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LIMS-1570: Remove unused app file #874

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LIMS-1570: Remove unused app file #874

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ca2241f
Remove touchscreen app
gfrn Nov 28, 2024
9814cee
Remove unused dependencies
gfrn Nov 28, 2024
a985c1d
Remove local version of jquery-flot-pie
gfrn Nov 28, 2024
71f1165
Remove aliased dependencies
gfrn Nov 29, 2024
6a130d3
Remove unused app file, dead dependencies
gfrn Dec 3, 2024
4303490
Remove unused vendor files
gfrn Dec 4, 2024
f024e33
Remove unused dependencies
gfrn Dec 10, 2024
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12 changes: 0 additions & 12 deletions api/config_sample.php
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Original file line number Diff line number Diff line change
Expand Up @@ -193,18 +193,6 @@
$in_contacts = array('Ind Contact' => '[email protected]'
);


# Beamline Sample Registration Machines
# - Used for touchscreen application (unauthenticated)
$blsr = array('1.2.3.4', # my touchscreen computer
);

# Beamline Sample Registration IP -> Beamline mapping
# - Third part of ip is used to identify beamline
#  x.x.103.x => i03
$ip2bl = array(103 => 'i03',
);

# Barcode readers
# - These clients use the android app (unauthenticated)
$bcr = array('1.2.3.4', # my android device
Expand Down
26 changes: 1 addition & 25 deletions api/src/Controllers/AssignController.php
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ class AssignController extends Page

public static $arg_list = array('visit' => '\w+\d+-\d+', 'cid' => '\d+', 'did' => '\d+', 'pos' => '\d+', 'bl' => '[\w\-]+');

public static $dispatch = array(array('/visits(/:visit)', 'get', 'getBeamlineVisits'),
public static $dispatch = array(
array('/assign', 'get', 'assignContainer'),
array('/unassign', 'get', 'unassignContainer'),
array('/deact', 'get', 'deactivateDewar'),
Expand Down Expand Up @@ -74,30 +74,6 @@ function deactivateDewar()
}
}


# ------------------------------------------------------------------------
# Return visits for beamline
function getBeamlineVisits($visit = null)
{
$visits = $this->blsr_visits();

if ($visit)
{
foreach ($visits as $i => $v)
{
if ($v['VISIT'] == $visit)
{
$this->_output($v);
return;
}
}
$this->_error('No such visit');
}
else
$this->_output($visits);
}


# ------------------------------------------------------------------------
# Puck names from puck scanner
# BL03I-MO-ROBOT-01:PUCK_01_NAME
Expand Down
11 changes: 1 addition & 10 deletions api/src/Controllers/AuthenticationController.php
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ function check()

private function checkAuthRequiredForSpecificSituations($parts): bool
{
global $blsr, $bcr, $img, $auto;
global $bcr, $img, $auto;

$need_auth = true;
# Work around to allow beamline sample registration without CAS authentication
Expand All @@ -102,10 +102,6 @@ private function checkAuthRequiredForSpecificSituations($parts): bool
# Allow formulatrix machines unauthorised access to inspections, certain IPs only
($parts[0] == 'imaging' && $parts[1] == 'inspection' && in_array($_SERVER["REMOTE_ADDR"], $img)) ||

# For use on the touchscreen computers in the hutch.
# Handles api calls: /assign/visits/<vist> e.g./assign/visits/mx1234-1
($parts[0] == 'assign' && $parts[1] == 'visits' && in_array($_SERVER["REMOTE_ADDR"], $blsr)) ||

# Allow barcode reader ips unauthorised access to add history
($parts[0] == 'shipment' && $parts[1] == 'dewars' && $parts[2] == 'history' && in_array($_SERVER["REMOTE_ADDR"], $bcr)) ||

Expand All @@ -129,11 +125,6 @@ private function checkAuthRequiredForSpecificSituations($parts): bool
else if (sizeof($parts) >= 2)
{
if (
# For use on the touchscreen computers in the hutch
# Handles api calls: /assign/assign, /assign/unassign, /assign/deact, /assign/visits
(($parts[0] == 'assign') && in_array($_SERVER["REMOTE_ADDR"], $blsr)) ||
(($parts[0] == 'shipment' && $parts[1] == 'containers') && in_array($_SERVER["REMOTE_ADDR"], $blsr)) ||

# Allow barcode reader unauthorised access, same as above, certain IPs only
($parts[0] == 'shipment' && $parts[1] == 'dewars' && in_array($_SERVER["REMOTE_ADDR"], $bcr)) ||

Expand Down
58 changes: 1 addition & 57 deletions api/src/Page.php
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Original file line number Diff line number Diff line change
Expand Up @@ -224,27 +224,7 @@ function auth($require_staff)

// Beamline Sample Registration
}
else if ($this->blsr() && !$this->user->loginId)
{
$auth = false;

if ($this->has_arg('visit'))
{
$blsr_visits = array();
foreach ($this->blsr_visits() as $v)
array_push($blsr_visits, $v['VISIT']);

if (in_array($this->arg('visit'), $blsr_visits))
$auth = True;

}
else
{
$auth = true;
}

// Barcode Scanners
}
// Barcode Scanners
else if ($this->bcr() && !$this->user->loginId)
{
$auth = true;
Expand Down Expand Up @@ -761,42 +741,6 @@ function pro()
}


# ------------------------------------------------------------------------
# Beamline sample registration: Get Beamline from IP
function ip2bl()
{
global $ip2bl;
$parts = explode('.', $_SERVER['REMOTE_ADDR']);

if ($parts && sizeof($parts) > 1 && array_key_exists($parts[2], $ip2bl))
{
return $ip2bl[$parts[2]];
}
}


