diff --git a/src/linkaheadadvancedtools/bloxberg/bloxberg.py b/src/linkaheadadvancedtools/bloxberg/bloxberg.py
index 7169315bde1933067fd0edb45fae8457f644813c..a774a8b9dda2c21c96bccb0d83d38c659fd3a94c 100644
--- a/src/linkaheadadvancedtools/bloxberg/bloxberg.py
+++ b/src/linkaheadadvancedtools/bloxberg/bloxberg.py
@@ -23,7 +23,7 @@ import hashlib
import json
import secrets
-import caosdb as db
+import linkahead as db
from ..models.parser import parse_model_from_string
from . import swagger_client
@@ -158,7 +158,7 @@ def ensure_data_model(force=False):
def certify_entity(entity, json_filename=None):
- """Certify the given entity and store the result in the CaosDB.
+ """Certify the given entity and store the result in the LinkAhead.
Parameters
----------
@@ -176,7 +176,7 @@ json_filename : str
certificate = blx.certify(entity)
print("Certificate was successfully obtained.")
certificate.insert()
- print("Certificate was stored in CaosDB.")
+ print("Certificate was stored in LinkAhead.")
if json_filename:
with open(json_filename, "w") as json_file:
@@ -188,7 +188,7 @@ def demo_run():
print("Making sure that the remote data model is up to date.")
ensure_data_model()
print("Data model is up to date.")
- import caosdb as db
+ import linkahead as db
CertRT = db.RecordType(name="BloxbergCertificate").retrieve()
print("Certifying the `BloxbergCertificate` RecordType...")
json_filename = "/tmp/cert.json"
diff --git a/src/linkaheadadvancedtools/cache.py b/src/linkaheadadvancedtools/cache.py
index e4b30694df2210f0bd1e10fab8d97686af038900..56a0e2509ba30b68933f48d2567bc4d4348bd48a 100644
--- a/src/linkaheadadvancedtools/cache.py
+++ b/src/linkaheadadvancedtools/cache.py
@@ -32,7 +32,7 @@ from abc import ABC, abstractmethod
from hashlib import sha256
import warnings
-import caosdb as db
+import linkahead as db
from lxml import etree
import tempfile
@@ -286,7 +286,7 @@ class IdentifiableCache(AbstractCache):
Non-matching entities will be removed from the cache.
entities: When set to a db.Container or a list of Entities
- the IDs from the cache will not be retrieved from the CaosDB database,
+ the IDs from the cache will not be retrieved from the LinkAhead database,
but the versions from the cache will be checked against the versions
contained in that collection. Only entries in the cache that have
a corresponding version in the collection will be checked, all others
diff --git a/src/linkaheadadvancedtools/cfood.py b/src/linkaheadadvancedtools/cfood.py
index c5c504e62120e642e4e9e4e21d0b90bb9c4d8920..cca099656209fd2a4320c376524edac07eb67b55 100644
--- a/src/linkaheadadvancedtools/cfood.py
+++ b/src/linkaheadadvancedtools/cfood.py
@@ -23,17 +23,17 @@
#
# 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/>.
-""" Defines how something that shall be inserted into CaosDB is treated.
+""" Defines how something that shall be inserted into LinkAhead is treated.
-CaosDB can automatically be filled with Records based on some structure, a file
+LinkAhead can automatically be filled with Records based on some structure, a file
structure, a table or similar.
The Crawler will iterate over the respective items and test for each item
whether a CFood class exists that matches the file path, i.e. whether CFood
class wants to treat that pariticular item. If one does, it is instanciated to
treat the match. This occurs in basically three steps:
-1. Create a list of identifiables, i.e. unique representation of CaosDB Records
+1. Create a list of identifiables, i.e. unique representation of LinkAhead Records
(such as an experiment belonging to a project and a date/time).
-2. The identifiables are either found in CaosDB or they are created.
+2. The identifiables are either found in LinkAhead or they are created.
3. The identifiables are update based on the date in the file structure.
"""
@@ -43,9 +43,9 @@ import warnings
from abc import ABCMeta, abstractmethod
from datetime import datetime
-import caosdb as db
-from caosdb.common.models import Entity
-from caosdb.exceptions import (BadQueryError, EmptyUniqueQueryError,
+import linkahead as db
+from linkahead.common.models import Entity
+from linkahead.exceptions import (BadQueryError, EmptyUniqueQueryError,
QueryNotUniqueError, TransactionError)
from .datamodel_problems import DataModelProblems
@@ -63,7 +63,7 @@ logger = logging.getLogger(__name__)
def get_entity(name):
""" Returns the entity with a given name, preferably from a local cache.
