autoload.py: script implementation, easier to understand and use. small fixes...

autoload.py: script implementation, easier to understand and use. small fixes to workflow.py and main.py

autoload.py

+from bioblend import galaxy
+import bioblend
+import argparse
+import os
+import subprocess
+import sys
+import json
+import yaml
+import numpy
+import pandas
+import logging
+import re
+
+
+class Autoload:
+    """
+    Cleaner version for gga_auto_load (to use in production).
+
+    This class possesses most useful parameters to interact with GGA as attributes (as defined in __init__), so new
+    methods can be more easily implemented by copying already existing ones (i.e add new analysis, run a workflow, ...)
+
+    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)
+    """
+
+    def __init__(self, species_parameters_dictionary: dict):
+        self.species_parameters_dictionary = species_parameters_dictionary
+        self.species = species_parameters_dictionary["species"]
+        self.genus = species_parameters_dictionary["genus"]
+        self.strain = species_parameters_dictionary["strain"]
+        self.sex = species_parameters_dictionary["sex"]
+        self.common = species_parameters_dictionary["common"]
+        self.date = species_parameters_dictionary["date"]
+        self.performed = species_parameters_dictionary["performed by"]
+        self.genome_version = species_parameters_dictionary["genome version"]
+        self.ogs_version = species_parameters_dictionary["ogs version"]
+        self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
+        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: galaxy = None
+        self.history_id = None
+        self.library_id = None
+        self.main_dir = None
+        self.species_dir = None
+        self.org_id = None
+        self.genome_analysis_id = None
+        self.ogs_analysis_id = None
+        self.tool_panel = None
+
+        # Test the connection to the galaxy instance for the current species
+        # Additionally set some class attributes
+        # TODO: auth issues with nginx
+        self.instance = galaxy.GalaxyInstance(url=self.instance_url,
+                                              key="3b36455cb16b4d0e4348e2c42f4bb934",
+                                              email="alebars@sb-roscoff.fr",
+                                              password="pouet",
+                                              verify=True)
+        logging.info("testing connection to the galaxy instance ...")
+        try:
+            self.instance.histories.get_histories()
+            self.tool_panel = self.instance.tools.get_tool_panel()
+        except bioblend.ConnectionError:
+            logging.info("cannot connect to galaxy instance @ " + self.instance_url)
+            sys.exit()
+        else:
+            logging.info("successfully connected to galaxy instance @ " + self.instance_url)
+
+        self.main_dir = os.getcwd() + "/"
+        self.species_dir = os.path.join(self.main_dir, self.genus_species) + "/"
+
+    def load_data_in_galaxy(self, method):
+        """
+        - create the src_data directory tree for the species
+        - change headers for pep file
+        - load data into the galaxy container with the galaxy_data_libs_SI.py script
+
+        :param method:
+        :return:
+        """
+        os.chdir(self.main_dir)
+        try:
+            os.mkdir(self.species_dir)
+        except FileExistsError:
+            logging.debug("directory " + self.species_dir + " already exists")
+        try:
+            os.chdir(self.species_dir)
+            working_dir = os.getcwd()
+        except OSError:
+            logging.info("cannot access " + self.species_dir + ", run with higher privileges")
+            sys.exit()
+
+        src_data_folders = ["annotation", "genome"]
+        species_folder_name = "_".join([self.genus_lowercase, self.species, self.strain, self.sex])
+        try:
+            os.mkdir("./src_data")
+            os.mkdir("./src_data/annotation")
+            os.mkdir("./src_data/genome")
+            os.mkdir("./src_data/annotation/" + species_folder_name)
+            os.mkdir("./src_data/genome/" + species_folder_name)
+        except FileExistsError:
+            logging.debug("src_data directory tree already exists")
+        except PermissionError:
+            logging.debug("insufficient permission to create src_data directory tree")
+
+        # Data import into galaxy
+        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)
+                    elif f.endswith("transcripts-gff.fa"):
+                        source_files["transcripts_file"] = os.path.join(d, f)
+                    elif f.endswith(".gff"):
+                        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)
+                logging.debug("source files found:")
+        for k, v in 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"]]
+        # 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"])
+        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"]],
+                           stdout=subprocess.PIPE,
+                           cwd=annotation_dir)
+        if os.path.exists(annotation_dir + "gmon.out"):
+            subprocess.run(["rm", annotation_dir + "/gmon.out"],
