Merge pull request #473 from ropable/master

Extend v2 API endpoints, add unit tests

Dockerfile

@@ -1,5 +1,5 @@
 # Prepare the base environment.
-FROM python:3.10.10-slim-bullseye as builder_base_wastd
+FROM python:3.10.12-slim-bookworm as builder_base_wastd
 MAINTAINER asi@dbca.wa.gov.au
 LABEL org.opencontainers.image.source https://github.com/dbca-wa/wastd
 
@@ -22,7 +22,7 @@ RUN curl -s https://packages.microsoft.com/keys/microsoft.asc | apt-key add - \
 # Install Python libs using Poetry.
 FROM builder_base_wastd as python_libs_wastd
 WORKDIR /app
-ENV POETRY_VERSION=1.2.2
+ENV POETRY_VERSION=1.5.1
 RUN pip install --upgrade pip && pip install "poetry==$POETRY_VERSION"
 COPY poetry.lock pyproject.toml /app/
 RUN poetry config virtualenvs.create false \
@@ -37,6 +37,7 @@ COPY wastd ./wastd
 COPY wamtram ./wamtram
 COPY tagging ./tagging
 RUN python manage.py collectstatic --noinput
+
 # Run the application as the www-data user.
 USER www-data
 EXPOSE 8080

observations/api_v2.py

@@ -1,27 +1,78 @@
+from django.http import HttpResponseBadRequest
 from wastd.utils import ListResourceView, DetailResourceView
 from .models import (
-    Encounter,
     Area,
     Survey,
     SurveyMediaAttachment,
+    Encounter,
+    AnimalEncounter,
+    TurtleNestEncounter,
     MediaAttachment,
+    TurtleNestObservation,
+    TurtleHatchlingEmergenceObservation,
+    NestTagObservation,
+    TurtleNestDisturbanceObservation,
+    LoggerObservation,
+    HatchlingMorphometricObservation,
+    TurtleHatchlingEmergenceOutlierObservation,
+    LightSourceObservation,
 )
 from .serializers_v2 import (
-    EncounterSerializer,
     AreaSerializer,
     SurveySerializer,
     SurveyMediaAttachmentSerializer,
+    EncounterSerializer,
+    AnimalEncounterSerializer,
+    TurtleNestEncounterSerializer,
     MediaAttachmentSerializer,
+    TurtleNestObservationSerializer,
+    TurtleHatchlingEmergenceObservationSerializer,
+    NestTagObservationSerializer,
+    TurtleNestDisturbanceObservationSerializer,
+    LoggerObservationSerializer,
+    HatchlingMorphometricObservationSerializer,
+    TurtleHatchlingEmergenceOutlierObservationSerializer,
+    LightSourceObservationSerializer,
 )
 
 
+class AreaListResource(ListResourceView):
+    model = Area
+    serializer = AreaSerializer
+
+
+class AreaDetailResource(DetailResourceView):
+    model = Area
+    serializer = AreaSerializer
+
+
+class SurveyListResource(ListResourceView):
+    model = Survey
+    serializer = SurveySerializer
+
+
+class SurveyDetailResource(DetailResourceView):
+    model = Survey
+    serializer = SurveySerializer
+
+
+class SurveyMediaAttachmentListResource(ListResourceView):
+    model = SurveyMediaAttachment
+    serializer = SurveyMediaAttachmentSerializer
+
+
+class SurveyMediaAttachmentDetailResource(DetailResourceView):
+    model = SurveyMediaAttachment
+    serializer = SurveyMediaAttachmentSerializer
+
+
 class EncounterListResource(ListResourceView):
     model = Encounter
     serializer = EncounterSerializer
 
     def get_queryset(self):
         # FIXME: permissions checking per object.
-        return Encounter.objects.all(
+        return self.model.objects.all(
         ).prefetch_related(
             'observer',
             'reporter',
@@ -36,41 +87,140 @@ class EncounterDetailResource(DetailResourceView):
     serializer = EncounterSerializer
 
 
-class AreaListResource(ListResourceView):
-    model = Area
-    serializer = AreaSerializer
+class AnimalEncounterListResource(EncounterListResource):
+    model = AnimalEncounter
+    serializer = AnimalEncounterSerializer
 
 
-class AreaDetailResource(DetailResourceView):
-    model = Area
-    serializer = AreaSerializer
+class AnimalEncounterDetailResource(EncounterDetailResource):
+    model = AnimalEncounter
+    serializer = AnimalEncounterSerializer
 
 
-class SurveyListResource(ListResourceView):
-    model = Survey
-    serializer = SurveySerializer
+class TurtleNestEncounterListResource(EncounterListResource):
+    model = TurtleNestEncounter
+    serializer = TurtleNestEncounterSerializer
 
