Merge pull request #149 from akash314/develop

Develop

app/db/005/downgrade.sql

@@ -0,0 +1,2 @@
+-- remove file type column
+ALTER TABLE SubjectFile DROP sfFileType;

app/db/005/upgrade.sql

@@ -0,0 +1,3 @@
+-- ensure there will be no duplicates user / user role pairs
+ALTER TABLE SubjectFile
+ADD sfFileType varchar(255) NOT NULL;

app/deploy/fabfile.py

@@ -352,7 +352,8 @@ def mysql_create_tables():
              '002/upgrade.sql',
              '002/data.sql',
              '003/upgrade.sql',
-             '004/upgrade.sql']
+             '004/upgrade.sql',
+             '005/upgrade.sql'	]
 
     with lcd('../db/'):
         for sql in files:
@@ -377,7 +378,8 @@ def mysql_drop_tables():
         abort(colors.red("Unable to drop tables in database '%(db_name)s'."
                          "The database does not exist" % env))
 
-    files = ['004/downgrade.sql',
+    files = ['005/downgrade.sql',
+             '004/downgrade.sql',
              '003/downgrade.sql',
              '002/downgrade.sql',
              '001/downgrade.sql']

app/fabfile.py

@@ -64,6 +64,7 @@ def init_db():
     local('sudo mysql ctsi_dropper_s < db/002/data.sql')
     local('sudo mysql ctsi_dropper_s < db/003/upgrade.sql')
     local('sudo mysql ctsi_dropper_s < db/004/upgrade.sql')
+    local('sudo mysql ctsi_dropper_s < db/005/upgrade.sql')
 
 
 @task
@@ -82,6 +83,7 @@ def reset_db():
     local('sudo mysql ctsi_dropper_s < db/002/data.sql')
     local('sudo mysql ctsi_dropper_s < db/003/upgrade.sql')
     local('sudo mysql ctsi_dropper_s < db/004/upgrade.sql')
+    local('sudo mysql ctsi_dropper_s < db/005/upgrade.sql')
 
 
 @task

app/redidropper/models/subject_file_entity.py

@@ -20,6 +20,7 @@ class SubjectFileEntity(db.Model, CRUDMixin):
     file_name = db.Column("sfFileName", db.String(255), nullable=False)
     file_check_sum = db.Column("sfFileCheckSum", db.String(32), nullable=False)
     file_size = db.Column("sfFileSize", db.String(255), nullable=False)
+    file_type = db.Column("sfFileType", db.String(255), nullable=False)
     uploaded_at = db.Column("sfUploadedAt", db.DateTime, nullable=False,
                             server_default='0000-00-00 00:00:00')
     user_id = db.Column("usrID", db.Integer, db.ForeignKey('User.usrID'),
@@ -100,12 +101,10 @@ def serialize(self):
             'file_name': self.file_name,
             'file_check_sum': self.file_check_sum,
             'file_size': self.file_size,
+            'file_type': self.file_type,  
             'uploaded_at': utils.localize_est_datetime(self.uploaded_at),
             'subject_id': self.subject_id,
             'event_id': self.event_id,
             'user_id': self.user_id,
-            'user_name': self.user.get_name(),
-            # 'subject': self.subject.serialize(),
-            # 'event': self.event.serialize(),
-            # 'user': self.user.serialize(),
+            'user_name': self.user.get_name()
         }

app/redidropper/routes/api.py

@@ -2,6 +2,7 @@
 Goal: Delegate requests to the `/api` path to the appropriate controller
 
 @authors:
+  Akash Agarwal           <agarwala989@gmail.com
   Andrei Sura             <sura.andrei@gmail.com>
   Ruchi Vivek Desai       <ruchivdesai@gmail.com>
   Sanath Pasumarthy       <sanath@ufl.edu>
@@ -182,7 +183,23 @@ def api_delete_file():
         response = utils.jsonify_error({"exception": ret_value})
 
     return response
+
+@app.route('/api/update_fileType', methods=['POST'])
+@login_required
+def api_update_fileType():
+    """ Updates the file type    """
+    #get the file from the response
+    subject_file_id = request.form.get('file_id')
+    subject_file_type = request.form.get('file_type')
+    try:
+        ret_value = file_manager.update_filetype(subject_file_id, subject_file_type)
+        #app.logger.debug("updated file id: {}".format(subject_file_id))
+        response = utils.jsonify_success({"file_id": ret_value[0], "file_type": ret_value[1]})
+
+    except:
+        response = utils.jsonify_error({"exception": ret_value})
 
