Merge branch 'merge-1.0.1' into 'master'

Merge 1.0.1

See merge request NCER-PD/scheduling-system!316

CHANGELOG

@@ -6,6 +6,22 @@ smasch (1.1.0~alpha.0-1) unstable; urgency=low
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 25 Feb 2021 17:00:00 +0200
 
+smasch (1.0.1-1) stable; urgency=low
+
+  * bug fix: gunicorn request length extended so dynamic table allows for more
+    columns (#381)
+  * bug fix: unfinish visit button was always disabled (#386)
+  * bug fix: generating documents for templates did not work for subjects
+    created before custom field was added to the study (#388)
+  * bug fix: readonly custom Date Field was improperly persisted in forms
+    (#383)
+  * bug fix: worker initials were not visible after changing appointments
+    calendar view from month to week (#377)
+  * bug fix: statics and npm files were not served properly when accessing by
+    docker
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 17 Mar 2021 10:00:00 +0200
+
 smasch (1.0.0-1) stable; urgency=low
 
   * backward incompatible: smasch is using python3 (#337)

Dockerfile

@@ -8,7 +8,18 @@ RUN pip install -r requirements.txt --default-timeout=180 -i https://pypi.lcsb.u
 ADD . /code/
 RUN cp local_settings_ci.py smash/smash/local_settings.py
 WORKDIR /code/smash
+ENV NODE_VERSION=12.6.0
+RUN apt install -y curl
+RUN curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.34.0/install.sh | bash
+ENV NVM_DIR=/root/.nvm
+RUN . "$NVM_DIR/nvm.sh" && nvm install ${NODE_VERSION}
+RUN . "$NVM_DIR/nvm.sh" && nvm use v${NODE_VERSION}
+RUN . "$NVM_DIR/nvm.sh" && nvm alias default v${NODE_VERSION}
+ENV PATH="/root/.nvm/versions/node/v${NODE_VERSION}/bin/:${PATH}"
+RUN node --version
+RUN npm --version
+RUN npm install
 
 ENTRYPOINT [ "/bin/sh" ]
-CMD [ "manage.py runserver 0.0.0.0:8002" ]
-EXPOSE 8002
+CMD [ "manage.py runserver 0.0.0.0:8888" ]
+EXPOSE 8888

debian-files/smasch.service

@@ -8,7 +8,7 @@ User=smasch
 Group=smasch
 WorkingDirectory=/usr/lib/smasch
 
-ExecStart=/usr/lib/smasch/env/bin/gunicorn -b :8888 --pid /run/smasch/pid smash.wsgi --error-logfile /var/log/smasch/gunicorn.log --log-level DEBUG --capture-output --limit-request-line 8192
+ExecStart=/usr/lib/smasch/env/bin/gunicorn -b :8888 --pid /run/smasch/pid smash.wsgi --error-logfile /var/log/smasch/gunicorn.log --log-level DEBUG --capture-output --limit-request-line 16384
 ExecReload=/bin/kill -s HUP $MAINPID
 ExecStop=/bin/kill -s TERM $MAINPID
 PrivateTmp=true

docker-compose.yml

@@ -13,21 +13,21 @@ services:
     web:
         build: .
         expose: 
-            - '8002'
+            - '8888'
         entrypoint: bash -c "sleep 5
                           && python manage.py makemigrations web 
                           && python manage.py migrate
                           && python manage.py migrate sessions
                           && python manage.py collectstatic --noinput
                           && echo && echo && echo 'The server will start now...'
-                          && gunicorn -b 0.0.0.0:8002 smash.wsgi:application --access-logfile access.log --error-logfile error.log"
+                          && gunicorn -b 0.0.0.0:8888 smash.wsgi:application --access-logfile access.log --error-logfile error.log"
                           ### To run the server through manage.py, use:
-                          #  && python manage.py runserver 0.0.0.0:8002"
+                          #  && python manage.py runserver 0.0.0.0:8888"
                           ### To run the verbose tests, uncomment:
                           # python manage.py test -v3"
         command: ""
         ports:
-            - "8002:8002"
+            - "8888:8888"
         volumes:
             - static_files:/tmp/static/
         depends_on:

docker/nginx/nginx.conf

@@ -43,7 +43,7 @@ http {
             proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
             proxy_set_header Host $http_host;
             proxy_redirect off;
-            proxy_pass http://web:8002;
+            proxy_pass http://web:8888;
         }
     }
 }

docker/nginx/smasch.conf

@@ -46,6 +46,6 @@ server {
             proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
             proxy_set_header Host $http_host;
             proxy_redirect off;
-            proxy_pass http://web:8002;
+            proxy_pass http://web:8888;
     }
 }

local_settings_ci.py

@@ -4,6 +4,8 @@ SECRET_KEY = 'Paste long random string here'  # Insert long random string
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True
 
