diff --git a/__pycache__/docker_compose_generator.cpython-38.pyc b/__pycache__/docker_compose_generator.cpython-38.pyc
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diff --git a/__pycache__/metadata_generator.cpython-38.pyc b/__pycache__/metadata_generator.cpython-38.pyc
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diff --git a/__pycache__/table_parser.cpython-38.pyc b/__pycache__/table_parser.cpython-38.pyc
new file mode 100644
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diff --git a/autoload.py b/autoload.py
index c26495b92f655999e35c657c3ed60a7988c0d549..29ff70210a63fc1e6cb8c0e705c5145e24f4c6f4 100644
--- a/autoload.py
+++ b/autoload.py
@@ -517,7 +517,8 @@ if __name__ == "__main__":
" modify headers (abims), generate blast banks (doesn't commit them: TODO), initialize GGA instance, load the data and run,"
" the main workflow. To update/add data to container, use --update in conjunction to --full (TODO)")
parser.add_argument("--init-instance",
- help="Initialization of galaxy instance. Run first in an empty instance")
+ help="Initialization of galaxy instance. Run first in an empty instance",
+ action="store_true")
parser.add_argument("--load-data",
help="Create src_data directory tree and load its data into the instance")
parser.add_argument("--run-main",
@@ -551,6 +552,7 @@ if __name__ == "__main__":
logging.basicConfig(level=logging.INFO)
if str(args.input).endswith(".json"):
+ print("JSON")
input_json = args.input
else:
tp = table_parser.TableParser()
@@ -564,6 +566,7 @@ if __name__ == "__main__":
for json_sp in json_sp_dict:
sp_dict_list.append(json_sp)
+ metadata = {}
for sp_dict in sp_dict_list:
al = Autoload(species_parameters_dictionary=sp_dict, args=args)
al.main_dir = os.path.abspath(args.dir)
@@ -574,7 +577,7 @@ if __name__ == "__main__":
metadata[genus_species_strain_sex]["initialized"] = True
if args.load_data:
logging.info("loading data into galaxy")
- al.load_data_in_galaxy()
+ # al.load_data()
metadata[genus_species_strain_sex]["data_loaded_in_instance"] = True
if args.run_main:
logging.info("running main workflow")
diff --git a/docker_compose_generator.py b/docker_compose_generator.py
index e76198bae1a8835096a1f326394aa338c7a4c022..c999460b8d0278003c7b8eecc81d248d18c90218 100644
--- a/docker_compose_generator.py
+++ b/docker_compose_generator.py
@@ -17,6 +17,8 @@ TODO: write the whole yml dict from scratch (would allow the script to be more r
more customizable while being clearer (instead of the default yml string or input docker-compose template)
TODO: read json
+
+API master key or galaxy: MASTER_API_KEY: XXXXXXX (alphanum, user prompt/git env variable)
"""
diff --git a/table_parser.py b/table_parser.py
index 0059fdbe72c3b08f63ea8f3b634f81b6e5545885..9c44cd8da9fee254e6de27335684b8e096d242bc 100755
--- a/table_parser.py
+++ b/table_parser.py
@@ -1,4 +1,5 @@
import os
+import sys
import pandas # xlrd required for excel files reading
import numpy
import json
@@ -28,54 +29,35 @@ class TableParser:
def parse_table(self, extension):
if extension == "xls":
pandas_table = pandas.DataFrame(pandas.read_excel(self.table_file))
- pandas_table = pandas_table.replace(numpy.nan, "", regex=True)
- for char in " ,.()-/":
- pandas_table = pandas_table.replace("\\" + char, "_", regex=True)
- pandas_table = pandas_table.replace("\\__", "_", regex=True)
- pandas_table.loc[pandas_table["genome version"] == "", "genome version"] = "1.0"
- pandas_table.loc[pandas_table["ogs version"] == "", "ogs version"] = "1.0"
- pandas_table.loc[pandas_table["version"] == "", "version"] = "1.0"
- pandas_table.loc[pandas_table["date"] == "", "date"] = datetime.today().strftime("%Y-%m-%d")
- with open(os.path.join(self.dir, self.json_file), 'w') as json_file:
- json_file.truncate(0)
- json_content = list()
- for organism in range(0, len(pandas_table.index)):
- organism_dict = pandas_table.iloc[organism].to_dict()
- for k, v in organism_dict.items():
- v = str(v).split(" ")
- v = "_".join(v)
- v = v.replace("__", "_")
- if v.endswith("_"):
- v = v[:-1]
- json_content.append(organism_dict)
- json.dump(json_content, json_file, indent=4)
-
elif extension == "csv":
pandas_table = pandas.DataFrame(pandas.read_csv(self.table_file))
- pandas_table = pandas_table.replace(numpy.nan, "", regex=True)
- for char in " ,.()-/":
- pandas_table = pandas_table.replace("\\" + char, "_", regex=True)
- pandas_table = pandas_table.replace("\\__", "_", regex=True)
- pandas_table.loc[pandas_table["genome version"] == "", "genome version"] = "1.0"
- pandas_table.loc[pandas_table["ogs version"] == "", "ogs version"] = "1.0"
- pandas_table.loc[pandas_table["version"] == "", "version"] = "1.0"
- pandas_table.loc[pandas_table["date"] == "", "date"] = datetime.today().strftime("%Y-%m-%d")
- with open(os.path.join(self.dir, self.json_file), 'w') as json_file:
- json_file.truncate(0)
- json_content = list()
- for organism in range(0, len(pandas_table.index)):
- organism_dict = pandas_table.iloc[organism].to_dict()
- for k, v in organism_dict.items():
- v = str(v).split(" ")
- v = "_".join(v)
- v = v.replace("__", "_")
- if v.endswith("_"):
- v = v[:-1]
- json_content.append(organism_dict)
- json.dump(json_content, json_file, indent=4)
-
else:
- logging.info("input tabulated file doesn't have the correct extension (supported extensions: xls, xlsx, csv)")
+ logging.info("wrong format: input tabulated file cannot be read (supported formats: xls, xlsx, csv)")
+ sys.exit()
+ pandas_table = pandas_table.replace(numpy.nan, "", regex=True)
+
+ for char in " ,.()-/":
+ pandas_table = pandas_table.replace("\\" + char, "_", regex=True)
+ pandas_table = pandas_table.replace("\\__", "_", regex=True)
+ pandas_table.loc[pandas_table["genome version"] == "", "genome version"] = "1.0"
+ pandas_table.loc[pandas_table["ogs version"] == "", "ogs version"] = "1.0"
+ pandas_table.loc[pandas_table["version"] == "", "version"] = "1.0"
+ pandas_table.loc[pandas_table["date"] == "", "date"] = datetime.today().strftime("%Y-%m-%d")
+ with open(os.path.join(self.dir, self.json_file), 'w') as json_file:
+ json_file.truncate(0)
+ json_content = list()
+ for organism in range(0, len(pandas_table.index)):
+ organism_dict = pandas_table.iloc[organism].to_dict()
+ for k, v in organism_dict.items():
+ v = str(v).split(" ")
+ v = "_".join(v)
+ v = v.replace("__", "_")
+ if v.endswith("_"):
+ v = v[:-1]
+ json_content.append(organism_dict)
+ json.dump(json_content, json_file, indent=4)
+
+
def write_json(self, data, filename):
with open(filename, 'w') as f:
diff --git a/templates/compose-template.yml b/templates/compose-template.yml
index ee3e04ebf89f21498de0f10ea2e46aa1ff5cc1bb..590923cd3b27ff536dd15d51931524783b5c52a3 100755
--- a/templates/compose-template.yml
+++ b/templates/compose-template.yml
@@ -110,6 +110,7 @@ services:
GALAXY_AUTO_UPDATE_DB: 1
GALAXY_AUTO_UPDATE_CONDA: 1
GALAXY_AUTO_UPDATE_TOOLS: "/galaxy-central/tools_1.yaml"
+ MASTER_API_KEY: dev
BLAT_ENABLED: 1
jbrowse:
diff --git a/templates/stack_template.yml b/templates/stack_template.yml
index 68adc74b0148d4a44c653e1e0b1f12b538a6064b..1844b7c958d481490e6258aca9d9d2bdab071edf 100755
--- a/templates/stack_template.yml
+++ b/templates/stack_template.yml
@@ -138,7 +138,7 @@ services:
GALAXY_AUTO_UPDATE_TOOLS: "/galaxy-central/tools_1.yaml"
GALAXY_SHARED_DIR: ""
BLAT_ENABLED: 1
- master_api_key: MASTERLOCK
+ MASTER_API_KEY: dev
networks:
- traefik
- genus_species