+                           stdout=subprocess.PIPE,
+                           cwd=annotation_dir)
+
+        setup_data_libraries = "docker-compose exec galaxy /tool_deps/_conda/bin/python /opt/setup_data_libraries.py"
+        try:
+            logging.info("loading data into the galaxy container")
+            subprocess.run(setup_data_libraries,
+                           stdout=subprocess.PIPE,
+                           shell=True)
+        except subprocess.CalledProcessError:
+            logging.info("cannot load data into container for " + self.full_name)
+            pass
+        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.history_id = histories[0]["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
+        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
+        for i in instance_source_data_folders:
+            for k, v in i.items():
+                if k == "name":
+                    folders_ids[v] = 0
+                    current_fo_name = v
+                if k == "id":
+                    folders_ids[current_fo_name] = v
+        logging.info("folders and datasets IDs: ")
+        datasets = dict()
+        for k, v in folders_ids.items():
+            logging.info("\t" + k + ": " + v)
+            if k == "/genome":
+                sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
+                for k2, v2 in sub_folder_content.items():
+                    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"])
+            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():
+                    for e in v2:
+                        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"])
+                            elif e["name"].endswith("proteins.fasta"):
+                                datasets["proteins_file"] = e["ldda_id"]
+                                logging.info("\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"])
+                            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"])
+
+    def run_workflow(self, workflow_name, workflow_parameters):
+        """
+
+        :param workflow_ga_file:
+        :param workflow_parameters:
+        :return:
+        """
+
+        logging.debug("running workflow: " + str(workflow_name))
+        workflow_ga_file = self.main_dir + "Galaxy-Workflow-" + workflow_name + ".ga"
+        if self.strain != "":
+            custom_ga_file = "_".join([self.genus, self.species, self.strain]) + "_workflow.ga"
+            custom_ga_file_path = os.path.abspath(custom_ga_file)
+        else:
+            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
+            # 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}")
+            # 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
+
+    def init_instance(self):
+        """
+        Galaxy instance startup in preparation for running workflows
+        - remove Homo sapiens from the chado database.
+        - add organism and analyses into the chado database
+        - get any other existing organisms IDs (mainly used for testing)
+
+        :return:
+        """
+
+        # Delete Homo sapiens from 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)
+        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:
+            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")
+        except IndexError:
+            pass
+
+        # Add organism (species) to chado
+        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,
+                                                  "genus": self.genus,
+                                                  "species": self.species,
+                                                  "common": self.common})
+        # Add OGS analysis to chado
+        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,
+                                                  "program": "Performed by Genoscope",
+                                                  "programversion": str("OGS" + self.ogs_version),
+                                                  "sourcename": "Genoscope",
+                                                  "date_executed": self.date})
+
+        # Add genome analysis to chado
+        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,
+                                                  "program": "Performed by Genoscope",
+                                                  "programversion": str("genome v" + self.genome_version),
+                                                  "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})
+        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")
+
+        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
+        except IndexError:
+            logging.debug("no matching OGS analysis exists in the 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})
+        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
+        except IndexError:
+            logging.debug("no matching genome analysis exists in the Chado database")
+
+        logging.info("finished initializing instance")
+
+    def clean_instance(self):
+        """
+        TODO: function to purge the instance from analyses and organisms
+        :return:
+        """
+        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)
+