+    return response
 
 @app.route("/api/download_file", methods=['POST'])
 @login_required
@@ -200,6 +217,22 @@ def download_file():
     LogEntity.file_downloaded(session['uuid'], file_path)
     return send_file(file_path, as_attachment=True)
 
+@app.route("/api/all_files_info", methods=['GET'])
+@login_required
+def all_files_info():
+    """ Get the list of all uploaded files and their path """
+    all_files = db.session.query(SubjectFileEntity,EventEntity.redcap_event,SubjectEntity.redcap_id).join(EventEntity).join(SubjectEntity)
+    return_list = [__build_files_info_json(subject_file,event,subject) for subject_file,event,subject in all_files]
+    return utils.jsonify_success({'list_of_files' : return_list})
+
+def __build_files_info_json(subject_file,event,subject):
+    path = subject_file.get_full_path(app.config['REDIDROPPER_UPLOAD_SAVED_DIR'])
+    file_json = subject_file.serialize()
+    file_json['path'] = path
+    file_json['redcap_id'] = subject
+    file_json['redcap_event'] = event
+    return file_json
+
 def __extract_user_information(request):
     return {
         "email": request.form.get('email'),

app/redidropper/routes/file_manager.py

@@ -44,6 +44,7 @@ def init_from_request(cls):
         self.total_size = int(request.form['resumableTotalSize'])
         self.uniqueid = request.form['resumableIdentifier']
         self.file_name = secure_filename(request.form['resumableFilename'])
+        self.file_type = request.form['resumableFileType']
         self.afile = request.files['file']
         self.total_parts = int(request.form['resumableTotalChunks'])
         self.redcap_id = request.form['subject_id']  # @TODO: rename
@@ -73,6 +74,7 @@ def save_file_metadata(fchunk):
         file_name=fchunk.file_name,
         file_check_sum='pending',
         file_size=fchunk.total_size,
+        file_type=fchunk.file_type,
         uploaded_at=added_date,
         user_id=current_user.id)
     logger.debug("Saved metadata to the db: ".format(subject_file))
@@ -217,3 +219,10 @@ def delete_file(subject_file_id):
     file_entity.delete()
     db.session.commit()
     return (subject_file_id, file_path)
+
+def update_filetype(subject_file_id, subject_file_type):
+    """ Updates the type field of the file """
+    file_entity = SubjectFileEntity.query.filter_by(id=subject_file_id).one()
+    file_entity.update(file_type=subject_file_type)
+    db.session.commit()
+    return (subject_file_id, subject_file_type)

app/redidropper/static/css/dashboard.css

@@ -0,0 +1,5 @@
+.dash_drop{
+	width:75px;
+	height:30px;
+	padding: 30px 0 0 0;
+}

app/redidropper/static/js/dashboard.js

@@ -262,6 +262,11 @@ var FilesList = React.createClass({
     },
 
     deleteFile: function(file_id) {
+        var confirmed = confirm("Are you sure you want to delete the file?");
+        if(confirmed == false){
+            return;
+        }
+
         var request = Utils.api_post_json("/api/delete_file", {file_id: file_id}),
             self = this;
 
