diff --git a/gga_get_data.py b/gga_get_data.py
index f936657600ce098e1a9359ff524390e3467ffc70..e9eb11e50fbd4470d739872a6f86fbffd3ac833b 100644
--- a/gga_get_data.py
+++ b/gga_get_data.py
@@ -55,11 +55,7 @@ class GetData(speciesData.SpeciesData):
def get_source_data_files_from_path(self):
"""
- Find source data files in the parent_directory
- Link data files
-
- TODO: manage access to the "parent directory" subdirectories properly
- TODO: implement search/tests for individual file paths
+ Find source data files and copy them into the src_data dir tree
:return:
"""
@@ -92,11 +88,17 @@ class GetData(speciesData.SpeciesData):
# Copy dataset in the organism src_data dir tree correct folder
for k, v in datasets_to_get.items():
if k in genome_datasets:
- shutil.copyfile(os.path.abspath(v), os.path.join(organism_genome_dir, os.path.basename(v)))
- logging.info("Copied {0} into {1}".format(v, organism_genome_dir))
+ logging.info("Copying {0} into {1}".format(v, organism_genome_dir))
+ try:
+ shutil.copyfile(os.path.abspath(v), os.path.join(organism_genome_dir, os.path.basename(v)))
+ except Exception as exc:
+ logging.warning("Could not copy {1} ({2})".format(v, exc))
elif k in annotation_datasets:
- shutil.copyfile(os.path.abspath(v), os.path.join(organism_annotation_dir, os.path.basename(v)))
- logging.info("Copied {0} into {1}".format(v, organism_annotation_dir))
+ logging.info("Copying {0} into {1}".format(v, organism_annotation_dir))
+ try:
+ shutil.copyfile(os.path.abspath(v), os.path.join(organism_annotation_dir, os.path.basename(v)))
+ except Exception as exc:
+ logging.warning("Could not copy {1} ({2})".format(v, exc))
else:
pass
diff --git a/gga_init.py b/gga_init.py
index 95ee78171a08c8cb3c89304601b368854a3ab415..9c990af4106b4846d5b1c83fb71119bd5fa1ed7c 100644
--- a/gga_init.py
+++ b/gga_init.py
@@ -28,7 +28,6 @@ TODO
"""
-
class DeploySpeciesStack(speciesData.SpeciesData):
"""
Child of SpeciesData
@@ -40,7 +39,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
def make_directory_tree(self):
"""
- Generate the directory tree for an organism and move datasets into src_data
+ Generate the directory tree for an organism
:return:
"""
@@ -73,9 +72,12 @@ class DeploySpeciesStack(speciesData.SpeciesData):
else:
logging.debug("Using default banner for Tripal pages")
self.config.pop("banner_path", None)
+ else:
+ logging.debug("Using default banner for Tripal pages")
+ self.config.pop("banner_path", None)
# Create nginx dirs and write/re-write nginx conf
- self.make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
+ make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
try:
with open(os.path.abspath("./nginx/conf/default.conf"), 'w') as conf:
conf.write("server {\n\tlisten 80;\n\tserver_name ~.;\n\tlocation /download/ {\n\t\talias /project_data/; \n\t\tautoindex on;\n\t}\n}") # The species nginx conf
@@ -92,46 +94,21 @@ class DeploySpeciesStack(speciesData.SpeciesData):
logging.critical("Insufficient permission to create src_data directory tree")
sys.exit(exc)
-
- print(self.strain)
- print(self.species_folder_name)
-
# List of all the directories to create in src_data
src_data_dirs_li = ["./src_data", "./src_data/annotation", "./src_data/genome", "./src_data/tracks",
"./src_data/annotation/%s" % self.species_folder_name,
"./src_data/genome/%s" % self.species_folder_name,
"./src_data/annotation/{0}/OGS{1}/".format(self.species_folder_name, self.ogs_version),
"./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version)]
- self.make_dirs(dir_paths_li=src_data_dirs_li)
+ make_dirs(dir_paths_li=src_data_dirs_li)
# Return to main directory
os.chdir(self.main_dir)
logging.info("Directory tree generated for %s" % self.full_name)
