Processing

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/utils/management/commands/import_data.py

@@ -13,6 +13,7 @@ from ccdb.misc.models import MeasurementUnit, MeasurementType, Container, \
 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
 
 
 class Command(BaseCommand):
@@ -24,7 +25,7 @@ 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')
 
 
@@ -44,7 +45,7 @@ def _fetch_data(url, write):
                     out_file.write(chunk)
 
 
-def _import_data():
+def _import_admin_data():
     c = setup_sqlite()
     if c:
         # Projects
@@ -126,7 +127,7 @@ 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()
 
@@ -158,3 +159,15 @@ def _import_data():
             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;'):
+            r = Reagent(id=r[0], name=r[1], code=r[2], reagent_class=r[3],
+                sort_order=r[4])
+            r.save()

config/settings/base.py

@@ -44,6 +44,7 @@ LOCAL_APPS = (
     '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.
@@ -399,45 +374,6 @@ 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.
@@ -492,25 +428,6 @@ 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.