def site_upload(request):
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
selection_type = 'segments'
selection_subtype = 'site_residue'
if request.FILES == {}:
return render(request, 'common/selection_lists_sitesearch.html', '')
#Overwriting the existing selection
selection.clear(selection_type)
print(type(request.FILES['xml_file'].file))
wb=load_workbook(filename=request.FILES['xml_file'].file)
ws=wb.active
for row in ws.rows:
if len(row) < 5:
continue
group_id = int(row[0].value)
min_match = int(row[1].value)
try:
position = ResidueGenericNumberEquivalent.objects.get(label=row[2].value, scheme__slug=row[3].value)
except e:
print(e)
continue
feature = row[4].value
# update the selected group
selection.active_site_residue_group = group_id
print(selection.site_residue_groups)
if not selection.site_residue_groups:
selection.site_residue_groups = [[]]
selection.site_residue_groups[selection.active_site_residue_group - 1].append(1)
if len(selection.site_residue_groups) < group_id:
for x in group_id - len(selection.site_residue_groups):
selection.site_residue_groups.append([])
selection.site_residue_groups[group_id - 1][0] = min_match
selection_object = SelectionItem(selection_subtype, position)
selection_object.properties['feature'] = feature
selection_object.properties['site_residue_group'] = selection.active_site_residue_group
selection_object.properties['amino_acids'] = ','.join(definitions.AMINO_ACID_GROUPS[feature])
selection.add(selection_type, selection_subtype, selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return render(request, 'common/selection_lists_sitesearch.html', selection.dict(selection_type))
def SelectionAnnotation(request):
"""Updates the selected level of annotation"""
protein_source = request.GET['protein_source']
if protein_source == 'All':
pss = ProteinSource.objects.all()
else:
pss = ProteinSource.objects.filter(name=protein_source)
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# reset the annotation selection
selection.clear('annotation')
# add the selected items to the selection
for ps in pss:
selection_object = SelectionItem('annotation', ps)
selection.add('annotation', 'annotation', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return render(request, 'common/selection_filters_annotation.html', selection.dict('annotation'))
def SelectionAnnotation(request):
"""Updates the selected level of annotation"""
protein_source = request.GET['protein_source']
if protein_source == 'All':
pss = ProteinSource.objects.all()
else:
pss = ProteinSource.objects.filter(name=protein_source)
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# reset the annotation selection
selection.clear('annotation')
# add the selected items to the selection
for ps in pss:
selection_object = SelectionItem('annotation', ps)
selection.add('annotation', 'annotation', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return render(request, 'common/selection_filters_annotation.html', selection.dict('annotation'))
def ResiduesUpload(request):
"""Receives a file containing generic residue positions along with numbering scheme and adds those to the selection."""
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
selection_type = 'segments'
if request.FILES == {}:
return render(request, 'common/selection_lists.html', '')
#Overwriting the existing selection
selection.clear(selection_type)
#The excel file
o = []
workbook = xlrd.open_workbook(
file_contents=request.FILES['xml_file'].read())
worksheets = workbook.sheet_names()
for worksheet_name in worksheets:
worksheet = workbook.sheet_by_name(worksheet_name)
for row in worksheet.get_rows():
if len(row) < 2:
continue
try:
if row[0].value == 'residue':
position = ResidueGenericNumberEquivalent.objects.get(
label=row[2].value, scheme__slug=row[1].value)
o.append(position)
elif row[0].value == 'helix':
o.append(ProteinSegment.objects.get(slug=row[2].value))
except Exception as msg:
print(msg)
continue
for obj in o:
# add the selected item to the selection
if obj.__class__.__name__ == 'ResidueGenericNumberEquivalent':
selection_subtype = 'residue'
else:
selection_subtype = 'helix'
selection_object = SelectionItem(selection_subtype, obj)
selection.add(selection_type, selection_subtype, selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return render(request, 'common/selection_lists.html',
selection.dict(selection_type))
def SelectionGproteinPredefined(request):
"""Updates the selected g proteins to predefined sets (Gi/Go and all)"""
g_protein = request.GET['g_protein']
preferred = request.GET['preferred']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
all_gprots = ProteinGProtein.objects.all()
gprots = False
if g_protein == 'All':
gprots = []
if g_protein != 'All' and g_protein:
gprots = ProteinGProtein.objects.filter(name=g_protein)
if gprots != False:
# reset the g proteins selection
if preferred == 'true':
selection.clear('pref_g_proteins')
else:
selection.clear('g_proteins')
# add the selected items to the selection
for gprot in gprots:
selection_object = SelectionItem('g_protein', gprot)
if preferred == 'true':
selection.add('pref_g_proteins', 'g_protein', selection_object)
else:
selection.add('g_proteins', 'g_protein', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
if preferred == 'true':
context = selection.dict('pref_g_proteins')
else:
context = selection.dict('g_proteins')
context['gprots'] = ProteinGProtein.objects.all()
if preferred == 'true':
return render(request, 'common/selection_filters_pref_gproteins.html',
context)
else:
return render(request, 'common/selection_filters_gproteins.html',
context)
def ResiduesUpload(request):
"""Receives a file containing generic residue positions along with numbering scheme and adds those to the selection."""