- If the local cache does not contain the entity, retrieve it from CaosDB.
+ If the local cache does not contain the entity, retrieve it from LinkAhead.
"""
if name not in ENTITIES:
@@ -79,7 +79,7 @@ def get_property(name):
cache.
If the local cache does not contain the record type, try to
- retrieve it from CaosDB. If it does not exist, see whether it
+ retrieve it from LinkAhead. If it does not exist, see whether it
could be a record type used as a property.
"""
@@ -101,7 +101,7 @@ def get_record(name):
"""Returns the record with a given name, preferably from a local cache.
If the local cache does not contain the record, try to retrieve it
- from CaosDB.
+ from LinkAhead.
"""
@@ -118,7 +118,7 @@ def get_recordtype(name):
cache.
If the local cache does not contain the record type, try to
- retrieve it from CaosDB. If it does not exist, add it to the data
+ retrieve it from LinkAhead. If it does not exist, add it to the data
model problems
"""
diff --git a/src/linkaheadadvancedtools/cfoods/h5.py b/src/linkaheadadvancedtools/cfoods/h5.py
index 482e154d5f7b4bbcece5cbfeadd15bd00c54af74..2615040faaf6c5a8ccd071733120f95256798fff 100644
--- a/src/linkaheadadvancedtools/cfoods/h5.py
+++ b/src/linkaheadadvancedtools/cfoods/h5.py
@@ -36,12 +36,12 @@ Properties.
import re
from copy import deepcopy
-import caosdb as db
+import linkahead as db
import h5py
import numpy as np
from linkaheadadvancedtools.cfood import fileguide
-from caosdb.common.datatype import is_reference
-from caosdb.common.utils import uuid
+from linkahead.common.datatype import is_reference
+from linkahead.common.utils import uuid
from ..cfood import (AbstractFileCFood, assure_has_description,
assure_has_parent, assure_has_property,
@@ -51,7 +51,7 @@ from ..structure_mapping import (EntityMapping, collect_existing_structure,
def h5_attr_to_property(val):
- """ returns the value and datatype of a CaosDB Property for the given value
+ """ returns the value and datatype of a LinkAhead Property for the given value
1d arrays are converted to lists
diff --git a/src/linkaheadadvancedtools/collect_datamodel.py b/src/linkaheadadvancedtools/collect_datamodel.py
index 2b8a6f306f54f3229b2fd12ff5d0e7d82cfa3536..e06d19077c79f10c3db5090da772b90d9d535d95 100644
--- a/src/linkaheadadvancedtools/collect_datamodel.py
+++ b/src/linkaheadadvancedtools/collect_datamodel.py
@@ -25,8 +25,8 @@
import argparse
import os
-import caosdb as db
-from caosdb.apiutils import retrieve_entities_with_ids
+import linkahead as db
+from linkahead.apiutils import retrieve_entities_with_ids
from export_related import export
diff --git a/src/linkaheadadvancedtools/converter/labfolder_api.py b/src/linkaheadadvancedtools/converter/labfolder_api.py
index b91dedd6d51b0d586cc3936bbe794e3938ce977f..12e7d7269aa66313d8e67262f2c74c8bb8da1269 100644
--- a/src/linkaheadadvancedtools/converter/labfolder_api.py
+++ b/src/linkaheadadvancedtools/converter/labfolder_api.py
@@ -27,7 +27,7 @@ import time
import html2text
-import caosdb as db
+import linkahead as db
from labfolder.connection import configure_connection # pylint: disable=import-error
diff --git a/src/linkaheadadvancedtools/converter/labfolder_export.py b/src/linkaheadadvancedtools/converter/labfolder_export.py
index 461d260df9e2ae183825d615a5ddac3cf8ac9f28..7e6428da2a232b2018b091ed9bc1519c029ca41d 100644
--- a/src/linkaheadadvancedtools/converter/labfolder_export.py
+++ b/src/linkaheadadvancedtools/converter/labfolder_export.py
@@ -35,7 +35,7 @@ import requests
import yaml
from bs4 import BeautifulSoup
-import caosdb as db
+import linkahead as db
RERUN = False
# crawler = Crawler()
diff --git a/src/linkaheadadvancedtools/crawler.py b/src/linkaheadadvancedtools/crawler.py
index 8afab698e3902fd9f08d4a7f2cd5a75975dd1177..dc4e52e69bda8de71d7e7ae464ab8306c34ec2f2 100644
--- a/src/linkaheadadvancedtools/crawler.py
+++ b/src/linkaheadadvancedtools/crawler.py
@@ -25,16 +25,16 @@
#
# ** end header
#
-""" Crawls a file structure and inserts Records into CaosDB based on what is
+""" Crawls a file structure and inserts Records into LinkAhead based on what is
found.
