From b6043307c5f56d9aa5b08a0e38012c4b0df5fb76 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Tue, 11 May 2021 18:45:43 +0200
Subject: [PATCH] fix Object-oriented galaxy instance (for get_previews())
---
gga_load_data.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index 9d22770..655f78a 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -101,7 +101,7 @@ class LoadData(speciesData.SpeciesData):
return histories
- def setup_library(self, instance, data_dir_root='./src_data'):
+ def setup_library(self, data_dir_root='./src_data'):
"""
Create a "Project Data" library in galaxy, mirroring the "src_data" folder of the current organism
directory tree
@@ -111,7 +111,7 @@ class LoadData(speciesData.SpeciesData):
self.goto_species_dir()
- gio = GalaxyInstance(url=self.instance_url,
+ instance = GalaxyInstance(url=self.instance_url,
email=self.config["galaxy_default_admin_email"],
password=self.config["galaxy_default_admin_password"]
)
@@ -372,7 +372,7 @@ if __name__ == "__main__":
# Load the datasets into a galaxy library
logging.info("Setting up library for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species))
- load_data_for_current_species.setup_library(load_data_for_current_species.instance)
+ load_data_for_current_species.setup_library()
logging.debug("Successfully set up library in galaxy for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species))
# Set or get the history for the current organism
--
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