All tests passing

feup-infolab · Jul 3, 2018 · eb53d96 · eb53d96
1 parent 3afcccd
commit eb53d96
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Showing 54 changed files with 212 additions and 302 deletions.
diff --git a/conf/deployment_configs.json b/conf/deployment_configs.json
@@ -1626,7 +1626,7 @@
       "active": true,
       "reuse_checkpoints": true,
       "create_checkpoints": true,
-      "destroy_existing_images_at_start": false,
+      "destroy_existing_images_at_start": true,
       "start_and_stop_containers_automatically" : false
     },
     "virtualbox": {

diff --git a/src/bootup/app.js b/src/bootup/app.js
@@ -269,7 +269,7 @@ class App
         if (process.env.NODE_ENV !== "test")
         {
             // second arg = overwrite pid if exists
-            self.pid = npid.create(rlequire.absPathInApp("dendro","running.pid"), true);
+            self.pid = npid.create(rlequire.absPathInApp("dendro", "running.pid"), true);
             self.pid.removeOnExit();
         }
 
@@ -563,7 +563,7 @@ class App
         {
             Logger.log("Dumping heap snapshot!");
             const heapdump = require("heapdump");
-            const snapshotsFolder = rlequire.absPathInApp("dendro","profiling/snapshots");
+            const snapshotsFolder = rlequire.absPathInApp("dendro", "profiling/snapshots");
             const snapshotFile = path.join(snapshotsFolder, Date.now() + ".heapsnapshot");
 
             mkdirp.sync(snapshotsFolder);

diff --git a/src/bootup/load/load_repository_platforms.js b/src/bootup/load/load_repository_platforms.js
@@ -6,8 +6,8 @@ const rlequire = require("rlequire");
 const isNull = rlequire("dendro", "src/utils/null.js").isNull;
 const Config = rlequire("dendro", "src/models/meta/config.js").Config;
 const Logger = rlequire("dendro", "src/utils/logger.js").Logger;
-const repository_platform_configs_file_path = rlequire.absPathInApp("dendro","conf/repository_platform_configs.json");
-const active_config_file_path = rlequire.absPathInApp("dendro","conf/active_deployment_config.json");
+const repository_platform_configs_file_path = rlequire.absPathInApp("dendro", "conf/repository_platform_configs.json");
+const active_config_file_path = rlequire.absPathInApp("dendro", "conf/active_deployment_config.json");
 
 const loadRepositoryPlatforms = function (app, callback)
 {

diff --git a/src/bootup/middleware/load_misc_middlewares.js b/src/bootup/middleware/load_misc_middlewares.js
@@ -6,7 +6,7 @@ const appSecret = Config.crypto.secret,
     slug = require("slug"),
     favicon = require("serve-favicon"),
     YAML = require("yamljs"),
-    swaggerDocument = YAML.load(rlequire.absPathInApp("dendro","swagger.yaml")),
+    swaggerDocument = YAML.load(rlequire.absPathInApp("dendro", "swagger.yaml")),
     swaggerUi = require("swagger-ui-express"),
     bodyParser = require("body-parser"),
     methodOverride = require("method-override"),

diff --git a/src/controllers/admin.js b/src/controllers/admin.js
@@ -468,7 +468,7 @@ module.exports.logs = function (req, res)
 
 module.exports.configuration = function (req, res)
 {
-    const configFilePath = rlequire.absPathInApp("dendro","conf/deployment_configs.json");
+    const configFilePath = rlequire.absPathInApp("dendro", "conf/deployment_configs.json");
     const Config = rlequire("dendro", "src/models/meta/config.js").Config;
     if (req.originalMethod === "GET")
     {
@@ -545,10 +545,10 @@ module.exports.configuration = function (req, res)
     else if (req.originalMethod === "POST")
     {
         const config = req.body;
-        mkdirp(rlequire.absPathInApp("dendro","conf/deployment_config_backups"), function (err)
+        mkdirp(rlequire.absPathInApp("dendro", "conf/deployment_config_backups"), function (err)
         {
             // destination.txt will be created or overwritten by default
-            fs.copyFile(configFilePath, path.join(rlequire.absPathInApp("dendro","conf/deployment_config_backups"), path.basename(configFilePath) + "_" + slug(new Date().toISOString()) + ".bak"), function (err)
+            fs.copyFile(configFilePath, path.join(rlequire.absPathInApp("dendro", "conf/deployment_config_backups"), path.basename(configFilePath) + "_" + slug(new Date().toISOString()) + ".bak"), function (err)
             {
                 if (isNull(err))
                 {

