Merge branch 'develop' of https://github.com/stochss/stochss into dev…

…elop
StochSS · Jun 1, 2021 · 02fa237 · 02fa237
2 parents 2d586d6 + 530a979
commit 02fa237
Show file tree

Hide file tree

Showing 12 changed files with 163 additions and 88 deletions.
diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js
@@ -44,6 +44,7 @@ let FileBrowser = PageView.extend({
     'click [data-hook=file-browser-help]' : function () {
       let modal = $(modals.operationInfoModalHtml('file-browser')).modal();
     },
+    'click [data-hook=empty-trash]' : 'emptyTrash'
   },
   initialize: function (attrs, options) {
     PageView.prototype.initialize.apply(this, arguments)
@@ -78,7 +79,10 @@ let FileBrowser = PageView.extend({
           if(op === 'move_node' && more && more.ref && more.ref.type && !(more.ref.type == 'folder' || more.ref.type == 'root')){
             return false
           }
-          if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder'){
+          if(op === 'move_node' && more && more.ref && more.ref.original && path.dirname(more.ref.original._path).split("/").includes("trash")){
+            return false
+          }
+          if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder' && more.ref.text !== "trash"){
             if(!more.ref.state.loaded){
               return false
             }
@@ -110,6 +114,11 @@ let FileBrowser = PageView.extend({
                 node.original._path = path.join(newDir, file);
                 if(node.type === "folder") {
                   $('#models-jstree').jstree().refresh_node(node);
+                }else if(newDir.endsWith("trash")) {
+                  $(self.queryByHook('empty-trash')).prop('disabled', false);
+                  $('#models-jstree').jstree().refresh_node(par);
+                }else if(oldPath.split("/").includes("trash")) {
+                  $('#models-jstree').jstree().refresh_node(par);
                 }
               },
               error: function (err, response, body) {
@@ -763,7 +772,6 @@ let FileBrowser = PageView.extend({
         if(o && o.original && o.original.type !== "root"){
           parentPath = o.original._path
         }
-        console.log(parentPath)
         if(isModel) {
           let ext = isSpatial ? ".smdl" : ".mdl"
           let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + ext : input.value.trim() + ext;
@@ -853,6 +861,43 @@ let FileBrowser = PageView.extend({
       }
     });
   },
+  moveToTrash: function (o) {
+    if(document.querySelector('#moveToTrashConfirmModal')) {
+      document.querySelector('#moveToTrashConfirmModal').remove();
+    }
+    let self = this;
+    let modal = $(modals.moveToTrashConfirmHtml("model")).modal();
+    let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn');
+    yesBtn.addEventListener('click', function (e) {
+      modal.modal('hide');
+      let queryStr = "?srcPath=" + o.original._path + "&dstPath=" + path.join("trash", o.text)
+      let endpoint = path.join(app.getApiPath(), "file/move") + queryStr
+      app.getXHR(endpoint, {
+        always: function (err, response, body) {
+          $(self.queryByHook('empty-trash')).prop('disabled', false);
+          $('#models-jstree').jstree().refresh();
+        }
+      });
+    });
+  },
+  emptyTrash: function (e) {
+    if(document.querySelector("#emptyTrashConfirmModal")) {
+      document.querySelector("#emptyTrashConfirmModal").remove()
+    }
+    let self = this;
+    let modal = $(modals.emptyTrashConfirmHtml()).modal();
+    let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn');
+    yesBtn.addEventListener('click', function (e) {
+      modal.modal('hide');
+      let endpoint = path.join(app.getApiPath(), "file/empty-trash") + "?path=trash";
+      app.getXHR(endpoint, {
+        success: function (err, response, body) {
+          self.refreshJSTree();
+          $(self.queryByHook('empty-trash')).prop('disabled', true);
+        }
+      });
+    });
+  },
   setupJstree: function () {
     var self = this;
     $.jstree.defaults.contextmenu.items = (o, cb) => {
@@ -898,6 +943,17 @@ let FileBrowser = PageView.extend({
             self.duplicateFileOrDirectory(o, null)
           }
         },
+        "MoveToTrash" : {
+          "label" : "Move To Trash",
+          "_disabled" : false,
+          "separator_before" : false,
+          "separator_after" : false,
+          "action" : function (data) {
+            self.moveToTrash(o);
+          }
+        }
+      }
+      let delete_node = {
         "Delete" : {
           "label" : "Delete",
           "_disabled" : false,
@@ -1261,6 +1317,12 @@ let FileBrowser = PageView.extend({
       if (o.type === 'root'){
         return folder
       }
+      if (o.text === "trash") {
+        return {"Refresh": folder.Refresh}
+      }
+      if (o.original._path.split("/")[0] === "trash") {
+        return delete_node
+      }
       if (o.type ===  'folder') {
         return $.extend(folder, common)
       }
@@ -1319,26 +1381,28 @@ let FileBrowser = PageView.extend({
       var file = e.target.text
       var node = $('#models-jstree').jstree().get_node(e.target)
       var _path = node.original._path;
-      if(file.endsWith('.mdl') || file.endsWith('.smdl')){
-        window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path;
-      }else if(file.endsWith('.ipynb')){
-        var notebookPath = path.join(app.getBasePath(), "notebooks", _path)
-        window.open(notebookPath, '_blank')
-      }else if(file.endsWith('.sbml')){
-        var openPath = path.join(app.getBasePath(), "edit", _path)
-        window.open(openPath, '_blank')
-      }else if(file.endsWith('.proj')){
-        window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
-      }else if(file.endsWith('.wkfl')){
-        window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
-      }else if(file.endsWith('.domn')) {
-        let queryStr = "?domainPath=" + _path
-        window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr
-      }else if(node.type === "folder" && $('#models-jstree').jstree().is_open(node) && $('#models-jstree').jstree().is_loaded(node)){
-        $('#models-jstree').jstree().refresh_node(node)
-      }else if(node.type === "other"){
-        var openPath = path.join(app.getBasePath(), "view", _path);
-        window.open(openPath, "_blank");
+      if(!(_path.split("/")[0] === "trash")) {
+        if(file.endsWith('.mdl') || file.endsWith('.smdl')){
+          window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path;
+        }else if(file.endsWith('.ipynb')){
+          var notebookPath = path.join(app.getBasePath(), "notebooks", _path)
+          window.open(notebookPath, '_blank')
+        }else if(file.endsWith('.sbml')){
+          var openPath = path.join(app.getBasePath(), "edit", _path)
+          window.open(openPath, '_blank')
+        }else if(file.endsWith('.proj')){
+          window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
+        }else if(file.endsWith('.wkfl')){
+          window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
+        }else if(file.endsWith('.domn')) {
+          let queryStr = "?domainPath=" + _path
+          window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr
+        }else if(node.type === "folder" && $('#models-jstree').jstree().is_open(node) && $('#models-jstree').jstree().is_loaded(node)){
+          $('#models-jstree').jstree().refresh_node(node)
+        }else if(node.type === "other"){
+          var openPath = path.join(app.getBasePath(), "view", _path);
+          window.open(openPath, "_blank");
+        }
       }
     });
   }

diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js
@@ -229,7 +229,7 @@ let ProjectManager = PageView.extend({
     let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn');
     yesBtn.addEventListener('click', function (e) {
       modal.modal('hide');
-      let endpoint = path.join(app.getApiPath(), "project/empty-trash")+"?path="+path.join(self.model.directory, "trash");
+      let endpoint = path.join(app.getApiPath(), "file/empty-trash")+"?path="+path.join(self.model.directory, "trash");
       app.getXHR(endpoint, {
         success: function (err, response, body) {
           $(self.queryByHook('empty-project-trash')).prop('disabled', true);

diff --git a/client/templates/pages/fileBrowser.pug b/client/templates/pages/fileBrowser.pug
@@ -35,4 +35,6 @@ section.page
 
   button.btn.btn-primary.box-shadow(id="options-for-node" data-hook="options-for-node" disabled) Actions
 
-  button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh
+  button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh
+
+  button.btn.btn-primary.inline.box-shadow(id="empty-trash" data-hook="empty-trash") Empty Trash
diff --git a/client/views/edit-project.js b/client/views/edit-project.js
@@ -29,24 +29,25 @@ let template = require('../templates/includes/editProject.pug');
 module.exports = View.extend({
   template: template,
   events: {
-    'click [data-hook=remove-project-btn]' : 'handleRemoveProjectClick'
+    'click [data-hook=remove-project-btn]' : 'handleMoveToTrash'
   },
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
   },
   render: function (attrs, options) {
     View.prototype.render.apply(this, arguments);
   },
-  handleRemoveProjectClick: function (e) {
-    if(document.querySelector('#deleteFileModal')) {
-      document.querySelector('#deleteFileModal').remove();
+  handleMoveToTrash: function (e) {
+    if(document.querySelector('#moveToTrashConfirmModal')) {
+      document.querySelector('#moveToTrashConfirmModal').remove();
     }
     let self = this;
-    let endpoint = path.join(app.getApiPath(), "file/delete")+"?path="+this.model.directory;
-    let modal = $(modals.deleteFileHtml("project")).modal();
-    let yesBtn = document.querySelector('#deleteFileModal .yes-modal-btn');
+    let modal = $(modals.moveToTrashConfirmHtml("model")).modal();
+    let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn');
     yesBtn.addEventListener('click', function (e) {
       modal.modal('hide');
+      let queryStr = "?srcPath=" + self.model.directory + "&dstPath=" + path.join("trash", self.model.directory.split("/").pop());
+      let endpoint = path.join(app.getApiPath(), "file/move") + queryStr
       app.getXHR(endpoint, {
         success: function (err, response, body) {
           self.model.collection.remove(self.model);

diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js
@@ -1379,7 +1379,7 @@ module.exports = View.extend({
       if (o.text === "trash"){
         return refresh
       }
-      if (o.original._path.includes("trash")) {
+      if (o.original._path.includes(".proj/trash/")) {
         return {"Delete": common.Delete}
       }
       if (o.type ===  'folder') {
@@ -1441,26 +1441,28 @@ module.exports = View.extend({
         var file = e.target.text
         var node = $('#models-jstree-view').jstree().get_node(e.target)
         var _path = node.original._path;
-        if(file.endsWith('.mdl') || file.endsWith('.smdl')){
-          window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path;
-        }else if(file.endsWith('.ipynb')){
-          var notebookPath = path.join(app.getBasePath(), "notebooks", _path)
-          window.open(notebookPath, '_blank')
-        }else if(file.endsWith('.sbml')){
-          var openPath = path.join(app.getBasePath(), "edit", _path)
-          window.open(openPath, '_blank')
-        }else if(file.endsWith('.proj')){
-          window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
-        }else if(file.endsWith('.wkfl')){
-          window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
-        }else if(file.endsWith('.domn')) {
-          let queryStr = "?domainPath=" + _path
-          window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr
-        }else if(node.type === "folder" && $('#models-jstree-view').jstree().is_open(node) && $('#models-jstree-view').jstree().is_loaded(node)){
-          $('#models-jstree-view').jstree().refresh_node(node)
-        }else if(node.type === "other"){
-          var openPath = path.join(app.getBasePath(), "view", _path);
-          window.open(openPath, "_blank");
+        if(!_path.includes(".proj/trash/")){
+          if(file.endsWith('.mdl') || file.endsWith('.smdl')){
+            window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path;
+          }else if(file.endsWith('.ipynb')){
+            var notebookPath = path.join(app.getBasePath(), "notebooks", _path)
+            window.open(notebookPath, '_blank')
+          }else if(file.endsWith('.sbml')){
+            var openPath = path.join(app.getBasePath(), "edit", _path)
+            window.open(openPath, '_blank')
+          }else if(file.endsWith('.proj')){
+            window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
+          }else if(file.endsWith('.wkfl')){
+            window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
+          }else if(file.endsWith('.domn')) {
+            let queryStr = "?domainPath=" + _path
+            window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr
+          }else if(node.type === "folder" && $('#models-jstree-view').jstree().is_open(node) && $('#models-jstree-view').jstree().is_loaded(node)){
+            $('#models-jstree-view').jstree().refresh_node(node)
+          }else if(node.type === "other"){
+            var openPath = path.join(app.getBasePath(), "view", _path);
+            window.open(openPath, "_blank");
+          }
         }
       });
     })

diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py
@@ -58,6 +58,7 @@ def get_page_handlers(route_start):
         (r"/stochss/api/file/upload\/?", UploadFileAPIHandler),
         (r"/stochss/api/file/upload-from-link\/?", UploadFileFromLinkAPIHandler),
         (r"/stochss/api/file/move\/?", MoveFileAPIHandler),
+        (r"/stochss/api/file/empty-trash\/?", EmptyTrashAPIHandler),
         (r"/stochss/api/file/delete\/?", DeleteFileAPIHandler),
         (r"/stochss/api/file/rename\/?", RenameAPIHandler),
         (r"/stochss/api/file/download\/?", DownloadAPIHandler),
@@ -88,7 +89,6 @@ def get_page_handlers(route_start):
         (r"/stochss/api/project/add-existing-model\/?", AddExistingModelAPIHandler),
         (r"/stochss/api/project/extract-model\/?", ExtractModelAPIHandler),
         (r"/stochss/api/project/extract-workflow\/?", ExtractWorkflowAPIHandler),
-        (r"/stochss/api/project/empty-trash\/?", EmptyTrashAPIHandler),
         (r"/stochss/api/project/export-combine\/?", ExportAsCombineAPIHandler),
         (r"/stochss/api/project/meta-data\/?", ProjectMetaDataAPIHandler),
         (r"/stochss/api/project/save-annotation\/?", UpdateAnnotationAPIHandler),

diff --git a/stochss/handlers/file_browser.py b/stochss/handlers/file_browser.py
@@ -101,6 +101,35 @@ async def get(self):
         self.finish()
 
