Merge pull request #72 from carlosp420/dataset

only select needed values, not everything
VoSeq · Feb 2, 2015 · ef338ae · ef338ae
2 parents c0be86e + ef1288b
commit ef338ae
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Showing 7 changed files with 18 additions and 6 deletions.
diff --git a/test_db_dump.xml b/test_db_dump.xml
@@ -381,6 +381,7 @@
         <row>
             <field name="code">CP100-09</field>
             <field name="orden"></field>
+            <field name="superfamily">Papilionoidea</field>
             <field name="family">Nymphalidae</field>
             <field name="subfamily">Nymphalinae</field>
             <field name="tribe">NULL </field>
@@ -420,6 +421,7 @@
    	<row>
 		<field name="code">CP100-10</field>
 		<field name="orden">NULL</field>
+        <field name="superfamily">Papilionoidea</field>
 		<field name="family"></field>
 		<field name="subfamily"></field>
 		<field name="tribe">Melitaeini</field>

diff --git a/voseq/create_dataset/forms.py b/voseq/create_dataset/forms.py
@@ -86,6 +86,7 @@ class CreateDatasetForm(BaseDatasetForm):
         choices=[
             ('CODE', 'Code'),
             ('ORDER', 'Order'),
+            ('SUPERFAMILY', 'Superfamily'),
             ('FAMILY', 'Family'),
             ('SUBFAMILY', 'Subfamily'),
             ('TRIBE', 'Tribe'),

diff --git a/voseq/create_dataset/tests/tests_utils.py b/voseq/create_dataset/tests/tests_utils.py
@@ -20,7 +20,7 @@ def setUp(self):
             'taxonset': None,
             'voucher_codes': 'CP100-10\r\nCP100-11',
             'geneset': None,
-            'taxon_names': ['CODE', 'GENUS', 'SPECIES']
+            'taxon_names': ['CODE', 'SUPERFAMILY', 'GENUS', 'SPECIES']
         }
 
         self.c = Client()
@@ -33,8 +33,8 @@ def test_create_dataset(self):
 
     def test_get_taxon_names_for_taxa(self):
         expected = [
-            {'code': 'CP100-10', 'genus': 'Melitaea', 'species': 'diamina'},
-            {'code': 'CP100-11', 'genus': 'Melitaea', 'species': 'diamina'},
+            {'code': 'CP100-10', 'genus': 'Melitaea', 'species': 'diamina', 'superfamily': 'Papilionoidea'},
+            {'code': 'CP100-11', 'genus': 'Melitaea', 'species': 'diamina', 'superfamily': ''},
         ]
         result = self.dataset_creator.get_taxon_names_for_taxa()
 

diff --git a/voseq/create_dataset/utils.py b/voseq/create_dataset/utils.py
@@ -102,7 +102,10 @@ def get_taxon_names_for_taxa(self):
         vouchers_with_taxon_names = []
         append = vouchers_with_taxon_names.append
 
-        all_vouchers = Vouchers.objects.all().order_by('code').values()
+        all_vouchers = Vouchers.objects.all().order_by('code').values('code', 'orden', 'superfamily',
+                                                                      'family', 'subfamily', 'tribe',
+                                                                      'subtribe', 'genus', 'species',
+                                                                      'subspecies', 'auctor', 'hostorg',)
         for voucher in all_vouchers:
             code = voucher['code'].lower()
             if code in self.voucher_codes:

diff --git a/voseq/public_interface/management/commands/_migrate_db.py b/voseq/public_interface/management/commands/_migrate_db.py
@@ -25,7 +25,7 @@
 
 TZINFO = pytz.utc
 
-if settings.TESTING:
+if settings.TESTING is True:
     TESTING = True
 else:
     TESTING = False
@@ -429,6 +429,10 @@ def parse_table_vouchers(self, xml_string):
             item = dict()
             item['code'] = row.find("./field/[@name='code']").text
             item['orden'] = row.find("./field/[@name='orden']").text
+            try:
+                item['superfamily'] = row.find("./field/[@name='superfamily']").text
+            except AttributeError:
+                item['superfamily'] = ''
             item['family'] = row.find("./field/[@name='family']").text
             item['subfamily'] = row.find("./field/[@name='subfamily']").text
             item['tribe'] = row.find("./field/[@name='tribe']").text

diff --git a/voseq/public_interface/tests/test_migrate_db.py b/voseq/public_interface/tests/test_migrate_db.py
@@ -39,7 +39,7 @@ def test_orden_space(self):
 
     def test_superfamily(self):
         b = Vouchers.objects.get(code='CP100-10')
-        self.assertEqual('', b.superfamily)
+        self.assertEqual('Papilionoidea', b.superfamily)
 
     def test_family(self):
         b = Vouchers.objects.get(code='CP100-09')

diff --git a/voseq/voseq/settings/base.py b/voseq/voseq/settings/base.py
@@ -112,3 +112,5 @@
 
 # This VoSeq version
 VERSION = '2.0.0'
+
+TESTING = False