diff --git a/Deps/auth_service/app.js b/Deps/auth_service/app.js index 6c9ff050..6df279ac 100644 --- a/Deps/auth_service/app.js +++ b/Deps/auth_service/app.js @@ -2,13 +2,24 @@ const express = require('express') const rp = require('request-promise'); const app = express(); const fs = require("fs"); +var atob = require('atob'); var jwt = require('jsonwebtoken'); var jwkToPem = require('jwk-to-pem'); var cookieParser = require('cookie-parser'); +const jwksClient = require('jwks-rsa'); var PORT = process.env.PORT || 8010 var BASE_USER_URL = "http://ca-data:9099/services/caMicroscope/Authorization/query/getAuth?name=" var SECRET = process.env.SECRET var EXPIRY = process.env.EXPIRY || "1d" +var JWK_URL = process.env.JWKS + +var jwks_client = false +console.log(JWK_URL) +if (JWK_URL){ + jwks_client = jwksClient({ + jwksUri: JWK_URL +}); +} // get cookies app.use(cookieParser()) @@ -61,10 +72,42 @@ const getToken = function(req) { return req.cookies.token; } } + +function getJwtKid(token) { + var base64Url = token.split('.')[0]; + var base64 = base64Url.replace(/-/g, '+').replace(/_/g, '/'); + var jsonPayload = decodeURIComponent(atob(base64).split('').map(function(c) { + return '%' + ('00' + c.charCodeAt(0).toString(16)).slice(-2); + }).join('')); + + return JSON.parse(jsonPayload).kid; +}; + +function jwk_token_trade(check_key, sign_key){ + return function(req,res){ + var THISTOKEN = getToken(req) + if(!jwks_client){ + console.log("something wrong...") + token_trade(check_key, sign_key)(req,res) + } + jwks_client.getSigningKey(getJwtKid(THISTOKEN), (err,key)=>{ + console.log(key) + let use_key = key.publicKey || key.rsaPublicKey + if(err){ + res.status(401).send(err) + } else { + token_trade(use_key, sign_key)(req,res) + } + }) + } +} + + // curry these calls function token_trade(check_key, sign_key){ return function(req,res){ - jwt.verify(getToken(req), check_key, function(err, token){ + var THISTOKEN = getToken(req) + jwt.verify(THISTOKEN, check_key, function(err, token){ if (err){ res.status(401).send(err) } else { @@ -104,7 +147,7 @@ function token_trade(check_key, sign_key){ } // convert or "check" a token -app.get("/check", token_trade(SECRET, PRIKEY)) +app.get("/check", jwk_token_trade(SECRET, PRIKEY)) // renew a token app.get("/renew", token_trade(PUBKEY, PRIKEY)) diff --git a/Deps/auth_service/package-lock.json b/Deps/auth_service/package-lock.json index 09b4082d..a6858630 100644 --- a/Deps/auth_service/package-lock.json +++ b/Deps/auth_service/package-lock.json @@ -4,19 +4,96 @@ "lockfileVersion": 1, "requires": true, "dependencies": { + "@types/body-parser": { + "version": "1.17.0", + "resolved": "https://registry.npmjs.org/@types/body-parser/-/body-parser-1.17.0.tgz", + "integrity": "sha512-a2+YeUjPkztKJu5aIF2yArYFQQp8d51wZ7DavSHjFuY1mqVgidGyzEQ41JIVNy82fXj8yPgy2vJmfIywgESW6w==", + "requires": { + "@types/connect": "*", + "@types/node": "*" + } + }, + "@types/connect": { + "version": "3.4.32", + "resolved": "https://registry.npmjs.org/@types/connect/-/connect-3.4.32.tgz", + "integrity": "sha512-4r8qa0quOvh7lGD0pre62CAb1oni1OO6ecJLGCezTmhQ8Fz50Arx9RUszryR8KlgK6avuSXvviL6yWyViQABOg==", + "requires": { + "@types/node": "*" + } + }, + "@types/express": { + "version": "4.17.0", + "resolved": "https://registry.npmjs.org/@types/express/-/express-4.17.0.tgz", + "integrity": "sha512-CjaMu57cjgjuZbh9DpkloeGxV45CnMGlVd+XpG7Gm9QgVrd7KFq+X4HY0vM+2v0bczS48Wg7bvnMY5TN+Xmcfw==", + "requires": { + "@types/body-parser": "*", + "@types/express-serve-static-core": "*", + "@types/serve-static": "*" + } + }, + "@types/express-jwt": { + "version": "0.0.42", + "resolved": "https://registry.npmjs.org/@types/express-jwt/-/express-jwt-0.0.42.tgz", + "integrity": "sha512-WszgUddvM1t5dPpJ3LhWNH8kfNN8GPIBrAGxgIYXVCEGx6Bx4A036aAuf/r5WH9DIEdlmp7gHOYvSM6U87B0ag==", + "requires": { + "@types/express": "*", + "@types/express-unless": "*" + } + }, + "@types/express-serve-static-core": { + "version": "4.16.7", + "resolved": "https://registry.npmjs.org/@types/express-serve-static-core/-/express-serve-static-core-4.16.7.tgz", + "integrity": "sha512-847KvL8Q1y3TtFLRTXcVakErLJQgdpFSaq+k043xefz9raEf0C7HalpSY7OW5PyjCnY8P7bPW5t/Co9qqp+USg==", + "requires": { + "@types/node": "*", + "@types/range-parser": "*" + } + }, + "@types/express-unless": { + "version": "0.5.1", + "resolved": "https://registry.npmjs.org/@types/express-unless/-/express-unless-0.5.1.tgz", + "integrity": "sha512-5fuvg7C69lemNgl0+v+CUxDYWVPSfXHhJPst4yTLcqi4zKJpORCxnDrnnilk3k0DTq/WrAUdvXFs01+vUqUZHw==", + "requires": { + "@types/express": "*" + } + }, + "@types/mime": { + "version": "2.0.1", + "resolved": "https://registry.npmjs.org/@types/mime/-/mime-2.0.1.tgz", + "integrity": "sha512-FwI9gX75FgVBJ7ywgnq/P7tw+/o1GUbtP0KzbtusLigAOgIgNISRK0ZPl4qertvXSIE8YbsVJueQ90cDt9YYyw==" + }, + "@types/node": { + "version": "12.7.1", + "resolved": "https://registry.npmjs.org/@types/node/-/node-12.7.1.tgz", + "integrity": "sha512-aK9jxMypeSrhiYofWWBf/T7O+KwaiAHzM4sveCdWPn71lzUSMimRnKzhXDKfKwV1kWoBo2P1aGgaIYGLf9/ljw==" + }, + "@types/range-parser": { + "version": "1.2.3", + "resolved": "https://registry.npmjs.org/@types/range-parser/-/range-parser-1.2.3.tgz", + "integrity": "sha512-ewFXqrQHlFsgc09MK5jP5iR7vumV/BYayNC6PgJO2LPe8vrnNFyjQjSppfEngITi0qvfKtzFvgKymGheFM9UOA==" + }, + "@types/serve-static": { + "version": "1.13.2", + "resolved": "https://registry.npmjs.org/@types/serve-static/-/serve-static-1.13.2.tgz", + "integrity": "sha512-/BZ4QRLpH/bNYgZgwhKEh+5AsboDBcUdlBYgzoLX0fpj3Y2gp6EApyOlM3bK53wQS/OE1SrdSYBAbux2D1528Q==", + "requires": { + "@types/express-serve-static-core": "*", + "@types/mime": "*" + } + }, "accepts": { - 