Commit 0ad86a40 authored by Martina Locatelli's avatar Martina Locatelli 🍁
Browse files

Interactive shell for cluster jobs; validation set hierarchy tree bug; tuple...

Interactive shell for cluster jobs; validation set hierarchy tree bug; tuple of arguments for datasource
parent f04f67f6
......@@ -224,7 +224,9 @@ class Datasource(Base):
down.download()
@staticmethod
def download_hpc(job_path, only_essential=False, *kwargs):
def download_hpc(job_path, only_essential=False, **kwargs):
#Error: Tuple doesn't have get atttribute
#def download_hpc(job_path, only_essential=False, *kwargs):
"""Run HPC jobs downloading the resources.
Args:
......
......@@ -27,9 +27,9 @@ class sge():
jobFilenameSuffix = ".sh"
jobStatusSuffix = ".status"
# interactive shell is needed to source the .bashrc file correctly
templateScript = """\
#!/bin/bash
#!/bin/bash -i
#
#
......
......@@ -230,14 +230,13 @@ def parse_drugbank(ACTS=None, drugbank_xml=None):
def put_hierarchy(ACTS):
R = psql.qstring(
"SELECT protein_class_id, parent_id, pref_name FROM protein_classification", chembl_dbname)
G = nx.DiGraph()
for r in R:
G.add_edge(r[1], r[0]) # The tree
if r[1] is not None:
G.add_edge(r[1], r[0]) # The tree
R = psql.qstring("SELECT cs.accession, cc.protein_class_id FROM component_sequences cs, component_class cc WHERE cs.component_id = cc.component_id AND cs.accession IS NOT NULL", chembl_dbname)
......
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