def init(ctx, reset):
"""Initialize a database that store metadata
Check if "root" dir exists, otherwise create the directory and
build the database. If a database already exists, do nothing.
The behaviour will be different with different plugins. A config file
in YAML format will be created in puzzle/configs with information about
the database.
VCF:
A sqlite database will be built in the home directory of the user
GEMINI:
A sqlite database will be built in the home directory of the user
"""
puzzle_dir = ctx.obj['root']
if os.path.exists(puzzle_dir):
logger.debug("Found puzzle directory: {0}".format(puzzle_dir))
else:
logger.info("Create directory: {0}".format(puzzle_dir))
os.makedirs(puzzle_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(ctx.obj['db_path'])
store.set_up(reset=reset)
def init(ctx, reset, root, phenomizer):
"""Initialize a database that store metadata
Check if "root" dir exists, otherwise create the directory and
build the database. If a database already exists, do nothing.
The behaviour will be different with different plugins. A config file
in YAML format will be created in puzzle/configs with information about
the database.
VCF:
A sqlite database will be built in the home directory of the user
GEMINI:
A sqlite database will be built in the home directory of the user
"""
configs = {}
if root is None:
root = ctx.obj.get('root') or os.path.expanduser("~/.puzzle")
configs['root'] = root
print(phenomizer)
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
resource_dir = os.path.join(root, 'resources')
logger.info("resource dir is: {}".format(resource_dir))
if os.path.exists(resource_dir):
logger.debug("Found puzzle directory: {0}".format(root))
if os.path.exists(resource_dir) and not reset:
logger.warning("Puzzle db already in place")
ctx.abort()
else:
logger.info("Create directory: {0}".format(resource_dir))
os.makedirs(resource_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(db_path)
store.set_up(reset=reset)
if phenomizer:
phenomizer = [str(term) for term in phenomizer]
configs['phenomizer_auth'] = phenomizer
if not ctx.obj.get('config_path'):
logger.info("Creating puzzle config file in {0}".format(PUZZLE_CONFIG_PATH))
with codecs.open(PUZZLE_CONFIG_PATH, 'w', encoding='utf-8') as f:
f.write(yaml.dump(configs))
logger.debug("Config created")
def init(ctx, reset, root, phenomizer):
"""Initialize a database that store metadata
Check if "root" dir exists, otherwise create the directory and
build the database. If a database already exists, do nothing.
"""
configs = {}
if root is None:
root = ctx.obj.get('root') or os.path.expanduser("~/.puzzle")
configs['root'] = root
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
resource_dir = os.path.join(root, 'resources')
logger.info("resource dir is: {}".format(resource_dir))
if os.path.exists(resource_dir):
logger.debug("Found puzzle directory: {0}".format(root))
if os.path.exists(resource_dir) and not reset:
logger.warning("Puzzle db already in place")
ctx.abort()
else:
logger.info("Create directory: {0}".format(resource_dir))
os.makedirs(resource_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(db_path)
store.set_up(reset=reset)
if phenomizer:
phenomizer = [str(term) for term in phenomizer]
configs['phenomizer_auth'] = phenomizer
if not ctx.obj.get('config_path'):
logger.info("Creating puzzle config file in {0}".format(PUZZLE_CONFIG_PATH))
with codecs.open(PUZZLE_CONFIG_PATH, 'w', encoding='utf-8') as f:
f.write(yaml.dump(configs))
logger.debug("Config created")
def puzzle_dir(request, dir_path):
"""Return a puzzle dir with a database initialized"""
db_path = os.path.join(dir_path, 'puzzle_db.sqlite3')
logger.debug("db path is: {}".format(db_path))
resource_dir = os.path.join(dir_path, 'resources')
logger.debug("resource dir is: {}".format(resource_dir))
logger.debug("Create directory: {0}".format(resource_dir))
os.makedirs(resource_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(db_path)
store.set_up(reset=False)
# It's getting tear downed by dir_path()...
return dir_path
def init(ctx, reset, root):
"""Initialize a database that store metadata
Check if "root" dir exists, otherwise create the directory and
build the database. If a database already exists, do nothing.
The behaviour will be different with different plugins. A config file
in YAML format will be created in puzzle/configs with information about
the database.
