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Merge 2023-R5.1 into Master #696

Merged
merged 14 commits into from
Nov 23, 2023
Merged

Merge 2023-R5.1 into Master #696

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b8aeda5
LIMS-59: Never write null to DewarTransportHistory.storageLocation (#…
ndg63276 Oct 12, 2023
fc4295e
LIMS-95: Show max score for each drop in a plate (#621)
ndg63276 Oct 16, 2023
269cd3d
LIMS-95: Change label to match others (#682)
ndg63276 Oct 18, 2023
81fa9c0
LIMS-140: Fix pia_estimated_d_min display on VMXi grid scans (#678)
ndg63276 Oct 18, 2023
12777c9
Move discovery away from constructor, get cookie expiry dynamically
gfrn Oct 20, 2023
44b0dd0
Update api/src/Authentication/Type/OIDC.php
gfrn Nov 2, 2023
6f36e9f
LIMS-309: Remove the Create New button in the protein acronym field f…
ndg63276 Nov 2, 2023
9a0ad6f
LIMS-1074: Allow accessing zipped files (#684)
ndg63276 Nov 2, 2023
5fa8803
Merge branch 'prerelease' into fix/lims-1068/oidc-discovery-endpoint-fix
gfrn Nov 2, 2023
e0ac33d
Merge pull request #683 from DiamondLightSource/fix/lims-1068/oidc-di…
gfrn Nov 2, 2023
efe064c
Merge pull request #688 from DiamondLightSource/master
John-Holt-Tessella Nov 2, 2023
ab0c56e
LIMS-1009: Remove the word 'remote' from 'responsive remote' (#671)
ndg63276 Nov 2, 2023
4b7047c
On Build: Satisfy Psalm Config (#689)
John-Holt-Tessella Nov 2, 2023
6a64ee7
Merge pull request #690 from DiamondLightSource/prerelease
John-Holt-Tessella Nov 2, 2023
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47 changes: 33 additions & 14 deletions api/scripts/mtz2map.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,35 @@ export CLIBD=$CCP4_MASTER/lib/data
export CCP4_SCR=/tmp
export root=$CCP4_MASTER/bin

if [ -f $1 ]; then
mtz=$1
else
if [ -f $1.gz ]; then
mtz=/tmp/$2_$3.mtz
gunzip -c $1.gz > $mtz
else
echo "No mtz file found"
exit
fi
fi

if [ $3 == 'dimple' -o $3 == 'mrbump' ]; then

if [ -f $4 ]; then
pdb=$4
else
if [ -f $4.gz ]; then
pdb=/tmp/$2_$3.pdb
gunzip -c $4.gz > $pdb
else
echo "No pdb file found"
exit
fi
fi

if [ $3 == 'dimple' ]; then
# fofc2="F1=F SIG1=SIGF PHI=PH2FOFCWT W=FOM"
# fofc="F1=F SIG1=SIGF PHI=PHFOFCWT W=FOM"
# fofc2="F1=F SIG1=SIGF PHI=PHWT W=FOM"
# fofc="F1=F SIG1=SIGF PHI=PHDELWT W=FOM"

if $root/mtzinfo $1 | grep -q PH2FOFCWT; then
if $root/mtzinfo $mtz | grep -q PH2FOFCWT; then
fofc2="F1=2FOFCWT SIG1=SIGF PHI=PH2FOFCWT"
fofc="F1=F SIG1=SIGF PHI=PHFOFCWT W=FOM"
else
Expand All @@ -37,7 +57,7 @@ fi

# F SIGF FC PHIC FC_ALL PHIC_ALL FWT PHWT DELFWT PHDELWT FOM FC_ALL_LS PHIC_ALL_LS

$root/fft HKLIN $1 MAPOUT "/tmp/$2_$3_2fofc.map.tmp" << eof
$root/fft HKLIN $mtz MAPOUT "/tmp/$2_$3_2fofc.map.tmp" << eof
title $2 2fofc
xyzlim asu
scale F1 1.0
Expand All @@ -46,11 +66,11 @@ $fofc2
end
eof

