Merge pull request #96 from ODM2/development

Release 0.3.0

.gitignore

@@ -1,3 +1,4 @@
+/src/dataloaderinterface/static/data
 /src/WebSDL/.idea
 # Created by .ignore support plugin (hsz.mobi)
 ### Python template

requirements.txt

@@ -1,19 +1,17 @@
 beautifulsoup4==4.5.1
+codegen==1.0
 coverage==4.2
 Django==1.10.3
-django-autocomplete-light==3.2.1
-django-bootstrap-form==3.2.1
-django-crispy-forms==1.6.1
+django-debug-toolbar==1.6
 django-discover-runner==1.0
-django-filter==1.0.0
-django-formset-js==0.5.0
-django-jquery-js==2.1.4
 django-webtest==1.8.0
 django-widget-tweaks==1.4.1
 djangorestframework==3.5.3
 Markdown==2.6.7
-mysqlclient==1.3.9
+patterns==0.3
+psycopg2==2.7.1
 six==1.10.0
+sqlparse==0.2.2
 waitress==1.0.1
 WebOb==1.6.2
 WebTest==2.0.23

src/WebSDL/settings/base.py

@@ -32,22 +32,22 @@
     print("The secret key is required in the settings.json file.")
     exit(1)
 
-ALLOWED_HOSTS = []
+ALLOWED_HOSTS = ['*']
 
 
 # Application definition
 
 INSTALLED_APPS = [
+    'rest_framework',
+    'dataloader',
+    'dataloaderservices',
+    'dataloaderinterface',
     'django.contrib.admin',
     'django.contrib.auth',
     'django.contrib.contenttypes',
     'django.contrib.sessions',
     'django.contrib.messages',
     'django.contrib.staticfiles',
-    'rest_framework',
-    'dataloader',
-    'dataloaderservices',
-    'dataloaderinterface',
     'widget_tweaks'
 ]
 
@@ -131,14 +131,10 @@
 
 LANGUAGE_CODE = 'en-us'
 
-TIME_ZONE = 'UTC'
-
 USE_I18N = True
 
 USE_L10N = True
 
-USE_TZ = True
-
 LOGIN_URL = 'login'
 
 DATABASE_ROUTERS = ['WebSDL.db_routers.WebSDLRouter']
@@ -154,4 +150,17 @@
 
 RECAPTCHA_USER_KEY = data["recaptcha_user_key"] if "recaptcha_user_key" in data else ""
 
-RECAPTCHA_VERIFY_URL = "https://www.google.com/recaptcha/api/siteverify"
+RECAPTCHA_VERIFY_URL = "https://www.google.com/recaptcha/api/siteverify"
+
+
+EMAIL_SENDER = data['email_sender'] if 'email_sender' in data else '',
+
+DEFAULT_FROM_EMAIL = EMAIL_SENDER[0] if isinstance(EMAIL_SENDER, tuple) else EMAIL_SENDER
+
+EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
+
+EMAIL_SERVER = data['email_host'] if 'email_host' in data else '',
+
+EMAIL_HOST = EMAIL_SERVER[0] if isinstance(EMAIL_SERVER, tuple) else EMAIL_SERVER
+
+DATETIME_FORMAT = "N j, Y, H:m"

src/WebSDL/settings/development.py

@@ -4,9 +4,9 @@
 
 INTERNAL_IPS = (
     '127.0.0.1',
-    '129.123.51.198'
 )
 
+STATIC_ROOT = os.path.join(os.path.join(BASE_DIR, os.pardir), 'dataloaderinterface', 'static')
 STATIC_URL = '/static/'
 SITE_URL = ''
 

src/WebSDL/settings/settings_template.json

@@ -0,0 +1,28 @@
+{
+  "secret_key": "",
+  "host": "-optional",
+  "recaptcha_secret_key": "-optional",
+  "recaptcha_user_key": "-optional",
+  "email_sender": "password.reset@data.envirodiy.org",
+  "email_host": "mail.usu.edu",
+  "databases": [
+    {
+      "name": "default",
+      "schema": "",
+      "engine": "",
+      "user": "",
+      "password": "",
+      "host": "",
+      "port": ""
+    },
+    {
+      "name": "odm2",
+      "schema": "",
+      "engine": "",
+      "user": "",
+      "password": "",
+      "host": "",
+      "port": ""
+    }
+  ]
+}

src/WebSDL/urls.py

@@ -14,15 +14,13 @@
     2. Add a URL to urlpatterns:  url(r'^blog/', include('blog.urls'))
 """
 from django.conf import settings
-from django.contrib.auth import views as auth_views
 from django.conf.urls import url, include
 from django.contrib import admin
+from django.contrib.auth import views as auth_views
 from django.core.urlresolvers import reverse_lazy
-from django.views.generic.edit import CreateView
 
