autopep8 code

Former-commit-id: e4a2b89495247a4954b8046c445d85df5888f0b5

ippisite/ippidb/admin.py

@@ -2,44 +2,56 @@ from django.contrib import admin
 from .models import *
 from django.apps import apps
 
+
 @admin.register(Bibliography)
 class BibliographyAdmin(admin.ModelAdmin):
-    list_display = ('authors_list', 'title', 'journal_name', 'biblio_year', 'id_source')
+    list_display = ('authors_list', 'title',
+                    'journal_name', 'biblio_year', 'id_source')
+
 
 @admin.register(Protein)
 class ProteinAdmin(admin.ModelAdmin):
     list_display = ('uniprot_id', 'recommended_name_long')
 
+
 @admin.register(Taxonomy)
 class TaxonomyAdmin(admin.ModelAdmin):
     list_display = ('taxonomy_id', 'name')
 
+
 @admin.register(Domain)
 class DomainAdmin(admin.ModelAdmin):
     list_display = ('pfam_acc', 'pfam_id', 'pfam_description', 'domain_family')
 
+
 @admin.register(ProteinDomainBoundComplex)
 class ProteinDomainBoundComplexAdmin(admin.ModelAdmin):
     list_display = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p')
-    list_display_links = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p')
+    list_display_links = (
+        'protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p')
+
 
 @admin.register(ProteinDomainPartnerComplex)
 class ProteinDomainPartnerComplexAdmin(admin.ModelAdmin):
     list_display = ('protein', 'domain', 'ppc_copy_nb')
     list_display_links = ('protein', 'domain', 'ppc_copy_nb')
 
+
 @admin.register(Symmetry)
 class Symmetry(admin.ModelAdmin):
     list_display = ('code', 'description')
 
+
 @admin.register(MDDRCompoundImport)
 class MDDRCompoundImport(admin.ModelAdmin):
     list_display = ('mddr_name', 'dvpmt_phase', 'canonical_smile')
 
+
 @admin.register(Compound)
 class Compound(admin.ModelAdmin):
     list_display = ('iupac_name', 'common_name', 'canonical_smile')
 
+
 @admin.register(TestActivityDescription)
 class TextActivityDescription(admin.ModelAdmin):
     list_display = ('test_name', 'test_type', 'test_modulation_type')
@@ -57,5 +69,3 @@ admin.site.site_title = admin.site.site_header
 admin.site.index_header = 'iPPI-DB administration'
 
 admin.site.index_title = admin.site.index_header
-
-

ippisite/ippidb/forms.py

-from django.forms import ModelForm,modelformset_factory,formset_factory
+from django.forms import ModelForm, modelformset_factory, formset_factory
 from django import forms
 from django.db import models
 from django.core.exceptions import ValidationError
@@ -7,84 +7,102 @@ from django.core.validators import RegexValidator
 from .models import Bibliography, Protein, ProteinDomainComplex, Ppi, PpiComplex
 from .ws import pdb_entry_exists
 
+
 class IdForm(ModelForm):
+
     class Meta:
         model = Bibliography
-        fields = ['source','id_source']
+        fields = ['source', 'id_source']
         widgets = {
-        	'source' : forms.RadioSelect,
+            'source': forms.RadioSelect,
             'id_source': forms.TextInput(attrs={'placeholder': 'ID'}),
         }
 
+
 class BibliographyForm(ModelForm):
+
     class Meta:
         model = Bibliography
         exclude = ['authors_list', 'biblio_year']
         widgets = {
-        	'source': forms.TextInput(attrs={'readonly':'readonly','class':'readonly'}),
-            'id_source': forms.TextInput(attrs={'readonly':'readonly', 'class':'readonly'}),
-            'title': forms.TextInput(attrs={'readonly':'readonly', 'class':'readonly'}),
-            'journal_name': forms.TextInput(attrs={'readonly':'readonly', 'class':'readonly'}),
+            'source': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
+            'id_source': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
+            'title': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
+            'journal_name': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
         }
 