$root/mapmask MAPIN "/tmp/$2_$3_2fofc.map.tmp" MAPOUT "/tmp/$2_$3_2fofc.map" XYZIN "$4" << eof
$root/mapmask MAPIN "/tmp/$2_$3_2fofc.map.tmp" MAPOUT "/tmp/$2_$3_2fofc.map" XYZIN "$pdb" << eof
BORDER 5
eof

$root/fft HKLIN $1 MAPOUT "/tmp/$2_$3_fofc.map.tmp" << eof
$root/fft HKLIN $mtz MAPOUT "/tmp/$2_$3_fofc.map.tmp" << eof
title $2 fofc
xyzlim asu
scale F1 1.0
Expand All @@ -60,16 +80,17 @@ end
eof


$root/mapmask MAPIN "/tmp/$2_$3_fofc.map.tmp" MAPOUT "/tmp/$2_$3_fofc.map" XYZIN "$4" << eof
$root/mapmask MAPIN "/tmp/$2_$3_fofc.map.tmp" MAPOUT "/tmp/$2_$3_fofc.map" XYZIN "$pdb" << eof
BORDER 5
eof

gzip "/tmp/$2_$3_2fofc.map"
gzip "/tmp/$2_$3_fofc.map"

rm -f /tmp/$2_$3.pdb

else
$root/fft HKLIN $1 MAPOUT "/tmp/$2_$3.map" << eof
$root/fft HKLIN $mtz MAPOUT "/tmp/$2_$3.map" << eof
title $2 fofc
xyzlim asu
scale F1 1.0
Expand All @@ -78,10 +99,8 @@ F1=F SIG1=SIGF PHI=PHI W=FOM
end
eof

#$mm MAPIN "/tmp/$2_ep.map.tmp" MAPOUT "/tmp/$2_ep.map" XYZIN "$4" << eof
#BORDER 5
#eof

gzip "/tmp/$2_$3.map"

fi

rm -f /tmp/$2_$3.mtz
69 changes: 32 additions & 37 deletions api/src/Authentication/Type/OIDC.php
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -8,45 +8,41 @@

class OIDC extends AuthenticationParent implements AuthenticationInterface
{
private $providerConfig = array();
//** Cache for providerConfig */
private $providerConfigCache = null;

function __construct() {
private function getProviderConfig() {
global $sso_url, $oidc_client_id, $oidc_client_secret;

$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, 'https://' . $sso_url . '/.well-known/openid-configuration');
curl_setopt($ch, CURLOPT_HEADER, 0);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
$response = curl_exec($ch);
$http_code = curl_getinfo($ch, CURLINFO_HTTP_CODE);
$errno = curl_errno($ch);

if ($errno || $http_code != 200) {
error_log("Failed to connect to OIDC discovery endpoint. HTTP code: " . $http_code . ". CURL err. no.: " . $errno);
return;
}

curl_close($ch);
$newProviderConfig = json_decode($response);

if(!$newProviderConfig
|| !isset($newProviderConfig->userinfo_endpoint)
|| !isset($newProviderConfig->authorization_endpoint)
|| !isset($newProviderConfig->token_endpoint)) {
error_log("OIDC Authentication provider replied with invalid JSON discovery body");
return;
if (is_null($this->providerConfigCache)) {

$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, 'https://' . $sso_url . '/.well-known/openid-configuration');
curl_setopt($ch, CURLOPT_HEADER, 0);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
$response = curl_exec($ch);
curl_close($ch);
$newProviderConfig = json_decode($response);

if(!$newProviderConfig
|| !isset($newProviderConfig->userinfo_endpoint)
|| !isset($newProviderConfig->authorization_endpoint)
|| !isset($newProviderConfig->token_endpoint)) {
error_log("OIDC Authentication provider replied with invalid JSON body");
return null;
}
$newProviderConfig->b64ClientCreds = base64_encode(
$oidc_client_id . ":" . $oidc_client_secret
);

