From 5e0fb6906b0b0b6ff15f54c0185436dc36afb414 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Tue, 11 May 2021 18:43:33 +0200
Subject: [PATCH] fix Object-oriented galaxy instance (for get_previews())
---
gga_load_data.py | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index 6bffec7..9d22770 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -11,6 +11,7 @@ import json
import yaml
from bioblend import galaxy
+from bioblend.galaxy.objects import GalaxyInstance
import utilities
import speciesData
@@ -100,7 +101,7 @@ class LoadData(speciesData.SpeciesData):
return histories
- def setup_library(self, instance):
+ def setup_library(self, instance, data_dir_root='./src_data'):
"""
Create a "Project Data" library in galaxy, mirroring the "src_data" folder of the current organism
directory tree
@@ -110,10 +111,16 @@ class LoadData(speciesData.SpeciesData):
self.goto_species_dir()
+ gio = GalaxyInstance(url=self.instance_url,
+ email=self.config["galaxy_default_admin_email"],
+ password=self.config["galaxy_default_admin_password"]
+ )
+
+ logging.info("Looking for project data in %s" % data_dir_root)
folders = dict()
post_renaming = {}
- for root, dirs, files in os.walk("./src_data", followlinks=True):
+ for root, dirs, files in os.walk(data_dir_root, followlinks=True):
file_list = [os.path.join(root, filename) for filename in files]
folders[root] = file_list
@@ -132,7 +139,7 @@ class LoadData(speciesData.SpeciesData):
for fname, files in folders.items():
if fname and files:
- folder_name = fname[len("./src_data") + 1:]
+ folder_name = fname[len(data_dir_root) + 1:]
logging.info("Creating folder: %s" % folder_name)
folder = self.create_deep_folder(prj_lib, folder_name)
--
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