@@ -303,6 +308,20 @@ var FilesList = React.createClass({
         });
     },
 
+    changeType: function(fileId){
+        var request = Utils.api_post_json("/api/update_fileType", {file_id: fileId, file_type: event.target.value}),
+            self = this;
+
+        request.success((json) => {
+            obj = self.state.list_of_files.find(function(ele){return ele.id==json.data.file_id})
+            obj.file_type=json.data.file_type
+            self.setState({
+                list_of_files: self.state.list_of_files
+            });
+        });
+
+    },
+
     render: function() {
         return (
         <div className="table-responsive" >
@@ -313,7 +332,7 @@ var FilesList = React.createClass({
                         <th className="text-center"> File Size (MB)</th>
                         <th className="text-center"> Uploaded </th>
                         <th className="text-center"> Uploaded By </th>
-                        <th className="text-center"></th>
+                        <th className="text-center"> Image Type </th>
                     </tr>
                 </thead>
                 <tbody id="technician-table-body">
@@ -324,6 +343,13 @@ var FilesList = React.createClass({
                         <td>{(record.file_size / (1024 * 1024)).toFixed(2)}</td>
                         <td>{record.uploaded_at}</td>
                         <td>{record.user_name}</td>
+                        <td>
+                            <select className="dash_drop" value={record.file_type} onChange={this.changeType.bind(this,record.id)}>
+                                <option value="MRI">MRI</option>
+                                <option value="PET">PET</option>
+                                <option value="N/A">N/A</option>
+                            </select>
+                        </td>
                         <td>
                             <form method="POST" action="/api/download_file">
                                 <input type="hidden" name="file_id" value={record.id} />
@@ -333,15 +359,8 @@ var FilesList = React.createClass({
                         <td>
                             <button
                             onClick={this.deleteFile.bind(this, record.id)}
-                            disabled={!record.canDelete}
                             className="btn btn-primary">Delete File</button>
                         </td>
-                        <td>
-                            Enable delete file? <input type="checkbox"
-                            checked={!!record.canDelete}
-                            onChange={this.toggleCanDelete.bind(this, record.id)}
-                            ></input>
-                        </td>
                     </tr>);
                 })}
                 </tbody>

app/redidropper/static/js/resumable.js

@@ -454,6 +454,7 @@
       $.file = file;
       $.fileName = file.fileName||file.name; // Some confusion in different versions of Firefox
       $.size = file.size;
+      $.fileType = 'N/A';
       $.relativePath = file.webkitRelativePath || file.relativePath || $.fileName;
       $.uniqueIdentifier = $h.generateUniqueIdentifier(file);
       $._pause = false;
@@ -680,6 +681,7 @@
         params.push(['resumableType', encodeURIComponent($.fileObjType)].join('='));
         params.push(['resumableIdentifier', encodeURIComponent($.fileObj.uniqueIdentifier)].join('='));
         params.push(['resumableFilename', encodeURIComponent($.fileObj.fileName)].join('='));
+        params.push(['resumableFileType', encodeURIComponent($.fileObj.fileType)].join('='));
         params.push(['resumableRelativePath', encodeURIComponent($.fileObj.relativePath)].join('='));
         params.push(['resumableTotalChunks', encodeURIComponent($.fileObj.chunks.length)].join('='));
 
@@ -767,6 +769,7 @@
           resumableType: $.fileObjType,
           resumableIdentifier: $.fileObj.uniqueIdentifier,
           resumableFilename: $.fileObj.fileName,
+          resumableFileType: $.fileObj.fileType,
           resumableRelativePath: $.fileObj.relativePath,
           resumableTotalChunks: $.fileObj.chunks.length
         };

app/redidropper/templates/layout.html

@@ -15,6 +15,7 @@
     <link href="{{ url_for('static', filename='css/layout.css') }}" rel="stylesheet">
     <link href="{{ url_for('static', filename='css/start_upload.css') }}" rel="stylesheet">
     <link href="{{ url_for('static', filename='css/parallax.css') }}" rel="stylesheet">
+    <link href="{{ url_for('static', filename='css/dashboard.css') }}" rel="stylesheet">
     <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css">
 
 

app/tests/base_test_with_data.py

@@ -2,6 +2,7 @@
 Goal: Extend the base test class by inserting samle rows in the database
 
 Authors:
+    Akash Agarwal <agarwala989@gmail.com
     Andrei Sura <sura.andrei@gmail.com>
 
 """
@@ -116,6 +117,7 @@ def create_sample_data(self):
                 subject_id=subject.id,
                 event_id=fdata['event'],
                 file_name=fdata['name'],
+                file_type="N/A",
                 file_check_sum=utils.compute_text_md5(fdata['name']),
                 file_size=fdata['size'],
                 uploaded_at=added_date,

app/tests/test_api.py

@@ -2,6 +2,7 @@
 Goal: Simulate api calls
 
 Authors:
+    Akash Agarwal <agarwala989@gmail.com
     Patrick White <pfwhite9@gmail.com> <pfwhite@ufl.edu>
 
 """
@@ -12,8 +13,14 @@
 from .base_test_with_data import BaseTestCaseWithData
 from redidropper.main import app
 from redidropper.main import db
+from datetime import datetime
 
