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Rename candidate center id to registration center #4078

Merged
merged 11 commits into from
Jan 28, 2019
Merged

Rename candidate center id to registration center #4078

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7380ea0
Updated the default schema and created a new patch for existing proje…
cmadjar Nov 5, 2018
59ce872
included Xavier changes before force pushing
cmadjar Jan 11, 2019
364f05d
fixed Imaging Browser unit test that was failing Travis
cmadjar Jan 14, 2019
e96d851
first round of review modification from Rida
cmadjar Jan 15, 2019
e7e240f
fixed test plan of timepoint list accoring to the current behaviour
cmadjar Jan 15, 2019
cfdcd58
line length fix
xlecours Jan 21, 2019
92f6a2c
Merge pull request #2 from xlecours/rename_candidate_CenterID_to_Regi…
cmadjar Jan 21, 2019
2004aba
Xavier's good catch!
cmadjar Jan 21, 2019
0013677
Merge branch 'rename_candidate_CenterID_to_RegistrationCenterID' of h…
cmadjar Jan 21, 2019
1335346
fixing the MRI violation test script
cmadjar Jan 25, 2019
7f310c6
Update mri_violationsTest.php
ridz1208 Jan 25, 2019
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6 changes: 3 additions & 3 deletions SQL/0000-00-00-schema.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -272,7 +272,7 @@ CREATE TABLE `candidate` (
`DoB` date DEFAULT NULL,
`EDC` date DEFAULT NULL,
`Sex` enum('Male','Female') DEFAULT NULL,
`CenterID` integer unsigned NOT NULL DEFAULT '0',
`RegistrationCenterID` integer unsigned NOT NULL DEFAULT '0',
`ProjectID` int(11) DEFAULT NULL,
`Ethnicity` varchar(255) DEFAULT NULL,
`Active` enum('Y','N') NOT NULL DEFAULT 'Y',
Expand All @@ -291,11 +291,11 @@ CREATE TABLE `candidate` (
PRIMARY KEY (`CandID`),
UNIQUE KEY `ID` (`ID`),
UNIQUE KEY `ExternalID` (`ExternalID`),
KEY `FK_candidate_1` (`CenterID`),
KEY `FK_candidate_1` (`RegistrationCenterID`),
KEY `CandidateActive` (`Active`),
KEY `FK_candidate_2_idx` (`flagged_reason`),
KEY `PSCID` (`PSCID`),
CONSTRAINT `FK_candidate_1` FOREIGN KEY (`CenterID`) REFERENCES `psc` (`CenterID`),
CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`),
CONSTRAINT `FK_candidate_2` FOREIGN KEY (`flagged_reason`) REFERENCES `caveat_options` (`ID`) ON DELETE RESTRICT ON UPDATE CASCADE
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

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6 changes: 6 additions & 0 deletions SQL/New_patches/2018-11-05_rename_candidate_CenterID_to_RegistrationCenterID.sql
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@@ -0,0 +1,6 @@
ALTER TABLE `candidate` DROP FOREIGN KEY `FK_candidate_1`;
ALTER TABLE `candidate`
CHANGE COLUMN `CenterID` `RegistrationCenterID` integer unsigned NOT NULL DEFAULT '0';
ALTER TABLE `candidate`
ADD CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`);

2 changes: 1 addition & 1 deletion htdocs/api/v0.0.2/Candidates.php
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Expand Up @@ -77,7 +77,7 @@ public function handleGET()
$candidates = $this->DB->pselect(
"SELECT CandID, ProjectID, PSCID, s.Alias as Site,
EDC, DoB, Sex as Gender
FROM candidate c JOIN psc s on (s.CenterID=c.CenterID)
FROM candidate c JOIN psc s on (s.CenterID=c.RegistrationCenterID)
WHERE Active='Y'
",
[]
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2 changes: 1 addition & 1 deletion htdocs/api/v0.0.3-dev/Candidates.php
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Expand Up @@ -74,7 +74,7 @@ public function handleGET()
$candidates = $this->DB->pselect(
"SELECT CandID, ProjectID, PSCID, s.Alias as Site,
EDC, DoB, Sex
FROM candidate c JOIN psc s on (s.CenterID=c.CenterID)
FROM candidate c JOIN psc s on (s.CenterID=c.RegistrationCenterID)
WHERE Active='Y'
",
[]
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14 changes: 7 additions & 7 deletions modules/candidate_list/php/candidate_list.class.inc
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Expand Up @@ -66,7 +66,7 @@ class Candidate_List extends \NDB_Menu_Filter