 
+class EmptyTrashAPIHandler(APIHandler):
+    '''
+    ##############################################################################
+    Handler for a projects trash directory
+    ##############################################################################
+    '''
+    @web.authenticated
+    def get(self):
+        '''
+        Empty the trash directory.
+
+        Attributes
+        ----------
+        '''
+        self.set_header('Content-Type', 'application/json')
+        path = self.get_query_argument(name="path")
+        log.debug("Path to the trash directory: %s", path)
+        try:
+            log.info("Emptying the trash")
+            folder = StochSSFolder(path=path)
+            resp = folder.empty()
+            log.debug("Response message: %s", resp)
+            log.info("Successfully emptied the trash")
+            self.write(resp)
+        except StochSSAPIError as err:
+            report_error(self, log, err)
+        self.finish()
+
+
 class DeleteFileAPIHandler(APIHandler):
     '''
     ################################################################################################

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
@@ -315,7 +315,8 @@ async def get(self):
         self.set_header('Content-Type', 'application/json')
         try:
             folder = StochSSFolder(path="")
-            resp = folder.get_file_list(ext=".domn")
+            test = lambda ext, root, file: bool("trash" in root.split("/"))
+            resp = folder.get_file_list(ext=".domn", test=test)
             log.debug("Response: %s", resp)
             self.write(resp)
         except StochSSAPIError as err:
@@ -340,7 +341,8 @@ async def get(self):
         self.set_header('Content-Type', 'application/json')
         try:
             folder = StochSSFolder(path="")
-            resp = folder.get_file_list(ext=".txt")
+            test = lambda ext, root, file: bool("trash" in root.split("/"))
+            resp = folder.get_file_list(ext=".txt", test=test)
             log.debug("Response: %s", resp)
             self.write(resp)
         except StochSSAPIError as err:

diff --git a/stochss/handlers/project.py b/stochss/handlers/project.py
@@ -171,7 +171,7 @@ def get(self):
             folder = StochSSFolder(path="")
             # file will be excluded if test passes
             test = lambda ext, root, file: bool(".wkfl" in root or f"{path}" in root or \
-                                                "trash" in root)
+                                                "trash" in root.split("/"))
             data = folder.get_file_list(ext=[".mdl", ".smdl"], test=test)
             log.debug("List of models: %s", data)
             self.write(data)
@@ -276,35 +276,6 @@ def get(self):
         self.finish()
 
 
-class EmptyTrashAPIHandler(APIHandler):
-    '''
-    ##############################################################################
-    Handler for a projects trash directory
-    ##############################################################################
-    '''
-    @web.authenticated
-    def get(self):
-        '''
-        Empty the trash directory.
-
-        Attributes
-        ----------
-        '''
-        self.set_header('Content-Type', 'application/json')
-        path = self.get_query_argument(name="path")
-        log.debug("Path to the trash directory: %s", path)
-        try:
-            log.info("Emptying the trash")
-            folder = StochSSFolder(path=path)
-            resp = folder.empty()
-            log.debug("Response message: %s", resp)
-            log.info("Successfully emptied the trash")
-            self.write(resp)
-        except StochSSAPIError as err:
-            report_error(self, log, err)
-        self.finish()
-
-
 class ProjectMetaDataAPIHandler(APIHandler):
     '''
     ##############################################################################

diff --git a/stochss/handlers/util/stochss_base.py b/stochss/handlers/util/stochss_base.py
@@ -97,6 +97,8 @@ def get_new_path(self, dst_path):
             New path for the file object from the users home directory
         '''
         new_path = os.path.join(self.user_dir, dst_path)
+        if dst_path.startswith("trash/") and not "trash" in os.listdir(self.user_dir):
+            os.mkdir(os.path.join(self.user_dir, "trash"))
         if new_path.split().pop().replace('.', '', 5).isdigit():
             return new_path.replace(new_path.split().pop(), "").strip()
         if "trash/" in new_path and os.path.exists(new_path):