+
 def validate_pdb_exists(value):
     if not(pdb_entry_exists(value)):
-        raise ValidationError('PDB entry not found: %(value)s', params={'value': value}, code='invalid')
+        raise ValidationError(
+            'PDB entry not found: %(value)s', params={'value': value}, code='invalid')
+
 
 class PDBForm(forms.Form):
-    pdb_id = forms.CharField(label="PDB ID",max_length=4, widget=forms.TextInput(attrs={'placeholder': 'e.g 4HHB', 'required':'required'}), required=True, validators=[
-                RegexValidator('^[0-9][a-zA-Z0-9]{3}$', message='PDB ID must be 1 numeric + 3 alphanumeric characters'),
+    pdb_id = forms.CharField(label="PDB ID", max_length=4, widget=forms.TextInput(attrs={'placeholder': 'e.g 4HHB', 'required': 'required'}), required=True, validators=[
+        RegexValidator(
+        '^[0-9][a-zA-Z0-9]{3}$', message='PDB ID must be 1 numeric + 3 alphanumeric characters'),
                 validate_pdb_exists
-             ])
+    ])
 
 PDBFormSet = formset_factory(PDBForm)
-formset=PDBFormSet()
+formset = PDBFormSet()
+
 
 class ProteinForm(ModelForm):
-	class Meta:
-		model = Protein
-		exclude = ['recommended_name_long', 'short_name']
-		widgets = {
-        	'uniprot_id' : forms.TextInput(attrs={'readonly':'readonly','class':'readonly'}),
-        	'gene_name' : forms.TextInput(attrs={'readonly':'readonly','class':'readonly'}),
-        	'entry_name' : forms.TextInput(attrs={'readonly':'readonly','class':'readonly'}),
-            'organism': forms.TextInput(attrs={'readonly':'readonly','class':'readonly'}),
+
+    class Meta:
+        model = Protein
+        exclude = ['recommended_name_long', 'short_name']
+        widgets = {
+            'uniprot_id': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
+            'gene_name': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
+            'entry_name': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
+            'organism': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
         }
 
-ProteinFormSet = modelformset_factory(Protein, exclude=('recommended_name_long', 'short_name'), extra=0)
+ProteinFormSet = modelformset_factory(
+    Protein, exclude=('recommended_name_long', 'short_name'), extra=0)
 
 TYPE_CHOICES = (
-	('Hetero2merAB','Inhib_Hetero 2-mer AB'),
-	('Homo2merA2','Inhib_Homo 2-mer A2'),
-	('custom', 'Inhib_Custom your own'),
-	('Hetero2merAB','Stab_Hetero 2-mer AB'),
-	('Homo2merA2','Stab_Homo 2-mer A2'),
-	('HomoLike2mer','Stab_Homo-Like 2-mer A2'),
-	('Homo3merA3','Stab_Homo 3-mer A3'),
-	('Homo3merA2','Stab_Homo 3-mer A3 inhibited A2-dimer'),
-	('Homo4merA4','Stab_Homo 4-mer A4'),
-	('RingHomo3mer','Stab_Ring-Like 3-mer A3'),
-	('RingHomo5mer','Stab_Ring-Like 5-mer A5'),
-	('custom', 'Stab_Custom your own'),
-	)
+    ('Hetero2merAB', 'Inhib_Hetero 2-mer AB'),
+        ('Homo2merA2', 'Inhib_Homo 2-mer A2'),
+        ('custom', 'Inhib_Custom your own'),
+        ('Hetero2merAB', 'Stab_Hetero 2-mer AB'),
+        ('Homo2merA2', 'Stab_Homo 2-mer A2'),
+        ('HomoLike2mer', 'Stab_Homo-Like 2-mer A2'),
+        ('Homo3merA3', 'Stab_Homo 3-mer A3'),
+        ('Homo3merA2', 'Stab_Homo 3-mer A3 inhibited A2-dimer'),
+        ('Homo4merA4', 'Stab_Homo 4-mer A4'),
+        ('RingHomo3mer', 'Stab_Ring-Like 3-mer A3'),
+        ('RingHomo5mer', 'Stab_Ring-Like 5-mer A5'),
+        ('custom', 'Stab_Custom your own'),
+)
+
 
