def add_repos(ctx, filename):
"""
Add repositories to Augur's database
"""
app = ctx.obj
df = app.database.execute(
s.sql.text("SELECT repo_group_id FROM augur_data.repo_groups"))
repo_group_IDs = [group[0] for group in df.fetchall()]
insertSQL = s.sql.text("""
INSERT INTO augur_data.repo(repo_group_id, repo_git, repo_status,
tool_source, tool_version, data_source, data_collection_date)
VALUES (:repo_group_id, :repo_git, 'New', 'CLI', 1.0, 'Git', CURRENT_TIMESTAMP)
""")
with open(filename) as upload_repos_file:
data = csv.reader(upload_repos_file, delimiter=',')
for row in data:
logger.info(
f"Inserting repo with Git URL `{row[1]}` into repo group {row[0]}"
)
if int(row[0]) in repo_group_IDs:
result = app.database.execute(insertSQL,
repo_group_id=int(row[0]),
repo_git=row[1])
else:
logger.warn(
f"Invalid repo group id specified for {row[1]}, skipping.")
def check_for_upgrade(ctx):
"""
Upgrade the configured database to the latest version
"""
app = ctx.obj
check_pgpass_credentials(app.config)
current_db_version = get_db_version(app)
update_scripts_filenames = []
for (_, _, filenames) in walk('schema/generate'):
update_scripts_filenames.extend(
[file for file in filenames if 'update' in file])
# files_temp.extend([file.split("-")[1][14:].split(".")[0] for file in filenames if 'update' in file])
break
target_version_script_map = {}
for script in update_scripts_filenames:
upgrades_to = int(script.split("-")[1][14:].split(".")[0])
target_version_script_map[upgrades_to] = str(script)
target_version_script_map = OrderedDict(
sorted(target_version_script_map.items()))
most_recent_version = list(target_version_script_map.keys())[-1]
if current_db_version == most_recent_version:
logger.info("Database is already up to date.")
elif current_db_version < most_recent_version:
logger.info(
f"Current database version: v{current_db_version}\nPlease upgrade to the most recent version (v{most_recent_version}) with augur db upgrade-db-version."
)
elif current_db_version > most_recent_version:
logger.warn(
f"Unrecognized version: {current_db_version}\nThe most recent version is {most_recent_version}. Please contact your system administrator to resolve this error."
)
def __init__(self):
"""
Reads config, creates DB session, and initializes cache
"""
self.config_file_name = 'augur.config.json'
self.__shell_config = None
self.__export_file = None
self.__env_file = None
self.config = default_config
self.env_config = {}
self.root_augur_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
default_config_path = self.root_augur_dir + '/' + self.config_file_name
using_config_file = False
config_locations = [self.config_file_name, default_config_path, f"/opt/augur/{self.config_file_name}"]
if os.getenv('AUGUR_CONFIG_FILE') is not None:
config_file_path = os.getenv('AUGUR_CONFIG_FILE')
using_config_file = True
else:
for index, location in enumerate(config_locations):
try:
f = open(location, "r+")
config_file_path = os.path.abspath(location)
using_config_file = True
f.close()
break
except FileNotFoundError:
pass
if using_config_file:
try:
with open(config_file_path, 'r+') as config_file_handle:
self.config = json.loads(config_file_handle.read())
except json.decoder.JSONDecodeError as e:
logger.warn('%s could not be parsed, using defaults. Fix that file, or delete it and run this again to regenerate it. Error: %s', config_file_path, str(e))
else:
logger.warn('%s could not be parsed, using defaults.')
self.load_env_configuration()
# List of data sources that can do periodic updates
self.cache_config = {
'cache.type': 'file',
'cache.data_dir': 'runtime/cache/',
'cache.lock_dir': 'runtime/cache/'
}
if not os.path.exists(self.cache_config['cache.data_dir']):
os.makedirs(self.cache_config['cache.data_dir'])
if not os.path.exists(self.cache_config['cache.lock_dir']):
os.makedirs(self.cache_config['cache.lock_dir'])
cache_parsed = parse_cache_config_options(self.cache_config)
self.cache = CacheManager(**cache_parsed)
self.metrics = MetricDefinitions(self)
def get_api_key(ctx):
app = ctx.obj
get_api_key_sql = s.sql.text("""
SELECT value FROM augur_operations.augur_settings WHERE setting='augur_api_key';
""")
try:
print(app.database.execute(get_api_key_sql).fetchone()[0])
except TypeError:
logger.warn("No Augur API key found.")
def import_plugins(cls):
"""
Imports all plugins and datasources
"""
if not hasattr(cls, 'plugins'):
setattr(cls, 'plugins', {})
plugins = [augur.plugins, augur.datasources]
for module in plugins:
for importer, modname, ispkg in pkgutil.iter_modules(module.__path__):
if ispkg:
try:
importer.find_module(modname).load_module(modname)
except Exception as e:
logger.warn('Error when loading plugin {module.__name__}.{modname}:')
logger.exception(e)