+SERVE_STATIC = True
+
 # Database
 # https://docs.djangoproject.com/en/1.10/ref/settings/#databases
 

smash/web/docx_helper.py

@@ -26,23 +26,27 @@ def process_file(path_to_docx, path_to_new_docx, changes_to_apply):
 
     doc.save(path_to_new_docx)
 
+
 def merge_files(files, path_to_new_docx):
-    '''
-    When combining templates into a new Document object, python-docx does not properly copy the information of the images, then Word is not able to locate the original content referred by the XML tag in the document. To fix this problem (see #234 ) the first file is loaded and the rest of templates are concatenated to this. This way, the original image content and rId match and the images are shown adequately.
+    """
+    When combining templates into a new Document object, python-docx does not properly copy the information of the
+    images, then Word is not able to locate the original content referred by the XML tag in the document. To fix this
+    problem (see #234 ) the first file is loaded and the rest of templates are concatenated to this. This way, the
+    original image content and rId match and the images are shown adequately.
     See issue #235
-    '''
+    """
     first_file = files[0]
     files = files[1:]
-    merged_document = Document(first_file) #first file
+    merged_document = Document(first_file)  # first file
 
     if len(files) > 0:
         merged_document.add_page_break()
 
-    for index, file in enumerate(files): #rest of files if any
+    for index, file in enumerate(files):  # rest of files if any
         sub_doc = Document(file)
         if index < len(files) - 1:
             sub_doc.add_page_break()
         for element in sub_doc.element.body:
             merged_document.element.body.append(element)
-       
-    merged_document.save(path_to_new_docx)
+
+    merged_document.save(path_to_new_docx)
\ No newline at end of file

smash/web/forms/study_subject_forms.py

@@ -158,8 +158,9 @@ class StudySubjectAddForm(StudySubjectForm):
         instance = super(StudySubjectAddForm, self).save(commit)
         # we can add custom values only after object exists in the database
         for field_type in CustomStudySubjectField.objects.filter(study=self.study):
-            self.instance.set_custom_data_value(field_type, get_study_subject_field_value(field_type, self[
-                get_study_subject_field_id(field_type)]))
+            if not field_type.readonly:
+                self.instance.set_custom_data_value(field_type, get_study_subject_field_value(field_type, self[
+                    get_study_subject_field_id(field_type)]))
         return instance
 
     def build_screening_number(self, cleaned_data):
@@ -289,8 +290,9 @@ class StudySubjectEditForm(StudySubjectForm):
 
     def save(self, commit=True) -> StudySubject:
         for field_type in CustomStudySubjectField.objects.filter(study=self.study):
-            self.instance.set_custom_data_value(field_type, get_study_subject_field_value(field_type, self[
-                get_study_subject_field_id(field_type)]))
+            if not field_type.readonly:
+                self.instance.set_custom_data_value(field_type, get_study_subject_field_value(field_type, self[
+                    get_study_subject_field_id(field_type)]))
         return super(StudySubjectForm, self).save(commit)
 
     class Meta:

smash/web/models/mail_template.py

@@ -338,13 +338,13 @@ class MailTemplate(models.Model):
                 "##S_ADDRESS##": study_subject.subject.address,
                 "##S_CITY##": study_subject.subject.city,
                 "##S_COUNTRY##": str(study_subject.subject.country),
-                "##S_DIAGNOSIS_YEAR##": study_subject.get_custom_field_value('Year of diagnosis'),
+                "##S_DIAGNOSIS_YEAR##": str(study_subject.get_custom_field_value('Year of diagnosis')),
                 "##S_DATE_ADDED##": date_to_str(study_subject.date_added, DATE_FORMAT_SHORT),
                 "##S_DATE_BORN##": date_born,
-                "##S_DIAGNOSIS##": study_subject.get_custom_field_value('Diagnosis'),
+                "##S_DIAGNOSIS##": str(study_subject.get_custom_field_value('Diagnosis')),
                 "##S_EMAIL##": str(study_subject.subject.email),
                 "##S_SEX##": study_subject.subject.get_sex_display(),
-                "##S_MPOWER_ID##": study_subject.get_custom_field_value('MPower ID'),
+                "##S_MPOWER_ID##": str(study_subject.get_custom_field_value('MPower ID')),
                 "##S_ND_NUMBER##": study_subject.nd_number,
                 "##S_PHONE_NUMBER##": str(study_subject.subject.phone_number),
                 "##S_PHONE_NUMBER_2##": str(study_subject.subject.phone_number_2),

