Merge pull request #1 from thermokarst/collections

Collections

ccdb/collections_ccdb/__init__.py

@@ -0,0 +1 @@
+default_app_config = 'ccdb.collections_ccdb.apps.CollectionsAppConfig'

ccdb/collections_ccdb/admin.py

@@ -0,0 +1,60 @@
+from django.contrib import admin
+
+from .models import CollectionType, CollectionMethod, Flaw, ADFGPermit, \
+    DatasheetAttachment, CollectionTrap
+
+
+class CollectionTypeAdmin(admin.ModelAdmin):
+    list_display = ('name', 'code', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name', 'code')
+    list_per_page = 25
+    fields = ('name', 'code', 'sort_order')
+
+
+class CollectionMethodAdmin(admin.ModelAdmin):
+    list_display = ('name', 'code', 'collection_method_class', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name', 'code', 'collection_method_class')
+    list_per_page = 25
+    fields = ('name', 'code', 'collection_method_class', 'sort_order')
+
+
+class FlawAdmin(admin.ModelAdmin):
+    list_display = ('name', 'description', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name', 'description')
+    list_per_page = 25
+    fields = ('name', 'description')
+
+
+class ADFGPermitAdmin(admin.ModelAdmin):
+    list_display = ('name', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name',)
+    list_per_page = 25
+    fields = ('name', 'sort_order')
+
+
+class DatasheetAttachmentAdmin(admin.ModelAdmin):
+    list_display = ('collection', 'datasheet')
+    list_display_links = ('datasheet',)
+    list_per_page = 25
+    fields = ('collection', 'datasheet')
+
+
+class CollectionTrapAdmin(admin.ModelAdmin):
+    list_display = ('collection', 'number_of_traps', 'date_opened',
+        'time_opened', 'date_closed', 'time_closed')
+    list_display_links = ('number_of_traps',)
+    list_per_page = 25
+    fields = ('collection', 'number_of_traps', 'date_opened',
+        'time_opened', 'date_closed', 'time_closed')
+
+
+admin.site.register(CollectionType, CollectionTypeAdmin)
+admin.site.register(CollectionMethod, CollectionMethodAdmin)
+admin.site.register(Flaw, FlawAdmin)
+admin.site.register(ADFGPermit, ADFGPermitAdmin)
+admin.site.register(DatasheetAttachment, DatasheetAttachmentAdmin)
+admin.site.register(CollectionTrap, CollectionTrapAdmin)

ccdb/collections_ccdb/apps.py

@@ -0,0 +1,7 @@
+from django.apps import AppConfig
+
+
+# This is needed because 'collections' is part of the Python Std Lib
+class CollectionsAppConfig(AppConfig):
+    name = 'ccdb.collections_ccdb'
+    verbose_name = 'Collections'

