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Initial commit for project-level permissions
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@jacobpenny
jacobpenny committed Apr 11, 2017
1 parent 95bee3f commit 56fb468
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Showing 14 changed files with 297 additions and 104 deletions.
12 changes: 12 additions & 0 deletions SQL/Archive/17.1/2017-03-30_Project_level_permissions.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
CREATE TABLE `user_project_rel` (
`UserID` int(10) unsigned NOT NULL,
`ProjectID` int(2) NOT NULL,
PRIMARY KEY (`UserID`,`ProjectID`),
KEY `FK_user_project_rel_2` (`ProjectID`),
CONSTRAINT `FK_user_project_rel_2` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `FK_user_project_rel_1` FOREIGN KEY (`UserID`) REFERENCES `users` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

INSERT INTO user_project_rel (UserID, ProjectID) SELECT 1, ProjectID FROM Project;
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useProjectPermissions', "Enable project level permissions", 1, 0, 'boolean', ID, 'Use project-level permissions', 4 FROM ConfigSettings WHERE Name="study";
INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useProjectPermissions";
12 changes: 11 additions & 1 deletion modules/candidate_list/php/NDB_Menu_Filter_candidate_list.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -100,6 +100,7 @@ class NDB_Menu_Filter_Candidate_List extends NDB_Menu_Filter
$this->validFilters = array(
'pso.ID',
'c.CenterID',
'c.ProjectID',
'c.CandID',
'c.PSCID',
'c.Gender',
Expand Down Expand Up @@ -141,6 +142,11 @@ class NDB_Menu_Filter_Candidate_List extends NDB_Menu_Filter
$this->query .= " AND c.CenterID IN (" . $site_arr . ")";
}

if ($config->getSetting("useProjectPermissions")) {
$projectIds = $user->getProjectIds();
$this->query .= " AND c.ProjectID IN (" . implode(",", $projectIds) . ")";
}

//'COALESCE(pso.ID,1) AS Participant_Status',
$this->group_by = 'c.CandID, psc.Name, c.PSCID, c.Gender';
$this->order_by = 'c.PSCID ASC';
Expand Down Expand Up @@ -320,7 +326,11 @@ class NDB_Menu_Filter_Candidate_List extends NDB_Menu_Filter
// Project list, if applicable
if ($config->getSetting("useProjects")==="true") {
$list_of_projects = array(null => 'All');
$projectList = Utility::getProjectList();
if ($config->getSetting("useProjectPermissions")) {
$projectList = $user->getProjects();
} else {
$projectList = Utility::getProjectList();
}
foreach ($projectList as $key => $value) {
$list_of_projects[$key] =$value;
}
Expand Down
8 changes: 8 additions & 0 deletions modules/candidate_parameters/php/NDB_Form_candidate_parameters.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,14 @@ class NDB_Form_Candidate_Parameters extends NDB_Form
{
//create user object
$user =& User::singleton();
$config =& NDB_Config::singleton();
$candidate =& Candidate::singleton($this->identifier);

if ($config->getSetting("useProjectPermissions")) {
if (!$user->hasAccessToProject($candidate->getData("ProjectID"))) {
return false;
}
}

// Set global permission to control access
// to different modules of candidate_parameters page
Expand Down
8 changes: 7 additions & 1 deletion modules/create_timepoint/php/create_timepoint.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,15 @@ class Create_Timepoint extends \NDB_Form
{
// create user object
$user =& \User::singleton();

$config =& \NDB_Config::singleton();
$candidate =& \Candidate::singleton($this->identifier);

if ($config->getSetting("useProjectPermissions")) {
if (!$user->hasAccessToProject($candidate->getData("ProjectID"))) {
return false;
}
}

// check user permissions
return (
$user->hasPermission('data_entry') &&
Expand Down
140 changes: 41 additions & 99 deletions modules/dashboard/php/NDB_Form_dashboard.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -73,25 +73,34 @@ class NDB_Form_Dashboard extends NDB_Form
}
}

$useProjects = $config->getSetting('useProjects');
$useProjectPermissions = $config->getSetting('useProjectPermissions');
$projectIDs = $useProjectPermissions ?
$user->getProjectIds() :
array_keys(Utility::getProjectList());

$recruitmentTarget = $config->getSetting('recruitmentTarget');

$overallRecruitment = Project::getRecruitment($projectIDs);

$this->createProjectProgressBar(
'overall',
"Overall Recruitment",
$recruitmentTarget,
$this->getTotalRecruitment()
$overallRecruitment,
$projectIDs
);

