Merge pull request #114 from DESm1th/0.2.1

[ENH] Release v0.2.1

containers/Dockerfile

@@ -1,4 +1,4 @@
-FROM tigrlab/datman:0.1 as prod
+FROM tigrlab/datman:0.2.1 as prod
 
 # NOTE: When building this container, do it from
 # inside the dashboard folder and build with
@@ -12,6 +12,10 @@ COPY containers/entrypoint.sh /entrypoint.sh
 # that rebuilds are faster.
 COPY ./requirements.txt /
 
+# Install requirements for pip installing uwsgi
+RUN apt update && \
+    apt install -y --no-install-recommends gcc python3.11-dev
+
 RUN pip install --upgrade pip && \
     pip install -r /requirements.txt
 

containers/dashboard.env

@@ -23,8 +23,7 @@ POSTGRES_SRVR=dash_postgres
 POSTGRES_USER=dashboard
 POSTGRES_DATABASE=dashboard
 # POSTGRES_TEST_DATABASE=test_dashboard
-
-
+# POSTGRES_PORT=5432
 # TIMEZONE=-240
 
 
@@ -58,6 +57,11 @@ POSTGRES_DATABASE=dashboard
 # DASH_LOG_DIR=
 
 
+# Menu Configuration
+# ------------------
+# DASH_MENU_CONFIG=
+
+
 # Debugging settings
 # ------------------
 # FLASK_ENV=

containers/prod/docker-compose.yml

@@ -2,10 +2,7 @@ version: '3'
 services:
   app:
     container_name: dashboard
-    build:
-      context: ../../
-      dockerfile: containers/Dockerfile
-      target: prod
+    image: tigrlab/dashboard:0.2.1
     env_file: ../dashboard.env
     ports:
       - 5000:5000

dashboard/__init__.py

@@ -173,7 +173,7 @@ def create_app(config=None):
 
     load_blueprints(app)
 
-    if app.debug and app.env == 'development':
+    if app.debug and app.config['ENV'] == 'development':
         # Never run this on a production server!
         setup_devel_ext(app)
 

dashboard/blueprints/main/views.py

@@ -124,7 +124,7 @@ def study(study_id=None, active_tab=None):
     display_metrics = current_app.config['DISPLAY_METRICS']
 
     # get the study object from the database
-    study = Study.query.get(study_id)
+    study = db.session.get(Study, study_id)
 
     # this is used to update the readme text file
     form = StudyOverviewForm()
@@ -416,7 +416,7 @@ def analysis(analysis_id=None):
     if not analysis_id:
         analyses = Analysis.query.all()
     else:
-        analyses = Analysis.query.get(analysis_id)
+        analyses = db.session.get(Analysis, analysis_id)
 
     for analysis in analyses:
         # format the user objects for display on page

dashboard/blueprints/redcap/monitors.py

@@ -8,7 +8,7 @@
 
 from .emails import missing_session_data
 from dashboard.monitors import add_monitor, get_emails
-from dashboard.models import Session, User
+from dashboard.models import Session, User, db
 from dashboard.exceptions import MonitorException
 from dashboard.queue import submit_job
 
@@ -78,7 +78,7 @@ def check_scans(name, num, recipients=None):
         :obj:`dashboard.exceptions.MonitorException`: If a matching session
             can't be found.
     """
-    session = Session.query.get((name, num))
+    session = db.session.get(Session, (name, num))
     if not session:
         raise MonitorException("Monitored session {}_{:02d} is no "
                                "longer in database. Cannot verify whether "
@@ -151,7 +151,7 @@ def monitor_scan_download(session, end_time=None):
 
 
 def download_session(name, num, end_time):
-    session = Session.query.get((name, num))
+    session = db.session.get(Session, (name, num))
     if not session:
         raise MonitorException(
             "Monitored session {}_{} is no longer in database, aborting "

dashboard/blueprints/redcap/utils.py

@@ -8,7 +8,7 @@
 import redcap as REDCAP
 
 from .monitors import monitor_scan_import, monitor_scan_download
-from dashboard.models import Session, Timepoint, RedcapRecord, RedcapConfig
+from dashboard.models import Session, Timepoint, RedcapRecord, RedcapConfig, db
 from dashboard.queries import get_studies
 from dashboard.exceptions import RedcapException
 import datman.scanid
@@ -20,7 +20,7 @@ def get_redcap_record(record_id, fail_url=None):
     if not fail_url:
         fail_url = url_for('main.index')
 