+from redidropper import utils
 from redidropper.models.user_entity import UserEntity
+from redidropper.models.event_entity import EventEntity
+from redidropper.models.subject_entity import SubjectEntity
+from redidropper.models.subject_file_entity import SubjectFileEntity
+import json
 
 class TestAPI(BaseTestCaseWithData):
 
@@ -84,6 +91,54 @@ def test_edit_user(self):
             self.fail('user not existing')
         print('edit user test')
 
+    def test_update_fileType(self):
+        """ Verify that we can change file type"""
+        res_login = self.__login("admin@example.com")
+
+        added_date = datetime.today()
+        subject = SubjectEntity.create(
+            redcap_id="002",
+            added_at=added_date,
+            last_checked_at=added_date,
+            was_deleted=0)
+
+        # == Create events
+        evt = EventEntity.create(redcap_arm='Arm 2',
+                                 redcap_event='Event 2',
+                                 day_offset=1,
+                                 added_at=added_date)
+
+        files = [
+            {'name': 'x.png', 'size': '123', 'event': evt.id},
+            {'name': 'y.png', 'size': '1234', 'event': evt.id}
+        ]
+
+        for fdata in files:
+            subject_file = SubjectFileEntity.create(
+                subject_id=subject.id,
+                event_id=fdata['event'],
+                file_name=fdata['name'],
+                file_type="N/A",
+                file_check_sum=utils.compute_text_md5(fdata['name']),
+                file_size=fdata['size'],
+                uploaded_at=added_date,
+                user_id='1')
+
+        file_entity = SubjectFileEntity.query.filter_by(file_name='x.png').one()
+        postdata = {'file_id': file_entity.id, 'file_type': 'MRI'}
+        response = self.client.post("/api/update_fileType", data=postdata)
+        self.assertEqual(response._status_code, 200)
+
+        after_edit_file = SubjectFileEntity.query.filter_by(file_name='x.png').one()
+        self.assertEqual(after_edit_file.file_type, "MRI")
+        print('update file test')
+
+    def test_all_files_info(self):
+        response = self.client.get("/api/all_files_info")
+        self.assertEqual(response._status_code, 200)
+        jsondata = json.loads(response.data)
+        self.assertGreater(len(jsondata['data']['list_of_files']),1)
+
     def __get_file_list_data(self, response):
         d = Decoder()
         data = d.decode(response.data)

app/tests/test_subject_file.py

@@ -2,6 +2,7 @@
 Goal: test insert/search subject, subject file
 
 Authors:
+    Akash Agarwal <agarwala989@gmail.com
     Andrei Sura <sura.andrei@gmail.com>
 
 """
@@ -47,7 +48,7 @@ def test_subject(self):
         evt = EventEntity.create(redcap_arm='Arm 1', redcap_event='Event 1',
                                  added_at=added_date)
 
-        fdata = {'name': 'a.png', 'size': '1MB', 'event': evt.id}
+        fdata = {'name': 'a.png', 'size': '1MB', 'event': evt.id, 'file_type': 'MRI'}
         user = UserEntity.create(email="admin@example.com",
                                  first="",
                                  last="",
@@ -62,6 +63,7 @@ def test_subject(self):
             file_name=fdata['name'],
             file_check_sum=utils.compute_text_md5(fdata['name']),
             file_size=fdata['size'],
+            file_type=fdata['file_type'],
             uploaded_at=added_date,
             user_id=user.get_id())
         self.assertIsNotNone(subject_file.id)
@@ -74,4 +76,5 @@ def test_subject(self):
         self.assertEqual(1, actual_count)
 
         sfile = SubjectFileEntity.query.first()
-        self.assertEqual(user.id, sfile.user_id)
+        self.assertEqual(user.id, sfile.user_id) 
+        self.assertEqual('MRI', sfile.file_type)

vagrant/bootstrap_functions.sh

@@ -80,7 +80,10 @@ function install_dropper() {
         mysql ctsi_dropper_s   < db/003/upgrade.sql
         log "Execute sql: db/004/upgrade.sql"
         mysql ctsi_dropper_s   < db/004/upgrade.sql
-
+	    log "Execute sql: db/005/upgrade.sql"
+        mysql ctsi_dropper_s   < db/005/upgrade.sql
+
+
         log "Stop apache in order to disable the default site"
         service apache2 stop
         a2dissite 000-default