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"http-errors": "~1.6.3", - "iconv-lite": "0.4.23", + "http-errors": "1.7.2", + "iconv-lite": "0.4.24", "on-finished": "~2.3.0", - "qs": "6.5.2", - "raw-body": "2.3.3", - "type-is": "~1.6.16" + "qs": "6.7.0", + "raw-body": "2.4.0", + "type-is": "~1.6.17" } }, "brorand": { @@ -113,9 +195,9 @@ "integrity": "sha1-+OcRMvf/5uAaXJaXpMbz5I1cyBk=" }, "bytes": { - "version": "3.0.0", - "resolved": "https://registry.npmjs.org/bytes/-/bytes-3.0.0.tgz", - "integrity": "sha1-0ygVQE1olpn4Wk6k+odV3ROpYEg=" + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/bytes/-/bytes-3.1.0.tgz", + "integrity": "sha512-zauLjrfCG+xvoyaqLoV8bLVXXNGC4JqlxFCutSDWA6fJrTo2ZuvLYTqZ7aHBLZSMOopbzwv8f+wZcVzfVTI2Dg==" }, "caseless": { "version": "0.12.0", @@ -123,17 +205,20 @@ "integrity": "sha1-G2gcIf+EAzyCZUMJBolCDRhxUdw=" }, "combined-stream": { - "version": "1.0.7", - "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-1.0.7.tgz", - "integrity": "sha512-brWl9y6vOB1xYPZcpZde3N9zDByXTosAeMDo4p1wzo6UMOX4vumB+TP1RZ76sfE6Md68Q0NJSrE/gbezd4Ul+w==", + "version": "1.0.8", + "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-1.0.8.tgz", + "integrity": "sha512-FQN4MRfuJeHf7cBbBMJFXhKSDq+2kAArBlmRBvcvFE5BB1HZKXtSFASDhdlz9zOYwxh8lDdnvmMOe/+5cdoEdg==", "requires": { "delayed-stream": "~1.0.0" } }, "content-disposition": { - 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"version": "1.4.0", - "resolved": "https://registry.npmjs.org/statuses/-/statuses-1.4.0.tgz", - "integrity": "sha512-zhSCtt8v2NDrRlPQpCNtw/heZLtfUDqxBM1udqikb/Hbk52LK4nQSwr10u77iopCW5LsyHpuXS0GnEc48mLeew==" + "version": "1.5.0", + "resolved": "https://registry.npmjs.org/statuses/-/statuses-1.5.0.tgz", + "integrity": "sha1-Fhx9rBd2Wf2YEfQ3cfqZOBR4Yow=" }, "stealthy-require": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/stealthy-require/-/stealthy-require-1.1.1.tgz", "integrity": "sha1-NbCYdbT/SfJqd35QmzCQoyJr8ks=" }, + "toidentifier": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/toidentifier/-/toidentifier-1.0.0.tgz", + "integrity": "sha512-yaOH/Pk/VEhBWWTlhI+qXxDFXlejDGcQipMlyxda9nthulaxLZUNcUqFxokp0vcYnvteJln5FNQDRrxj3YcbVw==" + }, "tough-cookie": { - "version": "2.5.0", - "resolved": "https://registry.npmjs.org/tough-cookie/-/tough-cookie-2.5.0.tgz", - "integrity": "sha512-nlLsUzgm1kfLXSXfRZMc1KLAugd4hqJHDTvc2hDIwS3mZAfMEuMbc03SujMF+GEcpaX/qboeycw6iO8JwVv2+g==", + "version": "2.4.3", + "resolved": "https://registry.npmjs.org/tough-cookie/-/tough-cookie-2.4.3.tgz", + "integrity": "sha512-Q5srk/4vDM54WJsJio3XNn6K2sCG+CQ8G5Wz6bZhRZoAe/+TxjWB/GlFAnYEbkYVlON9FMk/fE3h2RLpPXo4lQ==", "requires": { - "psl": "^1.1.28", - "punycode": "^2.1.1" + "psl": "^1.1.24", + "punycode": "^1.4.1" + }, + "dependencies": { + "punycode": { + "version": "1.4.1", + "resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz", + "integrity": "sha1-wNWmOycYgArY4esPpSachN1BhF4=" + } } }, "tunnel-agent": { @@ -829,12 +1003,12 @@ "integrity": "sha1-WuaBd/GS1EViadEIr6k/+HQ/T2Q=" }, "type-is": { - "version": "1.6.16", - "resolved": "https://registry.npmjs.org/type-is/-/type-is-1.6.16.tgz", - "integrity": "sha512-HRkVv/5qY2G6I8iab9cI7v1bOIdhm94dVjQCPFElW9W+3GeDOSHmy2EBYe4VTApuzolPcmgFTN3ftVJRKR2J9Q==", + "version": "1.6.18", + "resolved": "https://registry.npmjs.org/type-is/-/type-is-1.6.18.tgz", + "integrity": "sha512-TkRKr9sUTxEH8MdfuCSP7VizJyzRNMjj2J2do2Jr3Kym598JVdEksuzPQCnlFPW4ky9Q+iA+ma9BGm06XQBy8g==", "requires": { "media-typer": "0.3.0", - "mime-types": "~2.1.18" + "mime-types": "~2.1.24" } }, "unpipe": { @@ -874,6 +1048,16 @@ "core-util-is": "1.0.2", "extsprintf": "^1.2.0" } + }, + "very-fast-args": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/very-fast-args/-/very-fast-args-1.1.0.tgz", + "integrity": "sha1-4W0dH6+KbllqJGQh/ZCneWPQs5Y=" + }, + "yallist": { + "version": "2.1.2", + "resolved": "https://registry.npmjs.org/yallist/-/yallist-2.1.2.tgz", + "integrity": "sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI=" } } } diff --git a/Deps/auth_service/package.json b/Deps/auth_service/package.json index 681788aa..61b6d79f 100644 --- a/Deps/auth_service/package.json +++ b/Deps/auth_service/package.json @@ -9,11 +9,13 @@ "author": "birm", "license": "UNLICENSED", "dependencies": { + "atob": "^2.1.2", "cookie-parser": "^1.4.4", "express": "^4.16.4", "express-promise": "^0.4.0", "jsonwebtoken": "^8.4.0", "jwk-to-pem": "^2.0.1", + "jwks-rsa": "^1.6.0", "request": "^2.88.0", "request-promise": "^4.2.4" } diff --git a/auth0_login.html b/auth0_login.html new file mode 100644 index 00000000..6015938c --- /dev/null +++ b/auth0_login.html @@ -0,0 +1,59 @@ + +

Redirecting...

