Finish up collections admin

ccdb/collections_ccdb/__init__.py

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

ccdb/collections_ccdb/admin.py

@@ -1,3 +1,60 @@
 from django.contrib import admin
 
-# Register your models here.
+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

@@ -3,27 +3,103 @@ from django.db import models
 from autoslug import AutoSlugField
 
 
-# class Collection(models.Model):
+class CollectionType(models.Model):
-#     project = models.ForeignKey('projects.Project')
+    name = models.CharField(max_length=100)
-#     study_location = models.ForeignKey('locations.StudyLocation')
+    code = models.CharField(max_length=10, blank=True)
-#     collection_type = models.ForeignKey(CollectionType)
+    sort_order = models.IntegerField(blank=True, null=True)
-#     collection_method = models.ForeignKey(CollectionMethod)
+    slug = AutoSlugField(populate_from='name')
-#     number_of_traps = models.IntegerField(blank=True, null=True)
+
-#     collection_start_date = models.DateField(blank=True, null=True)
+    def __str__(self):
-#     collection_start_time = models.TimeField(blank=True, null=True)
+        return self.name
-#     collection_end_date = models.DateField(blank=True, null=True)
+
-#     collection_end_time = models.TimeField(blank=True, null=True)
+    class Meta:
-#     storage_location = models.ForeignKey('locations.StorageLocation', blank=True, null=True)
+        unique_together = ('name', 'code')
-#     specimen_state = models.CharField(max_length=50, blank=True)
+        ordering = ['sort_order']
-#     process_type = models.ForeignKey('processing.ProcessType', blank=True, null=True)
+
-#     reagent = models.ForeignKey('processing.Reagent', blank=True, null=True)
+
-#     # adfg_permit = models.CharField(db_column='ADFG_Permit', max_length=25, blank=True, null=True)  # Field name made lowercase.
+class CollectionMethod(models.Model):
-#     # link_to_datasheets = models.CharField(db_column='Link_To_Datasheets', max_length=255, blank=True, null=True)  # Field name made lowercase.
+    name = models.CharField(max_length=100)
-#     flaw = models.ForeignKey(Flaw, blank=True, null=True)
+    code = models.CharField(max_length=10, blank=True)
-#
+    collection_method_class = models.CharField(max_length=50, blank=True)
-#     def __str__(self):
+    sort_order = models.IntegerField(blank=True, null=True)
-#         return "{project} {study_location} {collection_type} {collection_method}".format(**self)
+    slug = AutoSlugField(populate_from='name')
-#
+
-#     class Meta:
+    def __str__(self):
-#         unique_together = ('project', 'study_location', 'collection_type',
+        return self.name
-#             'collection_start_date', 'collection_end_date', 'collection_method')
+
+    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/utils/management/commands/import_data.py

@@ -14,6 +14,8 @@ 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):
@@ -168,6 +170,39 @@ def _import_admin_data():
 
         # Reagent
         for r in c.execute('SELECT * FROM tbl_lu_reagents;'):
-            r = Reagent(id=r[0], name=r[1], code=r[2], reagent_class=r[3],
+            rg = Reagent(id=r[0], name=r[1], code=r[2], reagent_class=r[3],
                 sort_order=r[4])
-            r.save()
+            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()

misc/existing.py

@@ -215,22 +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.
@@ -293,31 +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.