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medco-deployment/docker-images/i2b2-web/i2b2-web-writeconfig.sh
65a3ad40168bshrineremoved

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i2b2-web-writeconfig.sh
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#!/bin/bash
set -e
# meant to be called by Dockerfile of i2b2-web
# env var used: I2B2_DOMAIN_NAME, LIGHTTPD_WEB_ROOT
cat > "$LIGHTTPD_WEB_ROOT/i2b2-admin/i2b2_config_data.js" <<EOL
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
lstDomains: [ {
domain: "$I2B2_DOMAIN_NAME",
name: "Domain $I2B2_DOMAIN_NAME",
urlCellPM: "http://i2b2-server:8080/i2b2/services/PMService/",
allowAnalysis: true,
adminOnly: true,
debug: false
} ]
}
EOL
cat > "$LIGHTTPD_WEB_ROOT/i2b2-client/i2b2_config_data.js" <<EOL
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
lstDomains: [ {
domain: "$I2B2_DOMAIN_NAME",
name: "Domain $I2B2_DOMAIN_NAME",
urlCellPM: "http://i2b2-server:8080/i2b2/services/PMService/",
allowAnalysis: true,
debug: false
} ]
}
EOL
cat > "$LIGHTTPD_WEB_ROOT/index.html" <<EOL
<html><head><title>I2b2-web</title>
<script>
document.addEventListener('click', function(event) {
var target = event.target;
if (target.tagName.toLowerCase() == 'a')
{
var port = target.getAttribute('href').match(/^:(\d+)(.*)/);
if (port)
{
target.href = port[2];
target.port = port[1];
}
}
}, false);
</script>
</head><body>
<div align="center">
<p><a href="/shrine-client">SHRINE client (MedCo)</a></p>
<p><br /><br /></p>
<p><a href="/i2b2-admin">I2b2 admin</a></p>
<p><a href="/i2b2-client">I2b2 client</a></p>
<p><a href="/phppgadmin">PhpPgAdmin</a></p>
<p><a href="/phpmyadmin">PhpMyAdmin</a></p>
<p><a href=":9990">WildFly Management</a></p>
<p><a href=":8080/i2b2">I2b2 Axis2 Management</a></p>
<p><a href=":6443/manager">Tomcat Management</a></p>
<p><a href=":6443/shrine-dashboard">SHRINE Dashboard</a></p>
<p><a href=":6443/steward">SHRINE Data Steward</a></p>
<p><a href="/shrine-webclient-update.php">Pull last MedCo Webclient commits</a></p>
</div>
</body>
</html>
EOL
cat > "$LIGHTTPD_WEB_ROOT/shrine-webclient-update.php" <<EOL
<?php
echo '<html><head><title>Pull last commits?</title></head><body>';
echo '<form><input type="submit" name="btnSubmit" value="Do it" /></form>';
if (isset(\$_GET['btnSubmit']) or isset(\$_POST['btnSubmit'])) {
\$message=shell_exec("/opt/shrine-webclient-update.sh 2>&1");
echo '<p>';
print_r(\$message);
echo '</p>';
}
echo '</body></html>';
?>
EOL
cat > "$LIGHTTPD_WEB_ROOT/shrine-client/i2b2_config_data.js" <<EOL
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
loginTimeout: 15, // in seconds
username_label:"MedCo username:",
password_label:"MedCo password:",
lstDomains: [
{
domain: "$I2B2_DOMAIN_NAME",
name: "Domain $I2B2_DOMAIN_NAME",
debug: true,
allowAnalysis: true,
urlCellPM: "http://i2b2-server:8080/i2b2/services/PMService/",
isSHRINE: true
}
]
}
EOL
cat > "$LIGHTTPD_WEB_ROOT/shrine-client/js-i2b2/cells/SHRINE/cell_config_data.js" <<EOL
{
files: [
"SHRINE_ctrl.js",
"i2b2_msgs.js"
],
css: [],
config: {
name: "SHRINE Cell",
description: "SHRINE Cell",
category: ["core","cell","shrine"],
newTopicURL: "/steward/client/index.html",
readApprovedURL:"https://shrine-server:6443/shrine/rest/i2b2/request"
}
}
EOL
cat > "/etc/lighttpd/conf-enabled/10-ssl.conf" <<EOL
\$SERVER["socket"] == "0.0.0.0:443" {
ssl.engine = "enable"
ssl.ca-file = "$CONF_DIR/cacert.pem"
ssl.pemfile = "$CONF_DIR/srv$NODE_IDX.pem"
#todo: names in configuration profiles make more explicit
# todo: enable + get ssl only
# strict configuration from https://cipherli.st/
#ssl.honor-cipher-order = "enable"
#ssl.cipher-list = "EECDH+AESGCM:EDH+AESGCM:AES256+EECDH:AES256+EDH"
#ssl.use-compression = "disable"
#setenv.add-response-header = (
# "Strict-Transport-Security" => "max-age=15724800; includeSubdomains; preload",
# "X-Frame-Options" => "DENY",
# "X-Content-Type-Options" => "nosniff"
#)
#ssl.use-sslv2 = "disable"
#ssl.use-sslv3 = "disable"
# strict configuration from https://raymii.org/s/tutorials/Strong_SSL_Security_On_lighttpd.html
#ssl.dh-file = "/etc/ssl/certs/dhparam.pem"
#ssl.ec-curve = "secp384r1"
}
EOL
# webclients whitelist URLs
sed -i "s/\"http:\/\/localhost\"/\"http:\/\/i2b2-server:8080\"/" "$LIGHTTPD_WEB_ROOT/i2b2-admin/index.php"
sed -i "s/\"http:\/\/localhost\"/\"http:\/\/i2b2-server:8080\"/" "$LIGHTTPD_WEB_ROOT/i2b2-client/index.php"
sed -i "s/\"http:\/\/127.0.0.1\"/\"http:\/\/i2b2-server:8080\"/" "$LIGHTTPD_WEB_ROOT/shrine-client/index.php"
sed -i "s/\"http:\/\/localhost\"/\"https:\/\/shrine-server:6443\"/" "$LIGHTTPD_WEB_ROOT/shrine-client/index.php"
# shrine webclient fixes for integration in php environment
sed -i "s#default.htm#index.html#g" "$LIGHTTPD_WEB_ROOT/shrine-client/index.php"
sed -i '/CURLOPT_SSL_VERIFYPEER/i curl_setopt($proxyRequest, CURLOPT_SSL_VERIFYHOST, FALSE);' "$LIGHTTPD_WEB_ROOT/shrine-client/index.php"
sed -i "s#SHRINE_ONT_DB#$I2B2_DOMAIN_NAME#g" "$LIGHTTPD_WEB_ROOT/shrine-client/js-i2b2/cells/plugins/MedCo/php/sqlConnection.php"
sed -i "s#SHRINE_ONT_USER#shrine_ont#g" "$LIGHTTPD_WEB_ROOT/shrine-client/js-i2b2/cells/plugins/MedCo/php/sqlConnection.php"
sed -i "s#SHRINE_ONT_PW#$DB_PASSWORD#g" "$LIGHTTPD_WEB_ROOT/shrine-client/js-i2b2/cells/plugins/MedCo/php/sqlConnection.php"
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