From d636c45c5e69e81a4bdfb16829ea8c51480c248c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Thu, 4 Apr 2024 09:51:02 +0200
Subject: [PATCH] revert some lilnkahead renamings
---
.../test_crawl_with_datamodel_problems.py | 2 +-
src/caosadvancedtools/cache.py | 2 +-
src/caosadvancedtools/cfood.py | 8 +--
src/caosadvancedtools/crawler.py | 72 +++++++++----------
src/caosadvancedtools/datamodel_problems.py | 6 +-
src/caosadvancedtools/guard.py | 2 +-
src/caosadvancedtools/loadFiles.py | 13 +---
.../scifolder/experiment_cfood.py | 15 ++--
.../scifolder/publication_cfood.py | 10 +--
.../scifolder/result_table_cfood.py | 18 ++---
.../scifolder/simulation_cfood.py | 13 ++--
.../scifolder/software_cfood.py | 13 ++--
src/caosadvancedtools/scifolder/utils.py | 1 +
src/caosadvancedtools/scifolder/withreadme.py | 7 +-
.../serverside/generic_analysis.py | 4 +-
src/caosadvancedtools/serverside/helper.py | 7 +-
src/caosadvancedtools/utils.py | 4 +-
17 files changed, 95 insertions(+), 102 deletions(-)
diff --git a/integrationtests/test_crawl_with_datamodel_problems.py b/integrationtests/test_crawl_with_datamodel_problems.py
index 08c80ea1..8623d57d 100644
--- a/integrationtests/test_crawl_with_datamodel_problems.py
+++ b/integrationtests/test_crawl_with_datamodel_problems.py
@@ -25,7 +25,7 @@
"""
-import linkahead as db
+import caosdb as db
from caosadvancedtools import loadFiles
from caosadvancedtools.cfood import fileguide
from caosadvancedtools.crawler import FileCrawler
diff --git a/src/caosadvancedtools/cache.py b/src/caosadvancedtools/cache.py
index 0ffc7282..cf74e330 100644
--- a/src/caosadvancedtools/cache.py
+++ b/src/caosadvancedtools/cache.py
@@ -33,7 +33,7 @@ from abc import ABC, abstractmethod
from copy import deepcopy
from hashlib import sha256
-import linkahead as db
+import caosdb as db
from lxml import etree
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 7c71f8a4..c0da4f01 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -43,10 +43,10 @@ import warnings
from abc import ABCMeta, abstractmethod
from datetime import datetime
-import linkahead as db
-from linkahead.common.models import Entity
-from linkahead.exceptions import (BadQueryError, EmptyUniqueQueryError,
- QueryNotUniqueError, TransactionError)
+import caosdb as db
+from caosdb.common.models import Entity
+from caosdb.exceptions import (BadQueryError, EmptyUniqueQueryError,
+ QueryNotUniqueError, TransactionError)
from .datamodel_problems import DataModelProblems
from .guard import global_guard as guard
diff --git a/src/caosadvancedtools/crawler.py b/src/caosadvancedtools/crawler.py
index 6655919e..5e84bc8a 100644
--- a/src/caosadvancedtools/crawler.py
+++ b/src/caosadvancedtools/crawler.py
@@ -41,14 +41,14 @@ match. This occurs in basically three steps:
import logging
import os
+import subprocess
import traceback
import uuid
from datetime import datetime
from sqlite3 import IntegrityError
-from xml.sax.saxutils import escape
-import linkahead as db
-from linkahead.exceptions import BadQueryError, TransactionError
+import caosdb as db
+from caosdb.exceptions import BadQueryError
from .cache import IdentifiableCache, UpdateCache, get_pretty_xml
from .cfood import RowCFood, add_files, get_ids_for_entities_with_names
@@ -67,7 +67,7 @@ def separated(text):
return "-"*60 + "\n" + text
-def apply_list_of_updates(to_be_updated, update_flags=None,
+def apply_list_of_updates(to_be_updated, update_flags={},
update_cache=None, run_id=None):
"""Updates the `to_be_updated` Container, i.e., pushes the changes to CaosDB
after removing possible duplicates. If a chace is provided, uauthorized
@@ -87,8 +87,6 @@ def apply_list_of_updates(to_be_updated, update_flags=None,
Id with which the pending updates are cached. Only meaningful if
`update_cache` is provided. Default is None.
