diff --git a/dataloader.json b/dataloader.json
index 619b77e04685b7f0199345a622ef9f043db2bedc..a0006ff98e5a6e1d845db005c5965b19a6fbc37b 100644
--- a/dataloader.json
+++ b/dataloader.json
@@ -9,6 +9,6 @@
"performed by" : "Genoscope",
"genome version" : "1.0",
"ogs version" : "1.0",
- "date" : "2020-20-20"
+ "date" : "2020-01-01"
}
]
diff --git a/filetransfer.py b/filetransfer.py
index 9dae890ff808fdd635af453258e0276471d4e473..675bbc2fdbbf018cc81ae87fdae5a18cb48e6f4f 100644
--- a/filetransfer.py
+++ b/filetransfer.py
@@ -12,8 +12,5 @@ class FileTransfer:
user_host = [user, host]
subprocess.Popen(user_host)
-
-
def file(self):
return 0
-
diff --git a/main.py b/main.py
index 4cf3f17bdd9ab285bf5d3a40ac10396c99b34fda..3d0403fe3ca0a56d1d7990c5e078a0d4839334d2 100644
--- a/main.py
+++ b/main.py
@@ -7,6 +7,7 @@ import subprocess
import json
from workflow import Workflow
from filetransfer import FileTransfer
+from toolrunner import ToolRunner
# TODO: script description
@@ -85,7 +86,7 @@ def main():
key="0e993414b2f876515e74dd890f16ffc7",
email="alebars@sb-roscoff.fr",
password="pouet",
- verify=False)
+ verify=True)
"""
This part creates the current species directory and go to it
@@ -143,24 +144,25 @@ def main():
# else:
# print("Data successfully loaded into docker container for " + genus_species_strain)
- # TODO: datamapping to run workflow (get datasets from instance)
- datamap = {}
-
# generate workflow file and run it in the galaxy instance
workflow = Workflow(parameters_dict=sp_dict, instance=gi)
print("Generating custom workflow for " + genus_species_strain)
- wf_dict = workflow.generate(working_directory=wd, main_directory=main_dir)
+ wf_dict_json = workflow.generate(working_directory=wd, main_directory=main_dir)
gi.histories.create_history(name=str(genus_species_strain + "_" + genome_version))
hi = gi.histories.get_histories(name=str(genus_species_strain + "_" + genome_version))
hi_id = hi[0]["id"]
# print(hi)
+
li = gi.libraries.get_libraries() # only one library
# print(li)
+
li_id = gi.libraries.get_libraries()[0]["id"] # project data folder/library
# print(li_id)
+
fo_gi = gi.libraries.get_folders(library_id=li_id) # data location (project data)
# print(fo_gi)
+
fo_id = {}
current_fo_name = ""
# folders ids: access to data to run the first tools
@@ -171,8 +173,9 @@ def main():
current_fo_name = v
if k == "id":
fo_id[current_fo_name] = v
- print("IDs: ")
- datasets = {}
+
+ print("Folders and datasets IDs: ")
+ datasets = dict()
for k, v in fo_id.items():
print("\t" + k + ": " + v)
if k == "/genome":
@@ -205,18 +208,50 @@ def main():
datasets["gff_file"] = e["ldda_id"]
print("\t\t" + e["name"] + ": " + e["ldda_id"])
- current_hi = gi.histories.get_current_history()["id"]
- print("History ID:" + current_hi)
- gi.histories.upload_dataset_from_library(history_id=hi_id, lib_dataset_id=datasets["genome_file"])
- gi.histories.upload_dataset_from_library(history_id=hi_id, lib_dataset_id=datasets["gff_file"])
- gi.histories.upload_dataset_from_library(history_id=hi_id, lib_dataset_id=datasets["transcripts_file"])
- gi.histories.upload_dataset_from_library(history_id=hi_id, lib_dataset_id=datasets["proteins_file"])
- # print(gi.tools.get_tool_panel())
+ current_hi_id = gi.histories.get_current_history()["id"]
+ print("History ID: " + current_hi_id)
+ gi.histories.upload_dataset_from_library(history_id=current_hi_id, lib_dataset_id=datasets["genome_file"])
+ gi.histories.upload_dataset_from_library(history_id=current_hi_id, lib_dataset_id=datasets["gff_file"])
+ gi.histories.upload_dataset_from_library(history_id=current_hi_id, lib_dataset_id=datasets["transcripts_file"])
+ gi.histories.upload_dataset_from_library(history_id=current_hi_id, lib_dataset_id=datasets["proteins_file"])
+
+ tools = gi.tools.get_tool_panel() # tools panel -> alternative to wf
+ # print(tools)
+ wf_dict = json.loads(wf_dict_json) # doesn't work with eval()
# print(wf_dict)
- wf_dict_2 = json.loads(wf_dict) # add to workflow class
- gi.workflows.import_workflow_dict(workflow_dict=wf_dict_2) # doesn't work with eval()
+ # print(wf_dict_json.count("id"))
+ # TODO: fill in workflow inputs and attributes (doable?)
