def svgview(request, tree_id, tree_src=None):
with get_treestore() as treestore:
if not tree_src: tree_src = '/trees/%s/download?format=newick' % tree_id
return render_to_response(
'svgview.html',
{'tree_src': tree_src, 'tree_id': tree_id, 'tree_uri': uri_from_tree_id(tree_id)},
context_instance=RequestContext(request)
)
def view(request, tree_id=None):
with get_treestore() as treestore:
tree_uri = uri_from_tree_id(tree_id)
params = {
'tree_uri': tree_uri,
'tree_id': tree_id,
'formats': sorted(bp._io.supported_formats.keys()) + ['ascii'],
}
try:
all_tree_info = treestore.get_tree_info(tree_uri)
tree_info = {}
tree_info.update(all_tree_info[0])
tree_info['citation'] = []
for x in all_tree_info:
if x['citation']: tree_info['citation'].append(x['citation'])
except IndexError:
raise Http404
return not_found(request, tree_uri)
obj_info = treestore.get_object_info(tree_uri)
prefixes = treestore.prefixes
def add_prefix(x):
for prefix, uri in prefixes:
if x.startswith(uri):
if prefix == 'obo':
try: return 'cdao:%s (obo:%s)' % (obo_to_cdao[x[len(uri):]], x[len(uri):])
except: pass
return '%s:%s' % (prefix, x[len(uri):])
return x
obj_info = [sum([(x, add_prefix(x)) for x in row], ()) for row in obj_info]
params.update(tree_info)
params['obj_info'] = obj_info
return render_to_response(
'view.html',
params,
context_instance=RequestContext(request)
)
def download(request, tree_id=None):
with get_treestore() as treestore:
tree_uri = uri_from_tree_id(tree_id)
if 'format' in request.GET:
format = request.GET.get('format')
else: format = 'newick'
if format == 'taxa_list':
# download list of taxa
names = treestore.get_names(tree_uri)
spp_list = ','.join(names)
return download_plaintext(request, spp_list)
trees = treestore.get_trees(tree_uri=tree_uri)
response = HttpResponse(mimetype='text/plain')
if format == 'ascii':
bp._utils.draw_ascii(trees[0], file=response)
else:
bp.write(trees, response, format)
return download_plaintext(request, response=response)
def upload_approve(request, tree_id):
submission = TreeSubmission.objects.get(id=tree_id)
tree_id = submission.tree_id
file_path = submission.tree_file.path
try:
tree = bp.read(file_path, submission.format)
with get_treestore() as treestore:
treestore.add_trees(file_path, submission.format,
tree_uri=uri_from_tree_id(tree_id))
text = 'Successfully uploaded <b>%s</b>.' % (uri_from_tree_id(tree_id))
submission.delete()
except Exception as e:
text = '<b>ERROR:</b> <p>%s</p>' % e
response = HttpResponse(mimetype='text/html')
response.write(text)
return response
def tree_list(request):
with get_treestore() as treestore:
if request.method == 'POST':
form = SearchForm(request.POST)
if form.is_valid():
taxa = form.cleaned_data['taxa']
filter = form.cleaned_data['filter']
params = [(x, y) for x, y in form.cleaned_data.items()]
return redirect('/trees/?' + urllib.urlencode(params))
else:
taxa = request.GET.get('taxa')
filter = request.GET.get('filter')
filter = filter if filter else None
form = SearchForm(initial=request.GET)
form.full_clean()
taxa = [x.strip() for x in taxa.split(',')] if taxa else []
params = {'form': form, 'taxonomy':settings.DEFAULT_TAXONOMY}
params.update(csrf(request))
try:
trees = list(treestore.list_trees_containing_taxa(contains=taxa, filter=filter,
taxonomy=settings.DEFAULT_TAXONOMY, show_counts=True))
except Exception as e:
errors = form._errors.setdefault(NON_FIELD_ERRORS, ErrorList())
err_msg = "There was a problem with your search: %s" % e
errors.append(err_msg)
return render_to_response(
'list.html',
params,
context_instance=RequestContext(request)
)
trees = [(tree_id_from_uri(m[0]), int(m[1])) for m in trees]
paginator = Paginator(trees, TREES_PER_PAGE)
page = request.GET.get('page')
try:
tree_list = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
tree_list = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
tree_list = paginator.page(paginator.num_pages)
params.update({'tree_list': tree_list,
'max_match_count': len(taxa)})
num_pages = paginator.num_pages
page_range = [n for n in range(tree_list.number - 2, tree_list.number + 3)
if n >= 1 and n <= num_pages]
params.update({
'total_results': len(trees),
'low_result': TREES_PER_PAGE * (tree_list.number - 1) + 1,
'high_result': min(len(trees), TREES_PER_PAGE * tree_list.number)
})
