def handle(self, *args, **options):
conn = sqlite3.connect(options['userdb_path'][0])
"""
CREATE TABLE users (
0 login TEXT PRIMARY KEY,
1 firstname TEXT,
2 lastname TEXT,
3 email TEXT,
4 password TEXT,
5 path TEXT,
6 token TEXT,
7 accepted INTEGER,
8 project TEXT,
9 affiliation TEXT,
10 ip TEXT,
11 clearance TEXT,
12 date TEXT,
13 visit TEXT)
"""
print("Migrating users table...")
user_paths = {}
for row in conn.execute('SELECT * FROM users;'):
username = sanitize_username(row[0])
password = "******" + row[4]
email = row[3]
is_active = True
is_superuser = True if row[11] == 'admin' else False
user_paths[row[5]] = username
date_joined = datetime.strptime(
row[12], "%Y-%m-%d").replace(tzinfo=timezone.utc)
newuser = User(username=username,
password=password,
email=email,
is_active=is_active,
is_superuser=is_superuser,
is_staff=is_superuser,
date_joined=date_joined)
newuser.save()
fullname = "%s %s" % (row[1], row[2])
institution = row[9]
if len(fullname) < 2:
fullname = None
newuser_profile = UserProfile(user=newuser,
fullname=fullname,
orcid=None,
institution=institution)
newuser_profile.save()
print(" - Successful.")
print("Moving project files... ")
for path in user_paths:
username = user_paths[path]
# old user project dir
src = os.path.join(options['userfiles_path'][0], path)
#new user project dir
dst = os.path.join(settings.USER_DATA_DIR, username)
try:
shutil.copytree(src, dst)
except FileNotFoundError:
# if user path does not exists create empty dir for user
os.makedirs(dst)
print(" - Successful")
print("Migratins project table... ")
"""
CREATE TABLE projects (
0 name TEXT PRIMARY KEY,
1 path TEXT,
2 user TEXT,
3 description TEXT)
"""
for row in conn.execute('SELECT * FROM projects;'):
name = row[0]
slug = slugify(name).replace('-', '_')
path = row[1]
username = sanitize_username(row[2])
description = row[3]
#rename project files
fileTypes_old = [
'treeFile', 'dataFile', 'fastaFile', 'samplesOrderFile',
'samplesInformationFile'
]
fileTypes_new = [
'tree.txt', 'data.txt', 'fasta.fa', 'samples-order.txt',
'samples-info.txt'
]
for i in range(5):
try:
os.rename(
os.path.join(settings.USER_DATA_DIR, username, path,
fileTypes_old[i]),
os.path.join(settings.USER_DATA_DIR, username, path,
fileTypes_new[i]))
except:
pass
try:
if not description or not len(description) > 0:
description = ""
project = Project(name=name,
slug=slug,
user=User.objects.get(username=username),
secret=path)
samples_info = project.get_file_path('samples-order.txt',
default=None)
samples_order = project.get_file_path('samples-info.txt',
default=None)
if (samples_info
or samples_order) and not project.get_file_path(
'samples.db', default=None):
s = dbops.SamplesInformationDatabase(project.get_file_path(
'samples.db', dont_check_exists=True),
quiet=True)
s.create(samples_order, samples_info)
interactive = project.get_interactive()
# try to get number of leaves
try:
leaves = get_names_order_from_newick_tree(
project.get_file_path('tree.txt', default=None))
project.num_leaves = len(leaves) if leaves != [''] else 0
except:
project.num_leaves = 0
# try to get number of layers
try:
project.num_layers = len(
interactive.views['single']
[0]) - 1 # <- -1 because first column is contigs
except:
project.num_layers = 0
# store description
dbops.update_description_in_db(
project.get_file_path('profile.db', default=None),
description or '')
project.synchronize_num_states()
project.synchronize_num_collections()
project.save()