$this->providerConfigCache = $newProviderConfig;
}
$newProviderConfig->b64ClientCreds = base64_encode(
$oidc_client_id . ":" . $oidc_client_secret
);

$this->providerConfig = $newProviderConfig;
return $this->providerConfigCache;
}

private function getUser($token)
{
$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, $this->providerConfig->userinfo_endpoint);
curl_setopt($ch, CURLOPT_URL, $this->getProviderConfig()->userinfo_endpoint);
curl_setopt($ch, CURLOPT_HEADER, 0);
curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Bearer ' . $token));
curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
Expand Down Expand Up @@ -82,7 +78,7 @@ function authorise()
global $oidc_client_id;
$redirect_url = Utils::filterParamFromUrl($_SERVER["HTTP_REFERER"], "code");

return ( $this->providerConfig->authorization_endpoint .
return ( $this->getProviderConfig()->authorization_endpoint .
'?response_type=code&client_id=' . $oidc_client_id .
'&redirect_uri=' . $redirect_url
);
Expand All @@ -95,14 +91,14 @@ function authenticateByCode($code)
$redirect_url = Utils::filterParamFromUrl($_SERVER["HTTP_REFERER"], "code");

$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, $this->providerConfig->token_endpoint .
curl_setopt($ch, CURLOPT_URL, $this->getProviderConfig()->token_endpoint .
'?grant_type=authorization_code&redirect_uri=' .
$redirect_url .
"&code=" . $code
);
curl_setopt($ch, CURLOPT_HEADER, 0);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Basic ' . $this->providerConfig->b64ClientCreds));
curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Basic ' . $this->getProviderConfig()->b64ClientCreds));
$response = curl_exec($ch);
curl_close($ch);

Expand All @@ -113,14 +109,14 @@ function authenticateByCode($code)
}

$token = $response_json->access_token;

if(!$token) {
error_log("Invalid authentication attempt, provider returned no access token");
return false;
}

$cookieOpts = array (
'expires' => time() + 60*60*24,
'expires' => time() + $response_json->expires_in,
'path' => '/',
'secure' => true,
'httponly' => true,
Expand All @@ -131,4 +127,3 @@ function authenticateByCode($code)
return $this->getUser($token);
}
}

8 changes: 6 additions & 2 deletions api/src/Downstream/BigEPPhasing.php
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,17 @@ function results() {
}

$image = $this->_get_image();
$dat['IMAGE'] = file_exists($image);
$dat['IMAGE'] = file_exists($image) || file_exists($image.'.gz');

$model = $this->_get_attachments('big_ep_model_ispyb.json');
$dat['HASMODEL'] = $model && file_exists($model['FILE']);
$dat['HASMODEL'] = $model && (file_exists($model['FILE']) || file_exists($model['FILE'].'.gz'));
if ($model) {
if (file_exists($model['FILE'])) {
$json_str = file_get_contents($model['FILE']);
} elseif (file_exists($model['FILE'].'.gz')) {
$json_str = gzdecode(file_get_contents($model['FILE'].'.gz'));
}
if (isset($json_str)) {
$json_data = json_decode($json_str, true);
foreach (
array(
Expand Down
142 changes: 77 additions & 65 deletions api/src/Downstream/Type/FastEp.php
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,83 +16,95 @@ function results() {
$pdb = $this->_get_attachments("sad_fa.pdb");
if ($pdb) {
if (file_exists($pdb["FILE"])) {
$pdb = file_get_contents($pdb["FILE"]);
foreach (explode("\n", $pdb) as $l) {
if (strpos($l, 'HETATM') !== false) {
$parts = preg_split('/\s+/', $l);
array_push($ats, array(
$parts[1],
$parts[5],
$parts[6],
$parts[7],
$parts[8],
));
}
}
$pdb_cont = file_get_contents($pdb["FILE"]);
} elseif (file_exists($pdb['FILE'].'.gz')) {
$pdb_cont = gzdecode(file_get_contents($pdb['FILE'].'.gz'));
}
}