-CaosDB can automatically be filled with Records based on some file structure.
+LinkAhead can automatically be filled with Records based on some file structure.
The Crawler will iterate over the files and test for each file whether a CFood
exists that matches the file path. If one does, it is instanciated to treat the
match. This occurs in basically three steps:
-1. create a list of identifiables, i.e. unique representation of CaosDB Records
+1. create a list of identifiables, i.e. unique representation of LinkAhead Records
(such as an experiment belonging to a project and a date/time)
-2. the identifiables are either found in CaosDB or they are created.
+2. the identifiables are either found in LinkAhead or they are created.
3. the identifiables are update based on the date in the file structure
"""
@@ -47,8 +47,8 @@ import uuid
from datetime import datetime
from sqlite3 import IntegrityError
-import caosdb as db
-from caosdb.exceptions import BadQueryError
+import linkahead as db
+from linkahead.exceptions import BadQueryError
from .cache import IdentifiableCache, UpdateCache, get_pretty_xml
from .cfood import RowCFood, add_files, get_ids_for_entities_with_names
@@ -69,7 +69,7 @@ def separated(text):
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
+ """Updates the `to_be_updated` Container, i.e., pushes the changes to LinkAhead
after removing possible duplicates. If a chace is provided, uauthorized
updates can be cached for further authorization.
@@ -78,7 +78,7 @@ def apply_list_of_updates(to_be_updated, update_flags={},
to_be_updated : db.Container
Container with the entities that will be updated.
update_flags : dict, optional
- Dictionary of CaosDB server flags that will be used for the
+ Dictionary of LinkAhead server flags that will be used for the
update. Default is an empty dict.
update_cache : UpdateCache or None, optional
Cache in which the intended updates will be stored so they can be
@@ -147,7 +147,7 @@ class Crawler(object):
The Crawler will use those CFoods when crawling.
use_cache : bool, optional
Whether to use caching (not re-inserting probably existing
- objects into CaosDB), defaults to False.
+ objects into LinkAhead), defaults to False.
abort_on_exception : if true, exceptions are raise.
Otherwise the crawler continues if an exception occurs.
interactive : boolean, optional
@@ -271,7 +271,7 @@ class Crawler(object):
"""
This is the first phase of the crawl. It collects all cfoods that shall
be processed. The second phase is iterating over cfoods and updating
- CaosDB. This separate first step is necessary in order to allow a
+ LinkAhead. This separate first step is necessary in order to allow a
single cfood being influenced by multiple crawled items. E.g. the
FileCrawler can have a single cfood treat multiple files.
@@ -512,7 +512,7 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
Parameters:
-----------
- changes: The CaosDB entities in the version after the update.
+ changes: The LinkAhead entities in the version after the update.
path: the path defining the subtree that is crawled
"""
@@ -604,7 +604,7 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
Parameters:
-----------
- changes: The CaosDB entities in the version after the update.
+ changes: The LinkAhead entities in the version after the update.
filename: path to the html site that allow the authorization
"""
@@ -639,11 +639,11 @@ carefully and if the changes are ok, click on the following link:
@staticmethod
def find_or_insert_identifiables(identifiables):
""" Sets the ids of identifiables (that do not have already an id from the
- cache) based on searching CaosDB and retrieves those entities.
+ cache) based on searching LinkAhead and retrieves those entities.
The remaining entities (those which can not be retrieved) have no
- correspondence in CaosDB and are thus inserted.
+ correspondence in LinkAhead and are thus inserted.
"""
- # looking for matching entities in CaosDB when there is no valid id
+ # looking for matching entities in LinkAhead when there is no valid id
# i.e. there was none set from a cache
existing = []
@@ -692,7 +692,7 @@ carefully and if the changes are ok, click on the following link:
else:
logger.debug("Did not insert any new entities")
- logger.debug("Retrieving entities from CaosDB...")
+ logger.debug("Retrieving entities from LinkAhead...")
identifiables.retrieve(unique=True, raise_exception_on_error=False)
@staticmethod
@@ -728,7 +728,7 @@ carefully and if the changes are ok, click on the following link:
@staticmethod
def find_existing(entity):
- """searches for an entity that matches the identifiable in CaosDB
+ """searches for an entity that matches the identifiable in LinkAhead
Characteristics of the identifiable like, properties, name or id are
used for the match.
diff --git a/src/linkaheadadvancedtools/datainconsistency.py b/src/linkaheadadvancedtools/datainconsistency.py
index a90e8c612c017f340cbb9adcc452be873b87435d..26a4319253833a7171c0434233fc2f5d68d5951b 100644
--- a/src/linkaheadadvancedtools/datainconsistency.py
+++ b/src/linkaheadadvancedtools/datainconsistency.py
@@ -20,7 +20,7 @@
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""Implements an error to be used when there is a problem with the data to be
-read. I.e. something that users of CaosDB need to fix.