-    record = RedcapRecord.query.get(record_id)
+    record = db.session.get(RedcapRecord, record_id)
 
     if record is None:
         logger.error("Tried and failed to retrieve RedcapRecord with "
@@ -149,7 +149,7 @@ def set_session(name):
     name = ident.get_full_subjectid_with_timepoint()
     num = datman.scanid.get_session_num(ident)
 
-    session = Session.query.get((name, num))
+    session = db.session.get(Session, (name, num))
     if not session:
         timepoint = get_timepoint(ident)
         session = timepoint.add_session(num)
@@ -166,7 +166,8 @@ def find_study(ident):
 
 
 def get_timepoint(ident):
-    timepoint = Timepoint.query.get(ident.get_full_subjectid_with_timepoint())
+    timepoint = db.session.get(
+        Timepoint, ident.get_full_subjectid_with_timepoint())
     if not timepoint:
         study = find_study(ident)[0]
         timepoint = study.add_timepoint(ident)

dashboard/blueprints/timepoints/forms.py

@@ -1,5 +1,5 @@
 from flask_wtf import FlaskForm
-from wtforms import SubmitField, TextAreaField, TextField, BooleanField
+from wtforms import SubmitField, TextAreaField, StringField, BooleanField
 from wtforms.validators import DataRequired
 
 
@@ -43,7 +43,7 @@ class TimepointCommentsForm(FlaskForm):
 
 
 class NewIssueForm(FlaskForm):
-    title = TextField(
+    title = StringField(
         "Title: ",
         validators=[DataRequired()],
         render_kw={'required': True})

dashboard/blueprints/timepoints/utils.py

@@ -1,8 +1,9 @@
 import logging
 
 from github import Github
+
 from flask import current_app, flash
-from ...models import Study
+from ...models import Study, db
 
 logger = logging.getLogger(__name__)
 
@@ -22,7 +23,7 @@ def search_issues(token, timepoint):
 
 def handle_issue(token, issue_form, study_id, timepoint):
     title = clean_issue_title(issue_form.title.data, timepoint)
-    study = Study.query.get(study_id)
+    study = db.session.get(Study, study_id)
 
     staff_member = study.choose_staff_contact()
     if staff_member:

dashboard/blueprints/users/forms.py

@@ -1,22 +1,21 @@
 from flask_wtf import FlaskForm
 
-from wtforms import (SubmitField, HiddenField, TextField, FormField,
-                     BooleanField, FieldList, RadioField, SelectMultipleField)
-from wtforms.fields.html5 import EmailField, TelField
-from wtforms.compat import iteritems
+from wtforms import (SubmitField, HiddenField, StringField, FormField,
+                     BooleanField, FieldList, RadioField, SelectMultipleField,
+                     EmailField, TelField)
 from wtforms.validators import DataRequired
 
