def view(ctx, host, port, debug, pattern, family_file, family_type,
variant_source, variant_type, root, mode):
"""Visualize DNA variant resources.
1. Look for variant source(s) to visualize and inst. the right plugin
2.
"""
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))
if variant_source is None:
if not os.path.exists(db_path):
logger.warn("database not initialized, run 'puzzle init'")
ctx.abort()
plugin = SqlStore(db_path)
BaseConfig.STORE_ENABLED = True
elif mode == 'vcf':
logger.info("Initialzing VCF plugin")
try:
plugin = VcfPlugin(
root_path=variant_source,
case_lines=family_file,
case_type=family_type,
pattern=pattern,
vtype=variant_type
)
except SyntaxError as e:
logger.error(e.message)
ctx.abort()
elif mode == 'gemini':
logger.info("Initialzing GEMINI plugin")
try:
plugin = GeminiPlugin(db=variant_source, vtype=variant_type)
except NameError:
logger.error("Need to have gemini installed to use gemini plugin")
ctx.abort()
except DatabaseError as e:
logger.error("{0} is not a valid gemini db".format(variant_source))
logger.info("variant-source has to point to a gemini databse")
ctx.abort()
logger.debug("Plugin setup was succesfull")
BaseConfig.PUZZLE_BACKEND = plugin
BaseConfig.ROOT_DIR = root
BaseConfig.UPLOAD_DIR = os.path.join(root, 'resources')
app = create_app(config_obj=BaseConfig)
app.run(host=host, port=port, debug=debug)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from flask.ext.script import Manager
from puzzle.factory import create_app
from puzzle.settings import DevConfig
app = create_app(config_obj=DevConfig)
manager = Manager(app)
if __name__ == '__main__':
manager.run()
def app(request):
app = create_app(config_obj=TestConfig)
return app
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from flask.ext.script import Manager
from puzzle.factory import create_app
from puzzle.settings import DevConfig
app = create_app(config_obj=DevConfig)
manager = Manager(app)
if __name__ == '__main__':
manager.run()
