Addressing failing tests

jeffersoncasimir · Feb 12, 2025 · 0adbe28 · 0adbe28
1 parent 81de941
commit 0adbe28
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Showing 7 changed files with 20 additions and 16 deletions.
diff --git a/modules/genomic_browser/php/provisioners/cnvprovisioner.class.inc b/modules/genomic_browser/php/provisioners/cnvprovisioner.class.inc
@@ -61,7 +61,7 @@ class CnvProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                     FROM session s
                     JOIN candidate c ON c.ID=s.CandidateID
                     GROUP BY
-                        c.CandID) AS cohort ON (cohort.CandidateID = candidate.ID)
+                        c.CandID) AS cohort ON (cohort.CandID = candidate.CandID)
                 LEFT JOIN psc ON (psc.CenterID = candidate.RegistrationCenterID)
                 JOIN CNV ON (candidate.ID = CNV.CandidateID)
                 LEFT JOIN genotyping_platform

diff --git a/modules/genomic_browser/php/provisioners/methylationprovisioner.class.inc b/modules/genomic_browser/php/provisioners/methylationprovisioner.class.inc
@@ -68,7 +68,7 @@ class MethylationProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisione
                     FROM session s
                     JOIN candidate c ON c.ID=s.CandidateID
                     GROUP BY
-                        c.CandID) AS cohort ON (cohort.CandidateID = candidate.ID)
+                        c.CandID) AS cohort ON (cohort.CandID = candidate.CandID)
                 LEFT JOIN psc ON (psc.CenterID = candidate.RegistrationCenterID)
                 LEFT JOIN genomic_sample_candidate_rel gscr
                     ON (gscr.CandidateID = candidate.ID)

diff --git a/modules/genomic_browser/php/provisioners/profileprovisioner.class.inc b/modules/genomic_browser/php/provisioners/profileprovisioner.class.inc
@@ -38,8 +38,8 @@ class ProfileProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                         genomicfileid
                     FROM
                         genomic_candidate_files_rel gcfr
-                    JOIN
-                        candidate c ON c.ID=gcfr.CandidateID THEN
+                    WHERE
+                        candidate.ID = gcfr.CandidateID) THEN
                     'Y'
                 ELSE
                     'N'
@@ -48,8 +48,8 @@ class ProfileProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                         snpid
                     FROM
                         SNP_candidate_rel scr
-                    JOIN
-                        candidate c ON c.ID=scr.CandidateID THEN
+                    WHERE
+                        candidate.ID = scr.CandidateID) THEN
                     'Y'
                 ELSE
                     'N'
@@ -58,19 +58,19 @@ class ProfileProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                         cnvid
                     FROM
                         CNV cnv
-                    JOIN
-                        candidate c ON c.ID=cnv.CandidateID THEN
+                    WHERE
+                        candidate.ID = cnv.CandidateID) THEN
                     'Y'
                 ELSE
                     'N'
                 END AS _CNV, CASE WHEN EXISTS (
                     SELECT
                         cpg_name
                     FROM
-                        genomic_sample_candidate_rel
+                        genomic_sample_candidate_rel gscr
                     LEFT JOIN genomic_cpg USING (sample_label)
                 WHERE
-                    candid = candidate.candid) THEN
+                    candidate.ID = gscr.CandidateID) THEN
                     'Y'
                 ELSE
                     'N'
@@ -84,7 +84,7 @@ class ProfileProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                     FROM session s
                     JOIN candidate c ON c.ID=s.CandidateID
                     GROUP BY
-                        c.CandID) AS cohort ON (cohort.CandidateID = candidate.ID)
+                        c.CandID) AS cohort ON (cohort.CandID = candidate.CandID)
                 LEFT JOIN cohort AS subproj
                     ON (cohort.CohortID = subproj.CohortID)
                 LEFT JOIN psc ON (psc.CenterID = candidate.RegistrationCenterID)

diff --git a/modules/genomic_browser/php/provisioners/snpprovisioner.class.inc b/modules/genomic_browser/php/provisioners/snpprovisioner.class.inc
@@ -65,7 +65,7 @@ class SnpProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                     FROM session s
                     JOIN candidate c ON c.ID=s.CandidateID
                     GROUP BY
-                        c.CandID) AS cohort ON (cohort.CandidateID = candidate.ID)
+                        c.CandID) AS cohort ON (cohort.CandID = candidate.CandID)
                 LEFT JOIN cohort AS subproj
                     ON (cohort.CohortID = subproj.CohortID)
                 LEFT JOIN psc ON (psc.CenterID = candidate.RegistrationCenterID)

diff --git a/modules/imaging_browser/test/imaging_browserTest.php b/modules/imaging_browser/test/imaging_browserTest.php
@@ -86,6 +86,7 @@ public function setUp(): void
         $this->DB->insert(
             "candidate",
             [
+                'ID'                    => 1,
                 'CandID'                => '000001',
                 'PSCID'                 => 'DCC0001',
                 'RegistrationCenterID'  => 1,
@@ -98,6 +99,7 @@ public function setUp(): void
         $this->DB->insert(
             "candidate",
             [
+                'ID'                    => 2,
                 'CandID'                => '000002',
                 'PSCID'                 => 'AOL0002',
                 'RegistrationCenterID'  => 253,
@@ -110,6 +112,7 @@ public function setUp(): void
         $this->DB->insert(
             "candidate",
             [
+                'ID'                    => 3,
                 'CandID'                => 000003,
                 'PSCID'                 => 'BOL0003',
                 'RegistrationCenterID'  => 254,
@@ -123,7 +126,7 @@ public function setUp(): void
             'session',
             [
                 'ID'            => 999997,
-                'CandID'        => 000001,
+                'CandidateID'   => 1,
                 'Visit_label'   => 'Test0',
                 'CenterID'      => 1,
                 'ProjectID'     => 1,
@@ -137,7 +140,7 @@ public function setUp(): void
             'session',
             [
                 'ID'            => 999998,
-                'CandID'        => 000002,
+                'CandidateID'   => 2,
                 'Visit_label'   => 'Test1',
                 'CenterID'      => 253,
                 'ProjectID'     => 1,
@@ -151,7 +154,7 @@ public function setUp(): void
             'session',
             [
                 'ID'            => 999999,
-                'CandID'        => 000003,
+                'CandidateID'   => 3,
                 'Visit_label'   => 'Test2',
                 'CenterID'      => 254,
                 'ProjectID'     => 1,

diff --git a/php/libraries/Candidate.class.inc b/php/libraries/Candidate.class.inc
@@ -1292,7 +1292,7 @@ class Candidate implements \LORIS\StudyEntities\AccessibleResource,
                 s.CenterID as SCenterID, s.ID as sessionID
             FROM candidate c LEFT JOIN session s ON (s.CandidateID=c.ID)
             WHERE c.Active='Y' AND COALESCE(s.Active, 'Y')='Y'
-                AND c.CandID IN (SELECT ID FROM accesscandidates)
+                AND c.CandID IN (SELECT CandID FROM accesscandidates)
             ORDER BY c.CandID",
             []
         );

diff --git a/test/unittests/CandidateTest.php b/test/unittests/CandidateTest.php
@@ -1199,6 +1199,7 @@ public function testParticipantStatusDescription()
                 ]
             ]
         );
+        echo "PSCID CandID: " . $this->_candidate->getPSCID() . ' ' . $this->_candidate->getCandID();
         $result = $this->_candidate->getParticipantStatusDescription($this->_DB);
         $this->_DB->run("DROP TEMPORARY TABLE participant_status_options");
         $this->_DB->run("DROP TEMPORARY TABLE participant_status");