+ + diff --git a/caMicroscope.yml b/caMicroscope.yml index 4d3ac1cf..538b5413 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -40,7 +40,7 @@ services: volumes: - ./images/:/images/ viewer: - build: "https://github.com/camicroscope/caMicroscope.git#v3.4.2" + build: "https://github.com/camicroscope/caMicroscope.git#v3.4.3" container_name: ca-front restart: unless-stopped volumes: @@ -48,7 +48,7 @@ services: logging: driver: none loader: - build: "https://github.com/camicroscope/SlideLoader.git#v3.2.0" + build: "https://github.com/camicroscope/SlideLoader.git#v3.4.3" container_name: ca-load restart: unless-stopped logging: @@ -71,6 +71,8 @@ services: volumes: - ./jwt_keys/:/keys/ container_name: ca-auth + environment: + JWKS: "https://www.googleapis.com/oauth2/v3/certs" restart: unless-stopped logging: driver: none diff --git a/config/httpd.conf.template b/config/httpd.conf.template index 3b4871ac..9456c34b 100644 --- a/config/httpd.conf.template +++ b/config/httpd.conf.template @@ -128,9 +128,9 @@ ServerAdmin root@localhost # documents. By default, all requests are taken from this directory, but # symbolic links and aliases may be used to point to other locations. # -DocumentRoot "/data/pathdb/quip/web" +DocumentRoot "/quip/web" # - + AllowOverride all Require all granted Options Indexes FollowSymLinks IncludesNOEXEC diff --git a/config/pathdb/settings.php b/config/pathdb/settings.php new file mode 100755 index 00000000..0ecc2e1b --- /dev/null +++ b/config/pathdb/settings.php @@ -0,0 +1,781 @@ + 'databasename', + * 'username' => 'sqlusername', + * 'password' => 'sqlpassword', + * 'host' => 'localhost', + * 'port' => '3306', + * 'driver' => 'mysql', + * 'prefix' => '', + * 'collation' => 'utf8mb4_general_ci', + * ]; + * @endcode + */ +$databases = []; + +/** + * Customizing database settings. + * + * Many of the values of the $databases array can be customized for your + * particular database system. Refer to the sample in the section above as a + * starting point. + * + * The "driver" property indicates what Drupal database driver the + * connection should use. This is usually the same as the name of the + * database type, such as mysql or sqlite, but not always. The other + * properties will vary depending on the driver. For SQLite, you must + * specify a database file name in a directory that is writable by the + * webserver. For most other drivers, you must specify a + * username, password, host, and database name. + * + * Transaction support is enabled by default for all drivers that support it, + * including MySQL. To explicitly disable it, set the 'transactions' key to + * FALSE. + * Note that some configurations of MySQL, such as the MyISAM engine, don't + * support it and will proceed silently even if enabled. If you experience + * transaction related crashes with such configuration, set the 'transactions' + * key to FALSE. + * + * For each database, you may optionally specify multiple "target" databases. + * A target database allows Drupal to try to send certain queries to a + * different database if it can but fall back to the default connection if not. + * That is useful for primary/replica replication, as Drupal may try to connect + * to a replica server when appropriate and if one is not available will simply + * fall back to the single primary server (The terms primary/replica are + * traditionally referred to as master/slave in database server documentation). + * + * The general format for the $databases array is as follows: + * @code + * $databases['default']['default'] = $info_array; + * $databases['default']['replica'][] = $info_array; + * $databases['default']['replica'][] = $info_array; + * $databases['extra']['default'] = $info_array; + * @endcode + * + * In the above example, $info_array is an array of settings described above. + * The first line sets a "default" database that has one primary database + * (the second level default). The second and third lines create an array + * of potential replica databases. Drupal will select one at random for a given + * request as needed. The fourth line creates a new database with a name of + * "extra". + * + * You can optionally set prefixes for some or all database table names + * by using the 'prefix' setting. If a prefix is specified, the table + * name will be prepended with its value. Be sure to use valid database + * characters only, usually alphanumeric and underscore. If no prefixes + * are desired, leave it as an empty string ''. + * + * To have all database names prefixed, set 'prefix' as a string: + * @code + * 'prefix' => 'main_', + * @endcode + * + * Per-table prefixes are deprecated as of Drupal 8.2, and will be removed in + * Drupal 9.0. After that, only a single prefix for all tables will be + * supported. + * + * To provide prefixes for specific tables, set 'prefix' as an array. + * The array's keys are the table names and the values are the prefixes. + * The 'default' element is mandatory and holds the prefix for any tables + * not specified elsewhere in the array. Example: + * @code + * 'prefix' => [ + * 'default' => 'main_', + * 'users' => 'shared_', + * 'sessions' => 'shared_', + * 'role' => 'shared_', + * 'authmap' => 'shared_', + * ], + * @endcode + * You can also use a reference to a schema/database as a prefix. This may be + * useful if your Drupal installation exists in a schema that is not the default + * or you want to access several databases from the same code base at the same + * time. + * Example: + * @code + * 'prefix' => [ + * 'default' => 'main.', + * 'users' => 'shared.', + * 'sessions' => 'shared.', + * 'role' => 'shared.', + * 'authmap' => 'shared.', + * ]; + * @endcode + * NOTE: MySQL and SQLite's definition of a schema is a database. + * + * Advanced users can add or override initial commands to execute when + * connecting to the database server, as well as PDO connection settings. For + * example, to enable MySQL SELECT queries to exceed the max_join_size system + * variable, and to reduce the database connection timeout to 5 seconds: + * @code + * $databases['default']['default'] = [ + * 'init_commands' => [ + * 'big_selects' => 'SET SQL_BIG_SELECTS=1', + * ], + * 'pdo' => [ + * PDO::ATTR_TIMEOUT => 5, + * ], + * ]; + * @endcode + * + * WARNING: The above defaults are designed for database portability. Changing + * them may cause unexpected behavior, including potential data loss. See + * https://www.drupal.org/developing/api/database/configuration for more + * information on these defaults and the potential issues. + * + * More details can be found in the constructor methods for each driver: + * - \Drupal\Core\Database\Driver\mysql\Connection::__construct() + * - \Drupal\Core\Database\Driver\pgsql\Connection::__construct() + * - \Drupal\Core\Database\Driver\sqlite\Connection::__construct() + * + * Sample Database configuration format for PostgreSQL (pgsql): + * @code + * $databases['default']['default'] = [ + * 'driver' => 'pgsql', + * 'database' => 'databasename', + * 'username' => 'sqlusername', + * 'password' => 'sqlpassword', + * 'host' => 'localhost', + * 'prefix' => '', + * ]; + * @endcode + * + * Sample Database configuration format for SQLite (sqlite): + * @code + * $databases['default']['default'] = [ + * 'driver' => 'sqlite', + * 'database' => '/path/to/databasefilename', + * ]; + * @endcode + */ + +/** + * Location of the site configuration files. + * + * The $config_directories array specifies the location of file system + * directories used for configuration data. On install, the "sync" directory is + * created. This is used for configuration imports. The "active" directory is + * not created by default since the default storage for active configuration is + * the database rather than the file system. (This can be changed. See "Active + * configuration settings" below). + * + * The default location for the "sync" directory is inside a randomly-named + * directory in the public files path. The setting below allows you to override + * the "sync" location. + * + * If you use files for the "active" configuration, you can tell the + * Configuration system where this directory is located by adding an entry with + * array key CONFIG_ACTIVE_DIRECTORY. + * + * Example: + * @code + * $config_directories = [ + * CONFIG_SYNC_DIRECTORY => '/directory/outside/webroot', + * ]; + * @endcode + */ +$config_directories = []; + +/** + * Settings: + * + * $settings contains environment-specific configuration, such as the files + * directory and reverse proxy address, and temporary configuration, such as + * security overrides. + * + * @see \Drupal\Core\Site\Settings::get() + */ + +/** + * Salt for one-time login links, cancel links, form tokens, etc. + * + * This variable will be set to a random value by the installer. All one-time + * login links will be invalidated if the value is changed. Note that if your + * site is deployed on a cluster of web servers, you must ensure that this + * variable has the same value on each server. + * + * For enhanced security, you may set this variable to the contents of a file + * outside your document root; you should also ensure that this file is not + * stored with backups of your database. + * + * Example: + * @code + * $settings['hash_salt'] = file_get_contents('/home/example/salt.txt'); + * @endcode + */ +$settings['hash_salt'] = ''; + +/** + * Deployment identifier. + * + * Drupal's dependency injection container will be automatically invalidated and + * rebuilt when the Drupal core version changes. When updating contributed or + * custom code that changes the container, changing this identifier will also + * allow the container to be invalidated as soon as code is deployed. + */ +# $settings['deployment_identifier'] = \Drupal::VERSION; + +/** + * Access control for update.php script. + * + * If you are updating your Drupal installation using the update.php script but + * are not logged in using either an account with the "Administer software + * updates" permission or the site maintenance account (the account that was + * created during installation), you will need to modify the access check + * statement below. Change the FALSE to a TRUE to disable the access check. + * After finishing the upgrade, be sure to open this file again and change the + * TRUE back to a FALSE! + */ +$settings['update_free_access'] = FALSE; + +/** + * External access proxy settings: + * + * If your site must access the Internet via a web proxy then you can enter the + * proxy settings here. Set the full URL of the proxy, including the port, in + * variables: + * - $settings['http_client_config']['proxy']['http']: The proxy URL for HTTP + * requests. + * - $settings['http_client_config']['proxy']['https']: The proxy URL for HTTPS + * requests. + * You can pass in the user name and password for basic authentication in the + * URLs in these settings. + * + * You can also define an array of host names that can be accessed directly, + * bypassing the proxy, in $settings['http_client_config']['proxy']['no']. + */ +# $settings['http_client_config']['proxy']['http'] = 'http://proxy_user:proxy_pass@example.com:8080'; +# $settings['http_client_config']['proxy']['https'] = 'http://proxy_user:proxy_pass@example.com:8080'; +# $settings['http_client_config']['proxy']['no'] = ['127.0.0.1', 'localhost']; + +/** + * Reverse Proxy Configuration: + * + * Reverse proxy servers are often used to enhance the performance + * of heavily visited sites and may also provide other site caching, + * security, or encryption benefits. In an environment where Drupal + * is behind a reverse proxy, the real IP address of the client should + * be determined such that the correct client IP address is available + * to Drupal's logging, statistics, and access management systems. In + * the most simple scenario, the proxy server will add an + * X-Forwarded-For header to the request that contains the client IP + * address. However, HTTP headers are vulnerable to spoofing, where a + * malicious client could bypass restrictions by setting the + * X-Forwarded-For header directly. Therefore, Drupal's proxy + * configuration requires the IP addresses of all remote proxies to be + * specified in $settings['reverse_proxy_addresses'] to work correctly. + * + * Enable this setting to get Drupal to determine the client IP from the + * X-Forwarded-For header. If you are unsure about this setting, do not have a + * reverse proxy, or Drupal operates in a shared hosting environment, this + * setting should remain commented out. + * + * In order for this setting to be used you must specify every possible + * reverse proxy IP address in $settings['reverse_proxy_addresses']. + * If a complete list of reverse proxies is not available in your + * environment (for example, if you use a CDN) you may set the + * $_SERVER['REMOTE_ADDR'] variable directly in settings.php. + * Be aware, however, that it is likely that this would allow IP + * address spoofing unless more advanced precautions are taken. + */ +# $settings['reverse_proxy'] = TRUE; + +/** + * Specify every reverse proxy IP address in your environment. + * This setting is required if $settings['reverse_proxy'] is TRUE. + */ +# $settings['reverse_proxy_addresses'] = ['a.b.c.d', ...]; + +/** + * Reverse proxy trusted headers. + * + * Sets which headers to trust from your reverse proxy. + * + * Common values are: + * - \Symfony\Component\HttpFoundation\Request::HEADER_X_FORWARDED_ALL + * - \Symfony\Component\HttpFoundation\Request::HEADER_FORWARDED + * + * Note the default value of + * @code + * \Symfony\Component\HttpFoundation\Request::HEADER_X_FORWARDED_ALL | \Symfony\Component\HttpFoundation\Request::HEADER_FORWARDED + * @endcode + * is not secure by default. The value should be set to only the specific + * headers the reverse proxy uses. For example: + * @code + * \Symfony\Component\HttpFoundation\Request::HEADER_X_FORWARDED_ALL + * @endcode + * This would trust the following headers: + * - X_FORWARDED_FOR + * - X_FORWARDED_HOST + * - X_FORWARDED_PROTO + * - X_FORWARDED_PORT + * + * @see \Symfony\Component\HttpFoundation\Request::HEADER_X_FORWARDED_ALL + * @see \Symfony\Component\HttpFoundation\Request::HEADER_FORWARDED + * @see \Symfony\Component\HttpFoundation\Request::setTrustedProxies + */ +# $settings['reverse_proxy_trusted_headers'] = \Symfony\Component\HttpFoundation\Request::HEADER_X_FORWARDED_ALL | \Symfony\Component\HttpFoundation\Request::HEADER_FORWARDED; + + +/** + * Page caching: + * + * By default, Drupal sends a "Vary: Cookie" HTTP header for anonymous page + * views. This tells a HTTP proxy that it may return a page from its local + * cache without contacting the web server, if the user sends the same Cookie + * header as the user who originally requested the cached page. Without "Vary: + * Cookie", authenticated users would also be served the anonymous page from + * the cache. If the site has mostly anonymous users except a few known + * editors/administrators, the Vary header can be omitted. This allows for + * better caching in HTTP proxies (including reverse proxies), i.e. even if + * clients send different cookies, they still get content served from the cache. + * However, authenticated users should access the site directly (i.e. not use an + * HTTP proxy, and bypass the reverse proxy if one is used) in order to avoid + * getting cached pages from the proxy. + */ +# $settings['omit_vary_cookie'] = TRUE; + + +/** + * Cache TTL for client error (4xx) responses. + * + * Items cached per-URL tend to result in a large number of cache items, and + * this can be problematic on 404 pages which by their nature are unbounded. A + * fixed TTL can be set for these items, defaulting to one hour, so that cache + * backends which do not support LRU can purge older entries. To disable caching + * of client error responses set the value to 0. Currently applies only to + * page_cache module. + */ +# $settings['cache_ttl_4xx'] = 3600; + +/** + * Expiration of cached forms. + * + * Drupal's