- @staticmethod
- def make_dirs(dir_paths_li):
- """
- Recursively create directories from a list of paths with a try-catch condition
- :param dir_paths_li:
- :return:
- """
- created_dir_paths_li = []
-
- for dir_path in dir_paths_li:
- try:
- os.mkdir(dir_path)
- except FileExistsError:
- logging.debug("%s directory already exists" % dir_path)
- except PermissionError as exc:
- logging.critical("Insufficient permission to create %s" % dir_path)
- sys.exit(exc)
- created_dir_paths_li.append(dir_path)
-
- return created_dir_paths_li
-
- def make_compose_files(self, force=False):
+ def make_compose_files(self):
"""
Create a formatted copy of the template compose file inside a species directory tree
@@ -167,80 +144,105 @@ class DeploySpeciesStack(speciesData.SpeciesData):
gspecies_compose_file.write(gspecies_compose_output)
# Create the volumes (directory) of the species docker-compose file
- self.create_mounts(working_dir=".")
+ create_mounts(working_dir=".", main_dir=self.main_dir)
# Return to main directory
os.chdir(self.main_dir)
- def make_traefik_compose_files(self):
+
+ def make_orthology_compose_files(self):
"""
- Create or update the traefik docker-compose file and authelia conf files
- Will only write new authelia conf files if the argument "--overwrite-all" is specified or
- the authelia directory doesn't contain conf files
:return:
"""
os.chdir(self.main_dir)
+ make_dirs["./orthology", "./orthology/src_data", "./orthology/src_data/genomes",
+ "./orthology/src_data/gff", "./orthology/src_data/newicks", "./orthology/src_data/proteomes"]
+
+
+def make_dirs(dir_paths_li):
+ """
+ Recursively create directories from a list of paths with a try-catch condition
+
+ :param dir_paths_li:
+ :return:
+ """
+ created_dir_paths_li = []
+
+ for dir_path in dir_paths_li:
+ try:
+ os.mkdir(dir_path)
+ except FileExistsError:
+ logging.debug("%s directory already exists" % dir_path)
+ except PermissionError as exc:
+ logging.critical("Insufficient permission to create %s" % dir_path)
+ sys.exit(exc)
+ created_dir_paths_li.append(dir_path)
+
+ return created_dir_paths_li
+
+def make_traefik_compose_files(config, main_dir):
+ """
+ Create or update the traefik directory, docker-compose file and authelia conf files
+ Only called when the argument "--traefik" is specified
+
+ :param config:
+ :param main_dir:
+ :return:
+ """
+
+ script_dir = os.path.dirname(os.path.realpath(sys.argv[0]))
+ render_vars = config
+
+ os.chdir(main_dir)
+
# Create directory tree
- self.make_dirs(["./traefik", "./traefik/authelia"])
+ make_dirs(["./traefik", "./traefik/authelia"])
# Render and try to write the traefik docker-compose file
# This new docker-compose file will not overwrite the one already present in the traefik dir
# unless the argument "--overwrite-all" is specified
# Jinja2 templating, handled using the python "jinja2" module
- file_loader = FileSystemLoader(self.script_dir + "/templates")
+ file_loader = FileSystemLoader(script_dir + "/templates")
env = Environment(loader=file_loader)
- if not os.path.isfile("./traefik/docker-compose.yml") or force:
+ if not os.path.isfile("./traefik/docker-compose.yml"):
traefik_compose_template = env.get_template("traefik_compose_template.yml.j2")
traefik_compose_output = traefik_compose_template.render(render_vars)
- with open(os.path.join(self.main_dir, "docker-compose.yml"), 'w') as traefik_compose_file:
+ with open(os.path.join(main_dir, "traefik/docker-compose.yml"), 'w') as traefik_compose_file:
logging.info("Writing traefik docker-compose.yml")
traefik_compose_file.truncate(0)
traefik_compose_file.write(traefik_compose_output)
- if self.config["authelia_config_path"]:
- if not self.config["authelia_config_path"] == "" or not self.config["authelia_config_path"] == "/path/to/authelia/config":
- if os.path.isfile(os.path.abspath(self.config["authelia_config_path"])):
+ if config["authelia_config_path"]:
+ if not config["authelia_config_path"] == "" or not config["authelia_config_path"] == "/path/to/authelia/config":
+ if os.path.isfile(os.path.abspath(config["authelia_config_path"])):
try:
- shutil.copy(os.path.abspath(self.config["authelia_config_path"]), "./traefik/authelia")
+ shutil.copy(os.path.abspath(config["authelia_config_path"]), "./traefik/authelia")
except Exception as exc:
- logging.critical("Cannot copy custom Authelia config file (%s)" % self.config["authelia_config_path"])
+ logging.critical("Cannot copy custom Authelia config file (%s)" % config["authelia_config_path"])
sys.exit(exc)
else:
- logging.critical("Custom Authelia config file not found (%s)" % self.config["authelia_config_path"])
+ logging.critical("Custom Authelia config file not found (%s)" % config["authelia_config_path"])
# Path to the authelia users in the repo
- authelia_users_path = self.script_dir + "/templates/authelia_users_template.yml"
+ authelia_users_path = script_dir + "/templates/authelia_users_template.yml"
# Copy authelia "users" file
- if not os.path.isfile("./traefik/authelia/users.yml") or force:
+ if not os.path.isfile("./traefik/authelia/users.yml"):
shutil.copy(authelia_users_path, "./traefik/authelia/users.yml")
# Create the mounts for the traefik and authelia services
- traefik_dir = os.path.abspath(os.path.join(self.main_dir, "traefik"))
- if not os.path.isdir(os.path.join(traefik_dir, "docker_data")) or force:
- self.create_mounts(working_dir=traefik_dir)
+ traefik_dir = os.path.abspath(os.path.join(main_dir, "traefik"))
+ if not os.path.isdir(os.path.join(traefik_dir, "docker_data")):
+ create_mounts(working_dir=traefik_dir, main_dir=main_dir)
# Return to main directory
- os.chdir(self.main_dir)
-
-
- def make_orthology_compose_files(self):
- """
-
- :return:
- """
-
- os.chdir(self.main_dir)
-
- self.make_dirs["./orthology", "./orthology/src_data", "./orthology/src_data/genomes",
- "./orthology/src_data/gff", "./orthology/src_data/newicks", "./orthology/src_data/proteomes"]
-
+ os.chdir(main_dir)
- def create_mounts(self, working_dir):
+def create_mounts(working_dir, main_dir):
"""
Create the folders (volumes) required by a container (to see required volumes, check their compose file)
@@ -285,12 +287,11 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Go back to the "main" directory
try:
- os.chdir(os.path.abspath(self.main_dir))
+ os.chdir(os.path.abspath(main_dir))
except OSError as exc:
- logging.critical("Cannot access %s, exiting" % self.main_dir)
+ logging.critical("Cannot access %s, exiting" % main_dir)
sys.exit(exc)
-
def deploy_stacks(input_list, main_dir):
"""
This function first deploys/redeploys the traefik stack, then deploys/redeploys the organism stack, then redeploys the traefik stack
@@ -367,8 +368,8 @@ if __name__ == "__main__":
type=str,
help="Where the stack containers will be located, defaults to current directory")
- parser.add_argument("--overwrite-all",
- help="Overwrite all docker-compose and conf files in the traefik and authelia directories (default=False)",
+ parser.add_argument("--traefik",
+ help="Initialize/wverwrite traefik directory all docker-compose and conf files in the traefik and authelia directories (default=False)",
action="store_true")
args = parser.parse_args()
@@ -392,6 +393,11 @@ if __name__ == "__main__":
sp_dict_list = utilities.parse_input(os.path.abspath(args.input))
+ # Create traefik directory and compose files if specified
