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Amandine PERRIN
pipeline_annotation
Commits
5ab9ef44
Commit
5ab9ef44
authored
Aug 01, 2021
by
Amandine PERRIN
Browse files
remove quote marks surrounding strings in configfile
parent
d3ec33c7
Pipeline
#62509
passed with stages
in 6 minutes and 8 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
PanACoTA/utils_argparse.py
View file @
5ab9ef44
...
...
@@ -193,28 +193,55 @@ def perc_id(param):
class
Conf_all_parser
(
configparser
.
ConfigParser
):
"""
Read configfile and return arguments found, according to required type
Parameters
----------
conffile : str
path to configuration file
readsec : list
list of sections of the config file to read
Attributes
----------
conffile : str
Path to configfile
sec_dicts : dict
{section1: {param: value}, {section2: {param:value}}}
"""
def
__init__
(
self
,
conffile
,
readsec
=
[]):
super
().
__init__
()
# If there is a config file specified, but it does not exist -> exit with error message
if
conffile
!=
""
and
not
os
.
path
.
isfile
(
conffile
):
print
(
f
"Error: config file
{
conffile
}
not found."
)
sys
.
exit
(
1
)
self
.
conffile
=
conffile
# Read the config file
try
:
self
.
read
(
conffile
)
except
configparser
.
DuplicateOptionError
as
err
:
print
(
err
)
sys
.
exit
(
1
)
self
.
sec_dicts
=
{}
# Convert configfile sections to dicts
for
sec
in
readsec
:
# If section in configfile, put its arguments and values to a dict
# If not, create empty section, and associate with empty dict
if
sec
in
dict
(
self
):
self
.
sec_dicts
[
sec
]
=
dict
(
self
[
sec
])
self
.
clean_strings
(
sec
)
else
:
self
.
sec_dicts
[
sec
]
=
{}
self
.
add_section
(
sec
)
def
clean_strings
(
self
,
section
):
"""
Remove quote marks surrounding strings
"""
for
param
in
self
.
sec_dicts
[
section
]:
initial
=
self
.
sec_dicts
[
section
][
param
]
self
.
sec_dicts
[
section
][
param
]
=
initial
.
strip
(
'"'
)
def
get_section_dict
(
self
,
section
):
"""
get dictionary of values for 'section' section
...
...
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