ccdb/collections_ccdb/migrations/0001_initial.py

@@ -0,0 +1,158 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import autoslug.fields
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('locations', '0002_remove_site_fk_dupes'),
+        ('projects', '0004_initial_grantreport'),
+        ('processing', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='ADFGPermit',
+            fields=[
+                ('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
+                ('name', models.CharField(max_length=200)),
+                ('sort_order', models.IntegerField(null=True, blank=True)),
+                ('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
+            ],
+            options={
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Collection',
+            fields=[
+                ('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
+                ('number_of_traps', models.IntegerField(null=True, blank=True)),
+                ('collection_start_date', models.DateField(null=True, blank=True)),
+                ('collection_start_time', models.TimeField(null=True, blank=True)),
+                ('collection_end_date', models.DateField(null=True, blank=True)),
+                ('collection_end_time', models.TimeField(null=True, blank=True)),
+                ('specimen_state', models.CharField(max_length=50, blank=True)),
+                ('adfg_permit', models.ForeignKey(to='collections_ccdb.ADFGPermit', blank=True, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='CollectionMethod',
+            fields=[
+                ('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
+                ('name', models.CharField(max_length=100)),
+                ('code', models.CharField(max_length=10, blank=True)),
+                ('collection_method_class', models.CharField(max_length=50, blank=True)),
+                ('sort_order', models.IntegerField(null=True, blank=True)),
+                ('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
+            ],
+            options={
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.CreateModel(
+            name='CollectionTrap',
+            fields=[
+                ('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
+                ('number_of_traps', models.IntegerField()),
+                ('date_opened', models.DateField()),
+                ('time_opened', models.TimeField()),
+                ('date_closed', models.DateField()),
+                ('time_closed', models.TimeField()),
+                ('collection', models.ForeignKey(to='collections_ccdb.Collection')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='CollectionType',
+            fields=[
+                ('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
+                ('name', models.CharField(max_length=100)),
+                ('code', models.CharField(max_length=10, blank=True)),
+                ('sort_order', models.IntegerField(null=True, blank=True)),
+                ('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
+            ],
+            options={
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.CreateModel(
+            name='DatasheetAttachment',
+            fields=[
+                ('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
+                ('datasheet', models.FileField(verbose_name='Datasheet', upload_to='collections/datasheets/%Y/%m/%d')),
+                ('collection', models.ForeignKey(to='collections_ccdb.Collection')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Flaw',
+            fields=[
+                ('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
+                ('name', models.CharField(max_length=200)),
+                ('description', models.CharField(max_length=255, blank=True)),
+                ('sort_order', models.IntegerField(null=True, blank=True)),
+                ('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
+            ],
+            options={
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.AlterUniqueTogether(
+            name='collectiontype',
+            unique_together=set([('name', 'code')]),
+        ),
+        migrations.AlterUniqueTogether(
+            name='collectionmethod',
+            unique_together=set([('name', 'code')]),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='collection_method',
+            field=models.ForeignKey(to='collections_ccdb.CollectionMethod'),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='collection_type',
+            field=models.ForeignKey(to='collections_ccdb.CollectionType'),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='flaw',
+            field=models.ForeignKey(to='collections_ccdb.Flaw', blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='process_type',
+            field=models.ForeignKey(to='processing.ProcessType', blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='project',
+            field=models.ForeignKey(to='projects.Project'),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='reagent',
+            field=models.ForeignKey(to='processing.Reagent', blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='storage_location',
+            field=models.ForeignKey(to='locations.StorageLocation', blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='study_location',
+            field=models.ForeignKey(to='locations.StudyLocation'),
+        ),
+        migrations.AlterUniqueTogether(
+            name='collectiontrap',
+            unique_together=set([('collection', 'date_opened', 'time_opened', 'date_closed', 'time_closed')]),
+        ),
+        migrations.AlterUniqueTogether(
+            name='collection',
+            unique_together=set([('project', 'study_location', 'collection_type', 'collection_start_date', 'collection_end_date', 'collection_method')]),
+        ),
+    ]

ccdb/collections_ccdb/models.py

@@ -0,0 +1,105 @@
+from django.db import models
+
+from autoslug import AutoSlugField
+
+
+class CollectionType(models.Model):
+    name = models.CharField(max_length=100)
+    code = models.CharField(max_length=10, blank=True)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='name')
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        unique_together = ('name', 'code')
+        ordering = ['sort_order']
+
+
+class CollectionMethod(models.Model):
+    name = models.CharField(max_length=100)
+    code = models.CharField(max_length=10, blank=True)
+    collection_method_class = models.CharField(max_length=50, blank=True)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='name')
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        unique_together = ('name', 'code')
+        ordering = ['sort_order']
+
+
+class Flaw(models.Model):
+    name = models.CharField(max_length=200)
+    description = models.CharField(max_length=255, blank=True)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='name')
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        ordering = ['sort_order']
+
+
+class ADFGPermit(models.Model):
+    name = models.CharField(max_length=200)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='name')
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        ordering = ['sort_order']
+
+
+class Collection(models.Model):
+    project = models.ForeignKey('projects.Project')
+    study_location = models.ForeignKey('locations.StudyLocation')
+    collection_type = models.ForeignKey(CollectionType)
+    collection_method = models.ForeignKey(CollectionMethod)
+    number_of_traps = models.IntegerField(blank=True, null=True)
+    collection_start_date = models.DateField(blank=True, null=True)
+    collection_start_time = models.TimeField(blank=True, null=True)
+    collection_end_date = models.DateField(blank=True, null=True)
+    collection_end_time = models.TimeField(blank=True, null=True)
+    storage_location = models.ForeignKey('locations.StorageLocation', blank=True, null=True)
+    specimen_state = models.CharField(max_length=50, blank=True)
+    process_type = models.ForeignKey('processing.ProcessType', blank=True, null=True)
+    reagent = models.ForeignKey('processing.Reagent', blank=True, null=True)
+    adfg_permit = models.ForeignKey(ADFGPermit, blank=True, null=True)
+    flaw = models.ForeignKey(Flaw, blank=True, null=True)
+
+    def __str__(self):
+        return "{} {} {} {} {} {}".format(self.project, self.study_location,
+            self.collection_start_date, self.collection_end_date,
+            self.collection_type, self.collection_method)
+
+    class Meta:
+        unique_together = ('project', 'study_location', 'collection_type',
+            'collection_start_date', 'collection_end_date', 'collection_method')
+
+
+class DatasheetAttachment(models.Model):
+    collection = models.ForeignKey(Collection)
+    datasheet = models.FileField("Datasheet",
+        upload_to='collections/datasheets/%Y/%m/%d')
+
+
+class CollectionTrap(models.Model):
+    collection = models.ForeignKey(Collection)
+    number_of_traps = models.IntegerField()
+    date_opened = models.DateField()
+    time_opened = models.TimeField()
+    date_closed = models.DateField()
+    time_closed = models.TimeField()
+
+    def __str__(self):
+        return "{collection} {number_of_traps} {date_opened} {date_closed}".format(self)
+
+    class Meta:
+        unique_together = ('collection', 'date_opened', 'time_opened', 'date_closed', 'time_closed')

