def index(self, organism=None, db_version=None):
global results_dir, uploads_dir, sett
if not organism: organism = sett["default_organism"]
if DEBUG_MODE or not organism in self._index_html:
tmpl = lookup.get_template("master.mako")
paths = PathNode()
paths.name = "Root"
[html_dbversion, db_version
] = grsnp_path.get_database_versions_html(sett["data_dir"],
db_version)
paths.organisms = self.get_org(db_version)
# Check if the organism actually exists in the current database.
# If it is not, select the default organism
if not organism in paths.organisms:
organism = sett["default_organism"]
custom_dir = os.path.join(
os.path.split(sett["data_dir"][db_version])[0], "custom_data")
# Use mako to render index.html
body = lookup.get_template("index.mako").render(
paths=paths,
default_background=paths.get_backgrounds_combo(
organism, custom_dir),
custom_gfs=paths.get_custom_gfs(organism, custom_dir),
demo_snps=paths.get_custom_fois(organism, custom_dir),
data_dir=os.path.join(sett["data_dir"][db_version], organism),
default_organism=organism,
database_versions=html_dbversion,
pct_scores=paths.get_scores(
os.path.split(sett["data_dir"][db_version])[0]))
script = lookup.get_template("index.js").render(
default_organism=organism)
self._index_html[organism] = tmpl.render(body=body, script=script)
return self._index_html[organism]
def __init__(self):
# go through each database directory and create custom_data if it does not exist.
for db_ver, db_dir in sett["data_dir"].items():
# create all directories in the custom_data dir if they do not already exist
for org in self.get_org(db_ver):
custom_dir = os.path.join(
os.path.split(db_dir)[0], "custom_data")
logger.info("Processing genomic features for {}".format(org))
if not os.path.exists(custom_dir): os.mkdir(custom_dir)
cust_sub_dir = [
"backgrounds", "gfs", "fois", "rsid_conversion"
]
for c in cust_sub_dir:
tmp = os.path.join(custom_dir, c)
if not os.path.exists(tmp): os.mkdir(tmp)
c_dir = os.path.join(custom_dir, c, org)
if not os.path.exists(c_dir): os.mkdir(c_dir)
# Read the genomic feature files and generate html files
paths = PathNode()
paths.name = "Root"
paths.organisms = self.get_org(db_ver)
paths.traverse(os.path.join(db_dir, org))
grsnp_path.write_treeview_json(os.path.join(db_dir, org))
self._index_html = {}