+read. I.e. something that users of LinkAhead need to fix.
"""
diff --git a/src/linkaheadadvancedtools/datamodel_problems.py b/src/linkaheadadvancedtools/datamodel_problems.py
index 32f32dfe831294d74ceb6466167bd42b30cc73ad..9605590275fc61e73d440169951331fa3340adcb 100644
--- a/src/linkaheadadvancedtools/datamodel_problems.py
+++ b/src/linkaheadadvancedtools/datamodel_problems.py
@@ -27,7 +27,7 @@ be inserted by hand or gueesed from possible exceptions when inserting
or updating entities with missing parents and/or properties.
"""
-from caosdb.exceptions import (EntityDoesNotExistError,
+from linkahead.exceptions import (EntityDoesNotExistError,
TransactionError,
UnqualifiedParentsError,
UnqualifiedPropertiesError)
diff --git a/src/linkaheadadvancedtools/example_cfood.py b/src/linkaheadadvancedtools/example_cfood.py
index 8e27c8bf246b433d388b51442d8f4668e111fb67..20021247eaa227b038a66b7b80373ba769248571 100644
--- a/src/linkaheadadvancedtools/example_cfood.py
+++ b/src/linkaheadadvancedtools/example_cfood.py
@@ -20,7 +20,7 @@
# 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 caosdb as db
+import linkahead as db
from .cfood import AbstractFileCFood, assure_has_property
diff --git a/src/linkaheadadvancedtools/export_related.py b/src/linkaheadadvancedtools/export_related.py
index 19181f783361efb20eea51749a2603148ee635d2..62a777aecc88e4adedee5dc820be9f5f1bba1158 100755
--- a/src/linkaheadadvancedtools/export_related.py
+++ b/src/linkaheadadvancedtools/export_related.py
@@ -24,7 +24,7 @@
"""
This file allows to create an xml representation of a complete dataset.
Using the given entity all related entities are collected and saved in a way
-that the data can be imported in another CaosDB instance.
+that the data can be imported in another LinkAhead instance.
Files that are smaller than 1MB are saved in a downloads folder and can be
imported along with the entities themselves.
@@ -32,9 +32,9 @@ imported along with the entities themselves.
import argparse
import os
-import caosdb as db
-from caosdb.apiutils import apply_to_ids, retrieve_entities_with_ids
-from caosdb.common.datatype import get_id_of_datatype, is_reference
+import linkahead as db
+from linkahead.apiutils import apply_to_ids, retrieve_entities_with_ids
+from linkahead.common.datatype import get_id_of_datatype, is_reference
from lxml import etree
diff --git a/src/linkaheadadvancedtools/guard.py b/src/linkaheadadvancedtools/guard.py
index 63b73dc8ef057b1de47a0a7885cd2df311af0ea3..649a776060308cb6bb81618262f7afd0cc308839 100644
--- a/src/linkaheadadvancedtools/guard.py
+++ b/src/linkaheadadvancedtools/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 caosdb as db
+import linkahead as db
RETRIEVE = 0
INSERT = 1
diff --git a/src/linkaheadadvancedtools/import_from_xml.py b/src/linkaheadadvancedtools/import_from_xml.py
index 816dc5ceab6d894f9eb30062a8ff2cd85a06c55b..3331e5346040e9716f81c8481cc7dc9303956dab 100755
--- a/src/linkaheadadvancedtools/import_from_xml.py
+++ b/src/linkaheadadvancedtools/import_from_xml.py
@@ -31,8 +31,8 @@ import argparse
import os
from tempfile import NamedTemporaryFile
-import caosdb as db
-from caosdb.apiutils import apply_to_ids
+import linkahead as db
+from linkahead.apiutils import apply_to_ids
from linkaheadadvancedtools.models.data_model import DataModel
diff --git a/src/linkaheadadvancedtools/loadFiles.py b/src/linkaheadadvancedtools/loadFiles.py
index 265a592148f0bec3a6b796c6e26d0d0399fe4f97..d57ac33c536e8e71e01b49c94c7066ec470bb02d 100755
--- a/src/linkaheadadvancedtools/loadFiles.py
+++ b/src/linkaheadadvancedtools/loadFiles.py
@@ -33,7 +33,7 @@ from argparse import ArgumentParser
from tempfile import NamedTemporaryFile
import shutil
-import caosdb as db
+import linkahead as db
logger = logging.getLogger(__name__)
timeout_fallback = 20
diff --git a/src/linkaheadadvancedtools/models/data_model.py b/src/linkaheadadvancedtools/models/data_model.py
index ddab5f2d52124703382474e2fa21b2cbaf4e83df..c9e344c6612a31ce363cfecd8802ee93f39982fe 100644