# Return visit list for blsr;
function blsr_visits()
{
$b = $this->ip2bl();

if (!$b)
return array();

$visits = $this->db->pq("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE TIMESTAMPDIFF('DAY', s.startdate, CURRENT_TIMESTAMP) < 1 AND TIMESTAMPDIFF('DAY', CURRENT_TIMESTAMP, s.enddate) < 2 AND s.beamlinename LIKE :1 ORDER BY s.startdate", array($b));
$v = $this->db->paginate("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE p.proposalcode LIKE 'cm' AND s.beamlinename LIKE :1 AND s.enddate <= CURRENT_TIMESTAMP ORDER BY s.startdate DESC", array($b, 0, 1));
$visits = array_merge($visits, $v);
return $visits;
}

# Beamline Sample Registration Machine
function blsr()
{
global $blsr;

return in_array($_SERVER['REMOTE_ADDR'], $blsr);
}

# Barcode Scanner Machines
function bcr()
{
Expand Down
50 changes: 0 additions & 50 deletions api/tests/Controllers/AssignControllerTest.php
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Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,6 @@ protected function setUp(): void
$this->assignController->shouldReceive('_setup_routes')->times(1)->andReturn(Mockery::self());
$this->assignController->__construct($this->slimStub, $this->dbStub, $this->user, $this->dataLayerStub);

global $ip2bl;
$ip2bl = array(103 => 'i03');

global $bl_puck_names;
$bl_puck_names = array(
'i03' => "BL03I-MO-ROBOT-01:PUCK_%'02d_NAME",
Expand Down Expand Up @@ -146,53 +143,6 @@ public function testDeactivateDewarReturnsOneWhenDewarFound(): void
$this->assertEquals(1, $response->getBody());
}

public function testGetBeamlineVisitsWithInvalidNoConfigReturnsNothing(): void
{
$response = $this->setUpCommonResponse();
$_SERVER['REMOTE_ADDR'] = '';

$this->assignController->getBeamlineVisits();
$this->assertEquals('[]', $response->getBody());
}

public function testGetBeamlineVisitsWithValidConfigReturnsNothing(): void
{
$response = $this->setUpCommonResponse();
$_SERVER['REMOTE_ADDR'] = 'www.diamond.103.com';
$this->dbStub->expects($this->exactly(1))->method('pq')->with("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE TIMESTAMPDIFF('DAY', s.startdate, CURRENT_TIMESTAMP) < 1 AND TIMESTAMPDIFF('DAY', CURRENT_TIMESTAMP, s.enddate) < 2 AND s.beamlinename LIKE :1 ORDER BY s.startdate", array('i03'))->willReturn(array());
$this->dbStub->expects($this->exactly(1))->method('paginate')->with("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE p.proposalcode LIKE 'cm' AND s.beamlinename LIKE :1 AND s.enddate <= CURRENT_TIMESTAMP ORDER BY s.startdate DESC", array('i03', 0, 1))->willReturn(array());

$this->assignController->getBeamlineVisits();
$this->assertEquals('[]', $response->getBody());
}

public function testGetBeamlineVisitsWithValidConfigAndVisitReturnsData(): void
{
$visitId = 123;
$response = $this->setUpCommonResponse();
$_SERVER['REMOTE_ADDR'] = 'www.diamond.103.com';
$result = ['VISIT' => $visitId, 'BL' => 'test03'];
$this->dbStub->expects($this->exactly(1))->method('pq')->with("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE TIMESTAMPDIFF('DAY', s.startdate, CURRENT_TIMESTAMP) < 1 AND TIMESTAMPDIFF('DAY', CURRENT_TIMESTAMP, s.enddate) < 2 AND s.beamlinename LIKE :1 ORDER BY s.startdate", array('i03'))->willReturn(array($result));
$this->dbStub->expects($this->exactly(1))->method('paginate')->with("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE p.proposalcode LIKE 'cm' AND s.beamlinename LIKE :1 AND s.enddate <= CURRENT_TIMESTAMP ORDER BY s.startdate DESC", array('i03', 0, 1))->willReturn(array());

$this->assignController->getBeamlineVisits($visitId);
$this->assertEquals('{"VISIT":123,"BL":"test03"}', $response->getBody());
}

public function testGetBeamlineVisitsWithValidConfigAndInvalidVisitReturnsError(): void
{
$visitId = 123;
$_SERVER['REMOTE_ADDR'] = 'www.diamond.103.com';
$result = ['VISIT' => 1230, 'BL' => 'test03'];
$this->dbStub->expects($this->exactly(1))->method('pq')->with("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE TIMESTAMPDIFF('DAY', s.startdate, CURRENT_TIMESTAMP) < 1 AND TIMESTAMPDIFF('DAY', CURRENT_TIMESTAMP, s.enddate) < 2 AND s.beamlinename LIKE :1 ORDER BY s.startdate", array('i03'))->willReturn(array($result));
$this->dbStub->expects($this->exactly(1))->method('paginate')->with("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE p.proposalcode LIKE 'cm' AND s.beamlinename LIKE :1 AND s.enddate <= CURRENT_TIMESTAMP ORDER BY s.startdate DESC", array('i03', 0, 1))->willReturn(array());

$this->slimStub->shouldReceive('halt')->times(1)->with(400, '{"status":400,"message":"No such visit"}')->andThrow(new \Exception);
$this->expectException(\Exception::class);

$this->assignController->getBeamlineVisits($visitId);
}

public function testGetPuckNamesWithoutPropThrowsError(): void
{
$this->slimStub->shouldReceive('halt')->times(1)->with(400, '{"status":400,"message":"No proposal specified"}')->andThrow(new \Exception);
Expand Down
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