-from dataloader.models import Organization
-from dataloaderinterface.forms import UserRegistrationForm
-from dataloaderinterface.views import UserRegistrationView
+from dataloaderinterface.views import UserRegistrationView, UserUpdateView
+
 
 BASE_URL = settings.SITE_URL[1:]
 
@@ -34,11 +32,24 @@
     'next_page': reverse_lazy('home')
 }
 
+password_reset_configuration = {
+    'post_reset_redirect': 'password_reset_done'
+}
+
+password_done_configuration = {
+    'post_reset_redirect': 'password_reset_complete'
+}
+
 urlpatterns = [
+    url(r'^' + BASE_URL + 'password-reset/$', auth_views.password_reset, password_reset_configuration, name='password_reset'),
+    url(r'^' + BASE_URL + 'password-reset/done/$', auth_views.password_reset_done, name='password_reset_done'),
+    url(r'^' + BASE_URL + 'password-reset/(?P<uidb64>[0-9A-Za-z]+)-(?P<token>.+)/$', auth_views.password_reset_confirm, password_done_configuration, name='password_reset_confirm'),
+    url(r'^' + BASE_URL + 'password-reset/completed/$', auth_views.password_reset_complete, name='password_reset_complete'),
     url(r'^' + BASE_URL + 'admin/', admin.site.urls),
     url(r'^' + BASE_URL + 'login/$', auth_views.login, login_configuration, name='login'),
     url(r'^' + BASE_URL + 'logout/$', auth_views.logout, logout_configuration, name='logout'),
     url(r'^' + BASE_URL + 'register/$', UserRegistrationView.as_view(), name='user_registration'),
+    url(r'^' + BASE_URL + 'account/$', UserUpdateView.as_view(), name='user_account'),
     url(r'^' + BASE_URL + 'api-auth/', include('rest_framework.urls', namespace='rest_framework')),
     url(BASE_URL, include('dataloaderinterface.urls')),
     url(BASE_URL, include('dataloaderservices.urls')),

src/dataloader/models.py

@@ -1,15 +1,17 @@
 from __future__ import unicode_literals
 
+import inspect
+import sys
 import uuid
 
-from django.db import models
-from django.utils.encoding import python_2_unicode_compatible
-
 from dataloader.querysets import AffiliationQuerySet, RelatedActionManager, ResultManager, \
-    DataLoggerFileManager, EquipmentModelManager, DataLoggerFileColumnManager, InstrumentOutputVariableManager, \
+    DataLoggerFileManager, InstrumentOutputVariableManager, \
     EquipmentManager, CalibrationReferenceEquipmentManager, EquipmentUsedManager, MaintenanceActionManager, \
     RelatedEquipmentManager, CalibrationActionManager, ODM2QuerySet, ActionQuerySet, ActionByQuerySet, \
-    FeatureActionQuerySet, TimeSeriesValuesQuerySet
+    FeatureActionQuerySet, TimeSeriesValuesQuerySet, EquipmentModelQuerySet
+from django.conf import settings
+from django.db import models
+from django.utils.encoding import python_2_unicode_compatible
 
 
 # TODO: function to handle the file upload folder for file fields.
@@ -120,7 +122,7 @@ class ResultValue(models.Model):
     value_datetime_utc_offset = models.IntegerField(db_column='valuedatetimeutcoffset')
 
     def __str__(self):
-        return '%s %s' % self.value_datetime, self.data_value
+        return '%s %s' % (self.value_datetime, self.data_value)
 
     def __repr__(self):
         return "<%s('%s', '%s', Result['%s', '%s'], '%s')>" % (
@@ -137,7 +139,7 @@ class ResultValueAnnotation(models.Model):
     annotation = models.ForeignKey('Annotation', db_column='annotationid')
 
     def __str__(self):
-        return '%s %s' % self.value_datetime, self.data_value
+        return '%s %s' % (self.value_datetime, self.data_value)
 
     def __repr__(self):
         return "<%s('%s', Annotation['%s', '%s'], ResultValue['%s', '%s')>" % (
@@ -191,6 +193,9 @@ class XIntendedComponent(models.Model):
     intended_x_spacing = models.FloatField(db_column='intendedxspacing')
     intended_x_spacing_unit = models.ForeignKey('Unit', related_name='+', db_column='intendedxspacingunitsid', blank=True, null=True)
 
