From abdd1b5de9f167ce6fbe6147d5f3f0397e4b243f Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Fri, 13 Mar 2020 17:21:18 +0100
Subject: [PATCH] fix for class attributes
---
autoload.py | 325 ++++++++++++++++++++++++++++++++++------------------
1 file changed, 211 insertions(+), 114 deletions(-)
diff --git a/autoload.py b/autoload.py
index 346d51e..82779cd 100644
--- a/autoload.py
+++ b/autoload.py
@@ -1,4 +1,5 @@
from bioblend import galaxy
+import bioblend.galaxy.objects
import bioblend
import argparse
import os
@@ -21,10 +22,12 @@ class Autoload:
To run the workflows, place them in the same directory as this script, and add the method + the workflow
parameters in the main invocation (at the end of the file)
+ TODO: store workflow as string in
"""
- def __init__(self, species_parameters_dictionary: dict):
+ def __init__(self, species_parameters_dictionary: dict, args):
self.species_parameters_dictionary = species_parameters_dictionary
+ self.args = args
self.species = species_parameters_dictionary["species"]
self.genus = species_parameters_dictionary["genus"]
self.strain = species_parameters_dictionary["strain"]
@@ -38,7 +41,7 @@ class Autoload:
self.full_name = " ".join([self.genus_lowercase, self.species, self.strain, self.sex])
self.abbreviation = " ".join([self.genus_lowercase[0], self.species, self.strain, self.sex])
self.genus_species = self.genus_lowercase + "_" + self.species
- self.instance_url = "http://localhost/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/"
+ self.instance_url = "http://localhost/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/" # testing
self.instance: galaxy = None
self.history_id = None
self.library_id = None
@@ -48,6 +51,9 @@ class Autoload:
self.genome_analysis_id = None
self.ogs_analysis_id = None
self.tool_panel = None
+ self.datasets = dict()
+ self.source_files = dict()
+ self.workflow_name = None
# Test the connection to the galaxy instance for the current species
# Additionally set some class attributes
@@ -70,7 +76,7 @@ class Autoload:
self.main_dir = os.getcwd() + "/"
self.species_dir = os.path.join(self.main_dir, self.genus_species) + "/"
- def load_data_in_galaxy(self, method):
+ def load_data_in_galaxy(self):
"""
- create the src_data directory tree for the species
- change headers for pep file
@@ -105,40 +111,40 @@ class Autoload:
logging.debug("insufficient permission to create src_data directory tree")
# Data import into galaxy
- source_files = dict()
+ self.source_files = dict()
annotation_dir, genome_dir = None, None
for d in [i[0] for i in os.walk(os.getcwd() + "/src_data")]:
if "annotation/" in d:
annotation_dir = d
for f in os.listdir(d):
if f.endswith("proteins.fasta"):
- source_files["proteins_file"] = os.path.join(d, f)
+ self.source_files["proteins_file"] = os.path.join(d, f)
elif f.endswith("transcripts-gff.fa"):
- source_files["transcripts_file"] = os.path.join(d, f)
+ self.source_files["transcripts_file"] = os.path.join(d, f)
elif f.endswith(".gff"):
- source_files["gff_file"] = os.path.join(d, f)
+ self.source_files["gff_file"] = os.path.join(d, f)
elif "genome/" in d:
genome_dir = d
for f in os.listdir(d):
if f.endswith(".fa"):
- source_files["genome_file"] = os.path.join(d, f)
+ self.source_files["genome_file"] = os.path.join(d, f)
logging.debug("source files found:")
- for k, v in source_files.items():
+ for k, v in self.source_files.items():
logging.debug("\t" + k + "\t" + v)
# Changing headers in the *proteins.fasta file from >mRNA* to >protein*
# production version
modify_pep_headers = ["/usr/local/genome2/mmo/scripts/phaeoexplorer/phaeoexplorer-change_pep_fasta_header.sh",
- source_files["proteins_file"]]
+ self.source_files["proteins_file"]]
# test version
modify_pep_headers = ["/home/alebars/gga/phaeoexplorer-change_pep_fasta_header.sh",