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
selection_type = 'segments'
if request.FILES == {}:
return render(request, 'common/selection_lists.html', '')
#Overwriting the existing selection
selection.clear(selection_type)
#The excel file
o = []
workbook = xlrd.open_workbook(file_contents=request.FILES['xml_file'].read())
worksheets = workbook.sheet_names()
for worksheet_name in worksheets:
worksheet = workbook.sheet_by_name(worksheet_name)
for row in worksheet.get_rows():
if len(row) < 2:
continue
try:
if row[0].value == 'residue':
position = ResidueGenericNumberEquivalent.objects.get(label=row[2].value, scheme__slug=row[1].value)
o.append(position)
elif row[0].value == 'helix':
o.append(ProteinSegment.objects.get(slug=row[2].value))
except Exception as msg:
print(msg)
continue
for obj in o:
# add the selected item to the selection
if obj.__class__.__name__ == 'ResidueGenericNumberEquivalent':
selection_subtype = 'residue'
else:
selection_subtype = 'helix'
selection_object = SelectionItem(selection_subtype, obj)
selection.add(selection_type, selection_subtype, selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return render(request, 'common/selection_lists.html', selection.dict(selection_type))
def SelectionGproteinPredefined(request):
"""Updates the selected g proteins to predefined sets (Gi/Go and all)"""
g_protein = request.GET['g_protein']
preferred = request.GET['preferred']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
all_gprots = ProteinGProtein.objects.all()
gprots = False
if g_protein == 'All':
gprots = []
if g_protein != 'All' and g_protein:
gprots = ProteinGProtein.objects.filter(name=g_protein)
if gprots != False:
# reset the g proteins selection
if preferred == 'true':
selection.clear('pref_g_proteins')
else:
selection.clear('g_proteins')
# add the selected items to the selection
for gprot in gprots:
selection_object = SelectionItem('g_protein', gprot)
if preferred == 'true':
selection.add('pref_g_proteins', 'g_protein', selection_object)
else:
selection.add('g_proteins', 'g_protein', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
if preferred == 'true':
context = selection.dict('pref_g_proteins')
else:
context = selection.dict('g_proteins')
context['gprots'] = ProteinGProtein.objects.all()
if preferred == 'true':
return render(request, 'common/selection_filters_pref_gproteins.html', context)
else:
return render(request, 'common/selection_filters_gproteins.html', context)
def preserve_targets(request):
request.session['targets_pos'] = deepcopy(request.session.get('selection', False))
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
selection.clear('targets')
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return redirect('/seqsign/negativegroupselection',)
def preserve_targets(request):
request.session['targets_pos'] = deepcopy(request.session.get('selection', False))
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
selection.clear('targets')
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return redirect('/seqsign/negativegroupselection',)
def SelectionSchemesPredefined(request):
"""Updates the selected numbering_schemes to predefined sets (GPCRdb and All)"""
numbering_schemes = request.GET['numbering_schemes']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
all_gns = ResidueNumberingScheme.objects.exclude(
slug=settings.DEFAULT_NUMBERING_SCHEME)
gns = False
if numbering_schemes == 'All':
print(len(selection.numbering_schemes), all_gns.count())
if len(selection.numbering_schemes) == all_gns.count():
gns = []
else:
gns = all_gns
# reset the species selection
selection.clear('numbering_schemes')
# add the selected items to the selection
for gn in gns:
selection_object = SelectionItem('numbering_schemes', gn)
selection.add('numbering_schemes', 'numbering_schemes',
selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('numbering_schemes')
context['gns'] = all_gns
return render(request, 'common/selection_filters_numbering_schemes.html',
context)
def signature_selection(request):
# create full selection and import simple selection (if it exists)
simple_selection = request.session.get('selection', False)
selection_pos = Selection()
selection_pos.importer(deepcopy(simple_selection))
selection_pos.clear('targets')
selection_neg = Selection()
selection_neg.importer(deepcopy(simple_selection))
selection_neg.clear('targets')
if 'group1' in request.POST and 'group2' in request.POST:
up_names = request.POST['group1'].split('\r')
for up_name in up_names:
try:
