Merge pull request #85 from ITC-CRIB/update-remote

Push command

Author: manuGil

jupyter_fairly/jupyter_fairly/handlers.py

@@ -257,25 +257,79 @@ def post(self):
                 "message": 'completed',
                 }))
 
+
+class PushDataset(APIHandler):
+    """
+    Handler for pushing updates on files and metadata to data repository
+    """
+
+    @tornado.web.authenticated
     def patch(self):
-        """ Send updates on files and metadata to remore repository
+        """ Updates files and metadata in existing dataset in data repository
         
         Args:
     
-            local-dataset (str): path to root directory of initialized fairly dataset
+            localdataset (str): path to root directory of initialized fairly dataset
                              witch a remote registered in the manifest.yaml file
 
         Body example as JSON:
         {
             
-            "local-dataset": <path to root directory of fairly dataset>
+            "localdataset": <path to root directory of fairly dataset>
         }
         """
 
         data = self.get_json_body() 
+        print(data)
 
         try:
-            local_dataset = fairly.dataset(data["local-dataset"])
+            local_dataset = fairly.dataset(data["localdataset"])
+
+        except FileNotFoundError as e:
+            raise web.HTTPError(404, f"Manifest file is missing from current directory: {e}")
+        except NotADirectoryError as e:
+            raise web.HTTPError(404, f"Path to dataset is not a directory: {e}")
+
+        try:
+            local_dataset.push() # push updates (files and metadata) to remote repository
+        except ValueError:
+            raise web.HTTPError(405, f"The dataset doesn't have a remote. Make sure you're in the right directory or use `upload` option first.")
+        except KeyError as e:
+            raise web.HTTPError(400, f"Possible malformed manifest file. Missing {e}")
+        else:
+            self.finish(json.dumps({
+                "message": 'remote  dataset is up to date',
+                }))
+
+
+class PullDataset(APIHandler):
+    """
+    Handler for pulling updates on files and metadata to remore repository
+    """
+
+    @tornado.web.authenticated
+    def patch(self):
+        """ Updates files and metadata in local dataset based on changes in data repository.
+        
+        Args:
+    
+            localdataset (str): path to root directory of initialized fairly dataset
+                             witch a remote registered in the manifest.yaml file
+
+        Body example as JSON:
+        {
+            
+            "localdataset": <path to root directory of fairly dataset>
+        }
+        """
+        raise web.HTTPError(501, "Not implemented yet")
+
+        # TODO: implement save changes to manifest.yaml and files in local dataset
+        data = self.get_json_body() 
+        print(data)
+
+        try:
+            local_dataset = fairly.dataset(data["localdataset"])
 
         except FileNotFoundError as e:
             raise web.HTTPError(404, f"Manifest file is missing from current directory: {e}")
@@ -287,8 +341,10 @@ def patch(self):
         except ValueError:
             raise web.HTTPError(405, f"The dataset doesn't have a remote. Use the upload option first.")
         else:
+            # save changes to manifest.yaml
+    
             self.finish(json.dumps({
-                "message": 'remote was updated',
+                "message": 'local dataset is up to date',
                 }))
 
 
@@ -355,6 +411,8 @@ def setup_handlers(web_app):
     initialize_dataset_url = url_path_join(extension_url, "newdataset")
     clone_dataset_url = url_path_join(extension_url, "clone")
     upload_dataset_url = url_path_join(extension_url, "upload")
+    push_dataset_url = url_path_join(extension_url, "push")
+    pull_dataset_url = url_path_join(extension_url, "pull")
     register_token_url = url_path_join(extension_url, "repo-token")
 
 
@@ -364,6 +422,8 @@ def setup_handlers(web_app):
         (initialize_dataset_url, InitFairlyDataset),
         (clone_dataset_url, CloneDataset),
         (upload_dataset_url, UploadDataset),
+        (push_dataset_url, PushDataset),
+        (pull_dataset_url, PullDataset),
         (register_token_url, RegisterRepositoryToken)
     ]
 

jupyter_fairly/package.json

@@ -1,6 +1,6 @@
 {
     "name": "jupyter-fairly",
-    "version": "0.3.1",
+    "version": "0.4.0",
     "description": "A JupyterLab extension for seamless integration of Jupyter-based research environments and research data repositories",
     "keywords": [
         "jupyter",

jupyter_fairly/src/upload.ts

@@ -5,7 +5,9 @@ import {
 
 import {
   InputDialog,
-  Notification
+  Notification,
+  showDialog,
+  Dialog
 } from '@jupyterlab/apputils';
 
 import { 
@@ -17,13 +19,11 @@ import { PromiseDelegate, ReadonlyJSONValue } from '@lumino/coreutils';
 // Icons
 import {
   fileUploadIcon,
+  redoIcon
 } from '@jupyterlab/ui-components';
 import { requestAPI } from './handler';
 import { showErrorMessage } from '@jupyterlab/apputils';
 