--- a/src/linkaheadadvancedtools/models/data_model.py
+++ b/src/linkaheadadvancedtools/models/data_model.py
@@ -29,8 +29,8 @@ from copy import deepcopy
# remove this, when we drop support for old Python versions.
from typing import List
-import caosdb as db
-from caosdb.apiutils import compare_entities, describe_diff
+import linkahead as db
+from linkahead.apiutils import compare_entities, describe_diff
CAOSDB_INTERNAL_PROPERTIES = [
@@ -43,7 +43,7 @@ CAOSDB_INTERNAL_PROPERTIES = [
class DataModel(dict):
"""Provides tools for managing a data model.
- When constructing a data model the CaosDB representation can easily be
+ When constructing a data model the LinkAhead representation can easily be
created using the classes RecordType and Propery, storing them in a
Container and inserting it in CaoSDB. However, this has one drawback: You
cannot simply change someting and update the container. The container will
@@ -51,11 +51,11 @@ class DataModel(dict):
This class allows you to define your model as easily but also provides you
with a method (`sync_data_model`) that will sync with the data model in an
- existing CaosDB instance.
+ existing LinkAhead instance.
This is possible because entities, defined in this model, are identified
- with entities in CaosDB using names. I.e. a RecordType "Experiment" in this
- model will update an existing RecordType with name "Experiment" in CaosDB.
+ with entities in LinkAhead using names. I.e. a RecordType "Experiment" in this
+ model will update an existing RecordType with name "Experiment" in LinkAhead.
Thus, be carefull not to change existing Entities that were created for a
different purpose (e.g. someone else's experiment).
@@ -88,9 +88,9 @@ class DataModel(dict):
self.append(entity)
def sync_data_model(self, noquestion: bool = False, verbose: bool = True):
- """Synchronize this DataModel with a CaosDB instance.
+ """Synchronize this DataModel with a LinkAhead instance.
- Updates existing entities from the CaosDB instance and inserts
+ Updates existing entities from the LinkAhead instance and inserts
non-existing entities into the instance. Note: This allows to easily
overwrite changes that were made to an existing data model. Use this
function with care and double check its effect.
@@ -167,7 +167,7 @@ class DataModel(dict):
@staticmethod
def get_existing_entities(entities):
""" Return a list with those entities of the supplied iterable that
- exist in the CaosDB instance.
+ exist in the LinkAhead instance.
Args
----
diff --git a/src/linkaheadadvancedtools/models/parser.py b/src/linkaheadadvancedtools/models/parser.py
index 45cb178c4b00bc04bd4d315863dd19ddbfd15cb5..981455c5333d0fe107753908187c7a1906938b19 100644
--- a/src/linkaheadadvancedtools/models/parser.py
+++ b/src/linkaheadadvancedtools/models/parser.py
@@ -45,7 +45,7 @@ from typing import List
from warnings import warn
import jsonschema
-import caosdb as db
+import linkahead as db
from .data_model import CAOSDB_INTERNAL_PROPERTIES, DataModel
@@ -164,7 +164,7 @@ def parse_model_from_json_schema(filename: str):
-------
out : Datamodel
The datamodel generated from the input schema which then can be used for
- synchronizing with CaosDB.
+ synchronizing with LinkAhead.
Note
----
@@ -243,7 +243,7 @@ class Parser(object):
# Extern keyword:
# The extern keyword can be used to include Properties and RecordTypes
- # from existing CaosDB datamodels into the current model.
+ # from existing LinkAhead datamodels into the current model.
# Any name included in the list specified by the extern keyword
# will be used in queries to retrieve a property or (if no property exists)
# a record type with the name of the element.
@@ -708,12 +708,12 @@ class JsonSchemaParser(Parser):
raise JsonSchemaDefinitionError(
f"`type` is missing in element {name}.")
if name == "name":
- # This is identified with the CaosDB name property as long as the
+ # This is identified with the LinkAhead name property as long as the
# type is correct.
if not elt["type"] == "string":
raise JsonSchemaDefinitionError(
"The 'name' property must be string-typed, otherwise it cannot "
- "be identified with CaosDB's name property."
+ "be identified with LinkAhead's name property."