+    def get_queryset(self):
+        # Filtering options.
+        queryset = super().get_queryset()
+        if 'nest_type' in self.request.GET and self.request.GET['nest_type']:
+            queryset = queryset.filter(nest_type=self.request.GET['nest_type'])
+        if 'species' in self.request.GET and self.request.GET['species']:
+            queryset = queryset.filter(nest_type=self.request.GET['species'])
 
-class SurveyDetailResource(DetailResourceView):
-    model = Survey
-    serializer = SurveySerializer
+        return queryset
 
 
-class SurveyMediaAttachmentListResource(ListResourceView):
-    model = SurveyMediaAttachment
-    serializer = SurveyMediaAttachmentSerializer
+class TurtleNestEncounterDetailResource(EncounterDetailResource):
+    model = TurtleNestEncounter
+    serializer = TurtleNestEncounterSerializer
 
 
-class SurveyMediaAttachmentDetailResource(DetailResourceView):
-    model = SurveyMediaAttachment
-    serializer = SurveyMediaAttachmentSerializer
+class ObservationListResource(ListResourceView):
+
+    def dispatch(self, request, *args, **kwargs):
+        if 'encounter_id' in request.GET and request.GET['encounter_id']:
+            try:
+                int(request.GET['encounter_id'])
+            except:
+                return HttpResponseBadRequest()
+        return super().dispatch(request, *args, **kwargs)
+
+    def get_queryset(self):
+        queryset = super().get_queryset()
+
+        if 'encounter_id' in self.request.GET and self.request.GET['encounter_id']:
+            queryset = queryset.filter(encounter__pk=int(self.request.GET['encounter_id']))
 
+        return queryset
 
-class MediaAttachmentListResource(ListResourceView):
+
+class MediaAttachmentListResource(ObservationListResource):
     model = MediaAttachment
     serializer = MediaAttachmentSerializer
 
 
 class MediaAttachmentDetailResource(DetailResourceView):
     model = MediaAttachment
     serializer = MediaAttachmentSerializer
+
+
+class TurtleNestObservationListResource(ObservationListResource):
+    model = TurtleNestObservation
+    serializer = TurtleNestObservationSerializer
+
+
+class TurtleNestObservationDetailResource(DetailResourceView):
+    model = TurtleNestObservation
+    serializer = TurtleNestObservationSerializer
+
+
+class TurtleHatchlingEmergenceObservationListResource(ObservationListResource):
+    model = TurtleHatchlingEmergenceObservation
+    serializer = TurtleHatchlingEmergenceObservationSerializer
+
+
+class TurtleHatchlingEmergenceObservationDetailResource(DetailResourceView):
+    model = TurtleHatchlingEmergenceObservation
+    serializer = TurtleHatchlingEmergenceObservationSerializer
+
+
+class NestTagObservationListResource(ObservationListResource):
+    model = NestTagObservation
+    serializer = NestTagObservationSerializer
+
+
+class NestTagObservationDetailResource(DetailResourceView):
+    model = NestTagObservation
+    serializer = NestTagObservationSerializer
+
+
+class TurtleNestDisturbanceObservationListResource(ObservationListResource):
+    model = TurtleNestDisturbanceObservation
+    serializer = TurtleNestDisturbanceObservationSerializer
+
+
+class TurtleNestDisturbanceObservationDetailResource(DetailResourceView):
+    model = TurtleNestDisturbanceObservation
+    serializer = TurtleNestDisturbanceObservationSerializer
+
+
+class LoggerObservationListResource(ObservationListResource):
+    model = LoggerObservation
+    serializer = LoggerObservationSerializer
+
+
+class LoggerObservationDetailResource(DetailResourceView):
+    model = LoggerObservation
+    serializer = LoggerObservationSerializer
+
+
+class HatchlingMorphometricObservationListResource(ObservationListResource):
+    model = HatchlingMorphometricObservation
+    serializer = HatchlingMorphometricObservationSerializer
+
+
+class HatchlingMorphometricObservationDetailResource(DetailResourceView):
+    model = HatchlingMorphometricObservation
+    serializer = HatchlingMorphometricObservationSerializer
+
+
+class TurtleHatchlingEmergenceOutlierObservationListResource(ObservationListResource):
+    model = TurtleHatchlingEmergenceOutlierObservation
+    serializer = TurtleHatchlingEmergenceOutlierObservationSerializer
+
+
+class TurtleHatchlingEmergenceOutlierObservationDetailResource(DetailResourceView):
+    model = TurtleHatchlingEmergenceOutlierObservation
+    serializer = TurtleHatchlingEmergenceOutlierObservationSerializer
+
+
+class LightSourceObservationListResource(ObservationListResource):
+    model = LightSourceObservation
+    serializer = LightSourceObservationSerializer
+
+
+class LightSourceObservationDetailResource(DetailResourceView):
+    model = LightSourceObservation
+    serializer = LightSourceObservationSerializer

observations/lookups.py

@@ -8,7 +8,7 @@
     ("ntp-broome", "NTP Access DB Broome"),
     ("cet", "Cetacean strandings DB"),
     ("pin", "Pinniped strandings DB"),
-    ("reconstructed", "Reconstructed by WAStD"),
+    ("reconstructed", "Reconstructed automatically"),
 )
 
