       GROUP_CONCAT(DISTINCT bc2.Barcode)
                         as ParentSpecimenBarcodes,
-                      s.CandID as CandidateID,
+                      s.CandidateID,
                       c.PSCID as CandidatePSCID,
                       bs.SessionID,
                       s.CenterID as SessionCenterID,
@@ -154,7 +154,7 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
                LEFT JOIN session s
                  ON bs.SessionID=s.ID
                LEFT JOIN candidate c
-                 ON s.CandID=c.CandID
+                 ON s.CandidateID=c.ID
                LEFT JOIN biobank_specimen_pool_rel bspor
                  ON bs.SpecimenID=bspor.SpecimenID
                LEFT JOIN biobank_specimen_collection bsc
@@ -561,7 +561,7 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
             SELECT IFNULL(MAX(bs.SampleNumber), 0) AS max_sample_number
             FROM biobank_specimen bs
             JOIN session s ON bs.SessionID = s.ID
-            WHERE s.CandID = :candId
+            WHERE s.CandidateID = :candId
         ";
 
         $sampleNumber = $this->db->pselectOneInt($query, ['candId' => $candId]);