 class ProteinDomainComplexTypeForm(forms.Form):
     complexType = forms.ChoiceField(
         widget=forms.RadioSelect,
         choices=TYPE_CHOICES,
-        )
+    )
+
 
 class ProteinDomainComplexForm(ModelForm):
-	class Meta:
-		model = ProteinDomainComplex
-		fields = ['protein', 'domain', 'ppc_copy_nb']
+
+    class Meta:
+        model = ProteinDomainComplex
+        fields = ['protein', 'domain', 'ppc_copy_nb']
+
 
 class PpiForm(ModelForm):
-	class Meta:
-		model = Ppi
-		fields = ['pdb_id', 'symmetry']
+
+    class Meta:
+        model = Ppi
+        fields = ['pdb_id', 'symmetry']
+
 
 class PpiComplexForm(ModelForm):
-	class Meta:
-		model = PpiComplex
-		fields = ['complex', 'cc_nb']
+
+    class Meta:
+        model = PpiComplex
+        fields = ['complex', 'cc_nb']

ippisite/ippidb/gx.py

@@ -2,14 +2,17 @@ from bioblend.galaxy import GalaxyInstance
 from bioblend.galaxy.tools.inputs import inputs
 
 workflow_id = 'dad6103ff71ca4fe'
-galaxy_url = 'https://galaxy-dev.web.pasteur.fr' 
+galaxy_url = 'https://galaxy-dev.web.pasteur.fr'
 api_key = '21c2ce387688b1a785040762f7c9c331'
 
+
 def run_workflow_and_get_results(input_file):
     gi = GalaxyInstance(galaxy_url, key=api_key)
     gi.verify = False
     history_id = gi.histories.create_history("ippidb_history")['id']
-    dataset_id = gi.tools.upload_file(input_file, history_id)['outputs'][0]['id']
-    inputs = {'0':{'id':dataset_id, 'src': 'hda' }}
-    workflow_run = gi.workflows.invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
-    print(workflow_run) 
+    dataset_id = gi.tools.upload_file(
+        input_file, history_id)['outputs'][0]['id']
+    inputs = {'0': {'id': dataset_id, 'src': 'hda'}}
+    workflow_run = gi.workflows.invoke_workflow(
+        workflow_id, inputs=inputs, history_id=history_id)
+    print(workflow_run)

ippisite/ippidb/urls.py

-from django.conf.urls import include,url
+from django.conf.urls import include, url
 from . import views
-from ippidb.forms import IdForm, BibliographyForm,PDBForm,ProteinDomainComplexTypeForm,ProteinDomainComplexForm,PpiForm
-from ippidb.views import IppiWizard,FORMS
+from ippidb.forms import IdForm, BibliographyForm, PDBForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm
+from ippidb.views import IppiWizard, FORMS
 
 ippidb_wizard = IppiWizard.as_view(FORMS,
-    url_name='ippidb_step')
+                                   url_name='ippidb_step')
 