// set the class variables
$this->columns = array(
'psc.Name AS Site',
'psc.Name AS RegistrationSite',
'c.CandID AS DCCID',
'c.PSCID',
'c.Sex',
Expand All @@ -87,7 +87,7 @@ class Candidate_List extends \NDB_Menu_Filter
);

$this->formToFilter = array(
'centerID' => 'c.CenterID',
'centerID' => 'c.RegistrationCenterID',
'DCCID' => 'c.CandID',
'PSCID' => 'c.PSCID',
'Sex' => 'c.Sex',
Expand All @@ -96,7 +96,7 @@ class Candidate_List extends \NDB_Menu_Filter

$this->validFilters = array(
'pso.ID',
'c.CenterID',
'c.RegistrationCenterID',
'c.CandID',
'c.PSCID',
'c.Sex',
Expand All @@ -121,7 +121,7 @@ class Candidate_List extends \NDB_Menu_Filter
);

$this->query = " FROM candidate c
LEFT JOIN psc ON (c.CenterID=psc.CenterID)
LEFT JOIN psc ON (c.RegistrationCenterID=psc.CenterID)
LEFT JOIN session s ON (c.CandID = s.CandID AND s.Active = 'Y')
LEFT JOIN feedback_bvl_thread
ON (c.CandID=feedback_bvl_thread.CandID)
Expand All @@ -135,7 +135,7 @@ class Candidate_List extends \NDB_Menu_Filter
if (!$user->hasPermission('access_all_profiles')) {

$site_arr = implode(",", $user->getCenterIDs());
$this->query .= " AND c.CenterID IN (" . $site_arr . ")";
$this->query .= " AND c.RegistrationCenterID IN (" . $site_arr . ")";
}

//'COALESCE(pso.ID,1) AS Participant_Status',
Expand Down Expand Up @@ -167,7 +167,7 @@ class Candidate_List extends \NDB_Menu_Filter
);
$this->EqualityFilters = array(
's.SubprojectID',
'c.CenterID',
'c.RegistrationCenterID',
'c.ProjectID',
's.Scan_done',
's.Visit_label',
Expand Down Expand Up @@ -259,7 +259,7 @@ class Candidate_List extends \NDB_Menu_Filter
$visits = array_merge(array('' => 'All'), $visits);

// add form elements
$this->addSelect('centerID', 'Site', $list_of_sites);
$this->addSelect('centerID', 'Registration Site', $list_of_sites);
$this->addBasicText('PSCID', 'PSCID');
$this->addBasicText('DCCID', 'DCCID');
$this->addBasicText('candID', 'DCCID');
Expand Down
2 changes: 1 addition & 1 deletion modules/conflict_resolver/php/conflict_resolver.class.inc
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Expand Up @@ -242,7 +242,7 @@ class Conflict_Resolver extends \NDB_Menu_Filter_Form
if (!$user->hasPermission('access_all_profiles')) {
// restrict data to own site
$site_arr = implode(",", $user->getCenterIDs());
$this->query .= " AND candidate.CenterID IN (" . $site_arr . ")";
$this->query .= " AND session.CenterID IN (" . $site_arr . ")";
}

$this->group_by = '';
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2 changes: 1 addition & 1 deletion modules/conflict_resolver/php/resolved_conflicts.class.inc
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Expand Up @@ -90,7 +90,7 @@ class Resolved_Conflicts extends \NDB_Menu_Filter
if (!$user->hasPermission('access_all_profiles')) {
// restrict data to own site
$site_arr = implode(",", $user->getCenterIDs());
$this->query .= " AND candidate.CenterID IN (" . $site_arr . ")";
$this->query .= " AND session.CenterID IN (" . $site_arr . ")";
}

$this->group_by = '';
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6 changes: 5 additions & 1 deletion modules/create_timepoint/php/create_timepoint.class.inc
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Expand Up @@ -51,7 +51,11 @@ class Create_Timepoint extends \NDB_Form
// check user permissions
return (
$user->hasPermission('data_entry') &&
(in_array($candidate->getData('CenterID'), $user->getData('CenterIDs')))
(in_array(
$candidate->getData('RegistrationCenterID'),
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this is fine for now but should be bettered in phase 2

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I copied the link of that comment to issue #4058 so that it does not get lost when I do the second part of the implementation :).