+ gi.workflows.import_workflow_dict(workflow_dict=wf_dict)
+ print(gi.workflows.import_workflow_dict(workflow_dict=wf_dict))
+ wf_name = workflow.get_workflow_name()
+ wf_attr = gi.workflows.get_workflows(name=wf_name)
+ # print(wf_attr)
+ wf_id = wf_attr[0]["id"]
+ wf_show = gi.workflows.show_workflow(workflow_id=wf_id)
+ print("Workflow ID: " + wf_id)
+ print(wf_show["inputs"])
+
+ # toolrunner = ToolRunner(parameters_dict=sp_dict, instance=gi, history=current_hi_id)
+ # toolrunner.purge_organisms()
+
+ wf_params = workflow.set_params(datasets=datasets)
+
+ datamap = dict()
+ datamap["0"] = {"src": "hda", "id": datasets["genome_file"]}
+ datamap["1"] = {"src": "hda", "id": datasets["gff_file"]}
+ datamap["2"] = {"src": "hda", "id": datasets["transcripts_file"]}
+ datamap["4"] = {"src": "hda", "id": datasets["proteins_file"]}
+
+ # print(gi.workflows.show_workflow(wf_id))
+ gi.workflows.run_workflow(workflow_id=wf_id,
+ history_id=current_hi_id,
+ params=wf_params,
+ dataset_map=datamap)
+ # for testing, purge configured @ ~/config/galaxy.yml.docker_sample
+ # gi.histories.delete_history(history_id=current_hi_id, purge=True)
+ # gi.workflows.delete_workflow(workflow_id=wf_id)
# # PRE FILLED METHOD
# wf_id = workflow.store()
@@ -231,7 +266,6 @@ def main():
# tsi = gi.toolshed.get_repositories() # tool shed repo access point
# # print(gi.users.get_users()) # TODO: users management
# # print(gi.libraries.show_library(li_id))
- # # TODO: create a NEW history, import data to galaxy from library (src_data)
# fo_gi = gi.libraries.get_folders(library_id=li_id) # data location
# fo_id = {}
# current_fo_name = ""
@@ -250,8 +284,6 @@ def main():
# workflow.show()
# # gi.workflows.run_workflow(workflow_id=wf_id) # pre filled workflow, use the set on runtime approach instead
- # for testing, purge configured @ ~/config/galaxy.yml.docker_sample
- # gi.histories.delete_history(history_id=hi_id, purge=True)
os.chdir(main_dir)
print("\n")
diff --git a/toolrunner.py b/toolrunner.py
new file mode 100644
index 0000000000000000000000000000000000000000..6d2ee7e4c04ee68c805fdf5e4d3914b2b864bd52
--- /dev/null
+++ b/toolrunner.py
@@ -0,0 +1,59 @@
+from bioblend import galaxy
+from bioblend.galaxy import GalaxyInstance
+import os
+"""
+Methods to run 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.custom_ga_file = None
+ self.custom_ga_file_path = None
+ self.preset_ga_file = None
+ self.analysis = None
+ self.organism = None
+ self.program = None
+ self.ogs = str("OGS"+ self.ogs_version)
+ self.genome = str(self.full + " genome v" + self.genome_version)
+ 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])
+
+ 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_genome(self):
+ 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.genome,
+ "program": "Performed by Genoscope",
+ "programversion": str("genome v" + self.genome_version),
+ "sourcename": "Genoscope",
+ "date_executed": "2020-02-02"})
+
+ def show_pannel(self):
+ print(self.instance.tools.get_tool_panel())
+ return self.instance.tools.get_tool_panel()
diff --git a/workflow.py b/workflow.py
index f658f6a4dfcdb5891cb14d196f0c3ffa1205cef3..64be18750a860a7d34318b88b9b836cb15ce4b84 100644
--- a/workflow.py
+++ b/workflow.py
@@ -19,6 +19,7 @@ class Workflow:
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
@@ -33,7 +34,7 @@ class Workflow:
def generate(self, working_directory, main_directory):
"""
Generation of a galaxy workflow using the defined parameters in the .json input file
- Output format is .ga (basically a .json for galaxy)
+ Output format is a json dict
:param working_directory:
:param main_directory:
@@ -41,43 +42,89 @@ class Workflow:
"""