if page_range[0] == 2: page_range = [1] + page_range
elif page_range[0] > 2: page_range = [1, '...'] + page_range
if page_range[-1] == num_pages - 1: page_range += [num_pages]
elif page_range[-1] < num_pages - 1: page_range += ['...', num_pages]
pages = []
for page in page_range:
if page == '...': pages.append((page, None))
else:
p = []
for arg in ('taxa', 'filter'):
if arg in request.GET:
p += [(arg, request.GET.get(arg))]
p += [('page', page)]
pages.append((page, '/trees/?' + urllib.urlencode(p)))
params['pages'] = pages
return render_to_response(
'list.html',
params,
context_instance=RequestContext(request)
)
def query(request):
with get_treestore() as treestore:
tree_uri = None
params = {
'taxa': '',
'format': 'view',
'prune': True,
'tree': None,
'filter': '',
'taxonomy': settings.DEFAULT_TAXONOMY,
}
if request.method == 'POST':
form = QueryForm(request.POST)
if form.is_valid():
url = '/query/?' + urllib.urlencode(form.cleaned_data.items())
if len(url) < 200: return redirect(url)
params.update(form.cleaned_data)
submitted_query = True
else:
submitted_query = False
elif request.method == 'GET' and 'taxa' in request.GET:
submitted_query = True
taxa = request.GET.get('taxa')
params.update(request.GET.dict())
if 'prune' in request.GET: params['prune'] = params['prune'] == 'True'
form = QueryForm(initial=request.GET.dict())
form.full_clean()
else:
submitted_query = False
form = QueryForm(initial=request.GET.dict())
best_match = params['tree'] == 'best'
if submitted_query:
if best_match: tree_uri = None
else: tree_uri = uri_from_tree_id(params['tree']) if params['tree'] else None
taxonomy = uri_from_tree_id(params['taxonomy']) if params['taxonomy'] else None
if params['format'] == 'view' and tree_uri:
params['format'] = 'newick'
tree_src = '/query/?' + urllib.urlencode(params.items())
return treeview.views.svgview(request, params['tree'], tree_src=tree_src)
# execute the query and return the result as a plaintext tree
contains = [t.strip() for t in params['taxa'].split(',')]
e = None
response = None
if tree_uri is None:
# 'select automatically' was chosen; perform the disambiguation step
# if there are more than one matching tree
trees = None
matches = []
try:
for match in treestore.list_trees_containing_taxa(contains=contains,
show_counts=True,
taxonomy=taxonomy,
filter=params['filter']):
if int(match[1]) < 2 and params['prune']:
if not matches:
raise Exception("The top match only matched one taxon, which isn't enough to make a tree. Try unchecking the 'prune results' checkbox or changing your search.")
break
matches.append((match[0], int(match[1])))
if len(matches) >= (1 if best_match else MAX_DISAMBIG_MATCHES): break
except Exception as e:
trees = None
if matches and not e:
if best_match:
if params['format'] == 'view':
params['format'] = 'newick'
params['tree'] = matches[0][0]
tree_src = '/query/?' + urllib.urlencode(params.items())
return treeview.views.svgview(request, tree_id_from_uri(matches[0][0]),
tree_src=tree_src)
response = HttpResponse(mimetype='text/plain')
treestore.get_subtree(contains=contains,
tree_uri=matches[0][0],
format=params['format'],
prune=params['prune'],
filter=params['filter'],
taxonomy=taxonomy,
handle=response)
else: return query_disambiguate(request, matches, params)
elif not e:
trees = None
e = 'There were no trees that matched your query.'
else:
try:
response = HttpResponse(mimetype='text/plain')
treestore.get_subtree(contains=contains,
tree_uri=tree_uri,
format=params['format'],
prune=params['prune'],
filter=params['filter'],
taxonomy=taxonomy,
handle=response)
except Exception as e:
trees = None
exception = e
if response:
return download_plaintext(request, response=response)
elif trees:
return download_plaintext(request, trees)
else:
errors = form._errors.setdefault(NON_FIELD_ERRORS, ErrorList())
if e:
errors.append('There was a problem with your query: %s' % e)
else:
err_msg = "Your query didn't return a result. Try entering a new list of taxa"
if tree_uri: err_msg += ' or selecting a different tree'
err_msg += '.'
errors.append(err_msg)
# show the query builder page
params = {
'form': form,
'domain': settings.DOMAIN.rstrip('/'),
'tree_uri': settings.TREE_URI,
}
params.update(csrf(request))
return render_to_response(
'query.html',
params,
context_instance=RequestContext(request)
)