Add baseUrl parameter to settings

genepi · Dec 1, 2023 · 7f3d1ab · 7f3d1ab
1 parent b269c9b
commit 7f3d1ab
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Showing 38 changed files with 81 additions and 71 deletions.
diff --git a/src/main/html/webapp/components/admin/dashboard/dashboard.js b/src/main/html/webapp/components/admin/dashboard/dashboard.js
@@ -22,7 +22,7 @@ export default Control.extend({
       }));
       $(element).fadeIn();
 
-      $.getJSON("/api/v2/admin/server/statistics", {
+      $.getJSON("api/v2/admin/server/statistics", {
         days: 1
       }, function(mydata) {
 
@@ -55,7 +55,7 @@ export default Control.extend({
 
     var days = $("#day_combo").val();
     var that = this;
-    $.getJSON("/api/v2/admin/server/statistics", {
+    $.getJSON("api/v2/admin/server/statistics", {
       days: days
     }, function(mydata) {
 

diff --git a/src/main/html/webapp/components/admin/settings/logs/logs.js b/src/main/html/webapp/components/admin/settings/logs/logs.js
@@ -12,6 +12,6 @@ export default Control.extend({
     $(element).hide();
     $(element).html(template());
     $(element).fadeIn();
-    $("#log-cloudgene").load("/api/v2/admin/server/logs/cloudgene.log");
+    $("#log-cloudgene").load("api/v2/admin/server/logs/cloudgene.log");
   }
 });
diff --git a/src/main/html/webapp/components/core/job/detail/logs/logs.js b/src/main/html/webapp/components/core/job/detail/logs/logs.js
@@ -8,7 +8,7 @@ export default Control.extend({
 
   "init": function(element, options) {
 
-    $.get('/logs/' + options.job.attr('id'),function(data) {
+    $.get('logs/' + options.job.attr('id'),function(data) {
       $(element).html(template({
         content: data,
         job: options.job

diff --git a/src/main/html/webapp/components/core/job/submit/submit.stache b/src/main/html/webapp/components/core/job/submit/submit.stache
@@ -36,7 +36,7 @@
 <div class="container">
 
 
-<form id="parameters" class="form-horizontal" action="/api/v2/jobs/submit/{{application.id}}" method="POST" enctype="multipart/form-data" novalidate autocomplete="off">
+<form id="parameters" class="form-horizontal" action="api/v2/jobs/submit/{{application.id}}" method="POST" enctype="multipart/form-data" novalidate autocomplete="off">
 
 <div class="form-group row">
 	<label for="job-name" class="col-sm-2 col-form-label">Name</label>

diff --git a/src/main/html/webapp/components/core/user/activate/activate.stache b/src/main/html/webapp/components/core/user/activate/activate.stache
@@ -2,7 +2,7 @@
 <br>
 {{#data.success}}
     <div class="alert alert-success" id="success-message">
-    <b>Well done!</b> Your account is now active. <a href="/">Login now</a>.
+    <b>Well done!</b> Your account is now active. <a href="./">Login now</a>.
     <br>
     </div>
 {{else}}

diff --git a/src/main/html/webapp/components/core/user/login/login.js b/src/main/html/webapp/components/core/user/login/login.js
@@ -21,7 +21,7 @@ export default Control.extend({
     var password = $(element).find("[name='password']");
 
     $.ajax({
-      url: "/login",
+      url: "login",
       type: "POST",
       data: $(element).find("#signin-form").serialize(),
       dataType: 'json',
@@ -33,7 +33,7 @@ export default Control.extend({
           };
           localStorage.setItem('cloudgene', JSON.stringify(dataToken));
 
-          var redirect = '/';
+          var redirect = './';
           window.location = redirect;
 
       },

diff --git a/src/main/html/webapp/components/core/user/logout/logout.js b/src/main/html/webapp/components/core/user/logout/logout.js
@@ -10,7 +10,7 @@ export default Control.extend({
 
     localStorage.removeItem("cloudgene");
 
-    var redirect = '/';
+    var redirect = './';
     window.location = redirect;
   }
 

diff --git a/src/main/html/webapp/components/core/user/password-recovery/password-recovery.js b/src/main/html/webapp/components/core/user/password-recovery/password-recovery.js
@@ -40,7 +40,7 @@ export default Control.extend({
 
 
     $.ajax({
-      url: "/api/v2/users/update-password",
+      url: "api/v2/users/update-password",
       type: "POST",
       data: $(element).find("#update-password-form")
         .serialize(),

diff --git a/src/main/html/webapp/components/core/user/password-reset/password-reset.js b/src/main/html/webapp/components/core/user/password-reset/password-reset.js
@@ -18,7 +18,7 @@ export default Control.extend({
     var username = $(element).find("[name='username']");
 