# template workflow as a string
# template_workflow_str = '"{"uuid": "ea9c3050-416f-4098-a7ff-b05c952bcd73", "tags": [], "format-version": "0.1", "name": "test", "version": 2, "steps": {"0": {"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2", "tool_version": "2.3.2", "outputs": [{"type": "txt", "name": "results"}], "workflow_outputs": [{"output_name": "results", "uuid": "d9b75b03-49e7-4a81-a67c-eaf6a9671905", "label": null}], "input_connections": {}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"organism\": \"\\\"2\\\"\", \"psql_target\": \"{\\\"__current_case__\\\": 0, \\\"method\\\": \\\"remote\\\"}\"}", "id": 0, "tool_shed_repository": {"owner": "gga", "changeset_revision": "13da56fdaeb1", "name": "chado_organism_delete_organisms", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "f70569bc-9ac0-441a-a2d8-b547086a5bdf", "errors": null, "name": "Chado organism delete", "post_job_actions": {}, "label": "$ORGADELETE", "inputs": [], "position": {"top": 362, "left": 200}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2", "type": "tool"}, "1": {"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_add_organism/organism_add_organism/2.3.2", "tool_version": "2.3.2", "outputs": [{"type": "json", "name": "results"}], "workflow_outputs": [{"output_name": "results", "uuid": "8ca0b891-0f01-4787-9b7f-57105dc303b0", "label": null}], "input_connections": {}, "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"psql_target\": \"{\\\"__current_case__\\\": 0, \\\"method\\\": \\\"remote\\\"}\", \"common\": \"\\\"$COMMON\\\"\", \"genus\": \"\\\"$GENUS\\\"\", \"species\": \"\\\"$SPECIES\\\"\", \"abbr\": \"\\\"$ABBR\\\"\"}", "id": 1, "tool_shed_repository": {"owner": "gga", "changeset_revision": "0f4956cec445", "name": "chado_organism_add_organism", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "24f0e175-f932-4e48-8b42-a53d9a432d5e", "errors": null, "name": "Chado organism add", "post_job_actions": {}, "label": "$ORGADD", "inputs": [], "position": {"top": 361, "left": 467.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_add_organism/organism_add_organism/2.3.2", "type": "tool"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2", "tool_version": "2.3.2", "outputs": [{"type": "json", "name": "results"}], "workflow_outputs": [{"output_name": "results", "uuid": "8fa0e728-8803-4800-93b4-70f906f95f87", "label": null}], "input_connections": {}, "tool_state": "{\"__page__\": null, \"name\": \"\\\"$GENOME\\\"\", \"sourceuri\": \"\\\"\\\"\", \"sourcename\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"programversion\": \"\\\"\\\"\", \"psql_target\": \"{\\\"__current_case__\\\": 0, \\\"method\\\": \\\"remote\\\"}\", \"sourceversion\": \"\\\"\\\"\", \"program\": \"\\\"$PERFORMEDBY\\\"\", \"algorithm\": \"\\\"\\\"\", \"date_executed\": \"\\\"\\\"\", \"description\": \"\\\"\\\"\"}", "id": 2, "tool_shed_repository": {"owner": "gga", "changeset_revision": "3a1f3c9b755b", "name": "chado_analysis_add_analysis", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "76cbbd55-f1ac-4e48-be3c-c7bbda5add4c", "errors": null, "name": "Chado analysis add", "post_job_actions": {}, "label": "$ADDGENOME", "inputs": [], "position": {"top": 307, "left": 690}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2", "type": "tool"}, "3": {"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2", "tool_version": "2.3.2", "outputs": [{"type": "json", "name": "results"}], "workflow_outputs": [{"output_name": "results", "uuid": "5e7da027-0723-4077-8885-2dbe51cb5dda", "label": null}], "input_connections": {}, "tool_state": "{\"__page__\": null, \"name\": \"\\\"$OGS\\\"\", \"sourceuri\": \"\\\"\\\"\", \"sourcename\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"programversion\": \"\\\"\\\"\", \"psql_target\": \"{\\\"__current_case__\\\": 