Form API stores details of forms in a cache and these entries are + * kept for at least 6 hours by default. Expired entries are cleared by cron. + * + * @see \Drupal\Core\Form\FormCache::setCache() + */ +# $settings['form_cache_expiration'] = 21600; + +/** + * Class Loader. + * + * If the APC extension is detected, the Symfony APC class loader is used for + * performance reasons. Detection can be prevented by setting + * class_loader_auto_detect to false, as in the example below. + */ +# $settings['class_loader_auto_detect'] = FALSE; + +/* + * If the APC extension is not detected, either because APC is missing or + * because auto-detection has been disabled, auto-loading falls back to + * Composer's ClassLoader, which is good for development as it does not break + * when code is moved in the file system. You can also decorate the base class + * loader with another cached solution than the Symfony APC class loader, as + * all production sites should have a cached class loader of some sort enabled. + * + * To do so, you may decorate and replace the local $class_loader variable. For + * example, to use Symfony's APC class loader without automatic detection, + * uncomment the code below. + */ +/* +if ($settings['hash_salt']) { + $prefix = 'drupal.' . hash('sha256', 'drupal.' . $settings['hash_salt']); + $apc_loader = new \Symfony\Component\ClassLoader\ApcClassLoader($prefix, $class_loader); + unset($prefix); + $class_loader->unregister(); + $apc_loader->register(); + $class_loader = $apc_loader; +} +*/ + +/** + * Authorized file system operations: + * + * The Update Manager module included with Drupal provides a mechanism for + * site administrators to securely install missing updates for the site + * directly through the web user interface. On securely-configured servers, + * the Update manager will require the administrator to provide SSH or FTP + * credentials before allowing the installation to proceed; this allows the + * site to update the new files as the user who owns all the Drupal files, + * instead of as the user the webserver is running as. On servers where the + * webserver user is itself the owner of the Drupal files, the administrator + * will not be prompted for SSH or FTP credentials (note that these server + * setups are common on shared hosting, but are inherently insecure). + * + * Some sites might wish to disable the above functionality, and only update + * the code directly via SSH or FTP themselves. This setting completely + * disables all functionality related to these authorized file operations. + * + * @see https://www.drupal.org/node/244924 + * + * Remove the leading hash signs to disable. + */ +# $settings['allow_authorize_operations'] = FALSE; + +/** + * Default mode for directories and files written by Drupal. + * + * Value should be in PHP Octal Notation, with leading zero. + */ +# $settings['file_chmod_directory'] = 0775; +# $settings['file_chmod_file'] = 0664; + +/** + * Public file base URL: + * + * An alternative base URL to be used for serving public files. This must + * include any leading directory path. + * + * A different value from the domain used by Drupal to be used for accessing + * public files. This can be used for a simple CDN integration, or to improve + * security by serving user-uploaded files from a different domain or subdomain + * pointing to the same server. Do not include a trailing slash. + */ +# $settings['file_public_base_url'] = 'http://downloads.example.com/files'; + +/** + * Public file path: + * + * A local file system path where public files will be stored. This directory + * must exist and be writable by Drupal. This directory must be relative to + * the Drupal installation directory and be accessible over the web. + */ +# $settings['file_public_path'] = 'sites/default/files'; + +/** + * Private file path: + * + * A local file system path where private files will be stored. This directory + * must be absolute, outside of the Drupal installation directory and not + * accessible over the web. + * + * Note: Caches need to be cleared when this value is changed to make the + * private:// stream wrapper available to the system. + * + * See https://www.drupal.org/documentation/modules/file for more information + * about securing private files. + */ +# $settings['file_private_path'] = ''; + +/** + * Session write interval: + * + * Set the minimum interval between each session write to database. + * For performance reasons it defaults to 180. + */ +# $settings['session_write_interval'] = 180; + +/** + * String overrides: + * + * To override specific strings on your site with or without enabling the Locale + * module, add an entry to this list. This functionality allows you to change + * a small number of your site's default English language interface strings. + * + * Remove the leading hash signs to enable. + * + * The "en" part of the variable name, is dynamic and can be any langcode of + * any added language. (eg locale_custom_strings_de for german). + */ +# $settings['locale_custom_strings_en'][''] = [ +# 'forum' => 'Discussion board', +# '@count min' => '@count minutes', +# ]; + +/** + * A custom theme for the offline page: + * + * This applies when the site is explicitly set to maintenance mode through