def SelectResidueGroup(request):
"""Receives a selection request, updates the active residue group, and returns the updated selection"""
selection_type = request.GET['selection_type']
group_id = int(request.GET['group_id'])
# 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)
# update the selected group
selection.active_site_residue_group = group_id
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# context
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)
# template to load
template = 'common/selection_lists_sitesearch.html'
return render(request, template, context)
def SelectResidueGroup(request):
"""Receives a selection request, updates the active residue group, and returns the updated selection"""
selection_type = request.GET['selection_type']
group_id = int(request.GET['group_id'])
# 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)
# update the selected group
selection.active_site_residue_group = group_id
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# context
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)
# template to load
template = 'common/selection_lists_sitesearch.html'
return render(request, template, 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)
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 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)
