Merge pull request #148 from ctsit/master

Bring Develop up to master

AUTHORS.md

@@ -6,3 +6,5 @@
 * Taeber Rapczak          <taeber@ufl.edu>
 * Kevin S. Hanson         <hansonks@gmail.com>
 * Christopher P. Barnes   <senrabc@gmail.com>
+* Patrick White   	  <pfwhite9@gmail.com>
+* Samantha Davuluri 	  <samanthadavuluri4444@gmail.com> 

CHANGELOG.md

@@ -1,6 +1,31 @@
 # Change Log
 
 
+## [0.2.0] - 2016-10-11
+
+### New Features
+ * Admin Users can edit existing users.
+ * Deleter users can delete files that exist.
+ * The dashboard is easier to search.
+
+### Changed
+ * Fixes for pagination. (Patrick White)
+ * Use config to find out where the deleted files are (Patrick White)
+ * Delete File changes and additions (Patrick White)
+ * Fixed dashboard presentation. (Patrick White)
+ * Update README.md (Kevin Hanson)
+ * deploy/fabfile.py enhancement to allow for easy database upgrades and downgrades (Patrick White)
+ * Made both the app/fabfile.py and bootstrap_functions.sh apply the most recent database version. (Patrick White)
+ * Edit user logging (ndavuluri)
+ * Unit tests and client side edit form changes (Patrick White)
+ * UserID and Role should be unique, adding an Unique Index for usrID,rolID. (ndavuluri)
+ * Only Admin User is allowed to create and edit User (ndavuluri)
+ * Polling for new subject data (Patrick White)
+ * Filter function for dashboard subject search (Patrick White)
+ * Initial Changes for Edit User:Adding a new route and updating db and loging (ndavuluri)
+ * Edit user changes (Patrick White, ndavuluri)
+
+
 ## [0.1.2] - 2016-04-13
 
 ### Changed

app/db/003/README

@@ -0,0 +1,7 @@
+These database changes are from the editUser feature branch
+
+This schema change adds a unique constraint on the UserRole table to
+prevent duplicate roles for individual users
+
+It also adds a new log type to account for the edit_user api call
+

app/db/003/downgrade.sql

@@ -0,0 +1,14 @@
+-- temporarily remove foreign keys to remove unique index
+ALTER TABLE UserRole DROP FOREIGN KEY fk_User_usrID;
+ALTER TABLE UserRole DROP FOREIGN KEY fk_UserRole_rolID;
+
+-- remove unique index from UserRole
+ALTER TABLE UserRole DROP INDEX uc_UserIDRoleID;
+
+-- reapply the foreign key constraints
+ALTER TABLE UserRole ADD CONSTRAINT fk_User_usrID FOREIGN KEY (usrID) REFERENCES User (usrID) ON DELETE CASCADE;
+ALTER TABLE UserRole ADD CONSTRAINT fk_UserRole_rolID FOREIGN KEY (rolID) REFERENCES Role (rolID) ON DELETE CASCADE;
+
+-- remove the log type for the edit user api call
+DELETE FROM LogType
+WHERE logtType='account_updated';

app/db/003/upgrade.sql

@@ -0,0 +1,9 @@
+-- ensure there will be no duplicates user / user role pairs
+ALTER TABLE UserRole
+ADD CONSTRAINT uc_UserIDRoleID UNIQUE (usrID, rolID);
+
+-- add the logtype for the edit_user api call
+INSERT INTO LogType
+(logtType, logtDescription)
+VALUES
+('account_updated','');

app/db/004/README

@@ -0,0 +1,2 @@
+This change is to add the deleter role to the Role table.
+The deleter role is able to delete files

app/db/004/downgrade.sql

@@ -0,0 +1,7 @@
+-- remove the deleter permission
+DELETE FROM Role
+WHERE rolName='deleter';
+
+-- remove the log type for the edit user api call
+DELETE FROM LogType
+WHERE logtType='file_deleted';

app/db/004/upgrade.sql

@@ -0,0 +1,8 @@
+-- add the deleter permission
+INSERT INTO Role (rolName, rolDescription) VALUES ('deleter', 'Can delete files');
+
+-- add the file deleted log type
+INSERT INTO LogType
+(logtType, logtDescription)
+VALUES
+('file_deleted','');

app/deploy/fabfile.py

@@ -274,6 +274,57 @@ def mysql_list_tables():
     result = local(cmd, capture=True)
     print(result)
 
