From b59d2a28e70b59bb395e01b5197ad2b66413185d Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 30 May 2021 22:02:16 +0200
Subject: [PATCH] fix get_history
---
gga_load_data.py | 27 ++++-----------------------
speciesData.py | 1 +
utilities_bioblend.py | 17 ++++++++++-------
3 files changed, 15 insertions(+), 30 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index 2c00165..0aadf59 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -2,7 +2,6 @@
# -*- coding: utf-8 -*-
import re
-import bioblend
import argparse
import os
import logging
@@ -39,27 +38,6 @@ class LoadData(speciesData.SpeciesData):
self.bam_metadata_cache = {}
super().__init__(parameters_dictionary)
- def get_history(self):
- """
- Create or set the working history to the current species one
-
- :return:
- """
- try:
- histories = self.instance.histories.get_histories(name=str(self.genus_species))
- if len(histories) == 1:
- self.history_id = histories[0]["id"]
- logging.debug("History ID set for {0} {1}: {2}".format(self.genus, self.species, self.history_id))
- else:
- logging.critical("Multiple histories exists for {0}: {1}".format(self.genus, self.species))
- except IndexError:
- logging.info("Creating history for {0} {1}".format(self.genus, self.species))
- hist_dict = self.instance.histories.create_history(name=str(self.genus_species))
- self.history_id = hist_dict["id"]
- logging.debug("History ID set for {0} {1}: {2}".format(self.genus, self.species, self.history_id))
-
- return self.history_id
-
def remove_homo_sapiens_from_db(self):
"""
Run the GMOD tool to remove the "Homo sapiens" default organism from the original database
@@ -304,6 +282,7 @@ if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
+ logging.getLogger("urllib3").setLevel(logging.INFO)
# Parsing the config file if provided, using the default config otherwise
if args.config:
@@ -360,7 +339,9 @@ if __name__ == "__main__":
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
- load_data_for_current_species.get_history()
+ load_data_for_current_species.history_id = utilities_bioblend.get_history(
+ instance=load_data_for_current_species.instance,
+ history_name=load_data_for_current_species.history_name)
# Remove H. sapiens from database if here
# TODO: set a dedicated history for removing H. sapiens (instead of doing it into a species history)
diff --git a/speciesData.py b/speciesData.py
index 1e2a9f3..3d41670 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -139,4 +139,5 @@ class SpeciesData:
self.instance_url = None
self.instance = None
self.history_id = None
+ self.history_name = str(self.genus_species)
self.library_id = None
diff --git a/utilities_bioblend.py b/utilities_bioblend.py
index 3cfcc48..0c959bc 100644
--- a/utilities_bioblend.py
+++ b/utilities_bioblend.py
@@ -34,21 +34,24 @@ def get_galaxy_instance(instance_url, email, password):
return instance
+
def get_history(instance, history_name):
"""
Create or set the working history to the current species one
:return:
"""
- try:
- histories = instance.histories.get_histories(name=history_name)
- history_id = histories[0]["id"]
- logging.debug("History ID set for {0}: {1}".format(history_name, history_id))
- except IndexError:
+ histories = instance.histories.get_histories(name=str(history_name))
+ if len(histories) == 0:
logging.info("Creating history for %s" % history_name)
- history = instance.histories.create_history(name=history_name)
- history_id = history["id"]
+ hist_dict = instance.histories.create_history(name=str(history_name))
+ history_id = hist_dict["id"]
logging.debug("History ID set for {0}: {1}".format(history_name, history_id))
+ if len(histories) == 1:
+ history_id = histories[0]["id"]
+ logging.debug("History ID set for {0}: {1}".format(history_name, history_id))
+ else:
+ logging.critical("Multiple histories exists for {0}".format(history_name))
return history_id
--
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