selection_object = SelectionItem(
'protein',
Protein.objects.get(entry_name=up_name.strip().lower()))
selection_pos.add('targets', 'protein', selection_object)
except:
continue
down_names = request.POST['group2'].split('\r')
for down_name in down_names:
try:
selection_object = SelectionItem(
'protein',
Protein.objects.get(entry_name=down_name.strip().lower()))
selection_neg.add('targets', 'protein', selection_object)
except:
continue
# Set both the positive and negative target selections
request.session['targets_pos'] = selection_pos.exporter()
request.session['selection'] = selection_neg.exporter()
return JsonResponse({"response": "ok"})
else:
return JsonResponse({"response": "error"})
def SelectionSchemesPredefined(request):
"""Updates the selected numbering_schemes to predefined sets (GPCRdb and All)"""
numbering_schemes = request.GET['numbering_schemes']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
all_gns = ResidueNumberingScheme.objects.exclude(slug=settings.DEFAULT_NUMBERING_SCHEME)
gns = False
if numbering_schemes == 'All':
print(len(selection.numbering_schemes), all_gns.count())
if len(selection.numbering_schemes) == all_gns.count():
gns = []
else:
gns = all_gns
# reset the species selection
selection.clear('numbering_schemes')
# add the selected items to the selection
for gn in gns:
selection_object = SelectionItem('numbering_schemes', gn)
selection.add('numbering_schemes', 'numbering_schemes', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('numbering_schemes')
context['gns'] = all_gns
return render(request, 'common/selection_filters_numbering_schemes.html', context)
def get_context_data (self, **kwargs):
context = super(SuperpositionWorkflowIndex, self).get_context_data(**kwargs)
# get selection from session and add to context
# get simple selection from session
simple_selection = self.request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
#Clearing selections for fresh run
if 'clear' in self.kwargs.keys():
selection.clear('reference')
selection.clear('targets')
selection.clear('segments')
if 'alt_files' in self.request.session.keys():
del self.request.session['alt_files']
if 'ref_file' in self.request.session.keys():
del self.request.session['ref_file']
context['selection'] = {}
for selection_box, include in self.selection_boxes.items():
if include:
context['selection'][selection_box] = selection.dict(selection_box)['selection'][selection_box]
# get attributes of this class and add them to the context
context['form_code'] = str(self.form_code)
attributes = inspect.getmembers(self, lambda a:not(inspect.isroutine(a)))
for a in attributes:
if not(a[0].startswith('__') and a[0].endswith('__')):
context[a[0]] = a[1]
return context
def SelectionSpeciesPredefined(request):
"""Updates the selected species to predefined sets (Human and all)"""
species = request.GET['species']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
all_sps = Species.objects.all()
sps = False
if species == 'All':
sps = []
if species != 'All' and species:
sps = Species.objects.filter(common_name=species)
if sps != False:
# reset the species selection
selection.clear('species')
# add the selected items to the selection
for sp in sps:
selection_object = SelectionItem('species', sp)
selection.add('species', 'species', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('species')
context['sps'] = all_sps
return render(request, 'common/selection_filters_species.html', context)
def ClearSelection(request):
"""Clears all selected items of the selected type from the session"""
selection_type = request.GET['selection_type']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# remove the selected item to the selection
selection.clear(selection_type)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return render(request, 'common/selection_lists.html', selection.dict(selection_type))
def SelectionSpeciesPredefined(request):
"""Updates the selected species to predefined sets (Human and all)"""
species = request.GET['species']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
all_sps = Species.objects.all()
sps = False
if species == 'All':
sps = []
if species != 'All' and species:
sps = Species.objects.filter(common_name=species)
if sps != False:
# reset the species selection
selection.clear('species')
# add the selected items to the selection
for sp in sps:
selection_object = SelectionItem('species', sp)
selection.add('species', 'species', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('species')
