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Merge pull request #55 from carlosp420/create_dataset
"Create dataset" tool
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from django import forms | ||
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from public_interface.models import Genes | ||
from public_interface.models import GeneSets | ||
from public_interface.models import TaxonSets | ||
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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, | ||
) | ||
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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") | ||
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geneset = cleaned_data.get("geneset") | ||
gene_codes = cleaned_data.get("gene_codes") | ||
print(gene_codes) | ||
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if taxonset is None and voucher_codes.strip() == '': | ||
raise forms.ValidationError("You need to enter at least some " | ||
"voucher codes or select a taxonset.") | ||
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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.") |
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from django.contrib import admin | ||
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# Register your models here. |
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from django import forms | ||
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from core.forms import BaseDatasetForm | ||
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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', | ||
) | ||
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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, | ||
) | ||
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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, | ||
) | ||
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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, | ||
) | ||
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translations = forms.BooleanField( | ||
label='Degen(erated)', | ||
widget=forms.CheckboxInput(), | ||
required=False, | ||
) | ||
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aminoacids = forms.BooleanField( | ||
label='Amino acids', | ||
widget=forms.CheckboxInput(), | ||
required=False, | ||
) | ||
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degen_translations = forms.ChoiceField( | ||
label='Degenerated translations)', | ||
choices=[ | ||
('NORMAL', 'normal'), | ||
('S', 'S'), | ||
('Z', 'Z'), | ||
('SZ', 'SZ'), | ||
], | ||
widget=forms.RadioSelect(), | ||
initial='NORMAL', | ||
required=True, | ||
) | ||
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special = forms.BooleanField( | ||
label='Special', | ||
widget=forms.CheckboxInput(), | ||
required=False, | ||
) | ||
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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', | ||
) | ||
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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, | ||
) | ||
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number_genes = forms.IntegerField( | ||
label='Minimum number of genes', | ||
required=False, | ||
) | ||
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introns = forms.ChoiceField( | ||
choices=[ | ||
('YES', 'yes'), | ||
('NO', 'no'), | ||
], | ||
widget=forms.RadioSelect(), | ||
initial='YES', | ||
required=True, | ||
help_text='Ignore introns?', | ||
) |
Empty file.
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from django.db import models | ||
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# Create your models here. |
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