$useProjects = $config->getSetting('useProjects');
$this->tpl_data['useProjects'] = $useProjects;
if ($useProjects == "true") {
$projects = Utility::getProjectList();
foreach ($projects as $projectID => $project) {
foreach ($projectIDs as $projectID) {
$projectInfo = $config->getProjectSettings($projectID);
$this->createProjectProgressBar(
$projectID,
$projectInfo['Name'],
$projectInfo['recruitmentTarget'],
$this->getTotalRecruitmentByProject($projectID)
Project::getRecruitment(array($projectID)),
$projectIDs
);
}
}
Expand All @@ -102,8 +111,9 @@ class NDB_Form_Dashboard extends NDB_Form
LEFT JOIN session s ON (s.ID=f.SessionID)
LEFT JOIN candidate c ON (s.CandID=c.CandID)
WHERE s.Active='Y' AND c.Active='Y'
AND c.ProjectID IN (:projectIDs)
AND s.CenterID <> 1",
array()
array('projectIDs' => implode(',', $projectIDs))
);

// Tasks
Expand All @@ -118,8 +128,9 @@ class NDB_Form_Dashboard extends NDB_Form
LEFT JOIN candidate c ON (s.CandID=c.CandID)
WHERE fqc.QCStatus IS NULL
AND s.Active='Y' AND c.Active='Y'
AND c.ProjectID IN (:projectIDs)
AND s.CenterID <> 1",
array()
array('projectIDs' => implode(',', $projectIDs))
);
$this->tpl_data['new_scans_site'] = 'Sites: all';
}
Expand All @@ -133,8 +144,9 @@ class NDB_Form_Dashboard extends NDB_Form
LEFT JOIN session s ON (flag.SessionID=s.ID)
LEFT JOIN candidate c ON (s.CandID=c.CandID)
WHERE s.CenterID <> 1
AND c.ProjectID IN (:projectIDs)
AND s.Active='Y' AND c.Active='Y'",
array()
array('projectIDs' => implode(',', $projectIDs))
);
$this->tpl_data['conflicts_site'] = 'Sites: all';
} else {
Expand All @@ -145,8 +157,12 @@ class NDB_Form_Dashboard extends NDB_Form
LEFT JOIN candidate c ON (c.CandID=s.CandID)
LEFT JOIN psc ON (psc.CenterID=s.CenterID)
WHERE FIND_IN_SET(psc.CenterID, :siteID)
AND c.ProjectID IN (:projectIDs)
AND s.Active='Y' AND c.Active='Y'",
array('siteID' => implode(',', $siteID))
array(
'siteID' => implode(',', $siteID),
'projectIDs' => implode(',', $projectIDs)
)
);
$this->tpl_data['conflicts_site'] = 'Sites: All User Sites';
}
Expand All @@ -159,8 +175,9 @@ class NDB_Form_Dashboard extends NDB_Form
LEFT JOIN session s ON (s.ID=flag.SessionID)
LEFT JOIN candidate c ON (s.CandID=c.CandID)
WHERE flag.Data_entry='In Progress'
AND c.ProjectID IN (:projectIDs)
AND s.Active='Y' AND c.Active='Y' AND s.CenterID <> 1",
array()
array('projectIDs' => implode(',', $projectIDs))
);
$this->tpl_data['incomplete_forms_site'] = 'Sites: all';
} else {
Expand All @@ -171,8 +188,12 @@ class NDB_Form_Dashboard extends NDB_Form
LEFT JOIN psc ON (psc.CenterID=s.CenterID)
WHERE Data_entry='In Progress'
AND FIND_IN_SET(psc.CenterID, :siteID)
AND c.ProjectID IN (:projectIDs)
AND s.Active='Y' AND c.Active='Y'",
array('siteID' => implode(',', $siteID))
array(
'siteID' => implode(',', $siteID),
'projectIDs' => implode(',', $projectIDs)
)
);
$this->tpl_data['incomplete_forms_site'] = $site;
}
Expand All @@ -187,8 +208,9 @@ class NDB_Form_Dashboard extends NDB_Form
LEFT JOIN session s ON (s.ID=fg.SessionID)
LEFT JOIN candidate c ON (c.CandID=s.CandID)
WHERE Review_Done IS NULL
AND c.ProjectID IN (:projectIDs)
AND c.Active='Y' AND s.Active='Y'",
array()
array('projectIDs' => implode(',', $projectIDs))
);
$this->tpl_data['radiology_review_site'] = 'Sites: all';
}
Expand Down Expand Up @@ -222,10 +244,11 @@ class NDB_Form_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.CenterID, 0) <> 1
AND c.ProjectID IN (:projectIDs)",
/* include null CenterIDs so we don't accidentally
filter things out */
array()
array('projectIDs' => implode(',', $projectIDs))
);
$this->tpl_data['violated_scans_site'] = 'Sites: all';
}
Expand Down Expand Up @@ -308,87 +331,6 @@ class NDB_Form_Dashboard extends NDB_Form
}
}