loader.sh

-#!/usr/bin/env bash
\ No newline at end of file

main.py

@@ -53,6 +53,7 @@ def main():
         genus_species = genus_lower + "_" + species
         common = sp_dict["common"]
         strain = sp_dict["strain"]
+        sex = sp_dict["sex"]
         if strain != "":
             genus_species_strain = genus_species + "_" + strain
         else:
@@ -123,65 +124,84 @@ def main():
             print("Successfully connected to galaxy instance @ " + instance_url)
 
         # TODO: FTP/symlink stuff to retrieve the datasets + change headers in pep.fasta
-        setup_data_libraries_cl = "docker-compose exec galaxy /tool_deps/_conda/bin/python /opt/setup_data_libraries.py"
-        # try:
-        #     os.mkdir("./src_data")
-        # except FileExistsError:
-        #     print("src_data folder already exists for " + genus_species_strain)
-        #     print("Loading data into galaxy...")
-        #     try:
-        #         setup_data_libraries = subprocess.Popen(setup_data_libraries_cl.split(), stdout=subprocess.PIPE)
-        #         print("Output from setup_data_libraries.py")
-        #         print(setup_data_libraries.communicate())
-        #     except bb.ConnectionError:
-        #         print("Cannot load data into container for " + genus_species_strain)
-        #         break
-        #     else:
-        #         print("Data successfully loaded into docker container for " + genus_species_strain)
-        # else:
-        #     print("src_data folder created for " + genus_species_strain)
-        #     try:
-        #         setup_data_libraries = subprocess.Popen(setup_data_libraries_cl.split(), stdout=subprocess.PIPE)
-        #         print("Output from setup_data_libraries.py")
-        #         print(setup_data_libraries.communicate())
-        #     except bb.ConnectionError:
-        #         print("Cannot load data into container for " + genus_species_strain)
-        #         break
-        #     else:
-        #         print("Data successfully loaded into docker container for " + genus_species_strain)
-
-        genome_dir, annotation_dir = None, None
+
+        # ---------------------------------------------------------------------
+        # src_data directory tree creation
+        # ---------------------------------------------------------------------
+
+        src_data_folders = ["annotation", "genome"]
+        species_folder_name = "_".join([genus_lower, species, strain, sex])
+        try:
+            os.mkdir("./src_data")
+            os.mkdir("./src_data/annotation")
+            os.mkdir("./src_data/genome")
+            os.mkdir("./src_data/annotation/" + species_folder_name)
+            os.mkdir("./src_data/genome/" + species_folder_name)
+        except FileExistsError:
+            print("src_data directory tree already exists")
+            pass
+        except PermissionError:
+            print("Insufficient permission to create src_data directory tree")
+
+        # ---------------------------------------------------------------------
+        # Data import into galaxy
+        # ---------------------------------------------------------------------
+
+        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
-                annotation_dir_files = [f for f in os.listdir(d) if os.path.isfile(os.path.join(d, f))]
-                print("src_data annotation file(s):")
-                print(str('\t' + file) for file in annotation_dir_files)
+                for f in os.listdir(d):
+                    if f.endswith("proteins.fasta"):
+                        source_files["proteins_file"] = os.path.join(d, f)
+                    elif f.endswith("transcripts-gff.fa"):
+                        source_files["transcripts_file"] = os.path.join(d, f)
+                    elif f.endswith(".gff"):
+                        source_files["gff_file"] = os.path.join(d, f)
+                # annotation_dir_files = [f for f in os.listdir(d) if os.path.isfile(os.path.join(d, f))]
             elif "genome/" in d:
                 genome_dir = d
-                genome_dir_files = [f for f in os.listdir(d) if os.path.isfile(os.path.join(d, f))]
-                print("src_data genome file(s):")
-                print(str('\t' + file) for file in genome_dir_files)
-
-
-
-
-        modify_pep_headers = ["sh /usr/local/genome2/mmo/scripts/phaeoexplorer/phaeoexplorer-change_pep_fasta_header.sh"]
-
+                for f in os.listdir(d):
+                    if f.endswith(".fa"):
+                        source_files["genome_file"] = os.path.join(d, f)
+                # genome_dir_files = [f for f in os.listdir(d) if os.path.isfile(os.path.join(d, f))]
+                print("Source files found:")
+        for k, v in source_files.items():
+            print("\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"]]
+        # test version
+        modify_pep_headers = ["/home/alebars/gga/phaeoexplorer-change_pep_fasta_header.sh",
+                              source_files["proteins_file"]]
+        print("Changing fasta headers in " + 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"]],
+                           stdout=subprocess.PIPE,
+                           cwd=annotation_dir)
+        if os.path.exists(annotation_dir + "gmon.out"):
+            subprocess.run(["rm", annotation_dir + "/gmon.out"],
+                           stdout=subprocess.PIPE,
+                           cwd=annotation_dir)
 