- source_files["proteins_file"]]
- logging.info("changing fasta headers in " + source_files["proteins_file"])
+ self.source_files["proteins_file"]]
+ logging.info("changing fasta headers in " + self.source_files["proteins_file"])
subprocess.run(modify_pep_headers, stdout=subprocess.PIPE, cwd=annotation_dir)
# src_data cleaning
if os.path.exists(annotation_dir + "outfile"):
- subprocess.run(["mv", annotation_dir + "/outfile", source_files["proteins_file"]],
+ subprocess.run(["mv", annotation_dir + "/outfile", self.source_files["proteins_file"]],
stdout=subprocess.PIPE,
cwd=annotation_dir)
if os.path.exists(annotation_dir + "gmon.out"):
@@ -158,25 +164,43 @@ class Autoload:
else:
logging.info("data successfully loaded into docker container for " + self.full_name)
- # gi.histories.create_history(name=str(genus_species_strain + "_" + genome_version))
- histories = self.instance.histories.get_histories(name=str(self.full_name + "_" + self.genome_version))
+ self.get_instance_attributes()
+ # self.history_id = self.instance.histories.get_current_history()["id"]
+
+ # import all datasets into current history
+ self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["genome_file"])
+ self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["gff_file"])
+ self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["transcripts_file"])
+ self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["proteins_file"])
+
+ def get_instance_attributes(self):
+ """
+ retrieves a pre-existing instance attributes:
+ - working history ID
+ - libraries ID
+ -
+
+ :return:
+ """
+ histories = self.instance.histories.get_histories(name=str(self.full_name))
self.history_id = histories[0]["id"]
+ logging.debug("history ID: " + self.history_id)
libraries = self.instance.libraries.get_libraries() # normally only one library
self.library_id = self.instance.libraries.get_libraries()[0]["id"] # project data folder/library
+ logging.debug("library ID: " + self.history_id)
instance_source_data_folders = self.instance.libraries.get_folders(library_id=self.library_id)
folders_ids = {}
- current_fo_name = ""
- # folders ids: access to data to run the first tools
+ current_folder_name = ""
for i in instance_source_data_folders:
for k, v in i.items():
if k == "name":
folders_ids[v] = 0
- current_fo_name = v
+ current_folder_name = v
if k == "id":
- folders_ids[current_fo_name] = v
- logging.info("folders and datasets IDs: ")
- datasets = dict()
+ folders_ids[current_folder_name] = v
+ logging.debug("folders and datasets IDs: ")
+ self.datasets = dict()
for k, v in folders_ids.items():
logging.info("\t" + k + ": " + v)
if k == "/genome":
@@ -185,8 +209,8 @@ class Autoload:
for e in v2:
if type(e) == dict:
if e["name"].endswith(".fa"):
- datasets["genome_file"] = e["ldda_id"]
- logging.info("\t\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets["genome_file"] = e["ldda_id"]
+ logging.debug("\t\t" + e["name"] + ": " + e["ldda_id"])
elif k == "/annotation/" + self.genus_species:
sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
for k2, v2 in sub_folder_content.items():
@@ -194,31 +218,31 @@ class Autoload:
if type(e) == dict:
# TODO: manage several files of the same type and manage versions
if e["name"].endswith("transcripts-gff.fa"):
- datasets["transcripts_file"] = e["ldda_id"]
- logging.info("\t\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets["transcripts_file"] = e["ldda_id"]
+ logging.debug("\t\t" + e["name"] + ": " + e["ldda_id"])
elif e["name"].endswith("proteins.fasta"):
- datasets["proteins_file"] = e["ldda_id"]
- logging.info("\t\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets["proteins_file"] = e["ldda_id"]
+ logging.debug("\t\t" + e["name"] + ": " + e["ldda_id"])
elif e["name"].endswith(".gff"):
