Commit 536a3254 authored by Martina Locatelli's avatar Martina Locatelli 🍁
Browse files

Adding CC DB creation step to the update pipeline

parent d7f06c7c
Pipeline #2511 passed with stages
in 11 minutes and 53 seconds
...@@ -45,6 +45,7 @@ from chemicalchecker.database import Dataset, Datasource ...@@ -45,6 +45,7 @@ from chemicalchecker.database import Dataset, Datasource
from chemicalchecker.database import Molrepo, Calcdata from chemicalchecker.database import Molrepo, Calcdata
from chemicalchecker.util.pipeline import Pipeline, PythonCallable from chemicalchecker.util.pipeline import Pipeline, PythonCallable
from chemicalchecker.util.pipeline import CCFit, CCPredict from chemicalchecker.util.pipeline import CCFit, CCPredict
from chemicalchecker.pipeline.update_resources.create_database import create_db_dataset
# this is needed to export signaturizers at the end # this is needed to export signaturizers at the end
sys.path.insert(0, '/aloy/home/mbertoni/code/signaturizer') sys.path.insert(0, '/aloy/home/mbertoni/code/signaturizer')
...@@ -228,6 +229,15 @@ def main(args): ...@@ -228,6 +229,15 @@ def main(args):
'cpu': hpc_kwargs['proj2']['cpu'] 'cpu': hpc_kwargs['proj2']['cpu']
} }
# TASK: Create new CC DB
def create_db():
# Create a new database for the current CC update
create_db_dataset()
creating_db_task = PythonCallable(name="creating_db",
python_callable=create_db)
pp.add_task(creating_db_task)
############################################# #############################################
# TASK: Download all datasources # TASK: Download all datasources
def download_fn(tmpdir): def download_fn(tmpdir):
......
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