ccdb/locations/migrations/0002_remove_site_fk_dupes.py

@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('locations', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='municipallocation',
+            name='site',
+        ),
+        migrations.AlterField(
+            model_name='studylocation',
+            name='site',
+            field=models.ForeignKey(to='locations.Site'),
+        ),
+    ]

ccdb/locations/models.py

@@ -33,7 +33,6 @@ class Site(models.Model):
 
 
 class MunicipalLocation(models.Model):
-    site = models.ForeignKey(Site)
     name = models.CharField(max_length=100)
     code = models.CharField(max_length=10, blank=True)
     municipal_location_type = models.CharField(max_length=50, blank=True)
@@ -49,7 +48,7 @@ class MunicipalLocation(models.Model):
 
 
 class StudyLocation(models.Model):
-    site = models.ForeignKey(Site, blank=True, null=True)
+    site = models.ForeignKey(Site)
     name = models.CharField(max_length=100)
     code = models.CharField(max_length=10, blank=True)
     study_location_type = models.CharField(max_length=50, blank=True)

ccdb/processing/admin.py

@@ -0,0 +1,32 @@
+from django.contrib import admin
+
+from .models import ProcessType, Reagent, Flaw
+
+
+class ProcessTypeAdmin(admin.ModelAdmin):
+    list_display = ('name', 'code', 'description', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name', 'code', 'description')
+    list_per_page = 25
+    fields = ('name', 'code', 'description', 'sort_order')
+
+
+class ReagentAdmin(admin.ModelAdmin):
+    list_display = ('name', 'code', 'reagent_class', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name', 'code', 'reagent_class')
+    list_per_page = 25
+    fields = ('name', 'code', 'reagent_class', 'sort_order')
+
+
+class FlawAdmin(admin.ModelAdmin):
+    list_display = ('name', 'description', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name', 'description')
+    list_per_page = 25
+    fields = ('name', 'description')
+
+
+admin.site.register(ProcessType, ProcessTypeAdmin)
+admin.site.register(Reagent, ReagentAdmin)
+admin.site.register(Flaw, FlawAdmin)

