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142 | class fill_metadata(eHive.BaseRunnable):
def param_defaults(self):
return {
"division": "",
"ignore": [],
"copy": {},
}
def run(self):
# params
wd = self.param_required("work_dir")
division = self.param("division")
brc4_mode = self.param("brc4_mode")
ignore = self.param("ignore")
copy = self.param("copy")
genome_data = self.param_required("genome_data")
# update division and url
if "species" in genome_data:
sd = genome_data["species"]
# Add division, but not needed for BRC4
if ("division" not in sd) and not brc4_mode:
sd["division"] = division
if "url" not in sd:
if "production_name" in sd:
sd["url"] = sd["production_name"].capitalize()
# RETROCOMPATIBILITY
# provider name and url to assembly.provider_*: retrocompatibility
if "provider" in genome_data:
prov = genome_data["provider"]
if "name" in prov and not "provider_name" in genome_data["assembly"]:
genome_data["assembly"]["provider_name"] = prov["name"]
if "url" in prov and not "provider_url" in genome_data["assembly"]:
genome_data["assembly"]["provider_url"] = prov["url"]
del genome_data["provider"]
# BRC4 organism abbrev: move from species to BRC4 namespace
if "species" in genome_data:
sd = genome_data["species"]
if "BRC4_organism_abbrev" in sd:
if "BRC4" not in genome_data:
genome_data["BRC4"] = {}
if "organism_abbrev" not in genome_data["BRC4"]:
genome_data["BRC4"]["organism_abbrev"] = sd["BRC4_organism_abbrev"]
del genome_data["species"]["BRC4_organism_abbrev"]
# END RETROCOMPATIBILITY
# Set up display name if not set
if "species" in genome_data:
sd = genome_data["species"]
if not "display_name" in sd and "scientific_name" in sd:
genome_data["species"]["display_name"] = sd["scientific_name"]
# flattern and dump
flat = self.flattern(genome_data, ignore)
flat += list(map(lambda p: (copy[p[0]], p[1]), filter(lambda x: x[0] in copy, flat)))
flat = list(filter(lambda x: x[0] not in ignore, flat))
if len(flat) <= 0:
return
# dump
os.makedirs(wd, exist_ok=True)
sql_file = pj(wd, "insert_meta.sql")
with open(sql_file, "w") as sql:
print("insert ignore into meta (species_id, meta_key, meta_value) values", file=sql)
c = ""
for _key, _val in flat:
if isinstance(_val, bool):
_val = int(_val)
if isinstance(_val, str):
_val = '"%s"' % (_val)
print('%s (1, "%s", %s)' % (c, str(_key), str(_val)), file=sql)
c = ","
print(";", file=sql)
# run insert sql
self.run_sql_req(sql_file, log_pfx=sql_file, from_file=True)
def flattern(self, data, ignore_lst, pfx=None):
# vectors with values only
if isinstance(data, list):
return [(pfx, v) for v in data]
elif isinstance(data, dict):
ignore_lst = frozenset(ignore_lst)
res = []
for k, v in data.items():
new_pfx = ".".join(filter(lambda p: p != None, [pfx, k]))
res.append(self.flattern(v, ignore_lst, new_pfx))
return sum(res, [])
return data != None and [(pfx, data)] or []
def run_sql_req(self, sql, log_pfx, from_file=False):
os.makedirs(dirname(log_pfx), exist_ok=True)
sql_option = r""" -sql '{_sql}' """.format(_sql=sql)
if from_file:
sql_option = r""" < '{_sql}' """.format(_sql=sql)
cmd = r"""{_dbcmd} -url "{_srv}{_dbname}" {_sql_option} > {_out} 2> {_err}""".format(
_dbcmd="perl %s/scripts/db_cmd.pl" % os.getenv("EHIVE_ROOT_DIR"),
_srv=self.param("dbsrv_url"),
_dbname=self.param("db_name"),
_sql_option=sql_option,
_out=log_pfx + ".stdout",
_err=log_pfx + ".stderr",
)
print("running %s" % (cmd), file=sys.stderr)
return sp.run(cmd, shell=True, check=True)
def db_string(self):
return "-dbhost {host_} -dbport {port_} -dbuser {user_} -dbpass {pass_} -dbname {dbname_} ".format(
host_=self.param("dbsrv_host"),
port_=self.param("dbsrv_port"),
user_=self.param("dbsrv_user"),
pass_=self.param("dbsrv_pass"),
dbname_=self.param("db_name"),
)
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