 
 class UserForm(FlaskForm):
     id = HiddenField()
-    first_name = TextField('First Name: ',
+    first_name = StringField('First Name: ',
                            validators=[DataRequired()],
                            render_kw={
                                'required': True,
                                'maxlength': '64',
                                'placeholder': 'Jane'
                            })
-    last_name = TextField('Last Name: ',
+    last_name = StringField('Last Name: ',
                           validators=[DataRequired()],
                           render_kw={
                               'required': True,
@@ -34,7 +33,7 @@ class UserForm(FlaskForm):
                           validators=[DataRequired()],
                           choices=[('github', 'GitHub')],
                           default='github')
-    account = TextField('Username: ',
+    account = StringField('Username: ',
                         validators=[DataRequired()],
                         render_kw={
                             'required':
@@ -44,12 +43,12 @@ class UserForm(FlaskForm):
                             'placeholder':
                             'Username used on account ' + 'provider\'s site'
                         })
-    position = TextField('Position: ',
+    position = StringField('Position: ',
                          render_kw={
                              'maxlength': '64',
                              'placeholder': 'Job title or position'
                          })
-    institution = TextField('Institution: ',
+    institution = StringField('Institution: ',
                             render_kw={
                                 'maxlength':
                                 '128',
@@ -61,7 +60,7 @@ class UserForm(FlaskForm):
                          'maxlength': '20',
                          'placeholder': '555-555-5555'
                      })
-    ext = TextField('Extension: ',
+    ext = StringField('Extension: ',
                     render_kw={
                         'maxlength': '10',
                         'placeholder': 'XXXXXXXXXX'
@@ -71,7 +70,7 @@ class UserForm(FlaskForm):
                              'maxlength': '20',
                              'placeholder': '555-555-5555'
                          })
-    alt_ext = TextField('Alt. Extension: ',
+    alt_ext = StringField('Alt. Extension: ',
                         render_kw={
                             'maxlength': '10',
                             'placeholder': 'XXXXXXXXXX'
@@ -136,7 +135,7 @@ def process(self, formdata=None, obj=None, data=None, **kwargs):
             #     Temporarily, this can simply be merged with kwargs.
             kwargs = dict(data, **kwargs)
 
-        for name, field, in iteritems(self._fields):
+        for name, field, in self._fields.items():
             if obj is not None and hasattr(obj, name):
                 # This if statement is the only change made to the original
                 # code for BaseForm.process() - Dawn
@@ -158,7 +157,7 @@ def populate_obj(self, obj):
         default with the 'studies' field treated as a special case to
         account for the fact that it is a mapped collection
         """
-        for name, field in iteritems(self._fields):
+        for name, field in self._fields.items():
             if name == 'studies':
                 for study_form in self.studies.entries:
                     if study_form.site_id.data == '':

dashboard/blueprints/users/views.py

@@ -6,13 +6,13 @@
 from . import user_bp
 from .utils import get_user_form, parse_enabled_sites
 from .forms import UserForm
-from ...models import User, AccountRequest
+from ...models import User, AccountRequest, db
 from ...utils import report_form_errors, dashboard_admin_required
 
 
 @lm.user_loader
 def load_user(uid):
-    return User.query.get(int(uid))
+    return db.session.get(User, int(uid))
 
 
 @user_bp.before_app_request
@@ -58,7 +58,7 @@ def user(user_id=None):
         return redirect(url_for('users.user'))
 
     if user_id:
-        user = User.query.get(user_id)
+        user = db.session.get(User, user_id)
     else:
         user = current_user
 
@@ -74,7 +74,7 @@ def user(user_id=None):
             flash("You are not authorized to update other users' settings.")
             return redirect(url_for('users.user'))
 
-        updated_user = User.query.get(submitted_id)
+        updated_user = db.session.get(User, submitted_id)
 
         if form.update_access.data:
             # Give user access to a new study or site
@@ -123,7 +123,7 @@ def manage_users(user_id=None, approve=False):
         # URL gets parsed into unicode
         approve = False
 
-    user_request = AccountRequest.query.get(user_id)
+    user_request = db.session.get(AccountRequest, user_id)
     if not approve:
         try:
             user_request.reject()

dashboard/forms.py

@@ -8,7 +8,7 @@
 
 from flask_wtf import FlaskForm
 from wtforms import (SelectMultipleField, HiddenField, TextAreaField,
-                     TextField)
+                     StringField)
 from wtforms.validators import DataRequired
 
 
@@ -49,6 +49,6 @@ class AnalysisForm(FlaskForm):
 
     This feature has not yet been fully implemented.
     """
-    name = TextField('Brief name', validators=[DataRequired()])
+    name = StringField('Brief name', validators=[DataRequired()])
     description = TextAreaField('Description', validators=[DataRequired()])
     software = TextAreaField('Software')