     $.ajax({
-      url: "/api/v2/users/reset",
+      url: "api/v2/users/reset",
       type: "POST",
       data: $(element).find("#reset-form").serialize(),
       dataType: 'json',

diff --git a/src/main/html/webapp/components/core/user/profile/profile.js b/src/main/html/webapp/components/core/user/profile/profile.js
@@ -57,7 +57,7 @@ export default Control.extend({
     }
 
     $.ajax({
-      url: "/api/v2/users/me/profile",
+      url: "api/v2/users/me/profile",
       type: "POST",
       data: $(element).find("#account-form").serialize(),
       dataType: 'json',

diff --git a/src/main/html/webapp/components/core/user/signup/signup.js b/src/main/html/webapp/components/core/user/signup/signup.js
@@ -48,7 +48,7 @@ export default Control.extend({
     $('#save').button('loading');
 
     $.ajax({
-      url: "/api/v2/users/register",
+      url: "api/v2/users/register",
       type: "POST",
       data: $(element).find("#signon-form").serialize(),
       dataType: 'json',

diff --git a/src/main/html/webapp/models/application-settings.js b/src/main/html/webapp/models/application-settings.js
@@ -1,8 +1,8 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findOne: 'GET /api/v2/server/apps/{id}/settings',
-  update: 'PUT /api/v2/server/apps/{id}/settings'
+  findOne: 'GET api/v2/server/apps/{id}/settings',
+  update: 'PUT api/v2/server/apps/{id}/settings'
 }, {
 
 });
diff --git a/src/main/html/webapp/models/application.js b/src/main/html/webapp/models/application.js
@@ -1,11 +1,11 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findAll: 'GET /api/v2/server/apps',
-  findOne: 'GET /api/v2/server/apps/{tool}',
-  create: 'POST /api/v2/server/apps',
-  update: 'PUT /api/v2/server/apps/{id}',
-  destroy: 'DELETE /api/v2/server/apps/{id}'
+  findAll: 'GET api/v2/server/apps',
+  findOne: 'GET api/v2/server/apps/{tool}',
+  create: 'POST api/v2/server/apps',
+  update: 'PUT api/v2/server/apps/{id}',
+  destroy: 'DELETE api/v2/server/apps/{id}'
 }, {
 
   'updateBinding': function() {

diff --git a/src/main/html/webapp/models/cloudgene-application.js b/src/main/html/webapp/models/cloudgene-application.js
@@ -2,7 +2,7 @@ import Model from 'can-connect/can/model/model';
 
 
 export default Model.extend({
-  findAll: 'GET /api/v2/admin/server/cloudgene-apps',
+  findAll: 'GET api/v2/admin/server/cloudgene-apps',
 }, {
 
 });
diff --git a/src/main/html/webapp/models/cluster.js b/src/main/html/webapp/models/cluster.js
@@ -1,7 +1,7 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findOne: 'GET /api/v2/admin/server/cluster'
+  findOne: 'GET api/v2/admin/server/cluster'
 }, {
 
 });
diff --git a/src/main/html/webapp/models/counter.js b/src/main/html/webapp/models/counter.js
@@ -1,7 +1,7 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findOne: 'GET /api/v2/server/counters'
+  findOne: 'GET api/v2/server/counters'
 }, {
 
 });
diff --git a/src/main/html/webapp/models/group.js b/src/main/html/webapp/models/group.js
@@ -1,5 +1,5 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findAll: 'GET /api/v2/admin/groups',
+  findAll: 'GET api/v2/admin/groups',
 }, {});
diff --git a/src/main/html/webapp/models/job-admin-details.js b/src/main/html/webapp/models/job-admin-details.js
@@ -1,7 +1,7 @@
 import Job from 'models/job';
 
 export default Job.extend({
-  findAll: 'GET /api/v2/admin/jobs'
+  findAll: 'GET api/v2/admin/jobs'
 }, {
 
 });
diff --git a/src/main/html/webapp/models/job-details.js b/src/main/html/webapp/models/job-details.js
@@ -1,6 +1,6 @@
 import Job from 'models/job';
 
 export default Job.extend({
-  findOne: 'GET /api/v2/jobs/{id}',
-  destroy: 'DELETE /api/v2/jobs/{id}'
+  findOne: 'GET api/v2/jobs/{id}',
+  destroy: 'DELETE api/v2/jobs/{id}'
 }, {});
diff --git a/src/main/html/webapp/models/job-operation.js b/src/main/html/webapp/models/job-operation.js
@@ -1,5 +1,5 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  update: 'GET /api/v2/jobs/{id}/{action}'
+  update: 'GET api/v2/jobs/{id}/{action}'
 }, {});
diff --git a/src/main/html/webapp/models/job.js b/src/main/html/webapp/models/job.js
@@ -4,9 +4,9 @@ import Model from 'can-connect/can/model/model';
 
 
 export default Model.extend({
-  findAll: 'GET /api/v2/jobs',
-  findOne: 'GET /api/v2/jobs/{id}/status',
-  destroy: 'DELETE /api/v2/jobs/{id}',
+  findAll: 'GET api/v2/jobs',
+  findOne: 'GET api/v2/jobs/{id}/status',
+  destroy: 'DELETE api/v2/jobs/{id}',
 }, {
 