/**
* Gets the total count of candidates associated with a specific project
*
* @return int
*/
function getTotalRecruitment()
{
$DB = Database::singleton();
$totalRecruitment = $DB->pselectOne(
"SELECT COUNT(*) FROM candidate c
WHERE c.Active='Y' AND c.Entity_type='Human' AND c.CenterID <> 1",
array()
);
return $totalRecruitment;
}

/**
* Gets the total count of candidates associated with a specific project
*
* @param int $projectID Project ID
*
* @return int
*/
function getTotalRecruitmentByProject($projectID)
{
$DB = Database::singleton();
$totalRecruitment = $DB->pselectOne(
"SELECT COUNT(*)
FROM candidate c
WHERE c.Active='Y' AND c.ProjectID=:PID AND c.Entity_type='Human'
AND c.CenterID <> 1",
array('PID' => $projectID)
);
return $totalRecruitment;
}

/**
* Gets the total count of candidates of a specific gender
*
* @param string $gender gender (male or female)
*
* @return int
*/
function getTotalGender($gender)
{
$DB = Database::singleton();
$total = $DB->pselectOne(
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.Gender=:Gender AND c.Active='Y' AND c.Entity_type='Human'
AND c.CenterID <> 1",
array('Gender' => $gender)
);
return $total;
}

/**
* Gets the total count of candidates of a specific gender,
* associated with a specific project
*
* @param string $gender gender (male or female)
* @param int $projectID Project ID
*
* @return int
*/
function getTotalGenderByProject($gender, $projectID)
{
$DB = Database::singleton();
$total = $DB->pselectOne(
"SELECT COUNT(c.CandID)
FROM candidate c
WHERE c.Gender=:Gender AND c.Active='Y' AND c.ProjectID=:PID
AND c.Entity_type='Human' AND c.CenterID <> 1",
array(
'Gender' => $gender,
'PID' => $projectID,
)
);
return $total;
}

/**
* Creates the template data for a progress bar
*
Expand All @@ -411,18 +353,18 @@ class NDB_Form_Dashboard extends NDB_Form
= $recruitmentTarget;

if ($ID == 'overall') {
$totalFemales = $this->getTotalGender("Female");
$totalFemales = Project::getTotalFemales();
} else {
$totalFemales = $this->getTotalGenderByProject("Female", $ID);
$totalFemales = Project::getTotalFemales(array($ID));
}
$this->tpl_data['recruitment'][$ID]['female_total'] = $totalFemales;
$this->tpl_data['recruitment'][$ID]['female_percent']
= round($totalFemales / $recruitmentTarget * 100);

if ($ID == 'overall') {
$totalMales = $this->getTotalGender("Male");
$totalMales = Project::getTotalMales();
} else {
$totalMales = $this->getTotalGenderByProject("Male", $ID);
$totalMales = Project::getTotalMales(array($ID));
}
$this->tpl_data['recruitment'][$ID]['male_total'] = $totalMales;
$this->tpl_data['recruitment'][$ID]['male_percent']
Expand Down
12 changes: 11 additions & 1 deletion modules/imaging_browser/php/NDB_Menu_Filter_imaging_browser.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,11 @@ class NDB_Menu_Filter_Imaging_Browser extends NDB_Menu_Filter
$config =& NDB_Config::singleton();
$user =& User::singleton();
$DB = Database::singleton();

if ($config->getSetting("useProjectPermissions")) {
$this->query .= " AND c.ProjectID IN (" . implode(",", $user->getProjectIds()) . ")";
}

if (!$user->hasPermission('imaging_browser_view_allsites')) {
$site_arr = implode(",", $user->getCenterIDs());
$this->query .= " AND c.CenterID IN (" . $site_arr . ")";
Expand Down Expand Up @@ -269,7 +274,12 @@ class NDB_Menu_Filter_Imaging_Browser extends NDB_Menu_Filter
$config =& NDB_Config::singleton();
if ($config->getSetting('useProjects') === "true") {
$list_of_projects = $allAr;
$projectList = Utility::getProjectList();
if ($config->getSetting("useProjectPermissions")) {
$projectList = $user->getProjects();
} else {
$projectList = Utility::getProjectList();
}

foreach ($projectList as $key => $value) {
$list_of_projects[$key] =$value;
}
Expand Down
7 changes: 7 additions & 0 deletions modules/instrument_list/php/NDB_Menu_Filter_instrument_list.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -38,12 +38,19 @@ class NDB_Menu_Filter_Instrument_List extends NDB_Menu_Filter
{
// create user object
$user =& User::singleton();
$config =& NDB_Config::singleton();

$timePoint =& TimePoint::singleton($_REQUEST['sessionID']);
$candID = $timePoint->getCandID();

$candidate =& Candidate::singleton($candID);

if ($config->getSetting("useProjectPermissions")) {
if (!$user->hasAccessToProject($candidate->getData("ProjectID"))) {
return false;
}
}

// check user permissions
return ($user->hasPermission('access_all_profiles')
|| (in_array(
Expand Down
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