+def _is_valid_version(version_number):
+    """Checks if the version has the right number of digits"""
+    version_string = str(version_number)
+    return len(version_string) <= 3
+
+def _get_version_string(version_number):
+    """Produces a three char string that corresponds to the desired db folder"""
+    version_string = str(version_number)
+    while len(version_string) < 3:
+        version_string = '0' + version_string
+    return version_string
+
+def _step_to_version(version_number, is_upgrade):
+    """Step once to the passed version. Must be on adjacent version
+    Version numbers are given by the number for the folder
+    in app/db/
+    """
+    require('environment', provided_by=[production, staging])
+
+    exists = mysql_check_db_exists()
+    if not exists:
+        abort(colors.red("Unable to create tables in database '%(db_name)s'."
+                         "The database does not exist" % env))
+    if not _is_valid_version(version_number) is True:
+        abort(colors.red("Unable to upgrade to version {} '%(db_name)s'."
+                         "Please look in app/db for valid versions".format(version_number)
+                         % env))
+
+    login_path = _mysql_login_path()
+    sql_file = 'upgrade.sql' if is_upgrade else 'downgrade.sql'
+    sql = _get_version_string(version_number) + '/' + sql_file
+
+    with lcd('../db/'):
+        cmd = ("mysql --login-path={} %(db_name)s < {}"
+                .format(login_path, sql)
+                % env)
+        local(cmd)
+
+def mysql_version_upgrade(version_number):
+    """Upgrade to the passed version. Must be on adjacent version
+    Version numbers are given by the number for the folder
+    in app/db/
+    """
+    _step_to_version(version_number, True)
+
+def mysql_version_downgrade(version_number):
+    """Downgrade to the passed version. Must be on adjacent version
+    Version numbers are given by the number for the folder
+    in app/db/
+    """
+    _step_to_version(version_number, False)
 
 def mysql_create_tables():
     """ Create the application tables.
@@ -297,7 +348,11 @@ def mysql_create_tables():
                  .format(env.environment))
 
     login_path = _mysql_login_path()
-    files = ['001/upgrade.sql', '002/upgrade.sql', '002/data.sql']
+    files = ['001/upgrade.sql',
+             '002/upgrade.sql',
+             '002/data.sql',
+             '003/upgrade.sql',
+             '004/upgrade.sql']
 
     with lcd('../db/'):
         for sql in files:
@@ -322,7 +377,10 @@ def mysql_drop_tables():
         abort(colors.red("Unable to drop tables in database '%(db_name)s'."
                          "The database does not exist" % env))
 
-    files = ['002/downgrade.sql', '001/downgrade.sql']
+    files = ['004/downgrade.sql',
+             '003/downgrade.sql',
+             '002/downgrade.sql',
+             '001/downgrade.sql']
 
     with lcd('../db/'):
         for sql in files:

app/fabfile.py

@@ -62,6 +62,8 @@ def init_db():
     local('sudo mysql ctsi_dropper_s < db/001/upgrade.sql')
     local('sudo mysql ctsi_dropper_s < db/002/upgrade.sql')
     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')
 
 
 @task
@@ -78,6 +80,8 @@ def reset_db():
     local('sudo mysql ctsi_dropper_s < db/001/upgrade.sql')
     local('sudo mysql ctsi_dropper_s < db/002/upgrade.sql')
     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')
 
 
 @task

app/redidropper/database/crud_mixin.py

@@ -33,27 +33,23 @@ def get_by_id(cls, id):
             return cls.query.get(int(id))
         return None
 
-
     @classmethod
     def create(cls, **kwargs):
         """ Helper for session.add() + session.commit() """
         instance = cls(**kwargs)
         return instance.save()
 
-
     def update(self, commit=True, **kwargs):
         for attr, value in kwargs.iteritems():
             setattr(self, attr, value)
-        return commit and self.save() or self
-
+        return self.save() if commit else self
 
     def save(self, commit=True):
         db.session.add(self)
         if commit:
             db.session.commit()
         return self
 