- datasets["gff_file"] = e["ldda_id"]
- logging.info("\t\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets["gff_file"] = e["ldda_id"]
+ logging.debug("\t\t" + e["name"] + ": " + e["ldda_id"])
elif e["name"].endswith("MALE"):
- datasets["gff_file"] = e["ldda_id"]
- logging.info("\t\t" + e["name"] + ": " + e["ldda_id"])
-
- self.history_id = self.instance.histories.get_current_history()["id"]
- logging.debug("history ID: " + self.history_id)
- # import all datasets into current history
- self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=datasets["genome_file"])
- self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=datasets["gff_file"])
- self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=datasets["transcripts_file"])
- self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=datasets["proteins_file"])
+ self.datasets["gff_file"] = e["ldda_id"]
+ logging.debug("\t\t" + e["name"] + ": " + e["ldda_id"])
- def run_workflow(self, workflow_name, workflow_parameters):
+ def run_workflow(self, workflow_name, workflow_parameters, datamap):
"""
-
- :param workflow_ga_file:
+ Run the "main" workflow in the galaxy instance
+ - import data to library
+ - load fasta and gff
+ - sync with tripal
+ - add jbrowse + organism
+ - fill in the tripal views
+
+ TODO: map tool name to step id
+ :param workflow_name:
:param workflow_parameters:
+ :param datamap:
:return:
"""
@@ -231,20 +255,38 @@ class Autoload:
custom_ga_file = "_".join([self.genus, self.species]) + "_workflow.ga"
custom_ga_file_path = os.path.abspath(custom_ga_file)
with open(workflow_ga_file, 'r') as ga_in_file:
- ga_in = str(ga_in_file.readlines())
- ga_in = ga_in.replace('{\\\\\\\\\\\\"unique_id\\\\\\\\\\\\": \\\\\\\\\\\\"UNIQUE_ID\\\\\\\\\\\\"}',
- str('{\\\\\\\\\\\\"unique_id\\\\\\\\\\\\": \\\\\\\\\\\\"' + self.genus + " " + self.species) + '\\\\\\\\\\\\"')
- ga_in = ga_in.replace('\\\\\\\\\\\\"name\\\\\\\\\\\\": \\\\\\\\\\\\"NAME\\\\\\\\\\\\"',
- str('\\\\\\\\\\\\"name\\\\\\\\\\\\": \\\\\\\\\\\\"' + self.genus.lower()[0] + self.species) + '\\\\\\\\\\\\"')
- ga_in = ga_in.replace("\\\\", "\\") # to restore the correct amount of backslashes in the workflow string before import
+ workflow = str(ga_in_file.readlines())
+ workflow = workflow.replace('{\\\\\\\\\\\\"unique_id\\\\\\\\\\\\": \\\\\\\\\\\\"UNIQUE_ID\\\\\\\\\\\\"}',
+ str('{\\\\\\\\\\\\"unique_id\\\\\\\\\\\\": \\\\\\\\\\\\"' + self.genus + " " + self.species) + '\\\\\\\\\\\\"')
+ workflow = workflow.replace('\\\\\\\\\\\\"name\\\\\\\\\\\\": \\\\\\\\\\\\"NAME\\\\\\\\\\\\"',
+ str('\\\\\\\\\\\\"name\\\\\\\\\\\\": \\\\\\\\\\\\"' + self.genus.lower()[0] + self.species) + '\\\\\\\\\\\\"')
+ workflow = workflow.replace("\\\\", "\\") # to restore the correct amount of backslashes in the workflow string before import
# test
- ga_in = ga_in.replace('http://localhost/sp/genus_species/feature/Genus/species/mRNA/{id}',
- "http://localhost/sp/" + self.genus_lowercase+ "_" + self.species + "/feature/" + self.genus + "/mRNA/{id}")
+ workflow = workflow.replace('http://localhost/sp/genus_species/feature/Genus/species/mRNA/{id}',
+ "http://localhost/sp/" + self.genus_lowercase+ "_" + self.species + "/feature/" + self.genus + "/mRNA/{id}")
# production
- # ga_in = ga_in.replace('http://localhost/sp/genus_species/feature/Genus/species/mRNA/{id}',
- # "http://abims--gga.sb-roscoff.fr/sp/" + self.genus_lowercase + "_" + self.species + "/feature/" + self.genus + "/mRNA/{id}")
- ga_in = ga_in[2:-2] # if the line under doesn't outputs a correct json
- # ga_in = ga_in[:-2] # if the line above doesn't outputs a correct json
+ # workflow = workflow.replace('http://localhost/sp/genus_species/feature/Genus/species/mRNA/{id}',
+ # "http://abims--gga.sb-roscoff.fr/sp/" + self.genus_lowercase + "_" + self.species + "/feature/" + self.genus + "/mRNA/{id}")