   'syncTime': function () {

diff --git a/src/main/html/webapp/models/nextflow-config.js b/src/main/html/webapp/models/nextflow-config.js
@@ -1,7 +1,7 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findOne: 'GET /api/v2/admin/server/nextflow/config',
-  create: 'POST /api/v2/admin/server/nextflow/config/update',
-  update: 'POST /api/v2/admin/server/nextflow/config/update'
+  findOne: 'GET api/v2/admin/server/nextflow/config',
+  create: 'POST api/v2/admin/server/nextflow/config/update',
+  update: 'POST api/v2/admin/server/nextflow/config/update'
 }, {});
diff --git a/src/main/html/webapp/models/server.js b/src/main/html/webapp/models/server.js
@@ -1,5 +1,5 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findOne: 'GET /api/v2/server'
+  findOne: 'GET api/v2/server'
 }, {});
diff --git a/src/main/html/webapp/models/settings.js b/src/main/html/webapp/models/settings.js
@@ -1,7 +1,7 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findOne: 'GET /api/v2/admin/server/settings',
-  create: 'POST /api/v2/admin/server/settings/update',
-  update: 'POST /api/v2/admin/server/settings/update'
+  findOne: 'GET api/v2/admin/server/settings',
+  create: 'POST api/v2/admin/server/settings/update',
+  update: 'POST api/v2/admin/server/settings/update'
 }, {});
diff --git a/src/main/html/webapp/models/template.js b/src/main/html/webapp/models/template.js
@@ -1,9 +1,9 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findAll: 'GET /api/v2/admin/server/templates',
-  findOne: 'GET /api/v2/admin/server/templates/{key}',
-  destroy: 'POST /api/v2/admin/server/templates/delete',
-  create: 'POST /api/v2/admin/server/templates/{key}',
-  update: 'POST /api/v2/admin/server/templates/{key}'
+  findAll: 'GET api/v2/admin/server/templates',
+  findOne: 'GET api/v2/admin/server/templates/{key}',
+  destroy: 'POST api/v2/admin/server/templates/delete',
+  create: 'POST api/v2/admin/server/templates/{key}',
+  update: 'POST api/v2/admin/server/templates/{key}'
 }, {});
diff --git a/src/main/html/webapp/models/user-profile.js b/src/main/html/webapp/models/user-profile.js
@@ -4,7 +4,7 @@ export default Model.extend({
     destroy: function(user) {
 
         return $.ajax({
-            url: "/api/v2/users/" + user.username + "/profile",
+            url: "api/v2/users/" + user.username + "/profile",
             type: "DELETE",
             data: {
                 "username": user.username,

diff --git a/src/main/html/webapp/models/user-token.js b/src/main/html/webapp/models/user-token.js
@@ -1,6 +1,6 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  create: 'POST /api/v2/users/{user}/api-token?expiration={expiration}',
-  destroy: 'DELETE /api/v2/users/{user}/api-token',
+  create: 'POST api/v2/users/{user}/api-token?expiration={expiration}',
+  destroy: 'DELETE api/v2/users/{user}/api-token',
 }, {});
diff --git a/src/main/html/webapp/models/user.js b/src/main/html/webapp/models/user.js
@@ -1,10 +1,10 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  findOne: 'GET /api/v2/users/{user}/profile',
-  destroy: 'POST /api/v2/admin/users/{username}/delete',
-  update: 'POST /api/v2/admin/users/changegroup',
-  findAll: 'GET /api/v2/admin/users'
+  findOne: 'GET api/v2/users/{user}/profile',
+  destroy: 'POST api/v2/admin/users/{username}/delete',
+  update: 'POST api/v2/admin/users/changegroup',
+  findAll: 'GET api/v2/admin/users'
 }, {
 
   define: {

diff --git a/src/main/java/cloudgene/mapred/cli/StartServer.java b/src/main/java/cloudgene/mapred/cli/StartServer.java
@@ -85,7 +85,16 @@ public int run() {
 