-/**
- * Uploads metadata and files to data repository
- */
 
 
  function uploadDataset(directory: string,  repository: string) {
@@ -88,6 +88,54 @@ import { showErrorMessage } from '@jupyterlab/apputils';
 };
 
 
+function pushDataset(localDataset: string) {
+  /**
+   * upload local dataset to data reposotory
+   * @param localDataset - realtive path to directory of local dataset with remote metadata
+   */
+
+  /* ./ is necessary becaucause defaultBrowser.Model.path
+  * returns an empty string when fileBlowser is on the
+  * jupyterlab root directory     
+  */
+  let rootPath = './';
+
+  let payload = JSON.stringify({
+    localdataset: rootPath.concat(localDataset)
+  });
+
+  // notification
+  const delegate = new PromiseDelegate<ReadonlyJSONValue>();
+  const complete = "complete";
+  const failed = "failed"
+  
+  requestAPI<any>('push', {
+    method: 'PATCH', 
+    body: payload
+  }) 
+  .then(data => {
+    console.log(data);
+    delegate.resolve({ complete });
+  })
+  .catch(reason => {
+    delegate.reject({ failed });
+    // show error when 
+    showErrorMessage("Error when updating remote dataset", reason)
+  });
+
+  Notification.promise(delegate.promise, {
+    pending: { message: 'Pushing dataset to repository ...', options: { autoClose: false } },
+    success: {
+      message: (result: any) =>
+      `Remote dataset update ${result.complete}.`,
+      options: {autoClose: 3000}
+    },
+    error: {message: () => `Pushing has failed.`}
+  });
+
+};
+
+
 export const uploadDatasetPlugin: JupyterFrontEndPlugin<void> = {
   id: '@jupyter-fairly/upload',
   requires: [IFileBrowserFactory],
@@ -102,8 +150,9 @@ export const uploadDatasetPlugin: JupyterFrontEndPlugin<void> = {
     const fileBrowserModel = fileBrowser.model;
 
 
-    const archiveDatasetCommand = "uploadDataset"
-    app.commands.addCommand(archiveDatasetCommand, {
+    // ** Upload a new dataset to a data repository **
+    const uploadDatasetCommand = "uploadDataset"
+    app.commands.addCommand(uploadDatasetCommand, {
       label: 'Upload Dataset',
       isEnabled: () => true,
       isVisible: () => true, // activate only when current directory contains a manifest.yalm
@@ -144,11 +193,44 @@ export const uploadDatasetPlugin: JupyterFrontEndPlugin<void> = {
       }
     });
 
+    // ** Push changes made to a local dataset to a data repository **
+    const pushCommand = "pushDataset"
+    app.commands.addCommand(pushCommand, {
+      label: 'Push',
+      isEnabled: () => true,
+      isVisible: () => true, // activate only when current directory contains a manifest.yalm
+      icon: redoIcon,
+      execute: async() => {
+
+        let confirmAction = await showDialog({
+            title: 'Push changes', // Can be text or a react element
+            body: 'This will update the data repository using changes made here.', 
+            host: document.body, // Parent element for rendering the dialog
+            buttons: [Dialog.cancelButton(), Dialog.okButton({ label: 'Push' })],
+          })
+
+        if (confirmAction.button.accept){
+          await pushDataset(fileBrowserModel.path)
+        } else {
+          console.log('rejected');
+          return
+        };
+      }
+    });
+
     app.contextMenu.addItem({
-      command: archiveDatasetCommand,
+      command: uploadDatasetCommand,
       // matches anywhere in the filebrowser
       selector: '.jp-DirListing-content',
       rank: 104
-    });
+    }
+    );
+    app.contextMenu.addItem({
+      command: pushCommand,
+      // matches anywhere in the filebrowser
+      selector: '.jp-DirListing-content',
+      rank: 105
+    }
+    );
   }
 };