ccdb/processing/migrations/0001_initial.py

@@ -0,0 +1,92 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import autoslug.fields
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('misc', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Flaw',
+            fields=[
+                ('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
+                ('name', models.CharField(max_length=200)),
+                ('description', models.CharField(blank=True, max_length=255)),
+                ('sort_order', models.IntegerField(blank=True, null=True)),
+                ('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
+            ],
+            options={
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Processing',
+            fields=[
+                ('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
+                ('container_label', models.CharField(max_length=50)),
+                ('process_date', models.DateField(blank=True, null=True)),
+                ('process_time', models.TimeField(blank=True, null=True)),
+                ('reagent_volume', models.FloatField(blank=True, null=True)),
+                ('minutes_in_reagent', models.IntegerField(blank=True, null=True)),
+                ('container', models.ForeignKey(to='misc.Container')),
+                ('flaw', models.ForeignKey(to='processing.Flaw', blank=True, null=True)),
+                ('measurement_unit', models.ForeignKey(to='misc.MeasurementUnit', blank=True, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='ProcessType',
+            fields=[
+                ('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
+                ('name', models.CharField(max_length=100)),
+                ('code', models.CharField(blank=True, max_length=10)),
+                ('description', models.CharField(blank=True, max_length=255)),
+                ('sort_order', models.IntegerField(blank=True, null=True)),
+                ('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
+            ],
+            options={
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Reagent',
+            fields=[
+                ('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
+                ('name', models.CharField(max_length=100)),
+                ('code', models.CharField(blank=True, max_length=10)),
+                ('reagent_class', models.CharField(blank=True, max_length=50)),
+                ('sort_order', models.IntegerField(blank=True, null=True)),
+                ('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
+            ],
+            options={
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.AlterUniqueTogether(
+            name='reagent',
+            unique_together=set([('name', 'code')]),
+        ),
+        migrations.AlterUniqueTogether(
+            name='processtype',
+            unique_together=set([('name', 'code')]),
+        ),
+        migrations.AddField(
+            model_name='processing',
+            name='process_type',
+            field=models.ForeignKey(to='processing.ProcessType'),
+        ),
+        migrations.AddField(
+            model_name='processing',
+            name='reagent',
+            field=models.ForeignKey(to='processing.Reagent', blank=True, null=True),
+        ),
+        migrations.AlterUniqueTogether(
+            name='processing',
+            unique_together=set([('process_type', 'container', 'container_label', 'process_date', 'process_time', 'reagent')]),
+        ),
+    ]

ccdb/processing/models.py

@@ -0,0 +1,66 @@
+from django.db import models
+
+from autoslug import AutoSlugField
+
+
+class ProcessType(models.Model):
+    name = models.CharField(max_length=100)
+    code = models.CharField(max_length=10, blank=True)
+    description = models.CharField(max_length=255, blank=True)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='name')
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        unique_together = ('name', 'code')
+        ordering = ['sort_order']
+
+
+class Reagent(models.Model):
+    name = models.CharField(max_length=100)
+    code = models.CharField(max_length=10, blank=True)
+    reagent_class = models.CharField(max_length=50, blank=True)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='name')
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        unique_together = ('name', 'code')
+        ordering = ['sort_order']
+
+
+class Flaw(models.Model):
+    name = models.CharField(max_length=200)
+    description = models.CharField(max_length=255, blank=True)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='name')
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        ordering = ['sort_order']
+
+
+class Processing(models.Model):
+    process_type = models.ForeignKey(ProcessType)
+    container = models.ForeignKey('misc.Container')
+    container_label = models.CharField(max_length=50)
+    process_date = models.DateField(blank=True, null=True)
+    process_time = models.TimeField(blank=True, null=True)
+    reagent = models.ForeignKey(Reagent, blank=True, null=True)
+    reagent_volume = models.FloatField(blank=True, null=True)
+    measurement_unit = models.ForeignKey('misc.MeasurementUnit', blank=True, null=True)
+    minutes_in_reagent = models.IntegerField(blank=True, null=True)
+    flaw = models.ForeignKey(Flaw, blank=True, null=True)
+
+    def __str__(self):
+        return "{process_date} {process_type} {container_label}".format(**self)
+
+    class Meta:
+        unique_together = ('process_type', 'container', 'container_label',
+            'process_date', 'process_time', 'reagent')

ccdb/species/admin.py

@@ -0,0 +1,14 @@
+from django.contrib import admin
+
+from .models import Species
+
+
+class SpeciesAdmin(admin.ModelAdmin):
+    list_display = ('common_name', 'genus', 'species', 'parasite', 'sort_order')
+    list_display_links = ('common_name',)
+    search_fields = ('common_name', 'genus', 'species', 'parasite')
+    list_per_page = 25
+    fields = ('common_name', 'genus', 'species', 'parasite', 'sort_order')
+
+
+admin.site.register(Species, SpeciesAdmin)