 			}
 
-			// TODO: urlPrefix
+			String baseUrl = Application.settings.getBaseUrl();
+			if (!baseUrl.trim().isEmpty()) {
+				if (!baseUrl.startsWith("/") || baseUrl.endsWith("/")){
+					System.out.println("Error: baseUrl has wrong format. Example: \"/path\" or \"/path/subpath\".");
+					System.exit(1);
+				}
+				properties.put("micronaut.server.context-path", baseUrl);
+			} else {
+
+			}
 
 			if (new File("webapp").exists()) {
 
@@ -131,7 +140,7 @@ protected Settings loadSettings(Config config) throws FileNotFoundException, Yam
 		}
 
 		if (settings.getServerUrl() == null || settings.getServerUrl().trim().isEmpty()) {
-			System.out.println("serverUrl not set. Please set serverUrl in file '" + settingsFilename + "'");
+			System.out.println("Error: serverUrl not set. Please set serverUrl in file '" + settingsFilename + "'");
 			System.exit(1);
 		}
 

diff --git a/src/main/java/cloudgene/mapred/jobs/Environment.java b/src/main/java/cloudgene/mapred/jobs/Environment.java
@@ -20,7 +20,7 @@ public class Environment {
 
 	public Environment(Settings settings) {
 		add("SERVICE_NAME", settings.getName());
-		add("SERVICE_URL", settings.getServerUrl());
+		add("SERVICE_URL", settings.getServerUrl() + settings.getBaseUrl());
 		add("CONTACT_EMAIL", settings.getAdminMail());
 		add("CONTACT_NAME", settings.getAdminName());
 		if (settings.getMail() != null) {

diff --git a/src/main/java/cloudgene/mapred/jobs/workspace/S3Workspace.java b/src/main/java/cloudgene/mapred/jobs/workspace/S3Workspace.java
@@ -105,7 +105,6 @@ public InputStream download(String url) throws IOException {
 		String key = S3Util.getKey(url);
 
 		AmazonS3 s3 = S3Util.getAmazonS3();
-
 		S3Object o = s3.getObject(bucket, key);
 		S3ObjectInputStream s3is = o.getObjectContent();
 

diff --git a/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowCollector.java b/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowCollector.java
@@ -41,7 +41,7 @@ public String addContext(CloudgeneContext context) {
 		contexts.put(context.getPublicJobId(), context);
 		Settings settings = context.getSettings();
 		log.info("[Job {}] Register collector for public job id '{}'", context.getJobId(), context.getPublicJobId());
-		return settings.getServerUrl() + settings.getUrlPrefix() + COLLECTOR_ENDPOINT + context.getPublicJobId();
+		return settings.getServerUrl() + settings.getBaseUrl() + COLLECTOR_ENDPOINT + context.getPublicJobId();
 	}
 
 	public void addEvent(String job, Map<String, Object> event) throws IOException {

diff --git a/src/main/java/cloudgene/mapred/server/controller/DownloadController.java b/src/main/java/cloudgene/mapred/server/controller/DownloadController.java
@@ -108,7 +108,7 @@ public String downloadScript(String paramId, String hash) {
 		List<Download> downloads = dao.findAllByParameter(param);
 
 		String hostname = application.getSettings().getServerUrl();
-		hostname += application.getSettings().getUrlPrefix();
+		hostname += application.getSettings().getBaseUrl();
 
 		StringBuffer script = new StringBuffer();
 		script.append("#!/bin/bash\n");

diff --git a/src/main/java/cloudgene/mapred/server/responses/ServerResponse.java b/src/main/java/cloudgene/mapred/server/responses/ServerResponse.java
@@ -32,7 +32,7 @@ public static ServerResponse build(Settings settings) {
 		response.setName(settings.getName());
 		response.setAdminName(settings.getAdminName());
 		response.setAdminMail(settings.getAdminMail());
-		response.setServerUrl(settings.getServerUrl());
+		response.setServerUrl(settings.getServerUrl() + settings.getBaseUrl());
 		response.setBackgroundColor(settings.getColors().get("background"));
 		response.setForegroundColor(settings.getColors().get("foreground"));
 		response.setGoogleAnalytics(settings.getGoogleAnalytics());

diff --git a/src/main/java/cloudgene/mapred/server/services/UserService.java b/src/main/java/cloudgene/mapred/server/services/UserService.java
@@ -289,7 +289,7 @@ public MessageResponse resetPassword(String username) {
 			}
 
 			String hostname = application.getSettings().getServerUrl();
-			hostname += application.getSettings().getUrlPrefix();
+			hostname += application.getSettings().getBaseUrl();
 
 			String link = hostname + "/#!recovery/" + user.getUsername() + "/" + key;
 
@@ -362,7 +362,7 @@ public MessageResponse registerUser(String username, String mail, String new_pas
 		try {
 
 			String hostname = application.getSettings().getServerUrl();
-			hostname += application.getSettings().getUrlPrefix();
+			hostname += application.getSettings().getBaseUrl();
 
 			// if email server configured, send mails with activation link. Else
 			// activate user immediately.