the + * administration page or when the database is inactive due to an error. + * The template file should also be copied into the theme. It is located inside + * 'core/modules/system/templates/maintenance-page.html.twig'. + * + * Note: This setting does not apply to installation and update pages. + */ +# $settings['maintenance_theme'] = 'bartik'; + +/** + * PHP settings: + * + * To see what PHP settings are possible, including whether they can be set at + * runtime (by using ini_set()), read the PHP documentation: + * http://php.net/manual/ini.list.php + * See \Drupal\Core\DrupalKernel::bootEnvironment() for required runtime + * settings and the .htaccess file for non-runtime settings. + * Settings defined there should not be duplicated here so as to avoid conflict + * issues. + */ + +/** + * If you encounter a situation where users post a large amount of text, and + * the result is stripped out upon viewing but can still be edited, Drupal's + * output filter may not have sufficient memory to process it. If you + * experience this issue, you may wish to uncomment the following two lines + * and increase the limits of these variables. For more information, see + * http://php.net/manual/pcre.configuration.php. + */ +# ini_set('pcre.backtrack_limit', 200000); +# ini_set('pcre.recursion_limit', 200000); + +/** + * Active configuration settings. + * + * By default, the active configuration is stored in the database in the + * {config} table. To use a different storage mechanism for the active + * configuration, do the following prior to installing: + * - Create an "active" directory and declare its path in $config_directories + * as explained under the 'Location of the site configuration files' section + * above in this file. To enhance security, you can declare a path that is + * outside your document root. + * - Override the 'bootstrap_config_storage' setting here. It must be set to a + * callable that returns an object that implements + * \Drupal\Core\Config\StorageInterface. + * - Override the service definition 'config.storage.active'. Put this + * override in a services.yml file in the same directory as settings.php + * (definitions in this file will override service definition defaults). + */ +# $settings['bootstrap_config_storage'] = ['Drupal\Core\Config\BootstrapConfigStorageFactory', 'getFileStorage']; + +/** + * Configuration overrides. + * + * To globally override specific configuration values for this site, + * set them here. You usually don't need to use this feature. This is + * useful in a configuration file for a vhost or directory, rather than + * the default settings.php. + * + * Note that any values you provide in these variable overrides will not be + * viewable from the Drupal administration interface. The administration + * interface displays the values stored in configuration so that you can stage + * changes to other environments that don't have the overrides. + * + * There are particular configuration values that are risky to override. For + * example, overriding the list of installed modules in 'core.extension' is not + * supported as module install or uninstall has not occurred. Other examples + * include field storage configuration, because it has effects on database + * structure, and 'core.menu.static_menu_link_overrides' since this is cached in + * a way that is not config override aware. Also, note that changing + * configuration values in settings.php will not fire any of the configuration + * change events. + */ +# $config['system.file']['path']['temporary'] = '/tmp'; +# $config['system.site']['name'] = 'My Drupal site'; +# $config['system.theme']['default'] = 'stark'; +# $config['user.settings']['anonymous'] = 'Visitor'; + +/** + * Fast 404 pages: + * + * Drupal can generate fully themed 404 pages. However, some of these responses + * are for images or other resource files that are not displayed to the user. + * This can waste bandwidth, and also generate server load. + * + * The options below return a simple, fast 404 page for URLs matching a + * specific pattern: + * - $config['system.performance']['fast_404']['exclude_paths']: A regular + * expression to match paths to exclude, such as images generated by image + * styles, or dynamically-resized images. The default pattern provided below + * also excludes the private file system. If you need to add more paths, you + * can add '|path' to the expression. + * - $config['system.performance']['fast_404']['paths']: A regular expression to + * match paths that should return a simple 404 page, rather than the fully + * themed 404 page. If you don't have any aliases ending in htm or html you + * can add '|s?html?' to the expression. + * - $config['system.performance']['fast_404']['html']: The html to return for + * simple 404 pages. + * + * Remove the leading hash signs if you would like to alter this functionality. + */ +# $config['system.performance']['fast_404']['exclude_paths'] = '/\/(?:styles)|(?:system\/files)\//'; +# $config['system.performance']['fast_404']['paths'] = '/\.(?:txt|png|gif|jpe?g|css|js|ico|swf|flv|cgi|bat|pl|dll|exe|asp)$/i'; +# $config['system.performance']['fast_404']['html'] = '404 Not Found

Not Found

The requested URL "@path" was not found on this server.

