From da26e81a8ec2112618e4d26200e8df62a227d010 Mon Sep 17 00:00:00 2001
From: AJRubio-Montero <AJRubio-Montero@github.com>
Date: Thu, 15 Jul 2021 12:51:19 +0000
Subject: [PATCH] bugs corrected running simulations and analisys
---
wrappers/ARTIwrapper.py | 2 +-
wrappers/args_showers.py | 3 ++-
wrappers/do_showers_onedata.py | 11 +++++------
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/wrappers/ARTIwrapper.py b/wrappers/ARTIwrapper.py
index 95b3601..85b4bff 100644
--- a/wrappers/ARTIwrapper.py
+++ b/wrappers/ARTIwrapper.py
@@ -56,7 +56,7 @@ class ARTIwrapper():
if os.path.exists(onedata_path + id):
xattr.setxattr(onedata_path + id, 'onedata_json', md)
id_hidden = '/' + id.lstrip('/').replace('/','/.metadata/.')
- osUtils.write_file(onedata_path + id_hidden + '.jsonld', md)
+ osUtils._write_file(onedata_path + id_hidden + '.jsonld', md)
else:
print('CAUTION: '+ id +' is not in onedata, requeuing...' )
raise inst
diff --git a/wrappers/args_showers.py b/wrappers/args_showers.py
index 664629c..8f16fdb 100644
--- a/wrappers/args_showers.py
+++ b/wrappers/args_showers.py
@@ -72,10 +72,11 @@ def get_sys_args_S1():
parser.add_argument('-?', action='help', help='Shows this help and exit.')
#added, not equiv in do_showers:
+
parser.add_argument('-u', dest='u', required=True,
help='ORCID code describing user, plain usernames are \
no allowed for publication')
-
+
args = parser.parse_args()
args_dict = vars(args)
diff --git a/wrappers/do_showers_onedata.py b/wrappers/do_showers_onedata.py
index 9fb24de..6b4e670 100755
--- a/wrappers/do_showers_onedata.py
+++ b/wrappers/do_showers_onedata.py
@@ -37,7 +37,7 @@ def _get_pri_metadata(filecode):
args=['common_activity.json', 'dataset_arti_pri_output.json']
s = mdUtils.get_metadata_for_dataset(args)
- s = s.replace('FILENAME', filecode+'pri.bz2')
+ s = s.replace('FILENAME', filecode +'.pri.bz2')
# DCAT2 distribution:format & mediaType
s = s.replace('FORMAT', 'BIN') ## BIN or TXT
s = s.replace('MEDIATYPE', 'octet-stream') ## octect-stream or text
@@ -47,7 +47,7 @@ def _get_sec_metadata(filecode):
args=['common_activity.json', 'dataset_arti_sec_output.json']
s = mdUtils.get_metadata_for_dataset(args)
- s = s.replace('FILENAME', filecode+'sec.bz2')
+ s = s.replace('FILENAME', filecode + '.sec.bz2')
# DCAT2 distribution:format & mediaType
s = s.replace('FORMAT', 'BIN') ## BIN or TXT
s = s.replace('MEDIATYPE', 'octet-stream') ## octect-stream or text
@@ -57,7 +57,7 @@ def _get_shw_metadata(filecode):
args=['common_activity.json', 'dataset_arti_shw_output.json']
s = mdUtils.get_metadata_for_dataset(args)
- s = s.replace('FILENAME', filecode+'shw.bz2')
+ s = s.replace('FILENAME', filecode + '.shw.bz2')
# DCAT2 distribution:format & mediaType
s = s.replace('FORMAT', 'BIN') ## BIN or TXT
s = s.replace('MEDIATYPE', 'octet-stream') ## octect-stream or text
@@ -117,7 +117,7 @@ def producer_S1(catcodename, arti_params):
#
# This final execution is a PROBLEM.... I only centering on primaries
- with open(catcodename+'.run', 'r') as file1:
+ with open('./' + catcodename + '/'+ catcodename + '.run', 'r') as file1:
print(file1)
for z in file1.readlines():
if z != "":
@@ -127,8 +127,7 @@ def producer_S1(catcodename, arti_params):
# filecode = $i
# task = "cp remote_onedata/$i ." + z
print(z)
- z_aux = z.split(" ")
- filecode = z_aux[14].replace(';', '')
+ filecode = z.split("echo DAT")[1].split(" ")[0]
task = z
q.put((filecode, task))
--
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