 SIGHTING_STATUS_CHOICES = (

observations/management/commands/odk_download_track_nest_form.py → observations/management/commands/odk_download_turtle_forms.py

@@ -1,11 +1,16 @@
 from django.core.management.base import BaseCommand
 import logging
-from observations.odk import import_turtle_track_or_nest, import_site_visit_start, import_site_visit_end
+from observations.odk import (
+    import_turtle_track_or_nest,
+    import_site_visit_start,
+    import_site_visit_end,
+    import_marine_wildlife_incident,
+)
 from wastd.odk import get_auth_headers
 
 
 class Command(BaseCommand):
-    help = 'Runs ETL scripts to download submissions related to Turtle Track/Nest survey data from ODK'
+    help = 'Runs ETL scripts to download Turtle Monitoring form submissions from ODK Central'
 
     def add_arguments(self, parser):
         parser.add_argument(
@@ -30,3 +35,6 @@ def handle(self, *args, **options):
 
         logger.info('Downloading data from Site Visit End form, linking encounters')
         import_site_visit_end(duration_hr=options['duration'], auth_headers=auth_headers)
+
+        logger.info('Downloading data from Marine Wildlife Incident form')
+        import_marine_wildlife_incident(auth_headers=auth_headers)

observations/migrations/0008_auto_20230809_1310.py

@@ -0,0 +1,45 @@
+# Generated by Django 3.2.20 on 2023-08-09 05:10
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('observations', '0007_delete_dugongmorphometricobservation'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='turtlehatchlingemergenceobservation',
+            name='hatchling_path_to_sea',
+        ),
+        migrations.AlterField(
+            model_name='encounter',
+            name='encounter_type',
+            field=models.CharField(blank=True, choices=[('stranding', 'Stranding'), ('tagging', 'Tagging'), ('nest', 'Nest'), ('tracks', 'Tracks'), ('inwater', 'In water'), ('tag-management', 'Tag Management'), ('logger', 'Logger'), ('other', 'Other')], default='other', editable=False, help_text='The primary concern of this encounter.', max_length=300, null=True, verbose_name='Encounter type'),
+        ),
+        migrations.AlterField(
+            model_name='encounter',
+            name='source',
+            field=models.CharField(choices=[('direct', 'Direct entry'), ('paper', 'Paper data sheet'), ('odk', 'OpenDataKit mobile data capture'), ('wamtram', 'WAMTRAM 2 tagging DB'), ('ntp-exmouth', 'NTP Access DB Exmouth'), ('ntp-broome', 'NTP Access DB Broome'), ('cet', 'Cetacean strandings DB'), ('pin', 'Pinniped strandings DB'), ('reconstructed', 'Reconstructed automatically')], db_index=True, default='direct', help_text='Where was this record captured initially?', max_length=300, verbose_name='Data Source'),
+        ),
+        migrations.AlterField(
+            model_name='nesttagobservation',
+            name='status',
+            field=models.CharField(choices=[('applied-new', 'Applied new'), ('resighted', 'Re-sighted associated with nest')], default='resighted', help_text='The status this tag was seen in, or brought into.', max_length=300, verbose_name='Tag status'),
+        ),
+        migrations.AlterField(
+            model_name='survey',
+            name='source',
+            field=models.CharField(choices=[('direct', 'Direct entry'), ('paper', 'Paper data sheet'), ('odk', 'OpenDataKit mobile data capture'), ('wamtram', 'WAMTRAM 2 tagging DB'), ('ntp-exmouth', 'NTP Access DB Exmouth'), ('ntp-broome', 'NTP Access DB Broome'), ('cet', 'Cetacean strandings DB'), ('pin', 'Pinniped strandings DB'), ('reconstructed', 'Reconstructed automatically')], default='direct', help_text='Where was this record captured initially?', max_length=300, verbose_name='Data Source'),
+        ),
+        migrations.AlterField(
+            model_name='surveyend',
+            name='source',
+            field=models.CharField(choices=[('direct', 'Direct entry'), ('paper', 'Paper data sheet'), ('odk', 'OpenDataKit mobile data capture'), ('wamtram', 'WAMTRAM 2 tagging DB'), ('ntp-exmouth', 'NTP Access DB Exmouth'), ('ntp-broome', 'NTP Access DB Broome'), ('cet', 'Cetacean strandings DB'), ('pin', 'Pinniped strandings DB'), ('reconstructed', 'Reconstructed automatically')], default='direct', help_text='Where was this record captured initially?', max_length=300, verbose_name='Data Source'),
+        ),
+        migrations.DeleteModel(
+            name='PathToSea',
+        ),
+    ]