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Commit 73cc89a8 authored by Loraine Gueguen's avatar Loraine Gueguen
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Remove unused imports. Factorize goto_species_dir(), create_galaxy_instance.... 

Remove unused imports. Factorize goto_species_dir(), create_galaxy_instance. Move constants at the beginning. Use upload_from_galaxy_fs() instead of upload_from_local(). Add get_bam_label()
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2 merge requests!10Release 2.0,!9Release 2.0 (merge dev to master)
This commit is part of merge request !10. Comments created here will be created in the context of that merge request.
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gga_load_data.py
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− 90
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......@@ -4,18 +4,13 @@
import bioblend
import argparse
import os
import subprocess
import logging
import sys
import fnmatch
import time
import json
import re
import stat
import shutil
import yaml
from bioblend.galaxy.objects import GalaxyInstance
from bioblend import galaxy
import utilities
import speciesData
......@@ -23,11 +18,15 @@ import speciesData
"""
gga_load_data.py
Usage: $ python3 gga_init.py -i input_example.yml --config config.yml [OPTIONS]
Usage: $ python3 gga_load_data.py -i input_example.yml --config config.yml [OPTIONS]
Do not call this script before the galaxy container is ready
"""
# If this version if not found, Galaxy will use the one that is found
GET_ORGANISMS_TOOL = "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.4+galaxy0"
DELETE_ORGANISMS_TOOL = "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.4+galaxy0"
class LoadData(speciesData.SpeciesData):
"""
......@@ -39,23 +38,7 @@ class LoadData(speciesData.SpeciesData):
"""
def goto_species_dir(self):
"""
Go to the species directory (starting from the main dir)
:return:
"""
os.chdir(self.main_dir)
species_dir = os.path.join(self.main_dir, self.genus_species) + "/"
try:
os.chdir(species_dir)
except OSError:
logging.critical("Cannot access %s" % species_dir)
sys.exit(0)
return 1
def set_get_history(self):
def get_history(self):
"""
Create or set the working history to the current species one
......@@ -63,13 +46,15 @@ class LoadData(speciesData.SpeciesData):
"""
try:
histories = self.instance.histories.get_histories(name=str(self.genus_species))
self.history_id = histories[0]["id"]
logging.debug("History ID set for {0} {1}: {2}".format(self.genus, self.species, self.history_id))
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 {1}: {2}".format(self.genus, self.species))
except IndexError:
logging.info("Creating history for {0} {1}".format(self.genus, self.species))
self.instance.histories.create_history(name=str(self.genus_species))
histories = self.instance.histories.get_histories(name=str(self.genus_species))
self.history_id = histories[0]["id"]
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
......@@ -81,26 +66,20 @@ class LoadData(speciesData.SpeciesData):
"""
get_organism_tool = self.instance.tools.show_tool("toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.4+galaxy0")
delete_organism_tool = self.instance.tools.show_tool("toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.4+galaxy0")
get_organism_tool_version = get_organism_tool["version"]
delete_organism_tool_version = delete_organism_tool["version"]
logging.debug("Getting 'Homo sapiens' ID in instance's chado database")
logging.debug("Getting 'Homo sapiens' ID in chado database")
get_sapiens_id_job = self.instance.tools.run_tool(
tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/%s" % get_organism_tool_version,
tool_id=GET_ORGANISMS_TOOL,
history_id=self.history_id,
tool_inputs={"genus": "Homo", "species": "sapiens"})
get_sapiens_id_job_output = get_sapiens_id_job["outputs"][0]["id"]
get_sapiens_id_json_output = self.instance.datasets.download_dataset(dataset_id=get_sapiens_id_job_output)
get_sapiens_id_job_output_dataset_id = get_sapiens_id_job["outputs"][0]["id"]
get_sapiens_id_json_output = self.instance.datasets.download_dataset(dataset_id=get_sapiens_id_job_output_dataset_id)
try:
logging.debug("Deleting Homo 'sapiens' in the instance's chado database")
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
self.instance.tools.run_tool(
tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/%s" % delete_organism_tool_version,
tool_id=DELETE_ORGANISMS_TOOL,
history_id=self.history_id,
tool_inputs={"organism": str(sapiens_id)})
except bioblend.ConnectionError:
......@@ -125,7 +104,7 @@ class LoadData(speciesData.SpeciesData):
return histories
def setup_library(self):
def setup_library(self, instance):
"""
Create a "Project Data" library in galaxy, mirroring the "src_data" folder of the current organism
directory tree
......@@ -135,11 +114,6 @@ class LoadData(speciesData.SpeciesData):
self.goto_species_dir()
# Delete pre-existing lib (probably created by a previous call)
gio = GalaxyInstance(url=self.instance_url,
email=self.config["galaxy_default_admin_email"],
password=self.config["galaxy_default_admin_password"])
folders = dict()
post_renaming = {}
......@@ -149,14 +123,14 @@ class LoadData(speciesData.SpeciesData):
if folders:
# Delete pre-existing lib (probably created by a previous call)
existing = gio.libraries.get_previews(name='Project Data')
existing = instance.libraries.get_previews(name='Project Data')
for lib in existing:
if not lib.deleted:
logging.info('Pre-existing "Project Data" library %s found, removing it' % lib.id)
gio.libraries.delete(lib.id)
instance.libraries.delete(lib.id)
logging.info("Creating new 'Project Data' library")
prj_lib = gio.libraries.create('Project Data', 'Data for current genome annotation project')