+ if args.traefik:
+ config = utilities.parse_config(args.config)
+ make_traefik_compose_files(config=config, main_dir=main_dir)
+
logging.info("Deploying stacks for organisms in input file %s" % args.input)
for sp_dict in sp_dict_list:
@@ -428,7 +434,7 @@ if __name__ == "__main__":
logging.info("Successfully generated the directory tree for %s" % deploy_stack_for_current_organism.full_name)
# Make compose files
- deploy_stack_for_current_organism.make_compose_files(force=args.overwrite_all)
+ deploy_stack_for_current_organism.make_compose_files()
logging.info("Successfully generated the docker-compose files for %s" % deploy_stack_for_current_organism.full_name)
logging.info("Deploying stacks")
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 27ec5973e5f9fdaea84e4e6f2a21699bab55efc9..ead3c936153421ee3b5ad000712a256df72a605d 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -183,7 +183,8 @@ class RunWorkflow(speciesData.SpeciesData):
"sourcename": "Genoscope",
"date_executed": self.date})
- # Add Interpro analysis to chado
+ # Add Interpro analysis to chado
+ logging.info("Adding Interproscan 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/2.3.3",
history_id=self.history_id,
@@ -194,7 +195,8 @@ class RunWorkflow(speciesData.SpeciesData):
"date_executed": self.date})
- # Add Blastp (diamond) analysis to chado
+ # Add Blastp (diamond) analysis to chado
+ logging.info("Adding Blastp Diamond 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/2.3.3",
history_id=self.history_id,
@@ -255,7 +257,6 @@ class RunWorkflow(speciesData.SpeciesData):
history_id=self.history_id,
params=workflow_parameters,
inputs=datamap,
- inputs_by="",
allow_tool_state_corrections=True)
logging.info("Successfully imported and invoked workflow {0}, check the galaxy instance ({1}) for the jobs state".format(workflow_name, self.instance_url))
@@ -310,7 +311,7 @@ class RunWorkflow(speciesData.SpeciesData):
folders_ids[current_folder_name] = v
# Iterating over the folders to find datasets and map datasets to their IDs
- logging.info("Datasets IDs: ")
+ logging.debug("Datasets IDs: ")
for k, v in folders_ids.items():
if k == "/genome":
sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
@@ -320,29 +321,33 @@ class RunWorkflow(speciesData.SpeciesData):
if type(e) == dict:
if e["name"].endswith(".fa"):
self.datasets["genome_file"] = e["ldda_id"]
- logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
+ logging.debug("Genome file:\t" + e["name"] + ": " + e["ldda_id"])
if k == "/annotation":
sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
final_sub_folder_content = self.instance.folders.show_folder(folder_id=sub_folder_content["folder_contents"][0]["id"], contents=True)
for k2, v2 in final_sub_folder_content.items():
for e in v2:
+ # try:
+ # print(e["name"])
+ # except TypeError:
+ # print("TypeError")
if type(e) == dict:
# TODO: manage genome and ogs versions (differentiate between the correct folders using self.config)
if "transcripts" in e["name"]:
self.datasets["transcripts_file"] = e["ldda_id"]
- logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
- elif "proteins" in e["name"]:
+ logging.debug("Transcripts file:\t" + e["name"] + ": " + e["ldda_id"])
+ elif "proteins.fa" in e["name"]:
self.datasets["proteins_file"] = e["ldda_id"]
- logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
+ logging.debug("Proteins file:\t" + e["name"] + ": " + e["ldda_id"])
elif "gff" in e["name"]:
self.datasets["gff_file"] = e["ldda_id"]
- logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
- elif e["name"].endswith(".xml") and e["name"].startswith("Interpro"):
+ logging.debug("GFF file:\t" + e["name"] + ": " + e["ldda_id"])