         # 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)
+        setup_data_libraries = "docker-compose exec galaxy /tool_deps/_conda/bin/python /opt/setup_data_libraries.py"
+        try:
+            print("Loading data into the galaxy container")
+            subprocess.run(setup_data_libraries,
+                           stdout=subprocess.PIPE,
+                           shell=True)
+        except subprocess.CalledProcessError:
+            print("Cannot load data into container for " + genus_species_strain)
+            break
+        else:
+            print("Data successfully loaded into docker container for " + genus_species_strain)
 
         # generate workflow file and run it in the galaxy instance
 
@@ -202,8 +222,6 @@ def main():
                     current_fo_name = v
                 if k == "id":
                     fo_id[current_fo_name] = v
-
-        # TODO: turn data id parsing into a function
         print("Folders and datasets IDs: ")
         datasets = dict()
         for k, v in fo_id.items():
@@ -242,6 +260,9 @@ def main():
         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"])
 
+        toolrunner = ToolRunner(parameters_dict=sp_dict, instance=gi, history=current_hi_id)
+        # toolrunner.show_pannel()  # show tools pannel (with tool_id and versions)
+
         # ---------------------------------------------------------------------
         # Galaxy instance interaction
         # ---------------------------------------------------------------------
@@ -301,7 +322,7 @@ def main():
         # datamap["0"] = {"src": "hda", "id": datasets["genome_file"]}
         # datamap["1"] = {"src": "hda", "id": datasets["proteins_file"]}
         #
-        wf_dict_json = workflow.generate(working_directory=wd, main_directory=main_dir, workflow_name="jbrowse")
+        wf_dict_json = workflow.generate(working_directory=wd, main_directory=main_dir, workflow_name="main")
         wf_dict = json.loads(wf_dict_json)  # doesn't work with eval()
         #
         # gi.workflows.import_workflow_dict(workflow_dict=wf_dict)
@@ -311,10 +332,13 @@ def main():
         # print("Jbrowse workflow ID: " + wf_id)
         # wf_params = workflow.set_jbrowse_workflow_parameters()
         #
+        # allow_tool_state_correction makes galaxy fill missing tool states,
+        # because workflow was edited outside of galaxy with only some inputs (precaution parameter)
         # gi.workflows.invoke_workflow(workflow_id=wf_id,
         #                              history_id=current_hi_id,
         #                              params=wf_params,
-        #                              inputs=datamap)
+        #                              inputs=datamap,
+        #                              allow_tool_state_corrections=True)
         # gi.workflows.delete_workflow(workflow_id=wf_id)
 
         # remove active instance history for testing, purge configured @ ~/config/galaxy.yml.docker_sample

workflow.py

@@ -62,14 +62,15 @@ class Workflow:
             # 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('{\\\\\\\\\\\\"unique_id\\\\\\\\\\\\": \\\\\\\\\\\\"UNIQUEID\\\\\\\\\\\\"}',
+            print(ga_in)
+            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
-            ga_in = ga_in.replace("\\\\\\\\\\\\", "\\\\\\")
-            ga_in = ga_in.replace('http://localhost/sp/undaria_pinnatifida/feature/Undaria/pinnatifida/mRNA/{id}"',
-                                  "http://localhost/sp/" + self.genus.lower()[0] + self.genus[1:] + " " + self.species + "/feature/" + self.genus + "/mRNA/{id}")
+            # ga_in = ga_in.replace("\\\\\\\\\\\\", "\\\\\\")
+            ga_in = ga_in.replace('http://localhost/sp/genus_species/feature/Genus/species/mRNA/{id}',
+                                  "http://localhost/sp/" + self.genus.lower()[0] + self.genus[1:] + "_" + self.species + "/feature/" + self.genus + "/mRNA/{id}")
             # ga_in = ga_in.replace('"index\\\": \\\"false', '"index\\\": \\\"true')
             # workflow_name = '"name": "' + self.full + '"'
             # ga_in = ga_in.replace('"name": "preset_workflow"', '"name": "preset_workflow"')
@@ -77,7 +78,7 @@ class Workflow:
             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
             self.workflow = ga_in
-            print(ga_in)
+            # print(ga_in)
         return ga_in
 
     def set_main_workflow_parameters(self, datasets):