+ workflow = workflow[2:-2] # if the line under doesn't output a correct json
+ # workflow = workflow[:-2] # if the line above doesn't output a correct json
+
+ workflow_dict = json.loads(workflow) # doesn't work with eval()
+
+ self.instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
+ self.workflow_name = workflow_name
+ workflow_attributes = self.instance.workflows.get_workflows(name=workflow_name)
+ workflow_id = workflow_attributes[0]["id"]
+ show_workflow = self.instance.workflows.show_workflow(workflow_id=workflow_id)
+ logging.debug("workflow ID: " + workflow_id)
+
+ logging.debug("inputs:")
+ logging.debug(show_workflow["inputs"])
+ self.instance.workflows.invoke_workflow(workflow_id=workflow_id,
+ history_id=self.history_id,
+ params=workflow_parameters,
+ inputs=datamap,
+ inputs_by="")
+ self.instance.workflows.delete_workflow(workflow_id=workflow_id)
def init_instance(self):
"""
@@ -256,24 +298,36 @@ class Autoload:
:return:
"""
+ self.instance.histories.create_history(name=str(self.full_name))
+ histories = self.instance.histories.get_histories(name=str(self.full_name))
+ self.history_id = histories[0]["id"]
+ logging.debug("history ID: " + self.history_id)
+ libraries = self.instance.libraries.get_libraries() # normally only one library
+ self.library_id = self.instance.libraries.get_libraries()[0]["id"] # project data folder/library
+ logging.debug("library ID: " + self.history_id)
+ instance_source_data_folders = self.instance.libraries.get_folders(library_id=self.library_id)
# Delete Homo sapiens from Chado database
+ logging.info("getting sapiens ID in instance's 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/2.3.2",
- tool_inputs={"genus": "Homo", "species": "species"},
- history=self.history_id)
+ 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)
try:
+ logging.info("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/2.3.2",
history_id=self.history_id,
tool_inputs={"organism": str(sapiens_id)})
except bioblend.ConnectionError:
- logging.debug("homo sapiens isn't in the database")
+ logging.debug("Homo sapiens isn't in the instance's chado database")
except IndexError:
+ logging.debug("Homo sapiens isn't in the instance's chado database")
pass
# Add organism (species) to chado
+ logging.info("adding organism to the instance's chado database")
self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_add_organism/organism_add_organism/2.3.2",
history_id=self.history_id,
tool_inputs={"abbr": self.abbreviation,
@@ -281,6 +335,7 @@ class Autoload:
"species": self.species,
"common": self.common})
# Add OGS analysis to chado
+ logging.info("adding OGS analysis to the instance's chado database")
self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2",
history_id=self.history_id,
tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version,
@@ -290,6 +345,7 @@ class Autoload:
"date_executed": self.date})
# Add genome analysis to chado
+ logging.info("adding genome analysis to the instance's chado database")
self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2",
history_id=self.history_id,
tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version,
@@ -298,41 +354,56 @@ class Autoload:
"sourcename": "Genoscope",
"date_executed": self.date})
- # Get the ID from OGS analysis in chado
- org = self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.2",
- history_id=self.history_id,
- tool_inputs={"genus": self.genus, "species": self.species})
+ self.get_organism_and_analyses_ids()
+ logging.info("finished initializing instance")
+
+ def get_organism_and_analyses_ids(self):
+ """
+ Retrieve current organism ID and OGS and genome chado analyses IDs (needed to run some tools as Tripal/Chado
+ doesn't accept organism/analyses names as valid inputs
