From 039be6e75859be1915126f55bc858ff314931034 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 23 Mar 2021 11:31:40 +0100
Subject: [PATCH] logging url when connecting
---
gga_load_data.py | 3 ++-
run_workflow_phaeoexplorer.py | 9 ++++++---
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index d6f944a..52902a0 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -273,12 +273,13 @@ class LoadData(speciesData.SpeciesData):
Exit if we cannot connect to the instance
"""
+
+ logging.info("Connecting to the galaxy instance (%s)" % self.instance_url)
self.instance = galaxy.GalaxyInstance(url=self.instance_url,
email=self.config["galaxy_default_admin_email"],
password=self.config["galaxy_default_admin_password"]
)
self.instance.histories.get_histories()
- logging.info("Connecting to the galaxy instance...")
try:
self.instance.histories.get_histories()
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 786afe8..27645dc 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -106,25 +106,28 @@ class RunWorkflow(speciesData.SpeciesData):
return {"history_id": self.history_id, "library_id": library_id, "datasets": self.datasets}
+
def connect_to_instance(self):
"""
Test the connection to the galaxy instance for the current organism
Exit if we cannot connect to the instance
"""
+
+ logging.info("Connecting to the galaxy instance (%s)" % self.instance_url)
self.instance = galaxy.GalaxyInstance(url=self.instance_url,
email=self.config["galaxy_default_admin_email"],
password=self.config["galaxy_default_admin_password"]
)
+ self.instance.histories.get_histories()
- logging.info("Connecting to the galaxy instance %s" % self.instance_url)
try:
self.instance.histories.get_histories()
except bioblend.ConnectionError:
- logging.critical("Cannot connect to galaxy instance %s" % self.instance_url)
+ logging.critical("Cannot connect to galaxy instance (%s) " % self.instance_url)
sys.exit()
else:
- logging.info("Successfully connected to galaxy instance %s" % self.instance_url)
+ logging.info("Successfully connected to galaxy instance (%s) " % self.instance_url)
return 1
--
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