$dat['ATOMS'] = array_slice($ats, 0, 5);
if (isset($pdb_cont)) {
foreach (explode("\n", $pdb_cont) as $l) {
if (strpos($l, 'HETATM') !== false) {
$parts = preg_split('/\s+/', $l);
array_push($ats, array(
$parts[1],
$parts[5],
$parts[6],
$parts[7],
$parts[8],
));
}
}

$dat['ATOMS'] = array_slice($ats, 0, 5);

}

$lst = $this->_get_attachments("sad.lst");
if ($lst) {
if (file_exists($lst['FILE'])) {
$p1 = array();
$p2 = array();

$lst = file_get_contents($lst['FILE']);
$graph_vals = 0;
$gvals = array();
foreach (explode("\n", $lst) as $l) {
if (
strpos(
$l,
'Estimated mean FOM and mapCC as a function of resolution'
) !== false
) {
$graph_vals = 1;
}

if ($graph_vals && $graph_vals < 5) {
array_push($gvals, $l);
$graph_vals++;
}

if (
preg_match(
'/ Estimated mean FOM = (\d+.\d+)\s+Pseudo-free CC = (\d+.\d+)/',
$l,
$mat
)
) {
$dat['FOM'] = floatval($mat[1]);
$dat['CC'] = floatval($mat[2]);
}
$lst_cont = file_get_contents($lst['FILE']);
} elseif (file_exists($lst['FILE'].'.gz')) {
$lst_cont = gzdecode(file_get_contents($lst['FILE'].'.gz'));
}
}

if (isset($lst_cont)) {
$p1 = array();
$p2 = array();

$graph_vals = 0;
$gvals = array();
foreach (explode("\n", $lst_cont) as $l) {
if (
strpos(
$l,
'Estimated mean FOM and mapCC as a function of resolution'
) !== false
) {
$graph_vals = 1;
}

if (sizeof($gvals) > 0) {
$x = array_map(
'floatval',
array_slice(explode(' - ', $gvals[1]), 1)
);
$y = array_map(
'floatval',
array_slice(preg_split('/\s+/', $gvals[2]), 2)
);
$y2 = array_map(
'floatval',
array_slice(preg_split('/\s+/', $gvals[3]), 2)
);

foreach ($x as $i => $v) {
array_push($p1, array(1.0 / pow($v, 2), $y[$i]));
array_push($p2, array(1.0 / pow($v, 2), $y2[$i]));
}
if ($graph_vals && $graph_vals < 5) {
array_push($gvals, $l);
$graph_vals++;
}

$dat['PLOTS']['FOM'] = $p1;
$dat['PLOTS']['CC'] = $p2;
if (
preg_match(
'/ Estimated mean FOM = (\d+.\d+)\s+Pseudo-free CC = (\d+.\d+)/',
$l,
$mat
)
) {
$dat['FOM'] = floatval($mat[1]);
$dat['CC'] = floatval($mat[2]);
}
}

if (sizeof($gvals) > 0) {
$x = array_map(
'floatval',
array_slice(explode(' - ', $gvals[1]), 1)
);
$y = array_map(
'floatval',
array_slice(preg_split('/\s+/', $gvals[2]), 2)
);
$y2 = array_map(
'floatval',
array_slice(preg_split('/\s+/', $gvals[3]), 2)
);

foreach ($x as $i => $v) {
array_push($p1, array(1.0 / pow($v, 2), $y[$i]));
array_push($p2, array(1.0 / pow($v, 2), $y2[$i]));
}
}

$dat['PLOTS']['FOM'] = $p1;
$dat['PLOTS']['CC'] = $p2;

}

$results = new DownstreamResult($this);
Expand Down
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