0, \\\"method\\\": \\\"remote\\\"}\", \"sourceversion\": \"\\\"\\\"\", \"program\": \"\\\"$PERFORMEDBY\\\"\", \"algorithm\": \"\\\"\\\"\", \"date_executed\": \"\\\"\\\"\", \"description\": \"\\\"\\\"\"}", "id": 3, "tool_shed_repository": {"owner": "gga", "changeset_revision": "3a1f3c9b755b", "name": "chado_analysis_add_analysis", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "4d1ffee4-00b2-445d-b630-b7b774c17873", "errors": null, "name": "Chado analysis add", "post_job_actions": {}, "label": "$ADDOGS", "inputs": [], "position": {"top": 395, "left": 697}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2", "type": "tool"}, "4": {"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.2", "tool_version": "2.3.2", "outputs": [{"type": "json", "name": "results"}], "workflow_outputs": [{"output_name": "results", "uuid": "737dddc9-ae1b-463d-99fa-d9176053594d", "label": null}], "input_connections": {}, "tool_state": "{\"do_update\": \"\\\"false\\\"\", \"relationships\": \"{\\\"__current_case__\\\": 0, \\\"rel_type\\\": \\\"none\\\"}\", \"ext_db\": \"{\\\"db\\\": \\\"\\\", \\\"re_db_accession\\\": \\\"\\\"}\", \"analysis_id\": \"\\\"4\\\"\", \"re_uniquename\": \"\\\"\\\"\", \"match_on_name\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"psql_target\": \"{\\\"__current_case__\\\": 0, \\\"method\\\": \\\"remote\\\"}\", \"re_name\": \"\\\"\\\"\", \"fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"wait_for\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"organism\": \"\\\"2\\\"\", \"sequence_type\": \"\\\"contig\\\"\"}", "id": 4, "tool_shed_repository": {"owner": "gga", "changeset_revision": "1421dbc33a92", "name": "chado_feature_load_fasta", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "3d417ced-fc48-4c04-8a92-fdb7b9fecafc", "errors": null, "name": "Chado load fasta", "post_job_actions": {}, "label": "$LOADFASTA", "inputs": [{"name": "fasta", "description": "runtime parameter for tool Chado load fasta"}, {"name": "wait_for", "description": "runtime parameter for tool Chado load fasta"}], "position": {"top": 306, "left": 933.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.2", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}"'
+ # TODO: store workflow as a var instead of file
os.chdir(path=working_directory)
- self.preset_ga_file = main_directory + "preset_workflow.ga"
+ self.preset_ga_file = main_directory + "Galaxy-Workflow-preset_workflow.ga"
if self.strain != "":
self.custom_ga_file = "_".join([self.genus, self.species, self.strain]) + "_workflow.ga"
self.custom_ga_file_path = os.path.abspath(self.custom_ga_file)
- print("Workflow file @ " + self.custom_ga_file_path)
+ # print("Workflow file @ " + self.custom_ga_file_path)
else:
self.custom_ga_file = "_".join([self.genus, self.species]) + "_workflow.ga"
self.custom_ga_file_path = os.path.abspath(self.custom_ga_file)
- print("Workflow file @ " + self.custom_ga_file_path)
+ # print("Workflow file @ " + self.custom_ga_file_path)
with open(self.preset_ga_file, 'r') as ga_in_file:
- ga_in = str(ga_in_file.readlines())
- ga_in = ga_in.replace("$OGS", "OGS")
- ga_in = ga_in.replace("$VERSION", self.ogs_version)
- ga_in = ga_in.replace("$GENUS", self.genus)
- ga_in = ga_in.replace("$SPECIES", self.species)
- ga_in = ga_in.replace("$ABBR", self.abbr)
- ga_in = ga_in.replace("$STRAIN", self.strain)
- ga_in = ga_in.replace("$PERFORMEDBY", self.performed)
- ga_in = ga_in.replace("$COMMON", self.common)
- ga_in = ga_in.replace("$ORGA", self.full)
- ga_in = ga_in.replace("$ADDAN", "Add analysis")
- ga_in = ga_in.replace("\\\\", "\\") # restore the correct amount of backslashes in the ga file
+ ga_in: str = str(ga_in_file.readlines())
+ # Pre-filled workflow, useless for parameters and data set on runtime