 
 urlpatterns = [
@@ -12,14 +12,17 @@ urlpatterns = [
     url(r'^about$', views.about, name='about'),
      url(r'^about/general/$', views.general, name='general'),
     url(r'^about/pharmacology/$', views.pharmacology, name='pharmacology'),
-    url(r'^about/physicochemistry/$', views.physicochemistry, name='physicochemistry'),
-    url(r'^about/drug-candidate/$', views.drugCandidate, name='drug-candidate'),   
+    url(r'^about/physicochemistry/$',
+        views.physicochemistry, name='physicochemistry'),
+    url(r'^about/drug-candidate/$',
+        views.drugCandidate, name='drug-candidate'),
     url(r'^query$', views.query, name='query'),
     url(r'^query/pharma/$', views.pharma, name='pharma'),
     url(r'^query/chemical/$', views.chemical, name='chemical'),
     url(r'^tutorials$', views.tutorials, name='tutorials'),
-	url(r'^admin-session$', views.adminSession, name='admin-session'),
-    url(r'^admin-session/add/(?P<step>.+)/$', ippidb_wizard, name='ippidb_step'),
+        url(r'^admin-session$', views.adminSession, name='admin-session'),
+    url(r'^admin-session/add/(?P<step>.+)/$',
+        ippidb_wizard, name='ippidb_step'),
     url(r'^admin-session/add/$', ippidb_wizard, name='ippidb'),
 ]
 

ippisite/ippidb/views.py

@@ -2,50 +2,62 @@ import ippidb
 
 from django.shortcuts import render
 from django.http import HttpResponseRedirect
-from formtools.wizard.views import SessionWizardView,NamedUrlSessionWizardView
+from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
 
 from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, ProteinFormSet, PDBFormSet
 from .models import Protein, Bibliography
 from .ws import get_pdb_uniprot_mapping
 
+
 def index(request):
     return render(request, 'index.html')
 
+
 def about(request):
     return render(request, 'about.html')
 
+
 def general(request):
     return render(request, 'general.html')
 
+
 def pharmacology(request):
     return render(request, 'pharmacology.html')
 
+
 def physicochemistry(request):
     return render(request, 'physicochemistry.html')
 
+
 def drugCandidate(request):
     return render(request, 'drug-candidate.html')
 
+
 def query(request):
     return render(request, 'query.html')
 
+
 def pharma(request):
     return render(request, 'pharma.html')
 
+
 def chemical(request):
     return render(request, 'chemical.html')
 
+
 def tutorials(request):
     return render(request, 'tutorials.html')
 
+
 def adminSession(request):
     return render(request, 'admin-session.html')
 
 FORMS = [("IdForm", ippidb.forms.IdForm),
          ("BibliographyForm", ippidb.forms.BibliographyForm),
          ("PDBForm", ippidb.forms.PDBFormSet),
-         ("ProteinForm",ippidb.forms.ProteinFormSet),
-         ("ProteinDomainComplexTypeForm", ippidb.forms.ProteinDomainComplexTypeForm),
+         ("ProteinForm", ippidb.forms.ProteinFormSet),
+         ("ProteinDomainComplexTypeForm",
+          ippidb.forms.ProteinDomainComplexTypeForm),
          ("ProteinDomainComplexForm", ippidb.forms.ProteinDomainComplexForm),
          ("PpiForm", ippidb.forms.PpiForm)]
 
@@ -53,19 +65,21 @@ TEMPLATES = {"IdForm": "IdForm.html",
              "BibliographyForm": "BibliographyForm.html",
              "PDBForm": "PDBForm.html",
              "ProteinForm": "ProteinForm.html",
-             "ProteinDomainComplexTypeForm":"ProteinDomainComplexTypeForm.html",
+             "ProteinDomainComplexTypeForm": "ProteinDomainComplexTypeForm.html",
              "ProteinDomainComplexForm": "ProteinDomainComplexForm.html",
              "PpiForm": "PpiForm.html"}
 
+
 class IppiWizard(NamedUrlSessionWizardView):
+
     def get_template_names(self):
         return [TEMPLATES[self.steps.current]]
 
     def get_form_instance(self, step):
-        if self.steps.current=='BibliographyForm':
+        if self.steps.current == 'BibliographyForm':
             pk = self.storage.get_step_data('IdForm').get('pk')
             return Bibliography.objects.get(pk=pk)
-        if self.steps.current=='ProteinForm':
+        if self.steps.current == 'ProteinForm':
             pks = self.storage.get_step_data('PDBForm').get('pks')
             return Protein.objects.filter(id__in=pks)
 