ccdb/species/migrations/0001_initial.py

@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import autoslug.fields
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Species',
+            fields=[
+                ('id', models.AutoField(primary_key=True, verbose_name='ID', serialize=False, auto_created=True)),
+                ('common_name', models.CharField(max_length=100)),
+                ('genus', models.CharField(max_length=50, blank=True)),
+                ('species', models.CharField(max_length=50, blank=True)),
+                ('parasite', models.BooleanField(default=False)),
+                ('sort_order', models.IntegerField(blank=True, null=True)),
+                ('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='common_name')),
+            ],
+            options={
+                'ordering': ['sort_order'],
+                'verbose_name_plural': 'species',
+            },
+        ),
+        migrations.AlterUniqueTogether(
+            name='species',
+            unique_together=set([('common_name', 'species')]),
+        ),
+    ]

ccdb/species/models.py

@@ -0,0 +1,20 @@
+from django.db import models
+
+from autoslug import AutoSlugField
+
+
+class Species(models.Model):
+    common_name = models.CharField(max_length=100)
+    genus = models.CharField(max_length=50, blank=True)
+    species = models.CharField(max_length=50, blank=True)
+    parasite = models.BooleanField(default=False)
+    sort_order = models.IntegerField(blank=True, null=True)
+    slug = AutoSlugField(populate_from='common_name')
+
+    def __str__(self):
+        return self.common_name
+
+    class Meta:
+        unique_together = ('common_name', 'species')
+        ordering = ['sort_order']
+        verbose_name_plural = 'species'

ccdb/utils/management/commands/import_data.py

@@ -12,6 +12,10 @@ from ccdb.misc.models import MeasurementUnit, MeasurementType, Container, \
     Material, Color
 from ccdb.locations.models import Region, Site, MunicipalLocation, \
     StudyLocation, StorageLocation
+from ccdb.species.models import Species
+from ccdb.processing.models import ProcessType, Reagent, Flaw, Processing
+from ccdb.collections_ccdb.models import CollectionType, CollectionMethod, \
+    Flaw, ADFGPermit, Collection
 
 
 class Command(BaseCommand):
@@ -23,7 +27,7 @@ class Command(BaseCommand):
     def handle(self, **options):
         _fetch_data(options['manifest_url'], self.stdout.write)
         self.stdout.write('Fetched data')
-        _import_data()
+        _import_admin_data()
         self.stdout.write('Imported data')
 
 
@@ -43,7 +47,7 @@ def _fetch_data(url, write):
                     out_file.write(chunk)
 
 
-def _import_data():
+def _import_admin_data():
     c = setup_sqlite()
     if c:
         # Projects
@@ -125,7 +129,7 @@ def _import_data():
 
         # Municipal Locations
         for r in c.execute('SELECT * FROM tbl_lu_municipal_locations;'):
-            ml = MunicipalLocation(site_id=r[0], id=r[1], name=r[2], code=r[3],
+            ml = MunicipalLocation(id=r[1], name=r[2], code=r[3],
                 municipal_location_type=r[4], description=r[5], sort_order=r[6])
             ml.save()
 
@@ -151,3 +155,54 @@ def _import_data():
                 room=r[3], freezer=r[4], temp_c=r[5], code=code,
                 description=r[6], sort_order=r[7])
             sl.save()
+
+        # Species
+        for r in c.execute('SELECT * FROM tbl_lu_species;'):
+            s = Species(id=r[0], common_name=r[1], genus=r[2], species=r[3],
+                parasite=r[4], sort_order=r[5])
+            s.save()
+
+        # Processing Type
+        for r in c.execute('SELECT * FROM tbl_lu_process_types;'):
+            pt = ProcessType(id=r[0], name=r[1], code=r[2], description=r[3],
+                sort_order=r[4])
+            pt.save()
+
+        # Reagent
+        for r in c.execute('SELECT * FROM tbl_lu_reagents;'):
+            rg = Reagent(id=r[0], name=r[1], code=r[2], reagent_class=r[3],
+                sort_order=r[4])
+            rg.save()
+
+        # Collection Type
+        for r in c.execute('SELECT * FROM tbl_lu_collection_types;'):
+            ct = CollectionType(id=r[0], name=r[1], code=r[2], sort_order=r[3])
+            ct.save()
+
+        # Collection Method
+        for r in c.execute('SELECT * FROM tbl_lu_collection_methods;'):
+            cm = CollectionMethod(id=r[0], name=r[1], code=r[2],
+                collection_method_class=r[3], sort_order=r[4])
+            cm.save()
+
+        # Collection
+        for r in c.execute('''
+               SELECT *,
+                 collection_start_date AS "collection_start_date [dtdt]",
+                 collection_start_time AS "collection_start_time [dtdt]",
+                 collection_end_date   AS "collection_end_date [dtdt]",
+                 collection_end_time   AS "collection_end_time [dtdt]"
+               FROM tbl_collections;
+            '''):
+            if r[14] is not '':
+                permit, _ = ADFGPermit.objects.get_or_create(name=r[14])
+            else:
+                permit = None
+            col = Collection(project_id=r[0], id=r[1], study_location_id=r[2],
+                collection_type_id=r[3], collection_method_id=r[4],
+                number_of_traps=r[5], collection_start_date=r[17],
+                collection_start_time=r[18], collection_end_date=r[19],
+                collection_end_time=r[20], storage_location_id=r[10],
+                specimen_state=r[11], process_type_id=r[12], reagent_id=r[13],
+                adfg_permit=permit)
+            col.save()