)
return None, force_list
if "enum" in elt:
diff --git a/src/linkaheadadvancedtools/pandoc_header_tools.py b/src/linkaheadadvancedtools/pandoc_header_tools.py
index 200621f1d305871c3a02a1dee61e9dad75bab500..2ac8dd32b08718434b073f669b8932a769d54079 100644
--- a/src/linkaheadadvancedtools/pandoc_header_tools.py
+++ b/src/linkaheadadvancedtools/pandoc_header_tools.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python3
# This is taken from the file manage_header.py
-# in a CaosDB management repository. The file manage_header.py
+# in a LinkAhead management repository. The file manage_header.py
# is not released yet, but creating a library might be useful.
# A. Schlemmer, 04/2019
diff --git a/src/linkaheadadvancedtools/read_md_header.py b/src/linkaheadadvancedtools/read_md_header.py
index 68030d1d6e5b9966861313a38b1e8d6131a15a95..f65ead9c54fc069f6547c1f63b10da5c2793f5a6 100644
--- a/src/linkaheadadvancedtools/read_md_header.py
+++ b/src/linkaheadadvancedtools/read_md_header.py
@@ -34,7 +34,7 @@ def get_header(fn):
# import os
# import re
-# import caosdb as db
+# import linkahead as db
# import yaml
# from .cfood import AbstractCFood, get_entity
diff --git a/src/linkaheadadvancedtools/scifolder/analysis_cfood.py b/src/linkaheadadvancedtools/scifolder/analysis_cfood.py
index 1e203503299b6b1ef3f79e7809057d58ad0e2265..95d6c83dab0404935d3b467853628fb9f6024526 100644
--- a/src/linkaheadadvancedtools/scifolder/analysis_cfood.py
+++ b/src/linkaheadadvancedtools/scifolder/analysis_cfood.py
@@ -19,7 +19,7 @@
import os
from itertools import chain
-import caosdb as db
+import linkahead as db
from linkaheadadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
assure_has_property,
assure_object_is_in_list, get_entity)
@@ -51,7 +51,7 @@ class AnalysisCFood(AbstractFileCFood, WithREADME):
@staticmethod
def name_beautifier(name):
""" a function that can be used to rename the project. I.e. if
- the project in CaosDB shall be named differently than in the folder
+ the project in LinkAhead shall be named differently than in the folder
structure.
Use discouraged.
"""
diff --git a/src/linkaheadadvancedtools/scifolder/experiment_cfood.py b/src/linkaheadadvancedtools/scifolder/experiment_cfood.py
index fbf53c77225847e1afe76ebfb1794ec1e8e21995..044cef43cc7c45055c1254842840a71d86330548 100644
--- a/src/linkaheadadvancedtools/scifolder/experiment_cfood.py
+++ b/src/linkaheadadvancedtools/scifolder/experiment_cfood.py
@@ -16,7 +16,7 @@
# 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 caosdb as db
+import linkahead as db
from linkaheadadvancedtools.cfood import (AbstractFileCFood, assure_has_description,
assure_has_parent, assure_has_property,
assure_object_is_in_list, get_entity)
diff --git a/src/linkaheadadvancedtools/scifolder/publication_cfood.py b/src/linkaheadadvancedtools/scifolder/publication_cfood.py
index b7297915d654ae3a4402c4463a24dffec60a911c..8a82db0bca60bf563784a7f9992da97349b3879b 100644
--- a/src/linkaheadadvancedtools/scifolder/publication_cfood.py
+++ b/src/linkaheadadvancedtools/scifolder/publication_cfood.py
@@ -19,7 +19,7 @@
import os
from itertools import chain
-import caosdb as db
+import linkahead as db
from linkaheadadvancedtools.cfood import (AbstractFileCFood,
assure_object_is_in_list, fileguide,
get_entity)
diff --git a/src/linkaheadadvancedtools/scifolder/result_table_cfood.py b/src/linkaheadadvancedtools/scifolder/result_table_cfood.py
index e8184853a4906873c8b28b92f6257704b74770e3..eaf2549678297e382b17faaf635deb0c3f8d7452 100644
--- a/src/linkaheadadvancedtools/scifolder/result_table_cfood.py