"""
- if update_flags is None:
- update_flags = {}
if len(to_be_updated) == 0:
return
@@ -134,7 +132,7 @@ def apply_list_of_updates(to_be_updated, update_flags=None,
)
logger.debug(traceback.format_exc())
logger.debug(e)
- except TransactionError as e:
+ except Exception as e:
DataModelProblems.evaluate_exception(e)
@@ -222,27 +220,25 @@ class Crawler(object):
new_cont = db.Container.from_xml(new)
ids = []
tmp = db.Container()
- # TODO what was this for?
- # update_incomplete = False
+ update_incomplete = False
# remove duplicate entities
for el in new_cont:
if el.id not in ids:
ids.append(el.id)
tmp.append(el)
else:
- pass
- # update_incomplete = True
+ update_incomplete = True
new_cont = tmp
- if new_cont[0].version: # pylint: disable=no-member
+ if new_cont[0].version:
valids = db.Container()
nonvalids = db.Container()
for ent in new_cont:
remote_ent = db.Entity(id=ent.id).retrieve()
- if ent.version == remote_ent.version: # pylint: disable=no-member
+ if ent.version == remote_ent.version:
valids.append(ent)
else:
- # update_incomplete = True
+ update_incomplete = True
nonvalids.append(remote_ent)
valids.update(unique=False)
logger.info("Successfully updated {} records!".format(
@@ -321,10 +317,10 @@ class Crawler(object):
logger.debug(e)
# TODO: Generally: in which cases should exceptions be raised? When is
# errors_occured set to True? The expected behavior must be documented.
- except TransactionError as e:
+ except Exception as e:
try:
DataModelProblems.evaluate_exception(e)
- except BaseException: # pylint: disable=broad-exception-caught
+ except BaseException:
pass
logger.debug("Failed during execution of {}!".format(
Cfood.__name__))
@@ -353,12 +349,13 @@ class Crawler(object):
logger.info("Cannot access {}. However, it might be needed for"
" the correct execution".format(e.filename))
remove_cfoods.append(cfood)
- except TransactionError as e:
+ except Exception as e:
try:
DataModelProblems.evaluate_exception(e)
- except BaseException: # pylint: disable=broad-exception-caught
+ except BaseException:
pass
- logger.debug("Failed during execution of {}!".format(cfood.__name__))
+ logger.debug("Failed during execution of {}!".format(
+ Cfood.__name__))
logger.debug(traceback.format_exc())
logger.debug(e)
remove_cfoods.append(cfood)
@@ -418,8 +415,8 @@ class Crawler(object):
self.cache.insert_list(hashes, identifiables)
def crawl(self, security_level=RETRIEVE, path=None):
- run_id = uuid.uuid1()
- logger.info("Run Id: " + str(run_id))
+ self.run_id = uuid.uuid1()
+ logger.info("Run Id: " + str(self.run_id))
guard.set_level(level=security_level)
logger.info("Scanning the objects to be treated...")
@@ -438,17 +435,17 @@ class Crawler(object):
cfood.to_be_updated,
cfood.update_flags,
update_cache=self.update_cache,
- run_id=run_id)
+ run_id=self.run_id)
except FileNotFoundError as e:
logger.info("Cannot access {}. However, it might be needed for"
" the correct execution".format(e.filename))
except DataInconsistencyError as e:
logger.debug(traceback.format_exc())
logger.debug(e)
- except TransactionError as e:
+ except Exception as e:
try:
DataModelProblems.evaluate_exception(e)
- except Exception: # pylint: disable=broad-exception-caught
+ except Exception:
pass
logger.info("Failed during execution of {}!".format(
cfood.__class__.__name__))
@@ -460,7 +457,7 @@ class Crawler(object):
errors_occured = True
tbs.append(e)
- pending_changes = self.update_cache.get_updates(run_id)
+ pending_changes = self.update_cache.get_updates(self.run_id)
if pending_changes:
# Sending an Email with a link to a form to authorize updates is
@@ -468,7 +465,7 @@ class Crawler(object):
if "SHARED_DIR" in os.environ:
filename = Crawler.save_form([el[3]
- for el in pending_changes], path, run_id)
+ for el in pending_changes], path, self.run_id)
Crawler.send_mail([el[3] for el in pending_changes], filename)
for i, el in enumerate(pending_changes):
@@ -480,7 +477,7 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
logger.info("There where unauthorized changes (see above). An "
"email was sent to the curator.\n"
"You can authorize the updates by invoking the crawler"
- " with the run id: {rid}\n".format(rid=run_id))
+ " with the run id: {rid}\n".format(rid=self.run_id))
if len(DataModelProblems.missing) > 0:
err_msg = ("There were problems with one or more RecordType or "
@@ -491,9 +488,8 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
logger.error(err_msg)
logger.error('Crawler finished with Datamodel Errors')
elif errors_occured:
- msg = ("There were fatal errors during execution, please "
- "contact the system administrator!"