prj_lib = instance.libraries.create('Project Data', 'Data for current genome annotation project')
self.library_id = prj_lib.id # project data folder/library
logging.info("Library for {0}: {1}".format(self.full_name, self.library_id))
......@@ -165,6 +139,7 @@ class LoadData(speciesData.SpeciesData):
folder_name = fname[len("./src_data") + 1:]
logging.info("Creating folder: %s" % folder_name)
folder = self.create_deep_folder(prj_lib, folder_name)
for single_file in files:
ftype = 'auto'
......@@ -204,10 +179,12 @@ class LoadData(speciesData.SpeciesData):
continue
logging.info("Adding file '%s' with type '%s' and name '%s'" % (single_file, ftype, clean_name))
datasets = prj_lib.upload_from_local(
path=single_file,
datasets = prj_lib.upload_from_galaxy_fs(
single_file,
folder=folder,
file_type=ftype
link_data_only='link_to_files',
file_type=ftype,
tag_using_filenames=False
)
# Rename dataset
......@@ -272,7 +249,29 @@ class LoadData(speciesData.SpeciesData):
return new_folder
def connect_to_instance(self):
def get_bam_label(self, dirname, bam_file):
bam_id = bam_file
if bam_id.endswith('.bam'):
bam_id = bam_id[:-4]
if dirname in self.bam_metadata_cache:
if bam_id in self.bam_metadata_cache[dirname] and 'label' in self.bam_metadata_cache[dirname][bam_id] and self.bam_metadata_cache[dirname][bam_id]['label']:
return self.bam_metadata_cache[dirname][bam_id]['label']
else:
return None
else:
meta_file = os.path.join(dirname, 'metadata.yml')
if os.path.exists(meta_file):
with open(meta_file) as f:
self.bam_metadata_cache[dirname] = yaml.safe_load(f)
logging.info("Found metadata in %s " % meta_file)
else:
self.bam_metadata_cache[dirname] = {}
logging.info("Did not find metadata in %s " % meta_file)
return self.get_bam_label(dirname, bam_file)
def create_galaxy_instance(self):
"""
Test the connection to the galaxy instance for the current organism
Exit if we cannot connect to the instance
......@@ -280,11 +279,10 @@ class LoadData(speciesData.SpeciesData):
"""
logging.info("Connecting to the galaxy instance (%s)" % self.instance_url)
self.instance = galaxy.GalaxyInstance(url=self.instance_url,
self.instance = GalaxyInstance(url=self.instance_url,
email=self.config["galaxy_default_admin_email"],
password=self.config["galaxy_default_admin_password"]
)
self.instance.histories.get_histories()
try:
self.instance.histories.get_histories()
......@@ -294,19 +292,7 @@ class LoadData(speciesData.SpeciesData):
else:
logging.info("Successfully connected to galaxy instance (%s) " % self.instance_url)
def get_species_to_load(sp_dict_list):
"""
"""
utilities.get_unique_species_list(sp_dict_list)
return 1
return self.instance
if __name__ == "__main__":
......@@ -338,64 +324,56 @@ if __name__ == "__main__":
else:
logging.basicConfig(level=logging.INFO)
# Parsing the config file if provided, using the default config otherwise
if not args.config:
args.config = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])), "config")
else:
args.config = os.path.abspath(args.config)
config_file = os.path.abspath(args.config)
config = utilities.parse_config(config_file)
main_dir = None
if not args.main_directory:
args.main_directory = os.getcwd()
main_dir = os.getcwd()
else:
args.main_directory = os.path.abspath(args.main_directory)
main_dir = os.path.abspath(args.main_directory)
sp_dict_list = utilities.parse_input(args.input)
unique_sp_dict_list = utilities.get_unique_species_dict_list(sp_dict_list=sp_dict_list)
for sp_dict in unique_sp_dict_list:
# Creating an instance of load_data_for_current_species object
load_data_for_current_species = LoadData(parameters_dictionary=sp_dict)
# Starting
logging.info("gga_load_data.py called for %s" % load_data_for_current_species.full_name)
logging.info("gga_load_data.py called for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species))
# Setting some of the instance attributes
load_data_for_current_species.main_dir = args.main_directory
load_data_for_current_species.main_dir = main_dir
load_data_for_current_species.species_dir = os.path.join(load_data_for_current_species.main_dir,
load_data_for_current_species.genus_species +
"/")
# Parse the config yaml file
load_data_for_current_species.config = utilities.parse_config(args.config)
load_data_for_current_species.config = config
# Set the instance url attribute -- Does not work with localhost on scratch (ALB)
load_data_for_current_species.instance_url = "http://localhost:{0}/sp/{1}_{2}/galaxy/".format(
load_data_for_current_species.config["http_port"],
load_data_for_current_species.genus_lowercase,
load_data_for_current_species.species)
# Check the galaxy container state and proceed if the galaxy services are up and running
if utilities.check_galaxy_state(genus_lowercase=load_data_for_current_species.genus_lowercase,
species=load_data_for_current_species.species,
script_dir=load_data_for_current_species.script_dir):
# Load config file
load_data_for_current_species.config = utilities.parse_config(args.config)
# Testing connection to the instance
load_data_for_current_species.connect_to_instance()
# Create the Galaxy instance
load_data_for_current_species.instance = load_data_for_current_species.create_galaxy_instance()
# 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()
logging.info("Successfully set up library in galaxy 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)
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.set_get_history()
load_data_for_current_species.get_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)
......@@ -403,7 +381,6 @@ if __name__ == "__main__":
# 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"
# load_data_for_current_species.purge_histories() # Testing purposes
logging.info("Data successfully loaded and imported for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species))
......
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