From 07d45756bd4cc3c8216905570a64f93f50829765 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 30 May 2021 22:37:06 +0200
Subject: [PATCH] fix library_id
---
gga_load_data.py | 4 ++--
gga_run_workflow_phaeo_jbrowse.py | 12 +++++++++++-
speciesData.py | 1 -
3 files changed, 13 insertions(+), 4 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index f4e0818..726b4e9 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -86,8 +86,8 @@ class LoadData(speciesData.SpeciesData):
logging.info("Creating new %s library" % constants.GALAXY_LIBRARY_NAME)
prj_lib = gio.libraries.create(constants.GALAXY_LIBRARY_NAME, constants.GALAXY_LIBRARY_DESC)
- self.library_id = prj_lib.id # project data folder/library
- logging.info("Library for {0}: {1}".format(self.full_name, self.library_id))
+ library_id = prj_lib.id # project data folder/library
+ logging.info("Library for {0}: {1}".format(self.full_name, library_id))
for fname, files in folders.items():
if fname and files:
diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py
index e6eada5..b7a9a24 100644
--- a/gga_run_workflow_phaeo_jbrowse.py
+++ b/gga_run_workflow_phaeo_jbrowse.py
@@ -8,6 +8,7 @@ import logging
import sys
import json
import time
+from bioblend.galaxy.objects import GalaxyInstance
import utilities
import utilities_bioblend
@@ -185,7 +186,16 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
transcripts_hda_id = None
proteins_hda_id = None
- folder_dict_list = self.instance.libraries.get_folders(library_id=str(self.library_id))
+ gio = GalaxyInstance(url=self.instance_url,
+ email=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_EMAIL],
+ password=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_PASSWORD]
+ )
+ prj_lib = gio.libraries.get_previews(constants.GALAXY_LIBRARY_NAME)
+ if len(prj_lib) == 1:
+ library_id = prj_lib[0].id
+ else:
+ logging.error("Multiple (or no one) libraries '%s' exist" % constants.GALAXY_LIBRARY_NAME)
+ folder_dict_list = self.instance.libraries.get_folders(library_id=str(library_id))
folders_id_dict = {}
diff --git a/speciesData.py b/speciesData.py
index 3d41670..4102680 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -140,4 +140,3 @@ class SpeciesData:
self.instance = None
self.history_id = None
self.history_name = str(self.genus_species)
- self.library_id = None
--
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