Merge pull request #62 from carlosp420/dataset_form_inheritance

Dataset form inheritance, docs and setup.py

.gitignore

@@ -9,6 +9,12 @@ config.json
 *bak
 *.fasta
 
+# package builds
+VoSeq.egg-info
+build
+dist
+voseq.egg-info
+
 # coverage
 .coverage
 voseq/htmlcov

AUTHORS.rst

@@ -6,7 +6,8 @@ Development Lead
 ----------------
 
 * Carlos Peña <mycalesis@gmail.com>
-* Victor Solis <<vm_solism@yahoo.es>
+* Tobias Malm <tobemalm@gmail.com>
+* Victor Solis <vm_solism@yahoo.es>
 
 Contributors
 ------------

requirements/base.txt

@@ -1 +1,2 @@
 Django==1.7.3
+biopython==1.65

requirements/testing.txt

@@ -10,5 +10,5 @@ django-haystack==2.3.1
 elasticsearch==1.2.0
 coveralls==0.5
 django-debug-toolbar==1.2.2
-biopython==1.65
 pytz==2014.10
+Sphinx==1.2.3

setup.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+import voseq
+
+version = voseq.__version__
+
+setup(
+    name='VoSeq',
+    version=version,
+    author='Carlos Pena, Tobias Malm, Victor Mezarino',
+    author_email='carlosp420@gmail.com',
+    packages=[
+        'voseq',
+    ],
+    include_package_data=True,
+    install_requires=[
+        'Django==1.7.3',
+    ],
+    zip_safe=False,
+    scripts=['voseq/manage.py'],
+)

voseq/core/forms.py

@@ -6,6 +6,14 @@
 
 
 class BaseDatasetForm(forms.Form):
+    """Base class for datasets.
+
+    * Handles list of voucher codes including those from taxonsets.
+    * Handles list of gene codes including those from genesets.
+
+    Other dataset classes should inherit from this one.
+
+    """
     taxonset = forms.ModelChoiceField(
         TaxonSets.objects.all(),
         label='Choose taxonset',
@@ -31,7 +39,15 @@ class BaseDatasetForm(forms.Form):
     )
 
     def clean(self):
-        """Overwriting validator method of class form."""
+        """Overwriting validator method of class form.
+
+        Drops vouchers if their codes have been flagged by users with two
+            consecutive dashes ``--``.
+
+        Returns:
+            Sets of voucher and genes codes.
+
+        """
         cleaned_data = super(BaseDatasetForm, self).clean()
         taxonset = cleaned_data.get("taxonset")
         voucher_codes = cleaned_data.get("voucher_codes")

voseq/genbank_fasta/forms.py

@@ -1,49 +1,6 @@
-from django import forms
+from core.forms import BaseDatasetForm
 
-from public_interface.models import Genes
-from public_interface.models import GeneSets
-from public_interface.models import TaxonSets
 
-
-class GenBankFastaForm(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(GenBankFastaForm, 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.")
+class GenBankFastaForm(BaseDatasetForm):
+    """The methods needed by this class are very basic."""
+    pass