From 6c7b8ea0f6e44bb96003c49e1e2f37d4b34b5193 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 18 Feb 2020 12:07:10 +0100
Subject: [PATCH] main function
---
main.py | 229 +++++++++++++++++++++++++++++++++++++++++++-------------
1 file changed, 177 insertions(+), 52 deletions(-)
diff --git a/main.py b/main.py
index 72f2443..bf999a9 100644
--- a/main.py
+++ b/main.py
@@ -1,59 +1,184 @@
from bioblend import galaxy
+import bioblend as bb
import argparse
+import os
+import sys
+import subprocess
+import json
+from workflow import Workflow
+from filetransfer import FileTransfer
-"""
-
-
+# TODO: script description
"""
-
-parser = argparse.ArgumentParser(description="Input genus, species, strain, version")
-parser.add_argument("--name", help="Sample species name, format: genus-species",type=str, required=True)
-parser.add_argument("--strain", help="Strain of the sample species", type=str, required=True)
-parser.add_argument("--version", help="Data version (e.g 1.0, 1.2, ...)", type=str, required=True)
-parser.add_argument("--common-name", help="Vernacular/common name of the species",type=str, required=False)
-
-user_arguments = parser.parse_args()
-
-genus = user_arguments.name.split('-')[0]
-species = user_arguments.name.split('-')[1]
-strain = user_arguments.strain
-vernacular = user_arguments.common_name
-instance_url = "http://localhost/sp/" + genus + "_" + species + "/galaxy/"
-
-print("Species: " + genus + " " + species + " (Wakame)" +
- "\nStrain: " + strain +
- "\nAccessing " + instance_url + "...")
-
-gi = galaxy.GalaxyInstance(url=instance_url,
- key="291ec50b48dd1f006985b32e39bc3696",
- email="alebars@sb-roscoff.fr",
- password="pouet",
- verify=True)
-
-# gi = galaxy.GalaxyInstance(url="http://localhost/sp/undaria_pinnatifida/galaxy/",
-# # key="291ec50b48dd1f006985b32e39bc3696",
-# email="alebars@sb-roscoff.fr",
-# password="pouet",
-# verify=True)
-
-# gi = galaxy.GalaxyInstance(url="http://localhost/sp/undaria_pinnatifida/galaxy/",
-# key="291ec50b48dd1f006985b32e39bc3696",
-# email="alebars@sb-roscoff.fr",
-# password="pouet",
-# verify=True)
-
-# gi = galaxy.GalaxyInstance(url="http://abims-gga.sb-roscoff.fr/sp/ectocarpus_species1/galaxy/",
-# key="84dfbee3c0efa9155518f01fbeff57c8",
-# email="gga@sb-roscoff.fr",
-# password="Mmo,55k")
-
-try:
- hl = gi.histories.get_histories()
-except ConnectionError:
- print("Cannot connect to GGA instance @ " + instance_url + "")
-
-
-
+"""
+class Autoload:
+
+ def __init__(self, json_in):
+ self.json_in = json_in
+
+ def main(self):
+ return None
+
+
+def main():
+
+ parser = argparse.ArgumentParser(description="Input genus, species, strain, version")
+ parser.add_argument("json", type=str, help="Input JSON file")
+ parser.add_argument("--just-load", help="Only load data into galaxy, does not create nor run analyses in galaxy")
+
+ # CLI stuff
+ # parser.add_argument("--name", help="Sample species name, format: genus-species",type=str)
+ # parser.add_argument("--strain", help="Strain of the sample species", type=str)
+ # parser.add_argument("--version", help="Data version (e.g 1.0, 1.2, ...)", type=str)
+ # parser.add_argument("--common-name", help="Vernacular/common name of the species",type=str)
+
+ user_arguments = parser.parse_args()
+
+ # List that will hold all dicts from the JSON input file, containing parameters for each species
+ sp_dict_list = []
+
+ # JSON parsing and loading
+ with open(user_arguments.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)
+
+ # Get variables from the current species dict
+ for sp_dict in sp_dict_list:
+ sp_params_list = []
+ genus = sp_dict["genus"]
+ genus_lower = genus[0].lower() + genus[1:]
+ species = sp_dict["species"]
+ genus_species = genus_lower + "_" + species
+ common = sp_dict["common"]
+ strain = sp_dict["strain"]
+ if strain != "":
+ genus_species_strain = genus_species + "_" + strain
+ else:
+ genus_species_strain = genus_species