+
+ :return:
+ """
+ # Get the ID for the current organism in chado
+ org = self.instance.tools.run_tool(
+ tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.2",
+ history_id=self.history_id,
+ tool_inputs={"genus": self.genus, "species": self.species})
org_job_out = org["outputs"][0]["id"]
org_json_output = self.instance.datasets.download_dataset(dataset_id=org_job_out)
try:
org_output = json.loads(org_json_output)[0]
self.org_id = str(org_output["organism_id"]) # needs to be str to be recognized by chado tools
except IndexError:
- logging.debug("no organism matching " + self.full_name + " exists in the Chado database")
+ logging.debug("no organism matching " + self.full_name + " exists in the instance's chado database")
- ogs_analysis = self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.2",
- history_id=self.history_id,
- tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version})
+ # Get the ID for the OGS analysis in chado
+ ogs_analysis = self.instance.tools.run_tool(
+ tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.2",
+ history_id=self.history_id,
+ tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version})
ogs_analysis_job_out = ogs_analysis["outputs"][0]["id"]
ogs_analysis_json_output = self.instance.datasets.download_dataset(dataset_id=ogs_analysis_job_out)
try:
ogs_analysis_output = json.loads(ogs_analysis_json_output)[0]
- self.ogs_analysis_id = str(ogs_analysis_output["analysis_id"]) # needs to be str to be recognized by chado tools
+ self.ogs_analysis_id = str(
+ ogs_analysis_output["analysis_id"]) # needs to be str to be recognized by chado tools
except IndexError:
- logging.debug("no matching OGS analysis exists in the Chado database")
+ logging.debug("no matching OGS analysis exists in the instance's chado database")
- genome_analysis = self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.2",
- history_id=self.history_id,
- tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version})
+ # Get the ID for the genome analysis in chado
+ genome_analysis = self.instance.tools.run_tool(
+ tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.2",
+ history_id=self.history_id,
+ tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version})
genome_analysis_job_out = genome_analysis["outputs"][0]["id"]
genome_analysis_json_output = self.instance.datasets.download_dataset(dataset_id=genome_analysis_job_out)
try:
genome_analysis_output = json.loads(genome_analysis_json_output)[0]
- self.genome_analysis_id = str(genome_analysis_output["analysis_id"]) # needs to be str to be recognized by chado tools
+ self.genome_analysis_id = str(
+ genome_analysis_output["analysis_id"]) # needs to be str to be recognized by chado tools
except IndexError:
- logging.debug("no matching genome analysis exists in the Chado database")
-
- logging.info("finished initializing instance")
+ logging.debug("no matching genome analysis exists in the instance's chado database")
def clean_instance(self):
"""
@@ -342,43 +413,69 @@ class Autoload:
return None
-if __name__ == "main":
- parser = argparse.ArgumentParser(description="Input genus, species, strain, version")
- parser.add_argument("json", type=str, help="Input JSON file")
- parser.add_argument("-v", "--verbose", help="Increase output verbosity")
- parser.add_argument("--load-data", help="Create src_data directory tree and load data into galaxy")
- parser.add_argument("--main-workflow", help="Run main workflow (initialize galaxy instance, load data into chado,"
- "sync with tripal, create jbrowse and add organism to jbrowse")
- args = parser.parse_args()
-
- if args.verbose:
- logging.basicConfig(level=logging.DEBUG)
- else:
- logging.basicConfig(level=logging.INFO)
-
- sp_dict_list = list()
- with open(args.json, 'r') as infile:
- json_sp_dict = json.load(infile)
- json_sp_dump = json.dumps(json_sp_dict, indent=4, sort_keys=True)
- for json_sp in json_sp_dict:
- sp_dict_list.append(json_sp)
-
- for sp_dict in sp_dict_list:
- al = Autoload(species_parameters_dictionary=sp_dict)
- if args.main_workflow:
- workflow_parameters = dict()
- workflow_parameters["0"] = {}
- workflow_parameters["1"] = {}
- workflow_parameters["2"] = {}
- workflow_parameters["3"] = {}
- workflow_parameters["4"] = {"organism": al.org_id,
- "analysis_id": al.genome_analysis_id,
- "do_update": "true"} # the do_update parameter is to prevent assertion errors when loading the file, should always be set to "true"
- workflow_parameters["5"] = {"organism": al.org_id,
- "analysis_id": al.ogs_analysis_id}
- workflow_parameters["6"] = {"organism_id": al.org_id}
- workflow_parameters["7"] = {"analysis_id": al.ogs_analysis_id}
- workflow_parameters["8"] = {"analysis_id": al.genome_analysis_id}
- workflow_parameters["9"] = {"organism_id": al.org_id}
- al.run_workflow(workflow_name="main", workflow_parameters=workflow_parameters)
-
+parser = argparse.ArgumentParser(description="Input genus, species, strain, version")
+parser.add_argument("json", type=str, help="Input JSON file")
+parser.add_argument("-v", "--verbose",
+ help="Increase output verbosity",
+ action="store_true")
+parser.add_argument("--init-instance",
+ help="Initialization of galaxy instance. Run first in an empty instance",
+ action="store_true")
+parser.add_argument("--load-data",
+ help="Create src_data directory tree and load its data into the instance",
+ action="store_true")
+parser.add_argument("--run-main",
+ help="Run main workflow (load data into chado, sync all with tripal, "
+ "index tripal data, populate materialized view, "
+ "create a jbrowse for the current genus_species_strain_sex and add organism to jbrowse",
+ action="store_true")
+args = parser.parse_args()
+
+if args.verbose:
+ logging.basicConfig(level=logging.DEBUG)
+else:
+ logging.basicConfig(level=logging.INFO)
+
+sp_dict_list = list()
+with open(args.json, 'r') as infile:
+ json_sp_dict = json.load(infile)
+ json_sp_dump = json.dumps(json_sp_dict, indent=4, sort_keys=True)
+ for json_sp in json_sp_dict:
+ sp_dict_list.append(json_sp)
+
+for sp_dict in sp_dict_list:
+ al = Autoload(species_parameters_dictionary=sp_dict, args=args)
+ if args.init_instance:
+ logging.info("initializing the galaxy instance")
+ al.init_instance()
+ al.get_instance_attributes()
+ if args.load_data:
+ logging.info("loading data into galaxy")
+ al.load_data_in_galaxy()
+ if args.run_main:
+ logging.info("running main workflow")
+ al.get_organism_and_analyses_ids()
+ workflow_parameters = dict()
+ workflow_parameters["0"] = {}
+ workflow_parameters["1"] = {}
+ workflow_parameters["2"] = {}
+ workflow_parameters["3"] = {}
+ workflow_parameters["4"] = {"organism": al.org_id,
+ "analysis_id": al.genome_analysis_id,
+ "do_update": "true"}
+ workflow_parameters["5"] = {"organism": al.org_id,
+ "analysis_id": al.ogs_analysis_id}
+ workflow_parameters["6"] = {"organism_id": al.org_id}
+ workflow_parameters["7"] = {"analysis_id": al.ogs_analysis_id}
+ workflow_parameters["8"] = {"analysis_id": al.genome_analysis_id}
+ workflow_parameters["9"] = {"organism_id": al.org_id}
+ workflow_parameters["10"] = {}
+ workflow_parameters["11"] = {}
+
+ al.datamap = dict()
+ al.datamap["0"] = {"src": "hda", "id": al.datasets["genome_file"]}
+ al.datamap["1"] = {"src": "hda", "id": al.datasets["gff_file"]}
+ al.datamap["2"] = {"src": "hda", "id": al.datasets["proteins_file"]}
+ al.datamap["3"] = {"src": "hda", "id": al.datasets["transcripts_file"]}
+
+ al.run_workflow(workflow_name="main", workflow_parameters=workflow_parameters, datamap=al.datamap)
--
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