VCF:
A sqlite database will be built in the home directory of the user
GEMINI:
A sqlite database will be built in the home directory of the user
"""
if root is None:
root = os.path.expanduser("~/.puzzle")
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
resource_dir = os.path.join(root, 'resources')
logger.info("resource dir is: {}".format(resource_dir))
if os.path.exists(resource_dir):
logger.debug("Found puzzle directory: {0}".format(root))
if os.path.exists(resource_dir) and not reset:
logger.warning("Puzzle db already in place")
ctx.abort()
else:
logger.info("Create directory: {0}".format(resource_dir))
os.makedirs(resource_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(db_path)
store.set_up(reset=reset)
def puzzle_dir(request, dir_path):
"""Return a puzzle dir with a database initialized"""
db_path = os.path.join(dir_path, 'puzzle_db.sqlite3')
logger.debug("db path is: {}".format(db_path))
resource_dir = os.path.join(dir_path, 'resources')
logger.debug("resource dir is: {}".format(resource_dir))
logger.debug("Create directory: {0}".format(resource_dir))
os.makedirs(resource_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(db_path)
store.set_up(reset=False)
#It's getting tear downed by dir_path()...
return dir_path
def populated_puzzle_db(request, dir_path, case_obj):
"""Return a puzzle dir with a populated database"""
db_path = os.path.join(dir_path, 'puzzle_db.sqlite3')
logger.debug("db path is: {}".format(db_path))
resource_dir = os.path.join(dir_path, 'resources')
logger.debug("resource dir is: {}".format(resource_dir))
logger.debug("Create directory: {0}".format(resource_dir))
os.makedirs(resource_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(db_path)
store.set_up(reset=False)
store.add_case(case_obj, vtype='sv', mode='vcf')
#It's getting tear downed by dir_path()...
return dir_path
def populated_puzzle_db(request, dir_path, case_obj):
"""Return a puzzle dir with a populated database"""
db_path = os.path.join(dir_path, 'puzzle_db.sqlite3')
logger.debug("db path is: {}".format(db_path))
resource_dir = os.path.join(dir_path, 'resources')
logger.debug("resource dir is: {}".format(resource_dir))
logger.debug("Create directory: {0}".format(resource_dir))
os.makedirs(resource_dir)
logger.debug('Directory created')
logger.debug('Connect to database and create tables')
store = SqlStore(db_path)
store.set_up(reset=False)
store.add_case(case_obj, vtype='sv', mode='vcf')
#It's getting tear downed by dir_path()...
return dir_path
def sql_store():
"""Setup an in-memory database."""
_test_db = SqlStore('sqlite:///:memory:')
_test_db.set_up()
yield _test_db
_test_db.tear_down()
def sql_store():
"""Setup an in-memory database."""
_test_db = SqlStore('sqlite:///:memory:')
_test_db.set_up()
yield _test_db
_test_db.tear_down()
def view(ctx, host, port, debug, pattern, family_file, family_type,
variant_source, root, no_browser, phenomizer):
"""Visualize DNA variant resources.
1. Look for variant source(s) to visualize and inst. the right plugin
"""
root = root or ctx.obj.get('root') or os.path.expanduser("~/.puzzle")
phenomizer_auth = phenomizer or ctx.obj.get('phenomizer_auth')
BaseConfig.PHENOMIZER_AUTH = True if ctx.obj.get('phenomizer_auth') else False
BaseConfig.STORE_ENABLED = True
if variant_source is None:
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
if not os.path.exists(db_path):
logger.warn("database not initialized, run 'puzzle init'")
ctx.abort()
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
store = SqlStore(db_path, phenomizer_auth=phenomizer_auth)
for case_obj in store.cases():
if case_obj.variant_mode == 'gemini':
if not GEMINI:
logger.error("Need to have gemini instaled to view gemini database")
ctx.abort()
else:
logger.info("Using in memory database")
store = SqlStore('sqlite:///:memory:', phenomizer_auth=phenomizer_auth)
store.set_up()
cases = []
if os.path.isfile(variant_source):
file_type = get_file_type(variant_source)
#Test if gemini is installed
if file_type == 'unknown':
logger.error("File has to be vcf or gemini db")
ctx.abort()
elif file_type == 'gemini':
#Check if gemini is installed
if not GEMINI:
logger.error("Need to have gemini installed to use gemini plugin")
ctx.abort()
variant_type = get_variant_type(variant_source)
cases = get_cases(
variant_source=variant_source,
case_lines=family_file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type
)
else:
for file in path(variant_source).walkfiles(pattern):
file_type = get_file_type(file)
if file_type != 'unknown':
variant_type = get_variant_type(file)
#Test if gemini is installed
if file_type == 'gemini':
if not GEMINI:
logger.error("Need to have gemini installed to use gemini plugin")
ctx.abort()
for case in get_cases(
variant_source=file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type):
cases.append(case)
for case_obj in cases:
if store.case(case_obj.case_id) is not None:
logger.warn("{} already exists in the database"
.format(case_obj.case_id))
continue
# extract case information
logger.debug("adding case: {}".format(case_obj.case_id))
store.add_case(case_obj, vtype=case_obj.variant_type, mode=case_obj.variant_mode)
logger.debug("Plugin setup was succesfull")
BaseConfig.PUZZLE_BACKEND = store
BaseConfig.UPLOAD_DIR = os.path.join(root, 'resources')
app = create_app(config_obj=BaseConfig)
if not (no_browser or debug):
webbrowser.open_new_tab("http://{}:{}".format(host, port))
app.run(host=host, port=port, debug=debug)
def view(ctx, host, port, debug, pattern, family_file, family_type,
variant_source, root, no_browser, phenomizer):
"""Visualize DNA variant resources.
1. Look for variant source(s) to visualize and inst. the right plugin
"""
main_loop = (not debug) or (os.environ.get('WERKZEUG_RUN_MAIN') == 'true')
root = root or ctx.obj.get('root') or os.path.expanduser("~/.puzzle")
phenomizer_auth = phenomizer or ctx.obj.get('phenomizer_auth')
BaseConfig.PHENOMIZER_AUTH = True if ctx.obj.get(
'phenomizer_auth') else False
BaseConfig.STORE_ENABLED = True
if variant_source is None:
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
if not os.path.exists(db_path):
logger.warn("database not initialized, run 'puzzle init'")
ctx.abort()
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
store = SqlStore(db_path, phenomizer_auth=phenomizer_auth)
for case_obj in store.cases():
if case_obj.variant_mode == 'gemini':
if not GEMINI:
logger.error(
"Need to have gemini instaled to view gemini database")
ctx.abort()
else:
logger.info("Using in memory database")
tmpdir = tempfile.mkdtemp()
tmpdb = os.path.join(tmpdir, 'puzzle.sqlite3')
logger.info("building database: {}".format(tmpdb))
store = SqlStore("sqlite:///{}".format(tmpdb),
phenomizer_auth=phenomizer_auth)
if main_loop:
store.set_up()
cases = []
if os.path.isfile(variant_source):
file_type = get_file_type(variant_source)
#Test if gemini is installed
if file_type == 'unknown':
logger.error("File has to be vcf or gemini db")
ctx.abort()
elif file_type == 'gemini':
#Check if gemini is installed
if not GEMINI:
logger.error(
"Need to have gemini installed to use gemini plugin"
)
ctx.abort()
variant_type = get_variant_type(variant_source)
cases = get_cases(variant_source=variant_source,
case_lines=family_file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type)
else:
for file in path(variant_source).walkfiles(pattern):
file_type = get_file_type(file)
if file_type != 'unknown':
variant_type = get_variant_type(file)
#Test if gemini is installed
if file_type == 'gemini':
if not GEMINI:
logger.error(
"Need to have gemini installed to use gemini plugin"
)
ctx.abort()
for case in get_cases(variant_source=file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type):
cases.append(case)
for case_obj in cases:
if store.case(case_obj.case_id) is not None:
logger.warn("{} already exists in the database".format(
case_obj.case_id))
continue
# extract case information
logger.debug("adding case: {}".format(case_obj.case_id))
store.add_case(case_obj,
vtype=case_obj.variant_type,
mode=case_obj.variant_mode)
logger.debug("Plugin setup was succesfull")
BaseConfig.PUZZLE_BACKEND = store
BaseConfig.UPLOAD_DIR = os.path.join(root, 'resources')
app = create_app(config_obj=BaseConfig)
if no_browser is False:
webbrowser.open_new_tab("http://{}:{}".format(host, port))
app.run(host=host, port=port, debug=debug)