diff --git a/src/controllers/datasets.js b/src/controllers/datasets.js
@@ -6,7 +6,7 @@ const CKAN = require("ckan");
 const Config = rlequire("dendro", "src/models/meta/config.js").Config;
 const isNull = rlequire("dendro", "src/utils/null.js").isNull;
 
-const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
 const RepositoryPlatform = rlequire("dendro", "src/models/harvesting/repo_platform").RepositoryPlatform;
 const swordConnection = rlequire("dendro", "src/export_libs/sword-connection/index.js");
 const Figshare = rlequire("dendro", "src/export_libs/figshare/figshare.js");

diff --git a/src/controllers/files.js b/src/controllers/files.js
@@ -6,7 +6,7 @@ const Config = rlequire("dendro", "src/models/meta/config.js").Config;
 const isNull = rlequire("dendro", "src/utils/null.js").isNull;
 const Project = rlequire("dendro", "src/models/project.js").Project;
 const InformationElement = rlequire("dendro", "src/models/directory_structure/information_element.js").InformationElement;
-const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
 const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
 const Descriptor = rlequire("dendro", "src/models/meta/descriptor.js").Descriptor;
 const User = rlequire("dendro", "src/models/user.js").User;

diff --git a/src/controllers/projects.js b/src/controllers/projects.js
@@ -8,7 +8,7 @@ const isNull = rlequire("dendro", "src/utils/null.js").isNull;
 const Ontology = rlequire("dendro", "src/models/meta/ontology.js").Ontology;
 const Project = rlequire("dendro", "src/models/project.js").Project;
 const StorageConfig = rlequire("dendro", "src/models/storage/storageConfig.js").StorageConfig;
-const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
 const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
 const InformationElement = rlequire("dendro", "src/models/directory_structure/information_element.js").InformationElement;
 const Descriptor = rlequire("dendro", "src/models/meta/descriptor.js").Descriptor;

diff --git a/src/controllers/search.js b/src/controllers/search.js
@@ -9,7 +9,7 @@ const Elements = rlequire("dendro", "src/models/meta/elements.js").Elements;
 const Resource = rlequire("dendro", "src/models/resource.js").Resource;
 
 const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
-const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
 const User = rlequire("dendro", "src/models/user.js").User;
 const Project = rlequire("dendro", "src/models/project.js").Project;
 const Administrator = rlequire("dendro", "src/models/administrator.js").Administrator;

diff --git a/src/kb/db.js b/src/kb/db.js
@@ -194,7 +194,7 @@ const queryObjectToString = function (query, argumentsArray, callback)
 
 const recordQueryConclusionInLog = function (query, queryStartTime)
 {
-    const logParentFolder = rlequire.absPathInApp("dendro","profiling");
+    const logParentFolder = rlequire.absPathInApp("dendro", "profiling");
     const queryProfileLogFilePath = path.join(logParentFolder, "database_profiling_" + bootStartTimestamp + ".csv");
 
     if (Config.debug.database.log_query_times)
@@ -738,7 +738,7 @@ DbConnection.prototype.create = function (callback)
         {
             jinst.addOption("-Xrs");
             jinst.setupClasspath([
-                rlequire.absPathInApp("dendro","conf/virtuoso-jdbc/jdbc-4.2/virtjdbc4_2.jar")
+                rlequire.absPathInApp("dendro", "conf/virtuoso-jdbc/jdbc-4.2/virtjdbc4_2.jar")
             ]);
         }
 

diff --git a/src/models/directory_structure/file.js b/src/models/directory_structure/file.js
@@ -146,7 +146,7 @@ File.createBlankFileRelativeToAppRoot = function (relativePathToFile, callback)
 {
     const fs = require("fs");
 