'; + +/** + * Load services definition file. + */ +$settings['container_yamls'][] = $app_root . '/' . $site_path . '/services.yml'; + +/** + * Override the default service container class. + * + * This is useful for example to trace the service container for performance + * tracking purposes, for testing a service container with an error condition or + * to test a service container that throws an exception. + */ +# $settings['container_base_class'] = '\Drupal\Core\DependencyInjection\Container'; + +/** + * Override the default yaml parser class. + * + * Provide a fully qualified class name here if you would like to provide an + * alternate implementation YAML parser. The class must implement the + * \Drupal\Component\Serialization\SerializationInterface interface. + */ +# $settings['yaml_parser_class'] = NULL; + +/** + * Trusted host configuration. + * + * Drupal core can use the Symfony trusted host mechanism to prevent HTTP Host + * header spoofing. + * + * To enable the trusted host mechanism, you enable your allowable hosts + * in $settings['trusted_host_patterns']. This should be an array of regular + * expression patterns, without delimiters, representing the hosts you would + * like to allow. + * + * For example: + * @code + * $settings['trusted_host_patterns'] = [ + * '^www\.example\.com$', + * ]; + * @endcode + * will allow the site to only run from www.example.com. + * + * If you are running multisite, or if you are running your site from + * different domain names (eg, you don't redirect http://www.example.com to + * http://example.com), you should specify all of the host patterns that are + * allowed by your site. + * + * For example: + * @code + * $settings['trusted_host_patterns'] = [ + * '^example\.com$', + * '^.+\.example\.com$', + * '^example\.org$', + * '^.+\.example\.org$', + * ]; + * @endcode + * will allow the site to run off of all variants of example.com and + * example.org, with all subdomains included. + */ + +/** + * The default list of directories that will be ignored by Drupal's file API. + * + * By default ignore node_modules and bower_components folders to avoid issues + * with common frontend tools and recursive scanning of directories looking for + * extensions. + * + * @see file_scan_directory() + * @see \Drupal\Core\Extension\ExtensionDiscovery::scanDirectory() + */ +$settings['file_scan_ignore_directories'] = [ + 'node_modules', + 'bower_components', +]; + +/** + * The default number of entities to update in a batch process. + * + * This is used by update and post-update functions that need to go through and + * change all the entities on a site, so it is useful to increase this number + * if your hosting configuration (i.e. RAM allocation, CPU speed) allows for a + * larger number of entities to be processed in a single batch run. + */ +$settings['entity_update_batch_size'] = 50; + +/** + * Entity update backup. + * + * This is used to inform the entity storage handler that the backup tables as + * well as the original entity type and field storage definitions should be + * retained after a successful entity update process. + */ +$settings['entity_update_backup'] = TRUE; + +/** + * Load local development override configuration, if available. + * + * Use settings.local.php to override variables on secondary (staging, + * development, etc) installations of this site. Typically used to disable + * caching, JavaScript/CSS compression, re-routing of outgoing emails, and + * other things that should not happen on development and testing sites. + * + * Keep this code block at the end of this file to take full effect. + */ +# +# if (file_exists($app_root . '/' . $site_path . '/settings.local.php')) { +# include $app_root . '/' . $site_path . '/settings.local.php'; +# } +$config_directories['sync'] = '../config/sync'; +$settings['file_private_path'] = '/data/pathdb/files';$databases['default']['default'] = array ( 'database' => 'QuIP', 'username' => 'root', 'password' => '', 'prefix' => '', 'host' => 'localhost', 'port' => '', 'namespace' => 'Drupal\Core\Database\Driver\mysql', 'driver' => 'mysql',);$settings['hash_salt'] = '3163ca60-e485-41d7-80e6-d91788978ca9'; diff --git a/develop.yml b/develop.yml index 0c18de4a..e91b88db 100644 --- a/develop.yml +++ b/develop.yml @@ -57,4 +57,6 @@ services: build: "./Deps/auth_service/" volumes: - ./jwt_keys/:/keys/ + environment: + JWKS: "https://birmstuff.auth0.com/.well-known/jwks.json" container_name: ca-auth diff --git a/images/.gitignore b/images/.gitignore old mode 100644 new mode 100755 diff --git a/images/sample.svs b/images/sample.svs old mode 100644 new mode 100755 diff --git a/images/uploading/.gitignore b/images/uploading/.gitignore old mode 100644 new mode 100755 diff --git a/login.html b/login.html index 6015938c..ffd51600 100644 --- a/login.html +++ b/login.html @@ -1,23 +1,18 @@ -

Redirecting...

+ + +
+Sign out + diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 7ec53bf7..5b037d0f 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -53,19 +53,20 @@ services: logging: driver: none pathdb: - build: "https://github.com/SBU-BMI/PathDB.git#1.0.7" + build: "https://github.com/SBU-BMI/PathDB.git#1.0.9" container_name: quip-pathdb restart: unless-stopped ports: ["443:443","80:80"] volumes: - ./data:/data/ - ./images/:/data/pathdb/files/wsi + - ./config/pathdb:/quip/web/sites/default - ./jwt_keys/:/keys/ - ./config:/config command: - /config/pathdb_pre.sh imageloader: - build: "https://github.com/SBU-BMI/ImageLoader.git#1.0.0" + build: "https://github.com/SBU-BMI/ImageLoader.git#develop" container_name: quip-imageloader volumes: - ./data:/data/