- )
+ msg = "There were fatal errors during execution, please "
+ "contact the system administrator!"
if self.debug_file:
msg += "\nPlease provide the following path:\n{}".format(
@@ -520,6 +516,7 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
path: the path defining the subtree that is crawled
"""
+ from xml.sax.saxutils import escape
# TODO move path related stuff to sss_helper
form = """
@@ -596,7 +593,7 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
randname = os.path.basename(os.path.abspath(directory))
filepath = os.path.abspath(os.path.join(directory, filename))
filename = os.path.join(randname, filename)
- with open(filepath, "w", encoding="utf8") as f:
+ with open(filepath, "w") as f:
f.write(form)
return filename
@@ -676,7 +673,7 @@ carefully and if the changes are ok, click on the following link:
guard.safe_insert(missing, unique=False,
flags={"force-missing-obligatory": "ignore"})
inserted.append(ent)
- except TransactionError as e:
+ except Exception as e:
DataModelProblems.evaluate_exception(e)
if len(existing) > 0:
info = "Identified the following existing entities:\n"
@@ -777,13 +774,14 @@ class FileCrawler(Crawler):
path if path.endswith("/") else path + "/") + "**'"
q_info = "Sending the following query: '" + query_str + "'\n"
files = db.execute_query(query_str)
- logger.info(q_info + f"Found {len(files)} files that need to be processed.")
+ logger.info(
+ q_info + "Found {} files that need to be processed.".format(
+ len(files)))
return files
class TableCrawler(Crawler):
- """Crawler for table like data."""
def __init__(self, table, unique_cols, recordtype, **kwargs):
"""
@@ -798,7 +796,6 @@ class TableCrawler(Crawler):
# TODO I do not like this yet, but I do not see a better way so far.
class ThisRowCF(RowCFood):
- """CFood for rows."""
def __init__(self, item):
super().__init__(item, unique_cols, recordtype)
@@ -824,6 +821,7 @@ def get_value(prop):
if isinstance(prop.value, db.Entity):
return prop.value.id
- if isinstance(prop.value, datetime):
+ elif isinstance(prop.value, datetime):
return prop.value.isoformat()
- return prop.value
+ else:
+ return prop.value
diff --git a/src/caosadvancedtools/datamodel_problems.py b/src/caosadvancedtools/datamodel_problems.py
index a83da009..df5b7e56 100644
--- a/src/caosadvancedtools/datamodel_problems.py
+++ b/src/caosadvancedtools/datamodel_problems.py
@@ -28,9 +28,9 @@ or updating entities with missing parents and/or properties.
"""
from caosdb.exceptions import (EntityDoesNotExistError,
- TransactionError,
- UnqualifiedParentsError,
- UnqualifiedPropertiesError)
+ TransactionError,
+ UnqualifiedParentsError,
+ UnqualifiedPropertiesError)
class DataModelProblems(object):
diff --git a/src/caosadvancedtools/guard.py b/src/caosadvancedtools/guard.py
index 16cf7304..aa37448d 100644
--- a/src/caosadvancedtools/guard.py
+++ b/src/caosadvancedtools/guard.py
@@ -18,7 +18,7 @@
# 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 linkahead as db
+import caosdb as db
RETRIEVE = 0
INSERT = 1
diff --git a/src/caosadvancedtools/loadFiles.py b/src/caosadvancedtools/loadFiles.py
index 26b6c1c0..405b3d13 100755
--- a/src/caosadvancedtools/loadFiles.py
+++ b/src/caosadvancedtools/loadFiles.py
@@ -129,14 +129,7 @@ def create_re_for_file_list(files, localroot, remoteroot):
def loadpath(path, include, exclude, prefix, dryrun, forceAllowSymlinks, caosdbignore=None,
- localpath=None) -> dict:
- """
-Returns
--------
-
-inserted: dict
- A dict with the files to be included for each of the ``include`` elements.