$user->getData('CenterIDs')
)
)
);
}

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4 changes: 2 additions & 2 deletions modules/dashboard/ajax/get_recruitment_bar_data.php
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Expand Up @@ -24,14 +24,14 @@
$sexData['datasets']['female'][] = $DB->pselectOne(
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.CenterID=:Site AND c.Sex='female' AND c.Active='Y'
WHERE c.RegistrationCenterID=:Site AND c.Sex='female' AND c.Active='Y'
AND c.Entity_type='Human'",
array('Site' => $siteID)
);
$sexData['datasets']['male'][] = $DB->pselectOne(
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.CenterID=:Site AND c.Sex='male' AND c.Active='Y'
WHERE c.RegistrationCenterID=:Site AND c.Sex='male' AND c.Active='Y'
AND c.Entity_type='Human'",
array('Site' => $siteID)
);
Expand Down
2 changes: 1 addition & 1 deletion modules/dashboard/ajax/get_recruitment_line_data.php
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Expand Up @@ -94,7 +94,7 @@ function getRecruitmentData($siteID, $labels)
$data[] = $DB->pselectOne(
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.CenterID=:Site
WHERE c.RegistrationCenterID=:Site
AND MONTH(c.Date_registered)=:Month
AND YEAR(c.Date_registered)=:Year
AND c.Entity_type='Human'",
Expand Down
5 changes: 4 additions & 1 deletion modules/dashboard/ajax/get_recruitment_pie_data.php
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Expand Up @@ -24,7 +24,10 @@
$totalRecruitment = $DB->pselectOne(
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.CenterID=:Site AND c.Active='Y' AND c.Entity_type='Human'",
WHERE
c.RegistrationCenterID=:Site AND
c.Active='Y' AND
c.Entity_type='Human'",
array('Site' => $siteID)
);

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13 changes: 7 additions & 6 deletions modules/dashboard/php/dashboard.class.inc
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Expand Up @@ -144,7 +144,7 @@ class Dashboard extends \NDB_Form
LEFT JOIN session s ON (flag.SessionID=s.ID)
LEFT JOIN candidate c ON (c.CandID=s.CandID)
LEFT JOIN Project p ON (c.ProjectID=p.ProjectID )
WHERE FIND_IN_SET(c.CenterID, :siteID)
WHERE FIND_IN_SET(s.CenterID, :siteID)
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AND s.Active='Y' AND c.Active='Y'",
array('siteID' => implode(',', $siteID))
);
Expand Down Expand Up @@ -207,7 +207,7 @@ class Dashboard extends \NDB_Form
$this->tpl_data['violated_scans'] = $DB->pselectOne(
"SELECT COUNT(*) FROM mri_protocol_violated_scans
LEFT JOIN candidate c USING (CandID)
WHERE COALESCE(c.CenterID, 0) <> 1",
WHERE COALESCE(c.RegistrationCenterID, 0) <> 1",
/* include null CenterIDs so we don't accidentally
filter things out */
array()
Expand Down Expand Up @@ -307,7 +307,8 @@ class Dashboard extends \NDB_Form
$DB = \Database::singleton();
$totalRecruitment = $DB->pselectOne(
"SELECT COUNT(*) FROM candidate c
WHERE c.Active='Y' AND c.Entity_type='Human' AND c.CenterID <> 1",
WHERE c.Active='Y' AND c.Entity_type='Human'
AND c.RegistrationCenterID <> 1",
array()
);
return $totalRecruitment;
Expand All @@ -327,7 +328,7 @@ class Dashboard extends \NDB_Form
"SELECT COUNT(*)
FROM candidate c
WHERE c.Active='Y' AND c.ProjectID=:PID AND c.Entity_type='Human'
AND c.CenterID <> 1",
AND c.RegistrationCenterID <> 1",
array('PID' => $projectID)
);
return $totalRecruitment;
Expand All @@ -347,7 +348,7 @@ class Dashboard extends \NDB_Form
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.Sex=:sex AND c.Active='Y' AND c.Entity_type='Human'
AND c.CenterID <> 1",
AND c.RegistrationCenterID <> 1",
array('sex' => $sex)
);
return $total;
Expand All @@ -369,7 +370,7 @@ class Dashboard extends \NDB_Form
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.Sex=:sex AND c.Active='Y' AND c.ProjectID=:PID
AND c.Entity_type='Human' AND c.CenterID <> 1",
AND c.Entity_type='Human' AND c.RegistrationCenterID <> 1",
array(
'sex' => $sex,
'PID' => $projectID,
Expand Down
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