config/settings/base.py

@@ -42,6 +42,9 @@ LOCAL_APPS = (
     'ccdb.projects',
     'ccdb.misc',
     'ccdb.locations',
+    'ccdb.species',
+    'ccdb.collections_ccdb',
+    'ccdb.processing',
 )
 
 # See: https://docs.djangoproject.com/en/dev/ref/settings/#installed-apps

misc/existing.py

@@ -74,31 +74,6 @@ class TblBioReplicates(models.Model):
         db_table = 'tbl_Bio_Replicates'
 
 
-class TblCollections(models.Model):
-    projectid = models.ForeignKey('TblLuProjects', db_column='ProjectID')  # Field name made lowercase.
-    collectionid = models.AutoField(db_column='CollectionID', primary_key=True)  # Field name made lowercase.
-    study_locationid = models.ForeignKey('TblLuStudyLocations', db_column='Study_LocationID')  # Field name made lowercase.
-    collection_typeid = models.ForeignKey('TblLuCollectionTypes', db_column='Collection_TypeID')  # Field name made lowercase.
-    collection_methodid = models.ForeignKey('TblLuCollectionMethods', db_column='Collection_MethodID')  # Field name made lowercase.
-    number_of_traps = models.IntegerField(db_column='Number_Of_Traps', blank=True, null=True)  # Field name made lowercase.
-    collection_start_date = models.DateField(db_column='Collection_Start_Date', blank=True, null=True)  # Field name made lowercase.
-    collection_start_time = models.TimeField(db_column='Collection_Start_Time', blank=True, null=True)  # Field name made lowercase.
-    collection_end_date = models.DateField(db_column='Collection_End_Date', blank=True, null=True)  # Field name made lowercase.
-    collection_end_time = models.TimeField(db_column='Collection_End_Time', blank=True, null=True)  # Field name made lowercase.
-    storage_locationid = models.ForeignKey('TblLuStorageLocations', db_column='Storage_LocationID', blank=True, null=True)  # Field name made lowercase.
-    specimen_state = models.CharField(db_column='Specimen_State', max_length=50, blank=True, null=True)  # Field name made lowercase.
-    process_typeid = models.ForeignKey('TblLuProcessTypes', db_column='Process_TypeID', blank=True, null=True)  # Field name made lowercase.
-    reagentid = models.ForeignKey('TblLuReagents', db_column='ReagentID', blank=True, null=True)  # Field name made lowercase.
-    adfg_permit = models.CharField(db_column='ADFG_Permit', max_length=25, blank=True, null=True)  # Field name made lowercase.
-    link_to_datasheets = models.CharField(db_column='Link_To_Datasheets', max_length=255, blank=True, null=True)  # Field name made lowercase.
-    flawid = models.ForeignKey('TblLuRecordFlaws', db_column='FlawID', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_Collections'
-        unique_together = (('ProjectID', 'Study_LocationID', 'Collection_TypeID', 'Collection_Start_Date', 'Collection_End_Date', 'Collection_MethodID'),)
-
-
 class TblComments(models.Model):
     record_typeid = models.ForeignKey('TblLuRecordTypes', db_column='Record_TypeID')  # Field name made lowercase.
     foreign_key = models.AutoField(db_column='Foreign_Key')  # Field name made lowercase.
@@ -240,22 +215,6 @@ class TblHashCollectionSpecies(models.Model):
         unique_together = (('CollectionID', 'SpeciesID'),)
 