- """
+ localpath=None):
if caosdbignore:
# create list of files and create regular expression for small chunks
@@ -153,7 +146,6 @@ inserted: dict
else:
includes = [include]
- inserted = {}
# if no caosdbignore file is used, this iterates over a single include
for include in includes:
if dryrun:
@@ -185,9 +177,8 @@ inserted: dict
logger.info(
f"Made new files accessible: {len(files)}, combined size: {convert_size(totalsize)} ")
- inserted[include] = files
- return inserted
+ return
def main(argv=None):
diff --git a/src/caosadvancedtools/scifolder/experiment_cfood.py b/src/caosadvancedtools/scifolder/experiment_cfood.py
index 502314ad..38606b5f 100644
--- a/src/caosadvancedtools/scifolder/experiment_cfood.py
+++ b/src/caosadvancedtools/scifolder/experiment_cfood.py
@@ -16,16 +16,16 @@
# 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/>.
-from typing import TYPE_CHECKING, Tuple
-
import caosdb as db
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_property,
- assure_object_is_in_list)
+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 .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, WithREADME, get_glob
+from .withreadme import RESULTS, REVISIONOF, SCRIPTS, WithREADME, get_glob
class ExperimentCFood(AbstractFileCFood, WithREADME):
@@ -40,9 +40,6 @@ class ExperimentCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- self.project = db.Record()
- self.experiment = db.Record()
- self.people = []
WithREADME.__init__(self)
self.name_map = {},
@@ -55,7 +52,7 @@ class ExperimentCFood(AbstractFileCFood, WithREADME):
self.find_referenced_files([RESULTS])
@staticmethod
- def create_identifiable_experiment(match) -> Tuple[db.Record, db.Record]:
+ def create_identifiable_experiment(match):
# create the project identifiable
name = ExperimentCFood.name_beautifier(
match.group("project_identifier"))
diff --git a/src/caosadvancedtools/scifolder/publication_cfood.py b/src/caosadvancedtools/scifolder/publication_cfood.py
index b4bc70b8..fc78e5b7 100644
--- a/src/caosadvancedtools/scifolder/publication_cfood.py
+++ b/src/caosadvancedtools/scifolder/publication_cfood.py
@@ -16,14 +16,18 @@
# 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 (parse_responsibles,
+from .utils import (get_files_referenced_by_field, parse_responsibles,
reference_records_corresponding_to_files)
from .withreadme import DATAMODEL as dm
from .withreadme import (RESULTS, REVISIONOF, SCRIPTS, SOURCES, WithREADME,
@@ -53,8 +57,6 @@ class PublicationCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- self.publication = db.Record()
- self.people = []
WithREADME.__init__(self)
def collect_information(self):
diff --git a/src/caosadvancedtools/scifolder/result_table_cfood.py b/src/caosadvancedtools/scifolder/result_table_cfood.py
index 71668d3a..deaa2d00 100644
--- a/src/caosadvancedtools/scifolder/result_table_cfood.py
+++ b/src/caosadvancedtools/scifolder/result_table_cfood.py
@@ -20,12 +20,17 @@ import re
import caosdb as db
import pandas as pd
-from caosadvancedtools.cfood import (AbstractFileCFood,
- )
+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 ..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
@@ -43,8 +48,6 @@ class ResultTableCFood(AbstractFileCFood):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- self.recs = []
- self.experiment, self.project = (db.Record(), db.Record())
self.table = pd.read_csv(fileguide.access(self.crawled_path))
@staticmethod
@@ -57,7 +60,7 @@ class ResultTableCFood(AbstractFileCFood):
self.experiment, self.project = (
ExperimentCFood.create_identifiable_experiment(self.match))
- for _, row in self.table.iterrows():
+ for idx, row in self.table.iterrows():
rec = db.Record()
rec.add_parent(self.match.group("recordtype"))
@@ -74,11 +77,10 @@ class ResultTableCFood(AbstractFileCFood):
self.identifiables.extend([self.project, self.experiment])
def update_identifiables(self):
- for ii, (_, row) in enumerate(self.table.iterrows()):
+ for ii, (idx, 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/simulation_cfood.py b/src/caosadvancedtools/scifolder/simulation_cfood.py
index 24f4fdaf..c8f23f14 100644
--- a/src/caosadvancedtools/scifolder/simulation_cfood.py
+++ b/src/caosadvancedtools/scifolder/simulation_cfood.py
@@ -16,13 +16,17 @@
# 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,
+from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
assure_has_property,
- assure_object_is_in_list)
+ assure_object_is_in_list, get_entity)
+from caosadvancedtools.read_md_header import get_header
from .generic_pattern import full_pattern
-from .utils import (parse_responsibles,