-    const absPathToFile = rlequire.absPathInApp("dendro",relativePathToFile);
+    const absPathToFile = rlequire.absPathInApp("dendro", relativePathToFile);
     const parentFolder = path.resolve(absPathToFile, "..");
 
     fs.stat(absPathToFile, function (err, stat)

diff --git a/src/models/directory_structure/folder.js b/src/models/directory_structure/folder.js
@@ -502,7 +502,7 @@ Folder.prototype.bagit = function (bagItOptions, callback)
             },
             function (absolutePathOfFinishedFolder, parentFolderPath, cb)
             {
-                const gladstone = rlequire("dendro","/node_modules/gladstone/gladstone.js");
+                const gladstone = rlequire("dendro","node_modules/gladstone/gladstone.js");
                 gladstone.createBagDirectory(bagItOptions)
                     .then(function (result)
                     {

diff --git a/src/models/directory_structure/information_element.js b/src/models/directory_structure/information_element.js
@@ -81,7 +81,7 @@ InformationElement.prototype.getParent = function (callback)
                         if (!isNull(results[0].parent_folder))
                         {
                             result.uri = result.parent_folder;
-                            const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+                            const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
                             // let parent = new Folder(result);
                             // return callback(null, parent);
                             return Folder.findByUri(result.uri, function (err, parent)
@@ -240,7 +240,7 @@ InformationElement.prototype.getAllParentsUntilProject = function (callback)
             {
                 if (result instanceof Array)
                 {
-                    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+                    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
                     async.mapSeries(result, function (result, callback)
                     {
                         Folder.findByUri(result.uri, function (err, parentFolder)
@@ -327,7 +327,7 @@ InformationElement.prototype.needsRenaming = function (callback, newTitle, paren
         {
             parentUri = self.nie.isLogicalPartOf;
         }
-        const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+        const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
         const Project = rlequire("dendro", "src/models/project.js").Project;
 
         Folder.findByUri(parentUri, function (err, parentFolder)
@@ -497,7 +497,7 @@ InformationElement.prototype.rename = function (newTitle, callback, customGraphU
 
 InformationElement.prototype.moveToFolder = function (newParentFolder, callback)
 {
-    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
     const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
     const self = this;
 
@@ -1094,7 +1094,7 @@ InformationElement.prototype.getHumanReadableUri = function (callback)
 InformationElement.prototype.refreshChildrenHumanReadableUris = function (callback, customGraphUri)
 {
     const self = this;
-    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
     if (self.isA(Folder))
     {
         Folder.findByUri(self.uri, function (err, folder)

diff --git a/src/models/meta/config.js b/src/models/meta/config.js
@@ -165,7 +165,7 @@ if (path.isAbsolute(getConfigParameter("tempFilesDir")))
 }
 else
 {
-    Config.tempFilesDir = rlequire.absPathInApp("dendro",getConfigParameter("tempFilesDir"));
+    Config.tempFilesDir = rlequire.absPathInApp("dendro", getConfigParameter("tempFilesDir"));
 }
 
 if (path.isAbsolute(getConfigParameter("tempUploadsDir")))
@@ -174,7 +174,7 @@ if (path.isAbsolute(getConfigParameter("tempUploadsDir")))
 }
 else
 {
-    Config.tempUploadsDir = rlequire.absPathInApp("dendro",getConfigParameter("tempUploadsDir"));
+    Config.tempUploadsDir = rlequire.absPathInApp("dendro", getConfigParameter("tempUploadsDir"));
 }
 
 Config.tempFilesCreationMode = getConfigParameter("tempFilesCreationMode");

diff --git a/src/models/meta/permissions.js b/src/models/meta/permissions.js
@@ -8,7 +8,7 @@ const isNull = rlequire("dendro", "src/utils/null.js").isNull;
 const Resource = rlequire("dendro", "src/models/resource.js").Resource;
 const InformationElement = rlequire("dendro", "src/models/directory_structure/information_element.js").InformationElement;
 const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
-const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
 const User = rlequire("dendro", "src/models/user.js").User;
 const Project = rlequire("dendro", "src/models/project.js").Project;
 const Post = rlequire("dendro", "src/models/social/post.js").Post;