+ elif "Interpro" in e["name"]:
self.datasets["interproscan_file"] = e["ldda_id"]
- logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
- elif e["name"].endswith(".xml") and "diamond" in e["name"]:
+ logging.debug("Interproscan file:\t" + e["name"] + ": " + e["ldda_id"])
+ elif "diamond-blastp" in e["name"]:
self.datasets["blast_diamond_file"] = e["ldda_id"]
- logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
+ logging.debug("Blastp diamond file:\t" + e["name"] + ": " + e["ldda_id"])
logging.info("Uploading datasets into history %s" % self.history_id)
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["genome_file"])
@@ -397,10 +402,10 @@ class RunWorkflow(speciesData.SpeciesData):
elif dataset_dict["name"].endswith(".gff"):
gff_dataset_hda_id = dataset_dict["id"]
logging.debug("gff dataset hda ID: %s" % gff_dataset_hda_id)
- elif dataset_dict["name"].endwsith(".xml") and dataset["name"].startswith("Interpro"):
+ elif "Interpro" in dataset_dict["name"]:
interproscan_dataset_hda_id = dataset_dict["id"]
logging.debug("InterproScan dataset hda ID: %s" % gff_dataset_hda_id)
- elif dataset_dict["name"].endswith(".xml") and "diamond" in dataset_dict["name"]:
+ elif "diamond-blastp" in dataset_dict["name"]:
blast_diamond_dataset_hda_id = dataset_dict["id"]
logging.debug("Blast Diamond dataset hda ID: %s" % gff_dataset_hda_id)
else:
@@ -614,6 +619,7 @@ if __name__ == "__main__":
# Import datasets into history and retrieve their hda IDs
run_workflow_for_current_organism.import_datasets_into_history()
hda_ids = run_workflow_for_current_organism.get_datasets_hda_ids()
+ # run_workflow_for_current_organism.get_invocation_report(workflow_name="Chado load Tripal synchronize")
# Explicit workflow parameter names
GENOME_FASTA_FILE = "0"
@@ -634,6 +640,15 @@ if __name__ == "__main__":
workflow_parameters[GFF_FILE] = {}
workflow_parameters[PROTEINS_FASTA_FILE] = {}
workflow_parameters[TRANSCRIPTS_FASTA_FILE] = {}
+
+ print(run_workflow_for_current_organism.org_id)
+ print(run_workflow_for_current_organism.genome_analysis_id)
+ print(run_workflow_for_current_organism.ogs_analysis_id)
+ print(hda_ids["genome_hda_id"])
+ print(hda_ids["gff_hda_id"])
+ print(hda_ids["proteins_hda_id"])
+ print(hda_ids["transcripts_hda_id"])
+
workflow_parameters[LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
"analysis_id": run_workflow_for_current_organism.genome_analysis_id,
"do_update": "true"}
@@ -648,17 +663,16 @@ if __name__ == "__main__":
# Datamap for input datasets - dataset source (type): ldda (LibraryDatasetDatasetAssociation)
run_workflow_for_current_organism.datamap = {}
- run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
- run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
- run_workflow_for_current_organism.datamap[PROTEINS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
- run_workflow_for_current_organism.datamap[TRANSCRIPTS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
+ run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "hda", "id": hda_ids["genome_hda_id"]}
+ run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "hda", "id": hda_ids["gff_hda_id"]}
+ run_workflow_for_current_organism.datamap[PROTEINS_FASTA_FILE] = {"src": "hda", "id": hda_ids["proteins_hda_id"]}
+ run_workflow_for_current_organism.datamap[TRANSCRIPTS_FASTA_FILE] = {"src": "hda", "id": hda_ids["transcripts_hda_id"]}
run_workflow_for_current_organism.datamap = {}
- run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id":
+ run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "hda", "id":
run_workflow_for_current_organism.datasets["genome_file"]}
- run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda",