+++ b/src/linkaheadadvancedtools/scifolder/result_table_cfood.py
@@ -18,7 +18,7 @@
import re
-import caosdb as db
+import linkahead as db
import pandas as pd
from linkaheadadvancedtools.cfood import (AbstractFileCFood, assure_has_description,
assure_has_parent, assure_has_property,
diff --git a/src/linkaheadadvancedtools/scifolder/simulation_cfood.py b/src/linkaheadadvancedtools/scifolder/simulation_cfood.py
index 93599db2079b48d3571d68bdb8d56bf4245883f4..9f3561c9d068d5412758a7591354bca50c3b45e5 100644
--- a/src/linkaheadadvancedtools/scifolder/simulation_cfood.py
+++ b/src/linkaheadadvancedtools/scifolder/simulation_cfood.py
@@ -19,7 +19,7 @@
import os
from itertools import chain
-import caosdb as db
+import linkahead as db
from linkaheadadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
assure_has_property,
assure_object_is_in_list, get_entity)
diff --git a/src/linkaheadadvancedtools/scifolder/software_cfood.py b/src/linkaheadadvancedtools/scifolder/software_cfood.py
index c95f9276ad348a66d649d517309fbfc1650a2ac2..891e77ccf50d893918d66394c0e46df7bcc105a0 100644
--- a/src/linkaheadadvancedtools/scifolder/software_cfood.py
+++ b/src/linkaheadadvancedtools/scifolder/software_cfood.py
@@ -20,7 +20,7 @@
import os
from itertools import chain
-import caosdb as db
+import linkahead as db
from linkaheadadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
assure_has_property, assure_name_is,
assure_object_is_in_list, get_entity)
diff --git a/src/linkaheadadvancedtools/scifolder/utils.py b/src/linkaheadadvancedtools/scifolder/utils.py
index 03767ee7a6d14157324b1eb424c1b14a1be4e1cc..34cbcf36fb9b76cc3bdfae2b781f083e8af0daf0 100644
--- a/src/linkaheadadvancedtools/scifolder/utils.py
+++ b/src/linkaheadadvancedtools/scifolder/utils.py
@@ -21,7 +21,7 @@ import logging
import os
from itertools import chain
-import caosdb as db
+import linkahead as db
import pandas as pd
from linkaheadadvancedtools.cfood import assure_object_is_in_list, fileguide
from linkaheadadvancedtools.utils import (find_records_that_reference_ids,
diff --git a/src/linkaheadadvancedtools/scifolder/withreadme.py b/src/linkaheadadvancedtools/scifolder/withreadme.py
index 460fd8c71f0dd9e9884687a2c0e72a016456dc16..42d665608db02d4211ded73a4ff64a9906e45900 100644
--- a/src/linkaheadadvancedtools/scifolder/withreadme.py
+++ b/src/linkaheadadvancedtools/scifolder/withreadme.py
@@ -22,7 +22,7 @@ import logging
import os
from dataclasses import dataclass
-import caosdb as db
+import linkahead as db
from linkaheadadvancedtools.cfood import (assure_has_description, assure_has_parent,
assure_object_is_in_list, fileguide)
from linkaheadadvancedtools.read_md_header import get_header as get_md_header
diff --git a/src/linkaheadadvancedtools/serverside/examples/example_script.py b/src/linkaheadadvancedtools/serverside/examples/example_script.py
index 3a02e35c1a423bbfc7d2e5a5180eee386ebffed1..fe401cb3e861f232da92e747a6229113b67b7cd7 100755
--- a/src/linkaheadadvancedtools/serverside/examples/example_script.py
+++ b/src/linkaheadadvancedtools/serverside/examples/example_script.py
@@ -45,7 +45,7 @@ import sys
from argparse import RawTextHelpFormatter
from datetime import datetime
-import caosdb as db
+import linkahead as db
import matplotlib.pyplot as plt
import numpy as np
from linkaheadadvancedtools.cfood import assure_property_is
@@ -68,7 +68,7 @@ def send_mail(changes: [db.Entity], receipient: str):
Parameters:
-----------
- changes: The CaosDB entities in the version after the update.
+ changes: The LinkAhead entities in the version after the update.
receipient: The person who shall receive the mail.