# try to migrate old links.
for row_links in conn.execute(
'SELECT * FROM views WHERE project LIKE \'%s\';' %
(name)):
old_link = OldLinks(
name=row_links[0],
user=sanitize_username(row_links[1]),
project=Project.objects.filter(
name=row_links[2],
user__username=sanitize_username(row_links[1]))[0],
is_public=True if row_links[3] == 1 else False,
token=row_links[4])
old_link.save()
project_link = ProjectLink(project=old_link.project,
link=old_link.token)
project_link.save()
except Exception as e:
print(username + " " + name + " " + path +
" failed to create project, here is the exception " +
str(e))
shutil.rmtree(
os.path.join(settings.USER_DATA_DIR, username, path))
print(" - Successful")
def new_project(request):
if request.method == "POST":
try:
name = request.POST.get('name')
slug = slugify(name).replace('-', '_')
if len(slug) < 1:
raise Exception("Project name should not be empty.")
project = Project.objects.filter(user=request.user, slug=slug)
if project:
if request.POST.get('delete-if-exists'):
project[0].delete_project_path()
project[0].delete()
else:
raise Exception("Project with same name already exists, please give another name.")
project = Project(name=name,
slug=slug,
user=request.user,
secret=get_random_string(length=32))
project.create_project_path()
fileTypes = ['tree.txt', 'data.txt', 'fasta.fa',
'samples-order.txt', 'samples-info.txt',
'additional-layers.txt', 'state.json',
'bins.txt', 'bins-info.txt', 'items-order.txt']
for fileType in fileTypes:
if fileType in request.FILES:
put_project_file(project.get_path(), fileType, request.FILES[fileType])
interactive = project.get_interactive()
profile_db_path = project.get_file_path('profile.db', default=None)
samples_info = project.get_file_path('samples-info.txt', default=None)
if samples_info:
miscdata.MiscDataTableFactory(argparse.Namespace(target_data_table='layers', profile_db=profile_db_path)).populate_from_file(samples_info)
samples_order = project.get_file_path('samples-order.txt', default=None)
if samples_order:
miscdata.MiscDataTableFactory(argparse.Namespace(target_data_table='layer_orders', profile_db=profile_db_path)).populate_from_file(samples_order)
state_file = project.get_file_path('state.json', default=None)
if state_file:
interactive.states_table.store_state('default', open(state_file, 'r').read(), datetime.datetime.now().strftime("%d.%m.%Y %H:%M:%S"))
project.num_states = 1
bins_file = project.get_file_path('bins.txt', default=None)
bins_info_file = project.get_file_path('bins-info.txt', default=None)
if bins_file and bins_info_file:
collections_table = collections.TablesForCollections(profile_db_path)
bins = get_TAB_delimited_file_as_dictionary(bins_file, no_header = True, column_names = ['split_id', 'bin_name'])
bins_info = get_TAB_delimited_file_as_dictionary(bins_info_file, no_header = True, column_names = ['bin_name', 'source', 'html_color'])
bin_data = {}
for split_name in bins:
bin_name = bins[split_name]['bin_name']
if not bin_name in bin_data:
bin_data[bin_name] = set([])
bin_data[bin_name].add(split_name)
collections_table.append('default', bin_data, bins_info)
project.num_collections = 1
# try to get number of leaves
try:
project.num_leaves = len(interactive.displayed_item_names_ordered)
except:
project.num_leaves = 0
# try to get number of layers
try:
project.num_layers = len(interactive.views['single'][0]) - 1 # <- -1 because first column is contigs
except:
project.num_layers = 0
# store description
dbops.update_description_in_db(profile_db_path, request.POST.get('description') or '')
project.save()
return JsonResponse({'status': 0})
except Exception as e:
try:
project.delete_project_path()
except:
# slug is not unique, so there is no project instance or direcotry created.
pass
message = str(e.clear_text()) if 'clear_text' in dir(e) else str(e)
# trim the full path from exception message, show only file name
message = re.sub(r"(\'.*\/)(.+?)(\.txt\')", r"'\2'", message)
return JsonResponse({
'status': 1,
'message': message
})
return render(request, 'projects/new.html')