def store_description(args, d, request, response): if args.read_only: return description = request.forms.get('description') db_path = d.pan_db_path or d.profile_db_path dbops.update_description_in_db(db_path, description) d.p_meta['description'] = description
def store_description(self): if self.read_only: return description = request.forms.get('description') db_path = self.interactive.pan_db_path or self.interactive.profile_db_path dbops.update_description_in_db(db_path, description) self.interactive.p_meta['description'] = description return json.dumps("")
def migrate(db_path): if db_path is None: raise ConfigError("No database path is given.") # make sure someone is not being funny utils.is_contigs_db(db_path) # make sure the current version matches contigs_db = db.DB(db_path, None, ignore_version=True) if str(contigs_db.get_version()) != current_version: raise ConfigError( "Version of this contigs database is not %s (hence, this script cannot really do anything)." % current_version) progress.new("Trying to upgrade the contigs database") progress.update('...') contigs_db.remove_meta_key_value_pair('project_name') contigs_db.set_meta_value('project_name', "NO_NAME") contigs_db.commit() # set the version contigs_db.remove_meta_key_value_pair('version') contigs_db.set_version(next_version) # gene name changes: contigs_db._exec( '''UPDATE %s SET genes = replace(genes, '%s', '%s') WHERE source LIKE 'Rinke_et_al';''' % (t.hmm_hits_info_table_name, 'Ribosomal_S12', 'Ribosom_S12_S23')) contigs_db._exec( '''UPDATE %s SET genes = replace(genes, '%s', '%s') Where source LIKE 'Rinke_et_al';''' % (t.hmm_hits_info_table_name, 'UPF0027', 'RtcB')) contigs_db._exec( '''UPDATE %s SET genes = replace(genes, '%s', '%s') Where source LIKE 'Rinke_et_al';''' % (t.hmm_hits_info_table_name, '‐', '-')) # first - is not ASCII # bye contigs_db.disconnect() # bye to you too progress.end() dbops.update_description_in_db(db_path, 'No description is given') run.info_single("The contigs database is now %s! All this upgrade did was to associate your contigs db with a\ project name (which happened to be 'NO_NAME', because anvi'o likes you very much)" \ % (next_version), nl_after=1, nl_before=1, mc='green')
def migrate(db_path): if db_path is None: raise ConfigError("No database path is given.") # make sure someone is not being funny utils.is_contigs_db(db_path) # make sure the current version matches contigs_db = db.DB(db_path, None, ignore_version = True) if str(contigs_db.get_version()) != current_version: raise ConfigError("Version of this contigs database is not %s (hence, this script cannot really do anything)." % current_version) progress.new("Trying to upgrade the contigs database") progress.update('...') contigs_db.remove_meta_key_value_pair('project_name') contigs_db.set_meta_value('project_name', "NO_NAME") contigs_db.commit() # set the version contigs_db.remove_meta_key_value_pair('version') contigs_db.set_version(next_version) # gene name changes: contigs_db._exec('''UPDATE %s SET genes = replace(genes, '%s', '%s') WHERE source LIKE 'Rinke_et_al';''' % (t.hmm_hits_info_table_name, 'Ribosomal_S12', 'Ribosom_S12_S23')) contigs_db._exec('''UPDATE %s SET genes = replace(genes, '%s', '%s') Where source LIKE 'Rinke_et_al';''' % (t.hmm_hits_info_table_name, 'UPF0027', 'RtcB')) contigs_db._exec('''UPDATE %s SET genes = replace(genes, '%s', '%s') Where source LIKE 'Rinke_et_al';''' % (t.hmm_hits_info_table_name, '‐', '-')) # first - is not ASCII # bye contigs_db.disconnect() # bye to you too progress.end() dbops.update_description_in_db(db_path, 'No description is given') run.info_single("The contigs database is now %s! All this upgrade did was to associate your contigs db with a\ project name (which happened to be 'NO_NAME', because anvi'o likes you very much)" \ % (next_version), nl_after=1, nl_before=1, mc='green')
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')