 
-class TblHashCollectionTraps(models.Model):
-    colltrapid = models.AutoField(db_column='CollTrapID', primary_key=True)  # Field name made lowercase.
-    collectionid = models.ForeignKey(TblCollections, db_column='CollectionID')  # Field name made lowercase.
-    number_of_traps = models.IntegerField(db_column='Number_Of_Traps')  # Field name made lowercase.
-    date_opened = models.DateField(db_column='Date_Opened')  # Field name made lowercase.
-    time_opened = models.TimeField(db_column='Time_Opened')  # Field name made lowercase.
-    date_closed = models.DateField(db_column='Date_Closed')  # Field name made lowercase.
-    time_closed = models.TimeField(db_column='Time_Closed')  # Field name made lowercase.
-    reference = models.CharField(db_column='Reference', max_length=255, blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_HASH_Collection_Traps'
-        unique_together = (('CollectionID', 'Date_Opened', 'Time_Opened', 'Date_Closed', 'Time_Closed'),)
-
-
 class TblHashPeopleSets(models.Model):
     peoplesetid = models.AutoField(db_column='PeopleSetID', primary_key=True)  # Field name made lowercase.
     record_typeid = models.ForeignKey('TblLuRecordTypes', db_column='Record_TypeID')  # Field name made lowercase.
@@ -318,31 +277,6 @@ class TblLuBioMolecules(models.Model):
         unique_together = (('BioMolecule', 'BioMolecule_Code'),)
 
 
-class TblLuCollectionMethods(models.Model):
-    collection_methodid = models.AutoField(db_column='Collection_MethodID', primary_key=True)  # Field name made lowercase.
-    collection_method = models.CharField(db_column='Collection_Method', max_length=100)  # Field name made lowercase.
-    collection_method_code = models.CharField(db_column='Collection_Method_Code', max_length=10, blank=True, null=True)  # Field name made lowercase.
-    collection_method_class = models.CharField(db_column='Collection_Method_Class', max_length=50, blank=True, null=True)  # Field name made lowercase.
-    sort_order = models.IntegerField(db_column='Sort_Order', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_LU_Collection_Methods'
-        unique_together = (('Collection_Method', 'Collection_Method_Code'),)
-
-
-class TblLuCollectionTypes(models.Model):
-    collection_typeid = models.AutoField(db_column='Collection_TypeID', primary_key=True)  # Field name made lowercase.
-    collection_type = models.CharField(db_column='Collection_Type', max_length=100)  # Field name made lowercase.
-    collection_type_code = models.CharField(db_column='Collection_Type_Code', max_length=10, blank=True, null=True)  # Field name made lowercase.
-    sort_order = models.IntegerField(db_column='Sort_Order', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_LU_Collection_Types'
-        unique_together = (('Collection_Type', 'Collection_Type_Code'),)
-
-
 class TblLuCommentTypes(models.Model):
     comment_typeid = models.AutoField(db_column='Comment_TypeID', primary_key=True)  # Field name made lowercase.
     comment_type = models.CharField(db_column='Comment_Type', max_length=100)  # Field name made lowercase.
@@ -399,45 +333,6 @@ class TblLuPeople(models.Model):
         unique_together = (('First_Name', 'Middle_Initial', 'Last_Name'),)
 