smash/web/templates/appointments/index.html

@@ -117,7 +117,10 @@
                 startParam: "start_date",
                 endParam: "end_date",
                 dayRender: function (date, cell) {
-                    var element = document.createElement("div");
+                    var element = dayHeaders[$(cell[0]).attr("data-date")];
+                    if (element === undefined) {
+                        element = document.createElement("div");
+                    }
                     cell[0].appendChild(element);
                     dayHeaders[$(cell[0]).attr("data-date")] = element;
                 },
@@ -146,7 +149,7 @@
                     if (event.status) {
                         content += '<li>Status: ' + event.status + '</li>'
                     }
-                    
+
                     content += "</ul>";
                     $(element).popover({
                         title: event.title,

smash/web/templates/visits/details.html

@@ -70,7 +70,7 @@
                     <div class="col-md-6 form-group">
                         <label class="col-sm-4 control-label">
                             {% if visFinished %}
-                                <i title="Only visits with one inmediate future visit (without appointments) can be unfinished." class="fa fa-info-circle"></i> 
+                                <i title="Only visits with one immediate future visit (without appointments) can be unfinished." class="fa fa-info-circle"></i>
                             {% endif %}
                             Visit finished
                         </label>
@@ -95,7 +95,7 @@
 
                         {% if visFinished %}
                         <div class="col-sm-1">
-                            {% if "unfinish_visit" not in permissions %}
+                            {% if "delete_visit" not in permissions %}
                                 <div title="You don't have permissions to unfinish visits." class="btn btn-block btn-warning disabled">
                                     <i class="fa fa-undo"></i>
                                 </div>

smash/web/tests/models/test_mail_template.py

@@ -4,13 +4,14 @@ import io
 from django.test import TestCase
 from docx import Document
 
-from web.models import MailTemplate
+from web.models import MailTemplate, StudySubject, Language
 from web.models.constants import MAIL_TEMPLATE_CONTEXT_APPOINTMENT, MAIL_TEMPLATE_CONTEXT_VISIT, \
-    MAIL_TEMPLATE_CONTEXT_SUBJECT, MAIL_TEMPLATE_CONTEXT_VOUCHER
+    MAIL_TEMPLATE_CONTEXT_SUBJECT, MAIL_TEMPLATE_CONTEXT_VOUCHER, CUSTOM_FIELD_TYPE_TEXT
+from web.models.custom_data import CustomStudySubjectField
 from web.models.mail_template import DATE_FORMAT_SHORT
 from web.tests.functions import create_language, get_resource_path, create_appointment, create_user, \
     create_study_subject, \
-    create_visit, create_voucher, create_worker, create_flying_team
+    create_visit, create_voucher, create_worker, create_flying_team, get_test_study
 
 
 class MailTemplateModelTests(TestCase):
@@ -100,19 +101,32 @@ class MailTemplateModelTests(TestCase):
         self.check_doc_contains(doc, [flying_team_name])
 
     def test_apply_subject(self):
-        template_name_french = "test_fr"
         subject = create_study_subject()
-        subject_template_french = MailTemplate(name=template_name_french, language=self.french_language,
-                                               context=MAIL_TEMPLATE_CONTEXT_SUBJECT,
-                                               template_file=self.template_file)
-        stream = io.BytesIO()
-        subject_template_french.apply(subject, self.user, stream)
-        doc = Document(stream)
+        doc = self.create_doc_for_subject(subject, self.french_language, MAIL_TEMPLATE_CONTEXT_SUBJECT)
+        worker_name = str(self.user.worker)
+
+        self.check_doc_contains(doc, [worker_name, str(subject), str(subject.subject.country), subject.nd_number,
+                                      subject.type.name])
+
+    def test_apply_subject_with_non_existing_custom_field(self):
+        subject = create_study_subject()
+        field = CustomStudySubjectField.objects.create(name="Diagnosis", type=CUSTOM_FIELD_TYPE_TEXT,
+                                                       study=get_test_study(), unique=True)
+        doc = self.create_doc_for_subject(subject, self.french_language, MAIL_TEMPLATE_CONTEXT_SUBJECT)
         worker_name = str(self.user.worker)
 
         self.check_doc_contains(doc, [worker_name, str(subject), str(subject.subject.country), subject.nd_number,
                                       subject.type.name])
 
+    def create_doc_for_subject(self, subject: StudySubject, language: Language, context: str):
+        subject_template_french = MailTemplate(name="test_fr", language=language,
+                                               context=context,
+                                               template_file=self.template_file)
+        stream = io.BytesIO()
+        subject_template_french.apply(subject, self.user, stream)
+        doc = Document(stream)
+        return doc
+
     def test_apply_voucher(self):
         template_name_french = "test_without_language"
         subject = create_study_subject()