From 9468ac92d5d56f6c7027a4819ebc76d34f9cbb35 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 30 May 2021 22:18:54 +0200
Subject: [PATCH] fix get_history(). Change verbosity
---
gga_load_data.py | 79 ++++++++++++++++++++++++-------------------
utilities_bioblend.py | 2 +-
2 files changed, 45 insertions(+), 36 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index d664c70..f4e0818 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -38,33 +38,6 @@ class LoadData(speciesData.SpeciesData):
self.bam_metadata_cache = {}
super().__init__(parameters_dictionary)
- def remove_homo_sapiens_from_db(self):
- """
- Run the GMOD tool to remove the "Homo sapiens" default organism from the original database
- Will do nothing if H. sapiens isn't in the database
-
- """
-
- logging.debug("Getting 'Homo sapiens' ID in chado database")
- get_sapiens_id_json_output = utilities_bioblend.run_tool_and_download_single_output_dataset(
- self.instance,
- tool_id=constants.GET_ORGANISMS_TOOL, # If this version if not found, Galaxy will use the one that is found
- history_id=self.history_id,
- tool_inputs={"genus": "Homo", "species": "sapiens"})
-
- logging.info("Deleting Homo 'sapiens' in the instance's chado database")
- try:
- get_sapiens_id_final_output = json.loads(get_sapiens_id_json_output)[0]
- sapiens_id = str(get_sapiens_id_final_output["organism_id"]) # needs to be str to be recognized by the chado tool
- utilities_bioblend.run_tool(
- self.instance,
- tool_id=constants.DELETE_ORGANISMS_TOOL,
- history_id=self.history_id,
- tool_inputs={"organism": sapiens_id})
- except IndexError:
- logging.error("Homo sapiens isn't in the instance's chado database (IndexError)")
- pass
-
def purge_histories(self):
"""
Delete all histories in the instance
@@ -256,7 +229,33 @@ class LoadData(speciesData.SpeciesData):
logging.info("Did not find metadata in %s " % meta_file)
return self.get_bam_label(dirname, bam_file)
-
+def remove_homo_sapiens_from_db(instance, history_id):
+ """
+ Run the GMOD tool to remove the "Homo sapiens" default organism from the original database
+ Will do nothing if H. sapiens isn't in the database
+
+ """
+
+ logging.debug("Getting 'Homo sapiens' ID in chado database")
+ get_sapiens_id_json_output = utilities_bioblend.run_tool_and_download_single_output_dataset(
+ instance,
+ tool_id=constants.GET_ORGANISMS_TOOL, # If this version if not found, Galaxy will use the one that is found
+ history_id=history_id,
+ tool_inputs={"genus": "Homo", "species": "sapiens"})
+
+ logging.info("Deleting Homo 'sapiens' in the instance's chado database")
+ try:
+ get_sapiens_id_final_output = json.loads(get_sapiens_id_json_output)[0]
+ sapiens_id = str(get_sapiens_id_final_output["organism_id"]) # needs to be str to be recognized by the chado tool
+ utilities_bioblend.run_tool(
+ instance,
+ tool_id=constants.DELETE_ORGANISMS_TOOL,
+ history_id=history_id,
+ tool_inputs={"organism": sapiens_id})
+ except IndexError:
+ logging.error("Homo sapiens isn't in the instance's chado database (IndexError)")
+ pass
+
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Load data into Galaxy library")
@@ -268,6 +267,10 @@ if __name__ == "__main__":
help="Increase output verbosity",
action="store_true")
+ parser.add_argument("-vv", "--very_verbose",
+ help="Increase output verbosity",
+ action="store_true")
+
parser.add_argument("--config",
type=str,
help="Config path, default to 'examples/config.yml'")
@@ -278,11 +281,14 @@ if __name__ == "__main__":
args = parser.parse_args()
- if args.verbose:
+ if args.verbose or args.very_verbose:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
- logging.getLogger("urllib3").setLevel(logging.INFO)
+
+ if not args.very_verbose:
+ logging.getLogger("urllib3").setLevel(logging.INFO)
+ logging.getLogger("bioblend").setLevel(logging.INFO)
# Parsing the config file if provided, using the default config otherwise
if args.config:
@@ -338,14 +344,17 @@ if __name__ == "__main__":
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
- load_data_for_current_species.history_id = utilities_bioblend.get_history(
+ # Get default history
+ history_id = utilities_bioblend.get_history(
instance=load_data_for_current_species.instance,
- history_name=load_data_for_current_species.history_name)
-
+ history_name="Unnamed history")
+
# Remove H. sapiens from database if here
# TODO: set a dedicated history for removing H. sapiens (instead of doing it into a species history)
- load_data_for_current_species.remove_homo_sapiens_from_db()
+ remove_homo_sapiens_from_db(
+ instance=load_data_for_current_species.instance,
+ history_id=history_id
+ )
# logging.info("Importing datasets into history for %s" % load_data_for_current_species.full_name)
# load_data_for_current_species.import_datasets_into_history() # Option "--load-history"
diff --git a/utilities_bioblend.py b/utilities_bioblend.py
index 0c959bc..08bb1bd 100644
--- a/utilities_bioblend.py
+++ b/utilities_bioblend.py
@@ -47,7 +47,7 @@ def get_history(instance, history_name):
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:
+ elif len(histories) == 1:
history_id = histories[0]["id"]
logging.debug("History ID set for {0}: {1}".format(history_name, history_id))
else:
--
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