from bioblend import galaxy
from bioblend.galaxy import GalaxyInstance
import os
"""
Methods to run all Chado and Tripal tools on galaxy
"""
class ToolRunner:
def __init__(self, parameters_dict, instance, history):
self.history = history
self.instance = instance
self.parameters_dict = parameters_dict
self.genus = parameters_dict["genus"]
self.species = parameters_dict["species"]
self.strain = parameters_dict["strain"]
self.common = parameters_dict["common"]
self.performed = parameters_dict["performed by"]
self.genome_version = parameters_dict["genome version"]
self.ogs_version = parameters_dict["ogs version"]
self.sex = parameters_dict["sex"]
self.date = parameters_dict["date"]
self.custom_ga_file = None
self.custom_ga_file_path = None
self.preset_ga_file = None
self.analysis = None
self.organism = None
self.program = None
if self.strain != "":
self.abbr = self.genus[0].lower() + "_" + self.species + "_" + self.strain
self.full = "_".join([self.genus, self.species, self.strain, self.sex])
else:
self.abbr = self.genus[0].lower() + "_" + self.species
self.full = "_".join([self.genus, self.species, self.strain, self.sex])
self.ogs = str("OGS"+ self.ogs_version)
self.genome = str(self.full + " genome v" + self.genome_version)
def show_tool(self, tool_id):
print(self.instance.tools.show_tool(tool_id=tool_id, io_details=True))
return self.instance.tools.show_tool(tool_id=tool_id, io_details=True)
def purge_organism(self):
self.show_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2")
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,
tool_inputs={"name": self.organism})
def purge_analyses(self):
return None
def get_organism(self):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"genus": self.genus, "species": self.species})
def get_ogs_analysis(self):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version})
def get_genome_analysis(self):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version})
def add_organism(self):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"abbr": self.abbr,
"genus": self.genus,
"species": self.species,
"common": self.common
})
def add_ogs(self):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version,
"program": "Performed by Genoscope",
"programversion": str("OGS" + self.genome_version),
"sourcename": "Genoscope",
"date_executed": self.date
})
def add_genome(self):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version,
"program": "Performed by Genoscope",
"programversion": str("genome v" + self.genome_version),
"sourcename": "Genoscope",
"date_executed": self.date
})
def add_jbrowse(self, datasets):
return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.5+galaxy7",
history_id=self.history,
tool_inputs={"genomes": datasets["genome_file"]})
def add_organism_jbrowse(self):
return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
history_id=self.history,
tool_inputs={"multiple": "false",
"name": "foo",
"unique_id": "bar"})
# Homo sapiens deletion TODO: concat the 2 calls
def get_sapiens_id(self):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"genus": "Homo", "species": "species"})
def delete_sapiens(self, hs_id):
"""
Tool invocation must be as return (or else it executes but returns nothing when called)
:return:
"""
return 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,
tool_inputs={"organism": hs_id})
# def load_fasta(self, inputs_dict):
# """
#
# :return:
# """
# return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.2",
# history_id=self.history,
# tool_inputs=)
def show_pannel(self):
print(self.instance.tools.get_tool_panel())
return self.instance.tools.get_tool_panel()