From 365e2d3d06d741daa152f66e87ffcfa397cea3c4 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Thu, 4 Apr 2024 17:29:06 +0200
Subject: [PATCH] MAINT: Linting
---
.../converter/labfolder_export.py | 16 +++-----------
.../scifolder/experiment_cfood.py | 15 +++++++------
.../scifolder/publication_cfood.py | 21 ++++++++-----------
.../scifolder/result_table_cfood.py | 19 ++++++++---------
.../scifolder/software_cfood.py | 3 +++
5 files changed, 33 insertions(+), 41 deletions(-)
diff --git a/src/caosadvancedtools/converter/labfolder_export.py b/src/caosadvancedtools/converter/labfolder_export.py
index 172ed993..6e282218 100644
--- a/src/caosadvancedtools/converter/labfolder_export.py
+++ b/src/caosadvancedtools/converter/labfolder_export.py
@@ -22,17 +22,7 @@
""" Imports labfolder exports """
import os
-import re
-import shutil
-import subprocess
-import sys
-import tempfile
-import time
-import warnings
-from io import BytesIO, StringIO
-
-import requests
-import yaml
+
from bs4 import BeautifulSoup
import caosdb as db
@@ -73,8 +63,8 @@ def get_author_from_entry(entry):
def val_or_none(stuff):
if len(stuff) == 0:
return None
- else:
- return stuff[0].getText()
+
+ return stuff[0].getText()
def add_property_from_data_element(dbrecord, element):
diff --git a/src/caosadvancedtools/scifolder/experiment_cfood.py b/src/caosadvancedtools/scifolder/experiment_cfood.py
index 38606b5f..83329863 100644
--- a/src/caosadvancedtools/scifolder/experiment_cfood.py
+++ b/src/caosadvancedtools/scifolder/experiment_cfood.py
@@ -17,15 +17,15 @@
# along with this program. If not, see <https://www.gnu.org/licenses/>.
import caosdb as db
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_description,
- assure_has_parent, assure_has_property,
- assure_object_is_in_list, get_entity)
-from caosadvancedtools.read_md_header import get_header
+from caosadvancedtools.cfood import (AbstractFileCFood,
+ assure_has_property,
+ assure_object_is_in_list,
+ )
from .generic_pattern import full_pattern
from .utils import parse_responsibles, reference_records_corresponding_to_files
from .withreadme import DATAMODEL as dm
-from .withreadme import RESULTS, REVISIONOF, SCRIPTS, WithREADME, get_glob
+from .withreadme import RESULTS, REVISIONOF, WithREADME, get_glob
class ExperimentCFood(AbstractFileCFood, WithREADME):
@@ -42,7 +42,10 @@ class ExperimentCFood(AbstractFileCFood, WithREADME):
super().__init__(*args, **kwargs)
WithREADME.__init__(self)
- self.name_map = {},
+ self.name_map = ({}, )
+ self.experiment = None
+ self.people = None
+ self.project = None
@staticmethod
def get_re():
diff --git a/src/caosadvancedtools/scifolder/publication_cfood.py b/src/caosadvancedtools/scifolder/publication_cfood.py
index fc78e5b7..68e345ac 100644
--- a/src/caosadvancedtools/scifolder/publication_cfood.py
+++ b/src/caosadvancedtools/scifolder/publication_cfood.py
@@ -16,18 +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_object_is_in_list, fileguide,
- get_entity)
+ )
from caosadvancedtools.read_md_header import get_header
-from caosadvancedtools.utils import find_records_that_reference_ids
from .generic_pattern import date_suffix_pattern, readme_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,
@@ -37,16 +33,15 @@ from .withreadme import (RESULTS, REVISIONOF, SCRIPTS, SOURCES, WithREADME,
def folder_to_type(name):
if name == "Theses":
return "Thesis"
- elif name == "Articles":
+ if name == "Articles":
return "Article"
- elif name == "Posters":
+ if name == "Posters":
return "Poster"
- elif name == "Presentations":
+ if name == "Presentations":
return "Presentation"
- elif name == "Reports":
+ if name == "Reports":
return "Report"
- else:
- raise ValueError()
+ raise ValueError()
class PublicationCFood(AbstractFileCFood, WithREADME):
@@ -58,6 +53,8 @@ class PublicationCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
WithREADME.__init__(self)
+ self.people = None
+ self.publication = None
def collect_information(self):
self.find_referenced_files([RESULTS, SOURCES, SCRIPTS])
diff --git a/src/caosadvancedtools/scifolder/result_table_cfood.py b/src/caosadvancedtools/scifolder/result_table_cfood.py
index deaa2d00..e32cd0bd 100644
--- a/src/caosadvancedtools/scifolder/result_table_cfood.py
+++ b/src/caosadvancedtools/scifolder/result_table_cfood.py
@@ -20,17 +20,12 @@ import re
import caosdb as db
import pandas as pd
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_description,
- assure_has_parent, assure_has_property,
- assure_object_is_in_list, get_entity)
-from caosadvancedtools.read_md_header import get_header
+from caosadvancedtools.cfood import (AbstractFileCFood,
+ )
from ..cfood import assure_property_is, fileguide
from .experiment_cfood import ExperimentCFood
from .generic_pattern import date_pattern, date_suffix_pattern, project_pattern
-from .utils import parse_responsibles, reference_records_corresponding_to_files
-from .withreadme import DATAMODEL as dm
-from .withreadme import RESULTS, REVISIONOF, SCRIPTS, WithREADME, get_glob
# TODO similarities with TableCrawler
@@ -49,6 +44,9 @@ class ResultTableCFood(AbstractFileCFood):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.table = pd.read_csv(fileguide.access(self.crawled_path))
+ self.recs = []
+ self.experiment = None
+ self.project = None
@staticmethod
def get_re():
@@ -60,7 +58,7 @@ class ResultTableCFood(AbstractFileCFood):
self.experiment, self.project = (
ExperimentCFood.create_identifiable_experiment(self.match))
- for idx, row in self.table.iterrows():
+ for _, row in self.table.iterrows():
rec = db.Record()
rec.add_parent(self.match.group("recordtype"))
@@ -77,10 +75,11 @@ class ResultTableCFood(AbstractFileCFood):
self.identifiables.extend([self.project, self.experiment])
def update_identifiables(self):
- for ii, (idx, row) in enumerate(self.table.iterrows()):
+ for ii, (_, row) in enumerate(self.table.iterrows()):
for col in row.index:
match = re.match(ResultTableCFood.property_name_re, col)
- assure_property_is(self.recs[ii], match.group("pname"), row.loc[col], to_be_updated=self.to_be_updated)
+ assure_property_is(self.recs[ii], match.group("pname"), row.loc[col],
+ to_be_updated=self.to_be_updated)
assure_property_is(self.experiment, self.match.group("recordtype"),
self.recs, to_be_updated=self.to_be_updated,
datatype=db.LIST(self.match.group("recordtype")))
diff --git a/src/caosadvancedtools/scifolder/software_cfood.py b/src/caosadvancedtools/scifolder/software_cfood.py
index 4992fc54..d91817f1 100644
--- a/src/caosadvancedtools/scifolder/software_cfood.py
+++ b/src/caosadvancedtools/scifolder/software_cfood.py
@@ -40,6 +40,9 @@ class SoftwareCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
WithREADME.__init__(self)
+ self.people = None
+ self.software = None
+ self.softwareversion = None
def collect_information(self):
self.find_referenced_files([BINARIES, SOURCECODE])
--
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