+    class Meta:
+        abstract = True
+
 
 class YIntendedComponent(models.Model):
     intended_y_spacing = models.FloatField(db_column='intendedyspacing')
@@ -407,7 +412,7 @@ class Meta:
 class Organization(ODM2Model):
     organization_id = models.AutoField(db_column='organizationid', primary_key=True)
     organization_type = models.ForeignKey('OrganizationType', db_column='organizationtypecv')
-    organization_code = models.CharField(db_column='organizationcode', max_length=50)
+    organization_code = models.CharField(db_column='organizationcode', max_length=50, unique=True)
     organization_name = models.CharField(db_column='organizationname', max_length=255)
     organization_description = models.CharField(db_column='organizationdescription', blank=True, max_length=500)
     organization_link = models.CharField(db_column='organizationlink', blank=True, max_length=255)
@@ -447,7 +452,7 @@ def role_status(self):
         return 'Primary contact' if self.is_primary_organization_contact else 'Secondary contact'
 
     def __str__(self):
-        return '%s (%s) - %s' % (self.person, self.primary_email, self.organization)
+        return '%s - %s' % (self.person, self.organization)
 
     def __repr__(self):
         return "<Affiliation('%s', Person['%s', '%s'], Organization['%s', '%s'], '%s', '%s', '%s')>" % (
@@ -547,7 +552,7 @@ class SamplingFeature(models.Model):
     sampling_feature_id = models.AutoField(db_column='samplingfeatureid', primary_key=True)
     sampling_feature_uuid = models.UUIDField(default=uuid.uuid4, editable=False, db_column='samplingfeatureuuid')
     sampling_feature_type = models.ForeignKey('SamplingFeatureType', db_column='samplingfeaturetypecv')
-    sampling_feature_code = models.CharField(db_column='samplingfeaturecode', max_length=50)
+    sampling_feature_code = models.CharField(db_column='samplingfeaturecode', max_length=50, unique=True)
     sampling_feature_name = models.CharField(db_column='samplingfeaturename', blank=True, max_length=255)
     sampling_feature_description = models.CharField(db_column='samplingfeaturedescription', blank=True, max_length=500)
     sampling_feature_geo_type = models.ForeignKey('SamplingFeatureGeoType', db_column='samplingfeaturegeotypecv', blank=True, null=True)
@@ -562,6 +567,12 @@ class SamplingFeature(models.Model):
     external_identifiers = models.ManyToManyField('ExternalIdentifierSystem', related_name='sampling_features',
                                                   through='SamplingFeatureExternalIdentifier')
 
+    @property
+    def latest_updated_result(self):
+        return self.feature_actions.with_results()\
+            .filter(results__value_count__gt=0)\
+            .latest('results__result_datetime').results.first()
+
     def __str__(self):
         return '%s %s' % (self.sampling_feature_code, self.sampling_feature_name)
 
@@ -690,7 +701,7 @@ class Unit(models.Model):
     unit_link = models.CharField(db_column='unitslink', blank=True, max_length=255)
 
     def __str__(self):
-        return '%s: %s (%s)' % (self.unit_type_id, self.unit_abbreviation, self.unit_name)
+        return '%s: %s (%s)' % (self.unit_type_id, self.unit_name, self.unit_abbreviation)
 
     def __repr__(self):
         return "<Unit('%s', '%s', '%s', '%s')>" % (
@@ -717,7 +728,7 @@ class Variable(models.Model):
                                                   through='VariableExternalIdentifier')
 
     def __str__(self):
-        return '%s: %s (%s)' % (self.variable_name_id, self.variable_code, self.variable_type_id)
+        return '%s: %s' % (self.variable_name_id, self.variable_code)
 
