diff --git a/gseapy/biomart.py b/gseapy/biomart.py
index fd0858e..943458d 100644
--- a/gseapy/biomart.py
+++ b/gseapy/biomart.py
@@ -73,7 +73,7 @@ def __init__(self, host: str = "www.ensembl.org", verbose: bool = False):
self.reset()
# get supported marts
- self._marts = self.get_marts()["Mart"].to_list()
+ self._marts = None
def __del__(self):
handlers = self._logger.handlers[:]
@@ -84,31 +84,29 @@ def __del__(self):
def _set_host(self, host: str):
"""set host"""
- hosts = ["www.ensembl.org", "asia.ensembl.org", "useast.ensembl.org"]
+ hosts = ["useast.ensembl.org", "asia.ensembl.org"]
hosts.insert(0, host)
- secure = ""
-
- # if self._secure:
- # secure = "s"
+ secure = "s"
# if host not work, select next
i = 0
while i < len(hosts):
- url = "http{}://{}/biomart/martservice".format(secure, hosts[i])
- request = requests.head(url)
- if request.status_code in [200]:
+ url = "http{}://{}/biomart/martservice?type=registry".format(
+ secure, hosts[i]
+ )
+ request = requests.get(url)
+ # '\n\n\n Service unavailable\n
+ # "\n\n"
+ if request.ok and request.text.startswith("\n\n"):
self.host = hosts[i]
break
- else:
- self._logger.warning(
- "host {} is not reachable, will try {} ".format(
- hosts[i], hosts[i % len(hosts)]
- )
+ self._logger.warning(
+ "host {} is not reachable, try {} ".format(
+ hosts[i], hosts[(i + 1) % len(hosts)]
)
+ )
i += 1
if i == len(hosts):
- raise ValueError(
- "host is not reachable. Please check your input or try again later."
- )
+ self._logger.warning("hosts is not reachable. Please try again later.")
def add_filter(self, name: str, value: Iterable[str]):
"""
@@ -152,18 +150,21 @@ def get_marts(self):
host=self.host, i=self._id
)
resp = requests.get(url)
- if resp.ok:
- # marts = pd.read_xml(resp.text)
+ if resp.ok and resp.text.startswith("\n\n"):
marts = [e.attrib for e in ET.XML(resp.text)]
marts = pd.DataFrame(marts)
marts = marts.loc[:, ["database", "displayName", "name"]]
marts.columns = ["Version", "DisplayName", "Mart"]
+ # get supported marts
+ self._marts = marts["Mart"].to_list()
return marts.loc[:, ["Mart", "Version"]]
return resp.text
def get_datasets(self, mart: str = "ENSEMBL_MART_ENSEMBL"):
"""Get available datasets from mart you've selected"""
+ if self._marts is None:
+ self.get_marts()
if mart not in self._marts:
raise ValueError(
"Provided mart name (%s) is not valid. see 'names' attribute" % mart