From 4f3bf7429031406442b39d2b30603e3586112fcb Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Wed, 21 Feb 2024 17:01:36 +0100
Subject: [PATCH] MAINT: Documentation, formatting, typos, error messages,
linkahead
---
src/caoscrawler/converters.py | 2 +-
src/caoscrawler/crawl.py | 17 ++++++++---------
src/caoscrawler/hdf5_converter.py | 2 +-
src/caoscrawler/identifiable.py | 2 +-
src/caoscrawler/identifiable_adapters.py | 6 +++---
src/caoscrawler/scanner.py | 2 +-
src/caoscrawler/utils.py | 2 +-
unittests/test_crawler.py | 6 +++---
8 files changed, 19 insertions(+), 20 deletions(-)
diff --git a/src/caoscrawler/converters.py b/src/caoscrawler/converters.py
index dddb83a7..772f690b 100644
--- a/src/caoscrawler/converters.py
+++ b/src/caoscrawler/converters.py
@@ -36,7 +36,7 @@ from inspect import signature
from string import Template
from typing import Any, List, Optional, Tuple, Union
-import caosdb as db
+import linkahead as db
import pandas as pd
import yaml
import yaml_header_tools
diff --git a/src/caoscrawler/crawl.py b/src/caoscrawler/crawl.py
index e0bddb57..698a154f 100644
--- a/src/caoscrawler/crawl.py
+++ b/src/caoscrawler/crawl.py
@@ -207,14 +207,13 @@ def _treat_merge_error_of(newrecord, record):
# TODO can we also compare lists?
and not isinstance(this_p.value, list)
and not isinstance(that_p.value, list)):
- logger.error("The Crawler is trying to merge two entities "
- "because they should be the same object (same"
- " identifiables), but they have "
- "different values for the same Property."
- f"Problematic Property: {this_p.name}\n"
- f"Values: {this_p.value} and "
- f"{that_p.value}\n"
- f"{record}\n{newrecord}")
+ logger.error(
+ "The Crawler is trying to merge two entities because they should be the same "
+ "object (same identifiables), but they have different values for the same "
+ "Property.\n"
+ f"Problematic Property: {this_p.name}\n"
+ f"Values: {this_p.value} and {that_p.value}\n"
+ f"{record}\n{newrecord}")
raise RuntimeError("Cannot merge Entities")
@@ -1149,7 +1148,7 @@ class Crawler(object):
"""
if crawled_data is None:
warnings.warn(DeprecationWarning(
- "Calling synchronize without the data to be synchronized is depricated. Please "
+ "Calling synchronize without the data to be synchronized is deprecated. Please "
"use for example the Scanner to create this data."))
crawled_data = self.crawled_data
diff --git a/src/caoscrawler/hdf5_converter.py b/src/caoscrawler/hdf5_converter.py
index 506c7b39..5b1ff577 100644
--- a/src/caoscrawler/hdf5_converter.py
+++ b/src/caoscrawler/hdf5_converter.py
@@ -30,7 +30,7 @@ import numpy as np
from typing import Union
-import caosdb as db
+import linkahead as db
from .converters import (convert_basic_element, Converter, DictElementConverter,
match_name_and_value, SimpleFileConverter)
diff --git a/src/caoscrawler/identifiable.py b/src/caoscrawler/identifiable.py
index 75af5be8..cefdf4a0 100644
--- a/src/caoscrawler/identifiable.py
+++ b/src/caoscrawler/identifiable.py
@@ -20,7 +20,7 @@
#
from __future__ import annotations
-import caosdb as db
+import linkahead as db
from datetime import datetime
import json
from hashlib import sha256
diff --git a/src/caoscrawler/identifiable_adapters.py b/src/caoscrawler/identifiable_adapters.py
index d661b97a..da31fa39 100644
--- a/src/caoscrawler/identifiable_adapters.py
+++ b/src/caoscrawler/identifiable_adapters.py
@@ -84,13 +84,13 @@ class IdentifiableAdapter(metaclass=ABCMeta):
Some terms:
-- Registered identifiable is the definition of an identifiable which is:
+- *Registered identifiable* is defined as an identifiable with:
- A record type as the parent
- A list of properties
- A list of referenced by statements
-- Identifiable is the concrete identifiable, e.g. the Record based on
+- *Identifiable* is the concrete identifiable, e.g. the Record based on
the registered identifiable with all the values filled in.
-- Identified record is the result of retrieving a record based on the
+- *Identified record* is the result of retrieving a record based on the
identifiable from the database.
General question to clarify:
diff --git a/src/caoscrawler/scanner.py b/src/caoscrawler/scanner.py
index c4a8063c..5d92401a 100644
--- a/src/caoscrawler/scanner.py
+++ b/src/caoscrawler/scanner.py
@@ -39,7 +39,7 @@ import warnings
from collections.abc import Callable
from typing import Any, Optional, Type, Union
-import caosdb as db
+import linkahead as db
import yaml
from importlib_resources import files
from jsonschema import validate
diff --git a/src/caoscrawler/utils.py b/src/caoscrawler/utils.py
index 61b36309..c62f44ee 100644
--- a/src/caoscrawler/utils.py
+++ b/src/caoscrawler/utils.py
@@ -25,7 +25,7 @@
# Some utility functions, e.g. for extending pylib.
-import caosdb as db
+import linkahead as db
def has_parent(entity: db.Entity, name: str):
diff --git a/unittests/test_crawler.py b/unittests/test_crawler.py
index 26aa9e73..14185d45 100644
--- a/unittests/test_crawler.py
+++ b/unittests/test_crawler.py
@@ -51,9 +51,9 @@ from caoscrawler.scanner import (create_converter_registry, scan_directory,
from caoscrawler.stores import GeneralStore, RecordStore
from caoscrawler.structure_elements import (DictElement, DictListElement,
DictTextElement, File)
-from caosdb.apiutils import compare_entities
-from caosdb.cached import cache_clear
-from caosdb.exceptions import EmptyUniqueQueryError
+from linkahead.apiutils import compare_entities
+from linkahead.cached import cache_clear
+from linkahead.exceptions import EmptyUniqueQueryError
from pytest import raises
UNITTESTDIR = Path(__file__).parent
--
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