@@ -76,12 +90,12 @@ class IppiWizard(NamedUrlSessionWizardView):
         when appropriate
         """
         data = super(IppiWizard, self).process_step(form).copy()
-        if self.steps.current=='IdForm':
+        if self.steps.current == 'IdForm':
             form.instance.autofill()
         if self.steps.current in ['IdForm', 'Bibliography']:
             form.instance.save()
             data['pk'] = form.instance.id
-        if self.steps.current=='PDBForm':
+        if self.steps.current == 'PDBForm':
             pdb_ids = [form['pdb_id'] for form in form.cleaned_data]
             uniprot_ids = []
             protein_ids = []
@@ -103,4 +117,3 @@ class IppiWizard(NamedUrlSessionWizardView):
         return render(self.request, '/admin-session/add.html', {
             'form_data': [form.cleaned_data for form in form_list],
         })
-

ippisite/ippidb/ws.py

@@ -3,12 +3,15 @@ from bioservices.uniprot import UniProt
 import xml.etree.ElementTree as ET
 import requests
 
+
 def get_pubmed_info(pmid):
     eu = EUtils()
     r = eu.EFetch('pubmed', pmid, retmode='dict', rettype='abstract')
-    article = r['PubmedArticleSet']['PubmedArticle']['MedlineCitation']['Article']
+    article = r['PubmedArticleSet'][
+        'PubmedArticle']['MedlineCitation']['Article']
     title = article['ArticleTitle']
-    authors_list = [a['LastName']+ ' ' + a['Initials'] for a in article['AuthorList']['Author']]
+    authors_list = [a['LastName'] + ' ' + a['Initials']
+                    for a in article['AuthorList']['Author']]
     authors = ', '.join(authors_list)
     journal_name = article['Journal']['Title']
     biblio_date = article['Journal']['JournalIssue']['PubDate']
@@ -16,60 +19,76 @@ def get_pubmed_info(pmid):
         biblio_year = biblio_date['Year']
     else:
         biblio_year = biblio_date['MedlineDate'][0:3]
-    return {'title':title,
-            'journal_name':journal_name,
-            'biblio_year':biblio_year,
+    return {'title': title,
+            'journal_name': journal_name,
+            'biblio_year': biblio_year,
             'authors_list': authors}
 
+
 def get_epo_info(patent_number):
-    resp = requests.get('http://ops.epo.org/3.1/rest-services/published-data/publication/docdb/{}/biblio.json'.format(patent_number))
+    resp = requests.get(
+        'http://ops.epo.org/3.1/rest-services/published-data/publication/docdb/{}/biblio.json'.format(patent_number))
     data = resp.json()
-    exchange_doc = data['ops:world-patent-data']['exchange-documents']['exchange-document']
+    exchange_doc = data['ops:world-patent-data'][
+        'exchange-documents']['exchange-document']
     if isinstance(exchange_doc, list):
         exchange_doc = exchange_doc[0]
-    title = [el['$'] for el in exchange_doc['bibliographic-data']['invention-title'] if el['@lang']=='en']
-    authors = [i['inventor-name']['name']['$'] for i in exchange_doc['bibliographic-data']['parties']['inventors']['inventor'] if i['@data-format']=='original']
-    biblio_year = [el['date']['$'][:4] for el in exchange_doc['bibliographic-data']['publication-reference']['document-id'] if el['@document-id-type']=='epodoc'][0]
+    title = [el['$']
+             for el in exchange_doc['bibliographic-data']['invention-title'] if el['@lang'] == 'en']
+    authors = [i['inventor-name']['name']['$']
+               for i in exchange_doc['bibliographic-data']['parties']['inventors']['inventor'] if i['@data-format'] == 'original']
+    biblio_year = [el['date']['$'][:4]
+                   for el in exchange_doc['bibliographic-data']['publication-reference']['document-id'] if el['@document-id-type'] == 'epodoc'][0]
     return {'title': title,
             'journal_name': None,
             'biblio_year': biblio_year,
             'authors_list': authors}
 
