Merge pull request #55 from carlosp420/create_dataset

"Create dataset" tool

Makefile

@@ -1,5 +1,5 @@
 help:
-	@echo "serve - remove build artifacts"
+	@echo "serve - runserver for development"
 	@echo "test - use testing settings and SQlite3 database"
 
 serve: index stats
@@ -16,7 +16,7 @@ import:
 	python voseq/manage.py migrate_db --dumpfile=test_db_dump.xml --settings=voseq.settings.local
 
 index:
-	python voseq/manage.py rebuild_index
+	python voseq/manage.py rebuild_index --settings=voseq.settings.local
 
 stats:
 	python voseq/manage.py create_stats --settings=voseq.settings.local

voseq/core/forms.py

@@ -0,0 +1,49 @@
+from django import forms
+
+from public_interface.models import Genes
+from public_interface.models import GeneSets
+from public_interface.models import TaxonSets
+
+
+class BaseDatasetForm(forms.Form):
+    taxonset = forms.ModelChoiceField(
+        TaxonSets.objects.all(),
+        label='Choose taxonset',
+        required=False,
+        empty_label='Choose taxonset',
+    )
+    geneset = forms.ModelChoiceField(
+        GeneSets.objects.all(),
+        label='Choose geneset',
+        required=False,
+        empty_label='Choose geneset',
+    )
+    gene_codes = forms.ModelMultipleChoiceField(
+        Genes.objects.all(),
+        label='Check to select your alignment/gene',
+        required=False,
+        widget=forms.CheckboxSelectMultiple(),
+    )
+    voucher_codes = forms.CharField(
+        widget=forms.Textarea,
+        label='... and/or a list of voucher codes',
+        required=False,
+    )
+
+    def clean(self):
+        """Overwriting validator method of class form."""
+        cleaned_data = super(BaseDatasetForm, self).clean()
+        taxonset = cleaned_data.get("taxonset")
+        voucher_codes = cleaned_data.get("voucher_codes")
+
+        geneset = cleaned_data.get("geneset")
+        gene_codes = cleaned_data.get("gene_codes")
+        print(gene_codes)
+
+        if taxonset is None and voucher_codes.strip() == '':
+            raise forms.ValidationError("You need to enter at least some "
+                                        "voucher codes or select a taxonset.")
+
+        if geneset is None and len(gene_codes) < 1:
+            raise forms.ValidationError("You need to enter at least some "
+                                        "gene codes or select a geneset.")

voseq/create_dataset/admin.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

voseq/create_dataset/forms.py

@@ -0,0 +1,132 @@
+from django import forms
+
+from core.forms import BaseDatasetForm
+
+
+class CreateDatasetForm(BaseDatasetForm):
+    file_format = forms.ChoiceField(
+        label='Choose file format',
+        choices=[
+            ('TNT', 'TNT format'),
+            ('NEXUS', 'NEXUS format'),
+            ('PHY', 'PHYLIP format'),
+            ('FASTA', 'Unaligned FASTA format'),
+        ],
+        widget=forms.RadioSelect(),
+        required=True,
+        initial='FASTA',
+    )
+
+    outgroup = forms.CharField(
+        label='Outgroup (code, for NEXUS and TNT)',
+        help_text='Voucher code for using that specimen\'s sequence as '
+                  'outgroup in NEXUS and TNT datasets.',
+        required=False,
+    )
+
+    positions = forms.ChoiceField(
+        label='Positions',
+        help_text='codon positions',
+        choices=[
+            ('ALL', 'all'),
+            ('1st', '1st'),
+            ('2nd', '2nd'),
+            ('3rd', '3rd'),
+        ],
+        widget=forms.RadioSelect(),
+        initial='ALL',
+        required=True,
+    )
+
+    partition_by_positions = forms.ChoiceField(
+        label='Partition by positions',
+        choices=[
+            ('ONE', 'as one'),
+            ('EACH', 'each'),
+            ('1st-3rd', '1st-2nd, 3rd'),
+        ],
+        widget=forms.RadioSelect(),
+        initial='ONE',
+        required=True,
+    )
+
+    translations = forms.BooleanField(
+        label='Degen(erated)',
+        widget=forms.CheckboxInput(),
+        required=False,
+    )
+
+    aminoacids = forms.BooleanField(
+        label='Amino acids',
+        widget=forms.CheckboxInput(),
+        required=False,
+    )
+
+    degen_translations = forms.ChoiceField(
+        label='Degenerated translations)',
+        choices=[
+            ('NORMAL', 'normal'),
+            ('S', 'S'),
+            ('Z', 'Z'),
+            ('SZ', 'SZ'),
+        ],
+        widget=forms.RadioSelect(),
+        initial='NORMAL',
+        required=True,
+    )
+
+    special = forms.BooleanField(
+        label='Special',
+        widget=forms.CheckboxInput(),
+        required=False,
+    )
+
+    taxon_names = forms.MultipleChoiceField(
+        label='What info do you want in the taxon names?',
+        choices=[
+            ('CODE', 'Code'),
+            ('ORDER', 'Order'),
+            ('FAMILY', 'Family'),
+            ('SUBFAMILY', 'Subfamily'),
+            ('TRIBE', 'Tribe'),
+            ('SUBTRIBE', 'Subtribe'),
+            ('GENUS', 'Genus'),
+            ('SPECIES', 'Species'),
+            ('SUBSPECIES', 'Subspecies'),
+            ('AUCTOR', 'Auctor'),
+            ('HOSTORG', 'Host org.'),
+            ('GENECODE', 'Gene code'),
+        ],
+        widget=forms.CheckboxSelectMultiple(),
+        initial=['CODE', 'GENUS', 'SPECIES'],
+        required=False,
+        help_text='If taxon_names is None, use standart code_genus_species',
+    )
+
+    exclude = forms.ChoiceField(
+        help_text='If dataset is for single gene, exclude taxa missing this gene? '
+                  'Otherwise include taxon with ? as sequences.',
+        choices=[
+            ('YES', 'yes'),
+            ('NO', 'no'),
+        ],
+        widget=forms.RadioSelect(),
+        initial='YES',
+        required=True,
+    )
+
+    number_genes = forms.IntegerField(
+        label='Minimum number of genes',
+        required=False,
+    )
+
+    introns = forms.ChoiceField(
+        choices=[
+            ('YES', 'yes'),
+            ('NO', 'no'),
+        ],
+        widget=forms.RadioSelect(),
+        initial='YES',
+        required=True,
+        help_text='Ignore introns?',
+    )

voseq/create_dataset/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.