+from .utils import (get_files_referenced_by_field, parse_responsibles,
reference_records_corresponding_to_files)
from .withreadme import DATAMODEL as dm
from .withreadme import (RESULTS, REVISIONOF, SCRIPTS, SOURCES, WithREADME,
@@ -37,9 +41,6 @@ class SimulationCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- self.project = db.Record()
- self.simulation = db.Record()
- self.people = []
WithREADME.__init__(self)
def collect_information(self):
diff --git a/src/caosadvancedtools/scifolder/software_cfood.py b/src/caosadvancedtools/scifolder/software_cfood.py
index 47abda23..77fb4652 100644
--- a/src/caosadvancedtools/scifolder/software_cfood.py
+++ b/src/caosadvancedtools/scifolder/software_cfood.py
@@ -17,16 +17,20 @@
# 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,
+from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
assure_has_property, assure_name_is,
- assure_object_is_in_list)
+ assure_object_is_in_list, get_entity)
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 parse_responsibles
+from .utils import get_files_referenced_by_field, parse_responsibles
from .withreadme import BINARIES
+from .withreadme import DATAMODEL as dm
from .withreadme import SOURCECODE, WithREADME
@@ -39,9 +43,6 @@ class SoftwareCFood(AbstractFileCFood, WithREADME):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- self.software = db.Record()
- self.softwareversion = db.Record()
- self.people = []
WithREADME.__init__(self)
def collect_information(self):
diff --git a/src/caosadvancedtools/scifolder/utils.py b/src/caosadvancedtools/scifolder/utils.py
index cbf87c4b..50e897c7 100644
--- a/src/caosadvancedtools/scifolder/utils.py
+++ b/src/caosadvancedtools/scifolder/utils.py
@@ -26,6 +26,7 @@ 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 2b9108bc..e1968ba4 100644
--- a/src/caosadvancedtools/scifolder/withreadme.py
+++ b/src/caosadvancedtools/scifolder/withreadme.py
@@ -26,7 +26,8 @@ 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
+from caosadvancedtools.table_importer import (win_path_converter,
+ win_path_list_converter)
from caosadvancedtools.utils import return_field_or_property
from .utils import (get_entity_ids_from_include_file,
@@ -156,8 +157,8 @@ class WithREADME(object):
for f in sublist]
if len(flat_list) == 0:
- LOGGER.warning("ATTENTION: the field {} does not reference any "
- "known files".format(field.key))
+ LOGGER.warn("ATTENTION: the field {} does not reference any "
+ "known files".format(field.key))
self.attached_filenames.extend(flat_list) # pylint: disable=no-member
diff --git a/src/caosadvancedtools/serverside/generic_analysis.py b/src/caosadvancedtools/serverside/generic_analysis.py
index a0ff479d..85d0c860 100644
--- a/src/caosadvancedtools/serverside/generic_analysis.py
+++ b/src/caosadvancedtools/serverside/generic_analysis.py
@@ -87,8 +87,8 @@ import logging
import os
import sys
-import linkahead as db
-from linkahead.utils.server_side_scripting import run_server_side_script
+import caosdb as db
+from caosdb.utils.server_side_scripting import run_server_side_script
logger = logging.getLogger(__name__)
diff --git a/src/caosadvancedtools/serverside/helper.py b/src/caosadvancedtools/serverside/helper.py
index a5f82988..ba75739e 100644
--- a/src/caosadvancedtools/serverside/helper.py
+++ b/src/caosadvancedtools/serverside/helper.py
@@ -30,7 +30,7 @@ import sys
from email import message, policy, utils
from tempfile import NamedTemporaryFile
-import linkahead as db
+import caosdb as db
def wrap_bootstrap_alert(text, kind):
@@ -223,7 +223,6 @@ def init_data_model(entities):
"be a {}.".format(e.role, local_role))
raise DataModelError(e.name, info)
except db.exceptions.EntityDoesNotExistError:
- # pylint: disable-next=raise-missing-from
raise DataModelError(e.name, "This entity does not exist.")
return True
@@ -243,11 +242,11 @@ def get_data(filename, default=None):
Returns
-------
- out: dict
+ dict
Data from the given file.
"""
result = default.copy() if default is not None else {}
- with open(filename, "r", encoding="utf8") as fi:
+ with open(filename, 'r') as fi:
data = json.load(fi)
result.update(data)
diff --git a/src/caosadvancedtools/utils.py b/src/caosadvancedtools/utils.py
index d03583a1..4d6a4b36 100644
--- a/src/caosadvancedtools/utils.py
+++ b/src/caosadvancedtools/utils.py
@@ -27,8 +27,8 @@ import logging
import os
import pathlib
-import linkahead as db
-from linkahead.exceptions import TransactionError
+import caosdb as db
+from caosdb.exceptions import TransactionError
logger = logging.getLogger(__name__)
--
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