- "id": run_workflow_for_current_organism.datasets[
- "gff_file"]}
+ run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "hda",
+ "id": hda_ids["gff_hda_id"]}
# Run the Chado load Tripal sync workflow with the parameters set above
run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
@@ -739,7 +753,7 @@ if __name__ == "__main__":
run_workflow_for_current_organism.datamap = {}
- run_workflow_for_current_organism.datamap[INTERPRO_FILE] = {"src": "hda", "id": hda_ids["interproscan_hda_id"]}
+ run_workflow_for_current_organism.datamap[INTERPRO_FILE] = {"src": "hda", "id": run_workflow_for_current_organism.hda_ids["interproscan_hda_id"]}
# Run Interproscan workflow
run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
diff --git a/speciesData.py b/speciesData.py
index a099078fa620fa73232c101f14ebbd43da9fd298..287c8ccf92a839743cb5ec71b0a7a23ff3f65acc 100644
--- a/speciesData.py
+++ b/speciesData.py
@@ -18,11 +18,11 @@ class SpeciesData:
def __init__(self, parameters_dictionary):
# self.config_dictionary = None
self.parameters_dictionary = parameters_dictionary
- self.species = parameters_dictionary["description"]["species"]
- self.genus = parameters_dictionary["description"]["genus"]
- self.strain = parameters_dictionary["description"]["strain"]
- self.sex = parameters_dictionary["description"]["sex"]
- self.common = parameters_dictionary["description"]["common_name"]
+ self.species = parameters_dictionary["description"]["species"].replace("(", "_").replace(")", "_")
+ self.genus = parameters_dictionary["description"]["genus"].replace("(", "_").replace(")", "_")
+ self.strain = parameters_dictionary["description"]["strain"].replace("(", "_").replace(")", "_")
+ self.sex = parameters_dictionary["description"]["sex"].replace("(", "_").replace(")", "_")
+ self.common = parameters_dictionary["description"]["common_name"].replace("(", "_").replace(")", "_")
self.date = datetime.today().strftime("%Y-%m-%d")
self.origin = parameters_dictionary["description"]["origin"]
@@ -70,14 +70,16 @@ class SpeciesData:
self.workflow_name = None
self.metadata = dict()
self.api_key = None
- self.datasets = dict()
# API key used to communicate with the galaxy instance. Cannot be used to do user-tied actions
+ self.datasets = dict()
self.config = None
# Custom config used to set environment variables inside containers, defaults to the one in the repo
- if parameters_dictionary["data"]["parent_directory"] == "" or parameters_dictionary["data"]["parent_directory"] == "/path/to/closest/parent/dir":
- self.source_data_dir = "/shared/projects/phaeoexplorer/" # Testing path for phaeoexplorer data - TODO: REMOVE IN PRODUCTION
- else:
- self.source_data_dir = parameters_dictionary["data"]["parent_directory"]
+ self.source_data_dir = parameters_dictionary["data"]["parent_directory"]
self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase.lower(), self.species.lower(), self.sex.lower()])["not_empty"])
self.existing_folders_cache = {}
self.bam_metadata_cache = {}
+
+ # # Sanitize str attributes
+ # for var in vars(self):
+ # for attr in var if type(attr) == str:
+ # attr = attr.replace("(", "_").replace(")", "_")
diff --git a/workflows/Chado_load_Tripal_synchronize.ga b/workflows/Chado_load_Tripal_synchronize.ga
index 6571c65e4bbb10d7f7d66f5c7076cf74ebf09c2f..a04e7afff8cc0d0b0616fefd611fe3a24c66e862 100644
--- a/workflows/Chado_load_Tripal_synchronize.ga
+++ b/workflows/Chado_load_Tripal_synchronize.ga
@@ -2,7 +2,7 @@
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
- "name": "Chado load Tripal synchronize (imported from uploaded file)",
+ "name": "Chado load Tripal synchronize",
"steps": {
"0": {
"annotation": "",