context['sps'] = all_sps
return render(request, 'common/selection_filters_species.html', context)
def ClearSelection(request):
"""Clears all selected items of the selected type from the session"""
selection_type = request.GET['selection_type']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# remove the selected item to the selection
selection.clear(selection_type)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return render(request, 'common/selection_lists.html', selection.dict(selection_type))
def site_upload(request):
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
selection_type = 'segments'
selection_subtype = 'site_residue'
if request.FILES == {}:
return render(request, 'common/selection_lists_sitesearch.html', '')
#Overwriting the existing selection
selection.clear(selection_type)
workbook = xlrd.open_workbook(file_contents=request.FILES['xml_file'].read())
worksheets = workbook.sheet_names()
for worksheet_name in worksheets:
worksheet = workbook.sheet_by_name(worksheet_name)
for row in worksheet.get_rows():
#for row in ws.rows:
if len(row) < 5:
continue
group_id = int(row[0].value)
min_match = int(row[1].value)
try:
position = ResidueGenericNumberEquivalent.objects.get(label=row[2].value, scheme__slug=row[3].value)
except e:
print(e)
continue
feature = row[4].value
# update the selected group
if not selection.active_site_residue_group:
selection.active_site_residue_group = group_id
if not selection.site_residue_groups:
selection.site_residue_groups = [[]]
if len(selection.site_residue_groups) < group_id:
for x in group_id - len(selection.site_residue_groups):
selection.site_residue_groups[x].append([])
# selection.site_residue_groups[group_id - 1].append(1)
properties = {}
properties['feature'] = feature
properties['site_residue_group'] = selection.active_site_residue_group
properties['amino_acids'] = ','.join(definitions.AMINO_ACID_GROUPS[feature]) if feature != 'custom' else row[5].value
selection_object = SelectionItem(selection_subtype, position, properties)
selection.add(selection_type, selection_subtype, selection_object)
selection.site_residue_groups[group_id - 1][0] = min_match
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
context = selection.dict(selection_type)
# amino acid groups
amino_acid_groups = {
'amino_acid_groups': definitions.AMINO_ACID_GROUPS,
'amino_acid_group_names': definitions.AMINO_ACID_GROUP_NAMES }
context.update(amino_acid_groups)
return render(request, 'common/selection_lists_sitesearch.html', context)
def site_upload(request):
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
selection_type = 'segments'
selection_subtype = 'site_residue'
if request.FILES == {}:
return render(request, 'common/selection_lists_sitesearch.html', '')
#Overwriting the existing selection
selection.clear(selection_type)
workbook = xlrd.open_workbook(
file_contents=request.FILES['xml_file'].read())
worksheets = workbook.sheet_names()
for worksheet_name in worksheets:
worksheet = workbook.sheet_by_name(worksheet_name)
for row in worksheet.get_rows():
#for row in ws.rows:
if len(row) < 5:
continue
group_id = int(row[0].value)
min_match = int(row[1].value)
try:
position = ResidueGenericNumberEquivalent.objects.get(
label=row[2].value, scheme__slug=row[3].value)
except e:
print(e)
continue
feature = row[4].value
# update the selected group
if not selection.active_site_residue_group:
selection.active_site_residue_group = group_id
if not selection.site_residue_groups:
selection.site_residue_groups = [[]]
if len(selection.site_residue_groups) < group_id:
for x in group_id - len(selection.site_residue_groups):
selection.site_residue_groups[x].append([])
# selection.site_residue_groups[group_id - 1].append(1)
properties = {}
properties['feature'] = feature
properties[
'site_residue_group'] = selection.active_site_residue_group
properties['amino_acids'] = ','.join(
definitions.AMINO_ACID_GROUPS[feature]
) if feature != 'custom' else row[5].value
selection_object = SelectionItem(selection_subtype, position,
properties)
selection.add(selection_type, selection_subtype, selection_object)
selection.site_residue_groups[group_id - 1][0] = min_match
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
context = selection.dict(selection_type)
# amino acid groups
amino_acid_groups = {
'amino_acid_groups': definitions.AMINO_ACID_GROUPS,
'amino_acid_group_names': definitions.AMINO_ACID_GROUP_NAMES
}
context.update(amino_acid_groups)
return render(request, 'common/selection_lists_sitesearch.html', context)