"""
diff --git a/src/linkaheadadvancedtools/serverside/generic_analysis.py b/src/linkaheadadvancedtools/serverside/generic_analysis.py
index 85d0c860df75fce205c5eaad77731fc04eee9e40..a0ff479d2fb66969f6f8107957c2a77213366aac 100644
--- a/src/linkaheadadvancedtools/serverside/generic_analysis.py
+++ b/src/linkaheadadvancedtools/serverside/generic_analysis.py
@@ -87,8 +87,8 @@ import logging
import os
import sys
-import caosdb as db
-from caosdb.utils.server_side_scripting import run_server_side_script
+import linkahead as db
+from linkahead.utils.server_side_scripting import run_server_side_script
logger = logging.getLogger(__name__)
diff --git a/src/linkaheadadvancedtools/serverside/helper.py b/src/linkaheadadvancedtools/serverside/helper.py
index ba75739e0fdc0a83f235db6920471afb196f4246..0a6f32a0dbee5c063c8393a12ef6fd66baca2986 100644
--- a/src/linkaheadadvancedtools/serverside/helper.py
+++ b/src/linkaheadadvancedtools/serverside/helper.py
@@ -30,7 +30,7 @@ import sys
from email import message, policy, utils
from tempfile import NamedTemporaryFile
-import caosdb as db
+import linkahead as db
def wrap_bootstrap_alert(text, kind):
@@ -449,7 +449,7 @@ def get_file_via_download(ent, logger=logging.getLogger(__name__)):
logger.error("The checksum of the downloaded file with id={} did not "
"match.".format(ent.id))
raise e
- except db.CaosDBException as e:
+ except db.LinkAheadException as e:
logger.error("Cannot download the file with id={}.".format(ent.id))
raise e
diff --git a/src/linkaheadadvancedtools/structure_mapping.py b/src/linkaheadadvancedtools/structure_mapping.py
index b33d7332ca20593752694ddc40aef9c8867232d5..f4b3a17c27069b3b89507f8aaa6ca016a1e158b1 100644
--- a/src/linkaheadadvancedtools/structure_mapping.py
+++ b/src/linkaheadadvancedtools/structure_mapping.py
@@ -18,9 +18,9 @@
# 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 caosdb as db
-from caosdb.apiutils import resolve_reference
-from caosdb.common.utils import uuid
+import linkahead as db
+from linkahead.apiutils import resolve_reference
+from linkahead.common.utils import uuid
from .cfood import (assure_has_description, assure_has_parent,
assure_property_is)
diff --git a/src/linkaheadadvancedtools/table_converter.py b/src/linkaheadadvancedtools/table_converter.py
index d1bb62629a18648fca0d202d90eed4951efbe763..361dc3ab4940974119da22b8a4d62e329c024ab0 100644
--- a/src/linkaheadadvancedtools/table_converter.py
+++ b/src/linkaheadadvancedtools/table_converter.py
@@ -24,7 +24,7 @@ import argparse
import re
import sys
-import caosdb as db
+import linkahead as db
import pandas as pd
diff --git a/src/linkaheadadvancedtools/table_export.py b/src/linkaheadadvancedtools/table_export.py
index 24b5b0619080f7bfeba9c6ad375b3da85710bbf7..be544b4862611ceb8e59bf73becb3df52572e22a 100644
--- a/src/linkaheadadvancedtools/table_export.py
+++ b/src/linkaheadadvancedtools/table_export.py
@@ -22,7 +22,7 @@
#
# ** end header
#
-"""Collect optional and mandatory data from CaosDB records and prepare
+"""Collect optional and mandatory data from LinkAhead records and prepare
them for an export as a table, e.g., for the export to metadata
repositories.
@@ -30,7 +30,7 @@ repositories.
import json
import logging
-import caosdb as db
+import linkahead as db
FIND_FUNCTION = "find_func"
QUERY = "query"
@@ -38,7 +38,7 @@ QUERY = "query"
logger = logging.getLogger(__name__)
-class TableExportError(db.CaosDBException):
+class TableExportError(db.LinkAheadException):
"""Error that is raised in case of failing export, e.g., because of
missing mandatory entries.
diff --git a/src/linkaheadadvancedtools/table_importer.py b/src/linkaheadadvancedtools/table_importer.py
index 84f7ffa8c86b760221e0328aca141b8c81be5932..ea063cb5e7e5adfc37923c6f7637cb428d439b4d 100755
--- a/src/linkaheadadvancedtools/table_importer.py
+++ b/src/linkaheadadvancedtools/table_importer.py
@@ -31,7 +31,7 @@ import logging
import pathlib
from datetime import datetime
-import caosdb as db
+import linkahead as db
import numpy as np
import pandas as pd
from xlrd import XLRDError
@@ -335,7 +335,7 @@ class TableImporter():
if key not in df.columns:
continue
# Check for castable numeric types first: We unconditionally cast int to the default
- # float, because CaosDB does not have different sizes anyway.
+ # float, because LinkAhead does not have different sizes anyway.
col_dtype = df.dtypes[key]
if not strict and not np.issubdtype(col_dtype, datatype):
issub = np.issubdtype
diff --git a/src/linkaheadadvancedtools/utils.py b/src/linkaheadadvancedtools/utils.py
index 12f9d563aba7ac1186408123ba55740b879f7723..97f857cb50e7a0b7a7f40e1b0f0c90089ca4ab50 100644
--- a/src/linkaheadadvancedtools/utils.py
+++ b/src/linkaheadadvancedtools/utils.py
@@ -27,8 +27,8 @@ import logging
import os
import pathlib
-import caosdb as db
-from caosdb.exceptions import TransactionError
+import linkahead as db
+from linkahead.exceptions import TransactionError
logger = logging.getLogger(__name__)