     def __repr__(self):
         return "<Variable('%s', '%s', '%s', '%s')>" % (
@@ -777,7 +788,7 @@ class Meta:
 @python_2_unicode_compatible
 class DataLoggerProgramFile(models.Model):
     program_id = models.AutoField(db_column='programid', primary_key=True)
-    affiliation_id = models.ForeignKey('Affiliation', db_column='affiliationid')
+    affiliation = models.ForeignKey('Affiliation', db_column='affiliationid', related_name='data_logger_programs')
     program_name = models.CharField(db_column='programname', max_length=255)
     program_description = models.CharField(db_column='programdescription', blank=True, max_length=500)
     program_version = models.CharField(db_column='programversion', blank=True, max_length=50)
@@ -798,7 +809,7 @@ class Meta:
 @python_2_unicode_compatible
 class DataLoggerFile(models.Model):
     data_logger_file_id = models.AutoField(db_column='dataloggerfileid', primary_key=True)
-    program = models.ForeignKey('DataLoggerProgramFile', db_column='programid')
+    program = models.ForeignKey('DataLoggerProgramFile', db_column='programid', related_name='data_logger_files')
     data_logger_file_name = models.CharField(db_column='dataloggerfilename', max_length=255)
     data_logger_file_description = models.CharField(db_column='dataloggerfiledescription', blank=True, max_length=500)
     data_logger_file_link = models.FileField(db_column='dataloggerfilelink', blank=True)
@@ -833,8 +844,6 @@ class DataLoggerFileColumn(models.Model):
     recording_interval_unit = models.ForeignKey('Unit', related_name='recording_interval_data_logger_file_columns', db_column='recordingintervalunitsid', blank=True, null=True)
     aggregation_statistic = models.ForeignKey('AggregationStatistic', related_name='data_logger_file_columns', db_column='aggregationstatisticcv', blank=True)
 
-    objects = DataLoggerFileColumnManager()
-
     def __str__(self):
         return '%s %s' % (self.column_label, self.column_description)
 
@@ -861,10 +870,10 @@ class EquipmentModel(models.Model):
     output_variables = models.ManyToManyField('Variable', related_name='instrument_models', through='InstrumentOutputVariable')
     output_units = models.ManyToManyField('Unit', related_name='instrument_models', through='InstrumentOutputVariable')
 
-    objects = EquipmentModelManager()
+    objects = EquipmentModelQuerySet.as_manager()
 
     def __str__(self):
-        return '%s: %s' % (self.model_name, self.model_description)
+        return '%s %s' % (self.model_manufacturer, self.model_name)
 
     def __repr__(self):
         return "<EquipmentModel('%s', '%s', '%s', Organization[%s, %s])>" % (
@@ -1849,7 +1858,7 @@ class Meta:
         db_table = 'pointcoverageresults'
 
 
-class ProfileResult(ExtendedResult, AggregatedComponent, XOffsetComponent, YOffsetComponent, YIntendedComponent, ZIntendedComponent, TimeIntendedComponent):
+class ProfileResult(ExtendedResult, AggregatedComponent, XOffsetComponent, YOffsetComponent, ZIntendedComponent, TimeIntendedComponent):
     class Meta:
         db_table = 'profileresults'
 
@@ -2068,3 +2077,19 @@ class Meta:
         db_table = 'transectresultvalueannotations'
 
 # endregion
+
+
+# TODO: make something more sophisticated than this later on
+sql_schema_fix = 'odm2].['   # for SQL databases
+psql_schema_fix = 'odm2"."'  # for postgres databases
+clsmembers = inspect.getmembers(sys.modules[__name__], inspect.isclass)
+classes = [model for name, model in clsmembers if issubclass(model, models.Model)]
+database_manager = settings.DATABASES['odm2']['ENGINE']
+
+for model in classes:
+    if database_manager == u'sql_server.pyodbc':
+        model._meta.db_table = sql_schema_fix.upper() + model._meta.db_table
+    elif database_manager == u'django.db.backends.postgresql_psycopg2':
+        model._meta.db_table = psql_schema_fix + model._meta.db_table
+
+            # can add more fixes there depending on the database engine

src/dataloader/querysets.py

@@ -47,7 +47,7 @@ def for_display(self):
         return self.select_related('action').prefetch_related('sampling_feature')
 
     def with_results(self):
-        return self.prefetch_related('results__timeseriesresult__values', 'results__variable')
+        return self.prefetch_related('results__timeseriesresult__values', 'results__variable', 'results__unit')
 
 
 class RelatedActionManager(models.Manager):
@@ -80,10 +80,9 @@ def get_queryset(self):
 # region ODM2 Equipment Extension
 
 
-class EquipmentModelManager(models.Manager):
-    def get_queryset(self):
-        queryset = super(EquipmentModelManager, self).get_queryset()
-        return queryset.prefetch_related('model_manufacturer')
+class EquipmentModelQuerySet(ODM2QuerySet):
+    def for_display(self):
+        return self.prefetch_related('model_manufacturer')
 
 
 class InstrumentOutputVariableManager(models.Manager):

src/dataloader/tests/test_models.py

@@ -1,6 +1,6 @@
+from dataloader.models import *
 from django.test import TestCase
 
-from dataloader.models import *
 from dataloader.tests.data import data_manager
 
 models_data = data_manager.test_data['models']['data']