diff --git a/src/models/project.js b/src/models/project.js
@@ -11,7 +11,7 @@ const Cache = rlequire("dendro", "src/kb/cache/cache.js").Cache;
 const Resource = rlequire("dendro", "src/models/resource.js").Resource;
 const Elements = rlequire("dendro", "src/models/meta/elements.js").Elements;
 const Logger = rlequire("dendro", "src/utils/logger.js").Logger;
-const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
 const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
 const User = rlequire("dendro", "src/models/user.js").User;
 const Class = rlequire("dendro", "src/models/meta/class.js").Class;

diff --git a/src/models/resource.js b/src/models/resource.js
@@ -3187,7 +3187,7 @@ Resource.prototype.getLogicalParts = function (callback)
 {
     const self = this;
     const fs = require("fs");
-    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+    const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
     const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
 
     const childFoldersQuery =

diff --git a/src/utils/datasets/ckanUtils.js b/src/utils/datasets/ckanUtils.js
@@ -8,7 +8,7 @@ const Utils = rlequire("dendro", "public/js/utils.js").Utils;
 const isNull = rlequire("dendro", "src/utils/null.js").isNull;
 const Elements = rlequire("dendro", "src/models/meta/elements.js").Elements;
 const Logger = rlequire("dendro", "src/utils/logger.js").Logger;
-const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder
+const Folder = rlequire("dendro", "src/models/directory_structure/folder.js").Folder;
 const File = rlequire("dendro", "src/models/directory_structure/file.js").File;
 const Config = rlequire("dendro", "src/models/meta/config.js").Config;
 const generalDatasetUtils = rlequire("dendro", "src/utils/datasets/generalDatasetUtils.js");

diff --git a/src/utils/docker/docker_manager.js b/src/utils/docker/docker_manager.js
@@ -8,13 +8,13 @@ const isNull = rlequire("dendro", "src/utils/null.js").isNull;
 const Logger = rlequire("dendro", "src/utils/logger.js").Logger;
 
 const childProcess = require("child_process");
-const startContainersScript = rlequire.absPathInApp("dendro","conf/scripts/docker/start_containers.sh");
-const stopContainersScript = rlequire.absPathInApp("dendro","conf/scripts/docker/stop_containers.sh");
-const createCheckpointScript = rlequire.absPathInApp("dendro","conf/scripts/docker/create_checkpoint.sh");
-const restoreCheckpointScript = rlequire.absPathInApp("dendro","conf/scripts/docker/restore_checkpoint.sh");
-const restartContainersScript = rlequire.absPathInApp("dendro","conf/scripts/docker/restart_containers.sh");
-const nukeAndRebuildScript = rlequire.absPathInApp("dendro","conf/scripts/docker/nuke_and_rebuild.sh");
-const checkIfCheckpointExistsScript = rlequire.absPathInApp("dendro","conf/scripts/docker/check_if_checkpoint_exists.sh");
+const startContainersScript = rlequire.absPathInApp("dendro", "conf/scripts/docker/start_containers.sh");
+const stopContainersScript = rlequire.absPathInApp("dendro", "conf/scripts/docker/stop_containers.sh");
+const createCheckpointScript = rlequire.absPathInApp("dendro", "conf/scripts/docker/create_checkpoint.sh");
+const restoreCheckpointScript = rlequire.absPathInApp("dendro", "conf/scripts/docker/restore_checkpoint.sh");
+const restartContainersScript = rlequire.absPathInApp("dendro", "conf/scripts/docker/restart_containers.sh");
+const nukeAndRebuildScript = rlequire.absPathInApp("dendro", "conf/scripts/docker/nuke_and_rebuild.sh");
+const checkIfCheckpointExistsScript = rlequire.absPathInApp("dendro", "conf/scripts/docker/check_if_checkpoint_exists.sh");
 
 const DockerManager = function ()
 {

diff --git a/src/utils/logger.js b/src/utils/logger.js
@@ -70,7 +70,7 @@ Logger.init = function (startTime)
         const loggerLevel = (Config.logging.level) ? Config.logging.level : "debug";
         if (!isNull(Config.logging.app_logs_folder))
         {
-            const absPath = rlequire.absPathInApp("dendro",Config.logging.app_logs_folder);
+            const absPath = rlequire.absPathInApp("dendro", Config.logging.app_logs_folder);
 
             const exists = fs.existsSync(absPath);
             if (!exists)