 
-class TblLuProcessTypes(models.Model):
-    process_typeid = models.AutoField(db_column='Process_TypeID', primary_key=True)  # Field name made lowercase.
-    process_type = models.CharField(db_column='Process_Type', max_length=100)  # Field name made lowercase.
-    process_type_code = models.CharField(db_column='Process_Type_Code', max_length=10, blank=True, null=True)  # Field name made lowercase.
-    ptype_short_description = models.CharField(db_column='PType_Short_Description', max_length=255, blank=True, null=True)  # Field name made lowercase.
-    sort_order = models.IntegerField(db_column='Sort_Order', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_LU_Process_Types'
-        unique_together = (('Process_Type', 'Process_Type_Code'),)
-
-
-class TblLuReagents(models.Model):
-    reagentid = models.AutoField(db_column='ReagentID', primary_key=True)  # Field name made lowercase.
-    reagent = models.CharField(db_column='Reagent', max_length=100)  # Field name made lowercase.
-    reagent_code = models.CharField(db_column='Reagent_Code', max_length=10, blank=True, null=True)  # Field name made lowercase.
-    reagent_class = models.CharField(db_column='Reagent_Class', max_length=50, blank=True, null=True)  # Field name made lowercase.
-    sort_order = models.IntegerField(db_column='Sort_Order', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_LU_Reagents'
-        unique_together = (('Reagent', 'Reagent_Code'),)
-
-
-class TblLuRecordFlaws(models.Model):
-    flawid = models.AutoField(db_column='FlawID', primary_key=True)  # Field name made lowercase.
-    record_typeid = models.ForeignKey('TblLuRecordTypes', db_column='Record_TypeID')  # Field name made lowercase.
-    flaw = models.CharField(db_column='Flaw', max_length=200)  # Field name made lowercase.
-    flaw_short_description = models.CharField(db_column='Flaw_Short_Description', max_length=255, blank=True, null=True)  # Field name made lowercase.
-    sort_order = models.IntegerField(db_column='Sort_Order', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_LU_Record_Flaws'
-        unique_together = (('Record_TypeID', 'Flaw'),)
-
-
 class TblLuRecordTypes(models.Model):
     record_typeid = models.AutoField(db_column='Record_TypeID', primary_key=True)  # Field name made lowercase.
     record_type = models.CharField(db_column='Record_Type', unique=True, max_length=50)  # Field name made lowercase.
@@ -461,20 +356,6 @@ class TblLuSampleTypes(models.Model):
         unique_together = (('Sample_Type', 'Sample_Type_Code'),)
 
 
-class TblLuSpecies(models.Model):
-    speciesid = models.AutoField(db_column='SpeciesID', primary_key=True)  # Field name made lowercase.
-    common_name = models.CharField(db_column='Common_Name', max_length=100)  # Field name made lowercase.
-    genus = models.CharField(db_column='Genus', max_length=50, blank=True, null=True)  # Field name made lowercase.
-    species = models.CharField(db_column='Species', max_length=50, blank=True, null=True)  # Field name made lowercase.
-    parasite = models.BooleanField(db_column='Parasite')  # Field name made lowercase.
-    sort_order = models.IntegerField(db_column='Sort_Order', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_LU_Species'
-        unique_together = (('Common_Name', 'Species'),)
-
-
 class TblLuTreatmentTypes(models.Model):
     treatment_typeid = models.AutoField(db_column='Treatment_TypeID', primary_key=True)  # Field name made lowercase.
     experimentid = models.ForeignKey(TblLuExperiments, db_column='ExperimentID', blank=True, null=True)  # Field name made lowercase.
@@ -506,25 +387,6 @@ class TblLuUsers(models.Model):
         db_table = 'tbl_LU_Users'
 
 
-class TblProcessing(models.Model):
-    processid = models.AutoField(db_column='ProcessID', primary_key=True)  # Field name made lowercase.
-    process_typeid = models.ForeignKey(TblLuProcessTypes, db_column='Process_TypeID')  # Field name made lowercase.
-    containerid = models.ForeignKey(TblLuContainers, db_column='ContainerID')  # Field name made lowercase.
-    container_label = models.CharField(db_column='Container_Label', max_length=50)  # Field name made lowercase.
-    process_date = models.DateField(db_column='Process_Date', blank=True, null=True)  # Field name made lowercase.
-    process_time = models.TimeField(db_column='Process_Time', blank=True, null=True)  # Field name made lowercase.
-    reagentid = models.ForeignKey(TblLuReagents, db_column='ReagentID', blank=True, null=True)  # Field name made lowercase.
-    reagent_volume = models.FloatField(db_column='Reagent_Volume', blank=True, null=True)  # Field name made lowercase.
-    measurement_unitid = models.ForeignKey(TblLuMeasurementUnits, db_column='Measurement_UnitID', blank=True, null=True)  # Field name made lowercase.
-    time_in_reagent = models.CharField(db_column='Time_in_Reagent', max_length=10, blank=True, null=True)  # Field name made lowercase.
-    flawid = models.ForeignKey(TblLuRecordFlaws, db_column='FlawID', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_Processing'
-        unique_together = (('Process_TypeID', 'ContainerID', 'Container_Label', 'Process_Date', 'Process_Time', 'ReagentID'),)
-
-
 class TblSamples(models.Model):
     trrepid = models.ForeignKey('TblTreatmentReplicates', db_column='TrRepID')  # Field name made lowercase.
     sampleid = models.AutoField(db_column='SampleID', primary_key=True)  # Field name made lowercase.