+ ogs_version = sp_dict["ogs version"]
+ genome_version = sp_dict["genome version"]
+ performed_by = sp_dict["performed by"]
+
+ # CLI stuff
+ # genus = user_arguments.name.split('-')[0]
+ # genus_lower = genus[0].lower().genus[1:]
+ # genus_upper = genus[0].upper() + genus[1:]
+ # species = user_arguments.name.split('-')[1]
+ # strain = user_arguments.strain
+ # vernacular = user_arguments.common_name
+
+ # TODO: prompt y/n asking for the validity of info
+ # Test adress, change to abims-gga.sb-roscoff.fr/sp/ in production
+ instance_url = "http://localhost/sp/" + genus_lower + "_" + species + "/galaxy/"
+
+ print("Species: " + genus + " " + species + " (" + common + ")"
+ "\nStrain: " + strain +
+ "\nAccessing instance " + instance_url)
+
+ # Connect to the galaxy instance of the current species TODO: API key connection issues
+ gi = galaxy.GalaxyInstance(url=instance_url,
+ key="291ec50b48dd1f006985b32e39bc3696",
+ email="alebars@sb-roscoff.fr",
+ password="pouet",
+ verify=True)
+
+ """
+ This part creates the current species directory and go to it
+ If it already exists, just move to it
+ To be expanded when docker-swarm is implemented (or all config files are ready), not useful for now
+ """
+ main_dir = os.getcwd() + "/"
+ sp_dir = os.path.join(main_dir, genus_species) + "/"
+
+ try:
+ os.mkdir(sp_dir)
+ except FileExistsError:
+ print("Directory " + sp_dir + " already exists")
+ try:
+ os.chdir(sp_dir)
+ wd = os.getcwd()
+ except OSError:
+ print("Cannot access " + sp_dir + ", run with higher privileges")
+ break
+
+ # Production instance example TODO: secure pswd and API key? + manage API keys (if needed)
+ # gi = galaxy.GalaxyInstance(url="http://abims-gga.sb-roscoff.fr/sp/ectocarpus_species1/galaxy/",
+ # key="84dfbee3c0efa9155518f01fbeff57c8",
+ # email="gga@sb-roscoff.fr",
+ # password="****")
+
+ # Check connection to the current instance
+ try:
+ hl = gi.histories.get_histories()
+ except bb.ConnectionError:
+ print("Cannot connect to GGA instance @ " + instance_url)
+ else:
+ print("Successfully connected to instance " + instance_url)
+
+ # TODO: FTP stuff to retrieve the datasets (used in testing, not needed for production)
+ # try:
+ # os.mkdir("./src_data")
+ # except FileExistsError:
+ # print("src_data folder already exists for " + genus_species_strain)
+ # else:
+ # print("src_data folder created for " + genus_species_strain)
+ #
+ # TODO: load the data into the current species directory and load it into galaxy instance
+ # setup_data_libraries_cl = \
+ # "docker-compose exec galaxy /tool_deps/_conda/bin/python /opt/setup_data_libraries.py"
+ #
+ # try:
+ # setup_data_libraries = subprocess.Popen(setup_data_libraries_cl.split(), stdout=subprocess.PIPE)
+ # # output message from the data loading script
+ # setup_data_libraries_output = setup_data_libraries.communicate()
+ # except Exception:
+ # print("Cannot load data into container for " + genus_species_strain)
+ # break
+ # 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)
+ workflow.generate(working_directory=wd, main_directory=main_dir)
+ wf_id = workflow.store()
+ hi_id = gi.histories.get_histories()[0]["id"]
+ print("Workflow id: " + wf_id)
+ print("History id: " + hi_id)
+ wf_show = gi.workflows.show_workflow(workflow_id=wf_id)
+ print(wf_show["inputs"])
+
+ # workflow.port()
+ li_id = gi.libraries.get_libraries()[0]["id"]
+ # gi.folders.update_folder() # TODO: add method to enable data updates
+ 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))
+ fo_gi = gi.libraries.get_folders(library_id=li_id) # data location
+ fo_id = {}
+ current_fo_name = ""
+ print(fo_gi)
+ # folders ids: access to data to run the first tools
+ for i in fo_gi:
+ for k, v in i.items():
+ if k == "name":
+ fo_id[k] = 0
+ current_fo_name = k
+ if k == "id":
+ fo_id[current_fo_name] = v
+
+
+ os.chdir(main_dir)
+ print("\n")
+
+
+if __name__ == "__main__":
+ main()
--
GitLab