+
 def get_uniprot_info(uniprot_id):
     uniprot_client = UniProt()
-    ns = {'u':'http://uniprot.org/uniprot'}
+    ns = {'u': 'http://uniprot.org/uniprot'}
     resp = uniprot_client.retrieve(uniprot_id)
-    recommended_name = resp.root.findall('u:entry/u:protein/u:recommendedName/u:fullName', ns)[0].text
-    organism = resp.root.findall('u:entry/u:organism/u:dbReference[@type="NCBI Taxonomy"]', ns)[0].attrib['id']
-    gene = resp.root.findall('u:entry/u:gene/u:name[@type="primary"]', ns)[0].text
+    recommended_name = resp.root.findall(
+        'u:entry/u:protein/u:recommendedName/u:fullName', ns)[0].text
+    organism = resp.root.findall(
+        'u:entry/u:organism/u:dbReference[@type="NCBI Taxonomy"]', ns)[0].attrib['id']
+    gene = resp.root.findall(
+        'u:entry/u:gene/u:name[@type="primary"]', ns)[0].text
     entry_name = resp.root.findall('u:entry/u:name', ns)[0].text
     go_els = resp.root.findall('u:entry/u:dbReference[@type="GO"]', ns)
     molecular_functions = []
     for go_el in go_els:
-        term_property_value = go_el.findall('u:property[@type="term"]', ns)[0].attrib['value']
-        if term_property_value[0:2]=='F:':
-            molecular_functions.append('GO_'+go_el.attrib['id'][3:])
+        term_property_value = go_el.findall(
+            'u:property[@type="term"]', ns)[0].attrib['value']
+        if term_property_value[0:2] == 'F:':
+            molecular_functions.append('GO_' + go_el.attrib['id'][3:])
     return {'recommended_name': recommended_name,
             'organism': int(organism),
             'gene': gene,
             'entry_name': entry_name,
             'molecular_functions': molecular_functions
-           }
+            }
+
 
 def get_go_info(go_id):
-    resp = requests.get('https://www.ebi.ac.uk/ols/api/ontologies/go/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F{}'.format(go_id))
+    resp = requests.get(
+        'https://www.ebi.ac.uk/ols/api/ontologies/go/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F{}'.format(go_id))
     data = resp.json()
     label = data['label']
     return {'label': label}
 
+
 def get_taxonomy_info(taxonomy_id):
     eu = EUtils()
     r = eu.EFetch('taxonomy', taxonomy_id, retmode='dict')
     scientific_name = r['TaxaSet']['Taxon']['ScientificName']
     return {'scientific_name': scientific_name}
 
+
 def get_pfam_info(pfam_acc):
-    resp = requests.get('http://pfam.xfam.org/family/{}?output=xml'.format(pfam_acc))
+    resp = requests.get(
+        'http://pfam.xfam.org/family/{}?output=xml'.format(pfam_acc))
     root = ET.fromstring(resp.text)
     ns = {'pfam': 'http://pfam.xfam.org/'}
     entry = root.findall('pfam:entry', ns)[0]
@@ -79,14 +98,18 @@ def get_pfam_info(pfam_acc):
     return {'id': pfam_id,
             'description': description}
 
+
 def get_pdb_uniprot_mapping(pdb_id):
-    resp = requests.get('https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{}'.format(pdb_id.lower()))
+    resp = requests.get(
+        'https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{}'.format(pdb_id.lower()))
     uniprot_ids = list(resp.json()[pdb_id]['UniProt'].keys())
     return uniprot_ids
 
+
 def pdb_entry_exists(pdb_id):
     """ test if a PDB entry exists using EBI web services """
-    resp = requests.get('https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{}'.format(pdb_id.lower()))
+    resp = requests.get(
+        'https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{}'.format(pdb_id.lower()))
     # EBI sends back either a 404 or an empty json if the PDB does not exist
     if not(resp.ok):
         return False