From 80e96ec81bc915a3e823a30d849e6bf0bf23c089 Mon Sep 17 00:00:00 2001 From: Matthew Dillon Date: Mon, 1 Feb 2016 13:31:32 -0700 Subject: [PATCH] Trap species and collection species --- ccdb/species/admin.py | 20 ++++++++++- ccdb/species/migrations/0002_trapspecies.py | 29 ++++++++++++++++ .../migrations/0003_collectionspecies.py | 33 +++++++++++++++++++ ccdb/species/models.py | 29 ++++++++++++++++ ccdb/utils/management/commands/import_data.py | 12 ++++++- misc/existing.py | 26 --------------- 6 files changed, 121 insertions(+), 28 deletions(-) create mode 100644 ccdb/species/migrations/0002_trapspecies.py create mode 100644 ccdb/species/migrations/0003_collectionspecies.py diff --git a/ccdb/species/admin.py b/ccdb/species/admin.py index ab1991a..71b3995 100644 --- a/ccdb/species/admin.py +++ b/ccdb/species/admin.py @@ -1,6 +1,6 @@ from django.contrib import admin -from .models import Species +from .models import Species, TrapSpecies, CollectionSpecies class SpeciesAdmin(admin.ModelAdmin): @@ -11,4 +11,22 @@ class SpeciesAdmin(admin.ModelAdmin): fields = ('common_name', 'genus', 'species', 'parasite', 'sort_order') +class TrapSpeciesAdmin(admin.ModelAdmin): + list_display = ('collection_trap', 'species', 'sex', 'count', 'count_estimated') + list_display_links = ('count',) + search_fields = ('collection_trap', 'species', 'sex', 'count', 'count_estimated') + list_per_page = 25 + fields = ('collection_trap', 'species', 'sex', 'count', 'count_estimated') + + +class CollectionSpeciesAdmin(admin.ModelAdmin): + list_display = ('collection', 'species', 'sex', 'count', 'count_estimated') + list_display_links = ('count',) + search_fields = ('collection', 'species', 'sex', 'count', 'count_estimated') + list_per_page = 25 + fields = ('collection', 'species', 'sex', 'count', 'count_estimated') + + admin.site.register(Species, SpeciesAdmin) +admin.site.register(TrapSpecies, TrapSpeciesAdmin) +admin.site.register(CollectionSpecies, CollectionSpeciesAdmin) diff --git a/ccdb/species/migrations/0002_trapspecies.py b/ccdb/species/migrations/0002_trapspecies.py new file mode 100644 index 0000000..b181c95 --- /dev/null +++ b/ccdb/species/migrations/0002_trapspecies.py @@ -0,0 +1,29 @@ +# -*- coding: utf-8 -*- +from __future__ import unicode_literals + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('collections_ccdb', '0001_initial'), + ('species', '0001_initial'), + ] + + operations = [ + migrations.CreateModel( + name='TrapSpecies', + fields=[ + ('id', models.AutoField(auto_created=True, verbose_name='ID', primary_key=True, serialize=False)), + ('sex', models.CharField(blank=True, max_length=25)), + ('count', models.IntegerField(blank=True, null=True)), + ('count_estimated', models.BooleanField(default=False)), + ('collection_trap', models.ForeignKey(to='collections_ccdb.CollectionTrap')), + ('species', models.ForeignKey(to='species.Species')), + ], + options={ + 'verbose_name_plural': 'trap-species', + }, + ), + ] diff --git a/ccdb/species/migrations/0003_collectionspecies.py b/ccdb/species/migrations/0003_collectionspecies.py new file mode 100644 index 0000000..09145a5 --- /dev/null +++ b/ccdb/species/migrations/0003_collectionspecies.py @@ -0,0 +1,33 @@ +# -*- coding: utf-8 -*- +from __future__ import unicode_literals + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('collections_ccdb', '0001_initial'), + ('species', '0002_trapspecies'), + ] + + operations = [ + migrations.CreateModel( + name='CollectionSpecies', + fields=[ + ('id', models.AutoField(verbose_name='ID', primary_key=True, auto_created=True, serialize=False)), + ('sex', models.CharField(blank=True, max_length=25)), + ('count', models.IntegerField(null=True, blank=True)), + ('count_estimated', models.BooleanField(default=False)), + ('collection', models.ForeignKey(to='collections_ccdb.Collection')), + ('species', models.ForeignKey(to='species.Species')), + ], + options={ + 'verbose_name_plural': 'collection-species', + }, + ), + migrations.AlterUniqueTogether( + name='collectionspecies', + unique_together=set([('collection', 'species')]), + ), + ] diff --git a/ccdb/species/models.py b/ccdb/species/models.py index 60a9820..dc76629 100644 --- a/ccdb/species/models.py +++ b/ccdb/species/models.py @@ -18,3 +18,32 @@ class Species(models.Model): unique_together = ('common_name', 'species') ordering = ['sort_order'] verbose_name_plural = 'species' + + +class TrapSpecies(models.Model): + collection_trap = models.ForeignKey('collections_ccdb.CollectionTrap') + species = models.ForeignKey(Species) + sex = models.CharField(max_length=25, blank=True) + count = models.IntegerField(blank=True, null=True) + count_estimated = models.BooleanField(default=False) + + def __str__(self): + return "{} {}".format(self.collection_trap, self.species) + + class Meta: + verbose_name_plural = 'trap-species' + + +class CollectionSpecies(models.Model): + collection = models.ForeignKey('collections_ccdb.Collection') + species = models.ForeignKey(Species) + sex = models.CharField(max_length=25, blank=True) + count = models.IntegerField(blank=True, null=True) + count_estimated = models.BooleanField(default=False) + + def __str__(self): + return "{} {}".format(self.collection, self.species) + + class Meta: + unique_together = ('collection', 'species') + verbose_name_plural = 'collection-species' diff --git a/ccdb/utils/management/commands/import_data.py b/ccdb/utils/management/commands/import_data.py index f93773d..b2385d0 100644 --- a/ccdb/utils/management/commands/import_data.py +++ b/ccdb/utils/management/commands/import_data.py @@ -12,7 +12,7 @@ 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.species.models import Species, CollectionSpecies from ccdb.processing.models import ProcessType, Reagent, Flaw, Processing from ccdb.collections_ccdb.models import CollectionType, CollectionMethod, \ Flaw, ADFGPermit, Collection @@ -206,3 +206,13 @@ def _import_admin_data(): specimen_state=r[11], process_type_id=r[12], reagent_id=r[13], adfg_permit=permit) col.save() + + # Collection Species + for r in c.execute('SELECT * FROM tbl_hash_collection_species;'): + # No PK field in Andre's file + cs = CollectionSpecies(collection_id=r[0], species_id=r[1], + sex=r[2], count=r[3], count_estimated=r[4]) + try: + cs.save() + except IntegrityError: + pass diff --git a/misc/existing.py b/misc/existing.py index 2d2af04..66cebb7 100644 --- a/misc/existing.py +++ b/misc/existing.py @@ -202,19 +202,6 @@ class TblHashCollectionExperiments(models.Model): unique_together = (('CollectionID', 'ExperimentID'),) -class TblHashCollectionSpecies(models.Model): - collectionid = models.ForeignKey(TblCollections, db_column='CollectionID') # Field name made lowercase. - speciesid = models.ForeignKey('TblLuSpecies', db_column='SpeciesID') # Field name made lowercase. - sex = models.CharField(db_column='Sex', max_length=25, blank=True, null=True) # Field name made lowercase. - count = models.IntegerField(db_column='Count', blank=True, null=True) # Field name made lowercase. - count_estimated = models.BooleanField(db_column='Count_Estimated') # Field name made lowercase. - - class Meta: - managed = False - db_table = 'tbl_HASH_Collection_Species' - unique_together = (('CollectionID', 'SpeciesID'),) - - 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. @@ -226,19 +213,6 @@ class TblHashPeopleSets(models.Model): db_table = 'tbl_HASH_People_Sets' -class TblHashTrapSpecies(models.Model): - trapspeciesid = models.AutoField(db_column='TrapSpeciesID', primary_key=True) # Field name made lowercase. - colltrapid = models.ForeignKey(TblHashCollectionTraps, db_column='CollTrapID') # Field name made lowercase. - speciesid = models.ForeignKey('TblLuSpecies', db_column='SpeciesID') # Field name made lowercase. - sex = models.CharField(db_column='Sex', max_length=25, blank=True, null=True) # Field name made lowercase. - count = models.IntegerField(db_column='Count', blank=True, null=True) # Field name made lowercase. - count_estimated = models.BooleanField(db_column='Count_Estimated') # Field name made lowercase. - - class Meta: - managed = False - db_table = 'tbl_HASH_Trap_Species' - - class TblLuAffiliations(models.Model): affiliationid = models.AutoField(db_column='AffiliationID', primary_key=True) # Field name made lowercase. affiliation = models.CharField(db_column='Affiliation', max_length=100) # Field name made lowercase.