From 5f0ad95d3b66ef4e5d43eb59f976605c0636fbf5 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Thu, 4 Apr 2024 17:15:36 +0200
Subject: [PATCH] MAINT: Linting
---
src/caosadvancedtools/scifolder/analysis_cfood.py | 3 +++
.../scifolder/simulation_cfood.py | 14 +++++++-------
src/caosadvancedtools/scifolder/software_cfood.py | 12 ++++--------
src/caosadvancedtools/scifolder/utils.py | 1 -
src/caosadvancedtools/scifolder/withreadme.py | 5 ++---
src/caosadvancedtools/serverside/helper.py | 3 ++-
.../table_json_conversion/table_generator.py | 4 ++--
7 files changed, 20 insertions(+), 22 deletions(-)
diff --git a/src/caosadvancedtools/scifolder/analysis_cfood.py b/src/caosadvancedtools/scifolder/analysis_cfood.py
index 608054cf..adce7225 100644
--- a/src/caosadvancedtools/scifolder/analysis_cfood.py
+++ b/src/caosadvancedtools/scifolder/analysis_cfood.py
@@ -41,6 +41,9 @@ class AnalysisCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
WithREADME.__init__(self)
+ self.analysis = None
+ self.people = None
+ self.project = None
def collect_information(self):
self.find_referenced_files([RESULTS, SOURCES, SCRIPTS])
diff --git a/src/caosadvancedtools/scifolder/simulation_cfood.py b/src/caosadvancedtools/scifolder/simulation_cfood.py
index c8f23f14..f8f3d07e 100644
--- a/src/caosadvancedtools/scifolder/simulation_cfood.py
+++ b/src/caosadvancedtools/scifolder/simulation_cfood.py
@@ -16,17 +16,14 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
-import os
-from itertools import chain
-
import caosdb as db
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
+from caosadvancedtools.cfood import (AbstractFileCFood,
assure_has_property,
- assure_object_is_in_list, get_entity)
-from caosadvancedtools.read_md_header import get_header
+ assure_object_is_in_list,
+ )
from .generic_pattern import full_pattern
-from .utils import (get_files_referenced_by_field, parse_responsibles,
+from .utils import (parse_responsibles,
reference_records_corresponding_to_files)
from .withreadme import DATAMODEL as dm
from .withreadme import (RESULTS, REVISIONOF, SCRIPTS, SOURCES, WithREADME,
@@ -42,6 +39,9 @@ class SimulationCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
WithREADME.__init__(self)
+ self.people = None
+ self.project = None
+ self.simulation = None
def collect_information(self):
self.find_referenced_files([RESULTS, SOURCES, SCRIPTS])
diff --git a/src/caosadvancedtools/scifolder/software_cfood.py b/src/caosadvancedtools/scifolder/software_cfood.py
index 77fb4652..4992fc54 100644
--- a/src/caosadvancedtools/scifolder/software_cfood.py
+++ b/src/caosadvancedtools/scifolder/software_cfood.py
@@ -17,20 +17,16 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
-import os
-from itertools import chain
-
import caosdb as db
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
+from caosadvancedtools.cfood import (AbstractFileCFood,
assure_has_property, assure_name_is,
- assure_object_is_in_list, get_entity)
+ assure_object_is_in_list,
+ )
from caosadvancedtools.guard import global_guard as guard
-from caosadvancedtools.read_md_header import get_header
from .generic_pattern import full_pattern
-from .utils import get_files_referenced_by_field, parse_responsibles
+from .utils import parse_responsibles
from .withreadme import BINARIES
-from .withreadme import DATAMODEL as dm
from .withreadme import SOURCECODE, WithREADME
diff --git a/src/caosadvancedtools/scifolder/utils.py b/src/caosadvancedtools/scifolder/utils.py
index 50e897c7..cbf87c4b 100644
--- a/src/caosadvancedtools/scifolder/utils.py
+++ b/src/caosadvancedtools/scifolder/utils.py
@@ -26,7 +26,6 @@ import pandas as pd
from caosadvancedtools.cfood import assure_object_is_in_list, fileguide
from caosadvancedtools.utils import (find_records_that_reference_ids,
read_field_as_list,
- return_field_or_property,
string_to_person)
logger = logging.getLogger("caosadvancedtools")
diff --git a/src/caosadvancedtools/scifolder/withreadme.py b/src/caosadvancedtools/scifolder/withreadme.py
index e1968ba4..d8388e1d 100644
--- a/src/caosadvancedtools/scifolder/withreadme.py
+++ b/src/caosadvancedtools/scifolder/withreadme.py
@@ -26,8 +26,7 @@ import caosdb as db
from caosadvancedtools.cfood import (assure_has_description, assure_has_parent,
assure_object_is_in_list, fileguide)
from caosadvancedtools.read_md_header import get_header as get_md_header
-from caosadvancedtools.table_importer import (win_path_converter,
- win_path_list_converter)
+from caosadvancedtools.table_importer import (win_path_converter)
from caosadvancedtools.utils import return_field_or_property
from .utils import (get_entity_ids_from_include_file,
@@ -236,7 +235,7 @@ class WithREADME(object):
generic_references,
record,
prop_name,
- to_be_updated=self.to_be_updated,
+ to_be_updated=self.to_be_updated, # pylint: disable=no-member
datatype=db.LIST(db.REFERENCE),
)
diff --git a/src/caosadvancedtools/serverside/helper.py b/src/caosadvancedtools/serverside/helper.py
index ba75739e..b7289c7f 100644
--- a/src/caosadvancedtools/serverside/helper.py
+++ b/src/caosadvancedtools/serverside/helper.py
@@ -223,6 +223,7 @@ def init_data_model(entities):
"be a {}.".format(e.role, local_role))
raise DataModelError(e.name, info)
except db.exceptions.EntityDoesNotExistError:
+ # pylint: disable=raise-missing-from
raise DataModelError(e.name, "This entity does not exist.")
return True
@@ -246,7 +247,7 @@ def get_data(filename, default=None):
Data from the given file.
"""
result = default.copy() if default is not None else {}
- with open(filename, 'r') as fi:
+ with open(filename, mode="r", encoding="utf-8") as fi:
data = json.load(fi)
result.update(data)
diff --git a/src/caosadvancedtools/table_json_conversion/table_generator.py b/src/caosadvancedtools/table_json_conversion/table_generator.py
index 21bcc7ae..5caefc8d 100644
--- a/src/caosadvancedtools/table_json_conversion/table_generator.py
+++ b/src/caosadvancedtools/table_json_conversion/table_generator.py
@@ -269,8 +269,8 @@ class TableTemplateGenerator(ABC):
class XLSXTemplateGenerator(TableTemplateGenerator):
"""Class for generating XLSX tables from json schema definitions."""
- def __init__(self):
- pass
+ # def __init__(self):
+ # super().__init__()
def generate(self, schema: dict, foreign_keys: dict, filepath: str) -> None:
"""Generate a sheet definition from a given JSON schema.
--
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