+ # ga_in = ga_in.replace("$OGS", "OGS")
+ # ga_in = ga_in.replace("$VERSION", self.ogs_version)
+ # ga_in = ga_in.replace("$GENUS", self.genus)
+ # ga_in = ga_in.replace("$SPECIES", self.species)
+ # ga_in = ga_in.replace("$ABBR", self.abbr)
+ # ga_in = ga_in.replace("$STRAIN", self.strain)
+ # ga_in = ga_in.replace("$PERFORMEDBY", self.performed)
+ # ga_in = ga_in.replace("$COMMON", self.common)
+ # ga_in = ga_in.replace("$ORGA", self.full)
+ # ga_in = ga_in.replace("$ADDAN", "Add analysis")
+ ga_in = ga_in.replace("\\\\", "\\") # to restore the correct amount of backslashes in the workflow string before import
workflow_name = '"name": "' + self.full + '"'
- ga_in = ga_in.replace('"name": "preset"', workflow_name)
- ga_in = ga_in[2:]
- ga_in = ga_in[:-4]
+ # ga_in = ga_in.replace('"name": "preset_workflow"', '"name": "preset_workflow"')
+ # print(workflow_name)
+ ga_in = ga_in[2:-2]
+ # ga_in = ga_in[:-2]
self.workflow = ga_in
+ print(str(main_directory + "Galaxy-Workflow-preset_workflow.ga"))
return ga_in
- def dict_port(self):
+ def set_params(self, datasets):
"""
:return:
"""
+ params = dict()
+ # params["0"] = {}
+ # params["1"] = {}
+ # params["2"] = {}
+ # params["3"] = {}
+ params["4"] = {"confirm": "True"}
+ params["5"] = {"abbr": self.abbr, "genus": self.genus, "species": self.species, "common": self.common}
+ # params["2"] = {"analysis": str(self.genus + " " + self.species + " genome v" + self.genome_version)}
+ # params["3"] = {"analysis": str(self.genus + " " + self.species + " OGS" + self.ogs_version)}
+ params["6"] = {"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
+ }
+ params["7"] = {"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
+ }
+ params["8"] = {"genus": self.genus,
+ "species": self.species,
+ "common": self.common,
+ "abbr": self.abbr
+ }
+ params["9"] = {"name": self.genus + " " + self.species + " genome v" + self.genome_version,
+ "program": "Performed by Genoscope",
+ "programversion": str("genome v" + self.genome_version),
+ "sourcename": "Genoscope",
+ }
+ # params["10"] = {"organism": "13", "analysis": "2", "sequence": "contig"}
+ return params
+
+ def set_datamap(self):
+ gi = self.instance
+ def dict_port(self):
+ """
+ Import workflow into a galaxy instance from a json dict
+
+ :return:
+ """
try:
self.instance.workflows.import_workflow_dict(workflow_dict=self.workflow)
except ConnectionError:
@@ -86,8 +133,8 @@ class Workflow:
def port(self):
"""
- Import workflow into a galaxy instance
- Importing from string doesnt work (MUST be dict) -> TODO: handle dict import
+ Import workflow into a galaxy instance from a local file
+
:return:
"""
try:
@@ -97,9 +144,18 @@ class Workflow:
else:
return True
+ def get_workflow_name(self):
+ """
+ Name of the imported workflow
+
+ :return:
+ """
+ return str("preset_workflow")
+
def show(self):
"""
Print the instance's main workflow to stdout (dict form)
+
:return:
"""
workflow_id = self.instance.workflows.get_workflows()[0]['id']
@@ -108,33 +164,29 @@ class Workflow:
def store(self):
"""
Store the instance's workflow
+
:return:
"""
workflow_id = self.instance.workflows.get_workflows()[0]['id']
return workflow_id
-
def delete(self):
"""
+ Delete custom workflow
:return:
"""
return None
-
- def run(self):
+ def run(self, datamap, params):
"""
Run the custom workflow into a galaxy instance
Input datasets in the form of a list
+ Params
:return:
"""
- wf_id = self.show()
-
- datamap = {"genus": self.genus, "species": self.species, "strain": self.strain, "abbr": self.abbr,
- "full": self.full, "common": self.common, "ogs_version": self.ogs_version,
- "genome_version": self.genome_version, "sex": self.sex, "performed": self.performed}
return None
# def add_step(self, step_position, description, name):