-
     def delete(self, commit=True):
         db.session.delete(self)
         return commit and db.session.commit()

app/redidropper/models/log_entity.py

@@ -20,10 +20,12 @@
     LOG_TYPE_LOGOUT, \
     LOG_TYPE_LOGIN_ERROR, \
     LOG_TYPE_FILE_UPLOADED, \
+    LOG_TYPE_FILE_DELETED, \
     LOG_TYPE_FILE_DOWNLOADED, \
     LOG_TYPE_ACCOUNT_MODIFIED, \
     LOG_TYPE_REDCAP_SUBJECTS_IMPORTED, \
-    LOG_TYPE_REDCAP_EVENTS_IMPORTED
+    LOG_TYPE_REDCAP_EVENTS_IMPORTED, \
+    LOG_TYPE_ACCOUNT_UPDATED
 
 
 class LogEntity(db.Model, CRUDMixin):
@@ -92,6 +94,11 @@ def account_created(session_id, details=''):
         """ Log account creation """
         LogEntity._log(LOG_TYPE_ACCOUNT_CREATED, session_id, details)
 
+    @staticmethod
+    def account_updated(session_id, details=''):
+        """ Log account updated """
+        LogEntity._log(LOG_TYPE_ACCOUNT_UPDATED, session_id, details)
+
     @staticmethod
     def login(session_id, details=''):
         """ Log successful login """
@@ -112,6 +119,11 @@ def file_uploaded(session_id, details=''):
         """ Log file upload """
         LogEntity._log(LOG_TYPE_FILE_UPLOADED, session_id, details)
 
+    @staticmethod
+    def file_deleted(session_id, details=''):
+        """ Log account creation """
+        LogEntity._log(LOG_TYPE_FILE_DELETED, session_id, details)
+
     @staticmethod
     def file_downloaded(session_id, details=''):
         """ Log file download """

app/redidropper/models/log_type_entity.py

@@ -9,10 +9,12 @@
 LOG_TYPE_LOGOUT = 'logout'
 LOG_TYPE_LOGIN_ERROR = 'login_error'
 LOG_TYPE_FILE_UPLOADED = 'file_uploaded'
+LOG_TYPE_FILE_DELETED = 'file_deleted'
 LOG_TYPE_FILE_DOWNLOADED = 'file_downloaded'
 LOG_TYPE_ACCOUNT_MODIFIED = 'account_modified'
 LOG_TYPE_REDCAP_SUBJECTS_IMPORTED = 'redcap_subjects_impported'
 LOG_TYPE_REDCAP_EVENTS_IMPORTED = 'redcap_events_imported'
+LOG_TYPE_ACCOUNT_UPDATED = 'account_updated'
 # LOG_TYPE_ = ''
 
 

app/redidropper/models/role_entity.py

@@ -10,6 +10,7 @@
 ROLE_TECHNICIAN = 'technician'
 ROLE_RESEARCHER_ONE = 'researcher_one'
 ROLE_RESEARCHER_TWO = 'researcher_two'
+ROLE_DELETER = 'deleter'
 
 
 class RoleEntity(db.Model, CRUDMixin):  # RoleMixin

app/redidropper/models/subject_file_entity.py

@@ -8,7 +8,6 @@
 
 logger = app.logger
 
-
 class SubjectFileEntity(db.Model, CRUDMixin):
     """ Stores the uploaded file metadata """
     __tablename__ = 'SubjectFile'

app/redidropper/models/user_entity.py

@@ -33,7 +33,7 @@ class UserEntity(db.Model, UserMixin, CRUDMixin):
     modified_at = db.Column("usrModifiedAt", db.TIMESTAMP, nullable=False)
     email_confirmed_at = db.Column("usrEmailConfirmedAt", db.DateTime,
                                    nullable=False,
-                                   server_default='0000-00-00 00:00:00')
+                                   server_default='1901-10-04 11:17:00')
     active = db.Column("usrIsActive", db.Boolean(), nullable=False,
                        server_default='1')