src/caosadvancedtools/export_related.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2020 IndiScale GmbH, Henrik tom Wörden
 #
@@ -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
 
 
@@ -128,7 +128,7 @@ def export(cont, directory="."):
     xml = etree.tounicode(cont.to_xml(
         local_serialization=True), pretty_print=True)
 
-    with open(os.path.join(directory, "caosdb_data.xml"), "w") as fi:
+    with open(os.path.join(directory, "linkahead_data.xml"), "w") as fi:
         fi.write(xml)
 
 

src/caosadvancedtools/guard.py

 #!/usr/bin/env python
 # encoding: utf-8
 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2020 Henrik tom Wörden
 #
@@ -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

src/caosadvancedtools/import_from_xml.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2020 IndiScale GmbH, Henrik tom Wörden
 #
@@ -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 caosadvancedtools.models.data_model import DataModel
 
 

src/caosadvancedtools/json_schema_exporter.py

 #!/usr/bin/env python
 # encoding: utf-8
 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2023 Indiscale GmbH <info@indiscale.com>
 # Copyright (C) 2023 Florian Spreckelsen <f.spreckelsen@indiscale.com>

src/caosadvancedtools/loadFiles.py

@@ -2,7 +2,7 @@
 # encoding: utf-8
 #
 # ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -45,7 +45,7 @@ from argparse import ArgumentParser
 from tempfile import NamedTemporaryFile
 from typing import Union
 
-import caosdb as db
+import linkahead as db
 
 logger = logging.getLogger(__name__)
 timeout_fallback = 20

src/caosadvancedtools/models/data_model.py

 # encoding: utf-8
 #
 # ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -34,7 +34,7 @@ import linkahead.common.models as models
 from linkahead.apiutils import compare_entities, describe_diff, merge_entities
 
 
-CAOSDB_INTERNAL_PROPERTIES = [
+LINKAHEAD_INTERNAL_PROPERTIES = [
     "description",
     "name",
     "unit",
@@ -44,19 +44,19 @@ 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
+    Container and inserting it in LinkAhead. However, this has one drawback: You
     cannot simply change someting and update the container. The container will
     insist on having valid ids for all contained Entities.
 
     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).
 
@@ -90,9 +90,9 @@ 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.
@@ -138,7 +138,7 @@ class DataModel(dict):
             any_change = False
 
             for ent in existing_entities:
-                if ent.name in CAOSDB_INTERNAL_PROPERTIES:
+                if ent.name in LINKAHEAD_INTERNAL_PROPERTIES:
                     # Workaround for the usage of internal properties like name
                     # in via the extern keyword:
                     ref = db.Property(name=ent.name).retrieve()
@@ -146,7 +146,9 @@ class DataModel(dict):
                     query = db.Query(f"FIND ENTITY with id={ent.id}")
                     ref = query.execute(unique=True)
                 diff = (describe_diff(*compare_entities(ent, ref),
-                                      name=ent.name))
+                                      name=ent.name,
+                                      label_e0="version from the yaml file",
+                                      label_e1="version from LinkAhead"))
 
                 if diff != "":
                     if verbose:
@@ -169,7 +171,7 @@ 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
         ----

src/caosadvancedtools/models/parser.py

-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
 # Copyright (C) 2022 Florian Spreckelsen <f.spreckelsen@indiscale.com>
@@ -49,7 +49,7 @@ import jsonschema
 import linkahead as db
 
 from linkahead.common.datatype import get_list_datatype
-from .data_model import CAOSDB_INTERNAL_PROPERTIES, DataModel
+from .data_model import LINKAHEAD_INTERNAL_PROPERTIES, DataModel
 
 # Keywords which are allowed in data model descriptions.
 KEYWORDS = ["importance",
@@ -200,7 +200,7 @@ def parse_model_from_json_schema(
 
     out : Datamodel
         The datamodel generated from the input schema which then can be used for
-        synchronizing with CaosDB.
+        synchronizing with LinkAhead.
 
     Note
     ----
@@ -301,7 +301,7 @@ debug : bool, optional
 
         # 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.
@@ -312,7 +312,7 @@ debug : bool, optional
             ymlmodel["extern"] = []
 
         for name in ymlmodel["extern"]:
-            if name in CAOSDB_INTERNAL_PROPERTIES:
+            if name in LINKAHEAD_INTERNAL_PROPERTIES:
                 self.model[name] = db.Property(name=name).retrieve()
                 continue
             for role in ("Property", "RecordType", "Record", "File"):
@@ -610,7 +610,7 @@ debug : bool, optional
         iterate over properties and check whether it is a base datatype of a
         name that was defined in the model (or extern part)
 
-        the string representations are replaced with caosdb objects
+        the string representations are replaced with linkahead objects
 
         """
 
@@ -816,12 +816,12 @@ 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" and "string" not in elt["type"]:
                 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
         # LinkAhead suports null for all types, so in the very special case of

src/caosadvancedtools/pandoc_header_tools.py

@@ -6,7 +6,7 @@
 # A. Schlemmer, 04/2019
 
 # ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 
 # Copyright (C) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen

src/caosadvancedtools/read_md_header.py

@@ -2,7 +2,7 @@
 # encoding: utf-8
 #
 # ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C)
 # A. Schlemmer, 01/2019
@@ -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

src/caosadvancedtools/scifolder/analysis_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 caosadvancedtools.cfood import (AbstractFileCFood,
                                      assure_has_property,
                                      assure_object_is_in_list,
@@ -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.
         """

src/caosadvancedtools/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 caosadvancedtools.cfood import (AbstractFileCFood,
                                      assure_has_property,
                                      assure_object_is_in_list,

src/caosadvancedtools/scifolder/publication_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 caosadvancedtools.cfood import (AbstractFileCFood,
                                      assure_object_is_in_list, fileguide,
                                      )

src/caosadvancedtools/scifolder/result_table_cfood.py

@@ -18,7 +18,7 @@
 
 import re
 
-import caosdb as db
+import linkahead as db
 import pandas as pd
 from caosadvancedtools.cfood import (AbstractFileCFood,
                                      )

src/caosadvancedtools/scifolder/simulation_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 caosadvancedtools.cfood import (AbstractFileCFood,
                                      assure_has_property,
                                      assure_object_is_in_list,

src/caosadvancedtools/scifolder/software_cfood.py

@@ -17,7 +17,7 @@
 # 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 caosadvancedtools.cfood import (AbstractFileCFood,
                                      assure_has_property, assure_name_is,
                                      assure_object_is_in_list,

src/caosadvancedtools/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 caosadvancedtools.cfood import assure_object_is_in_list, fileguide
 from caosadvancedtools.utils import (find_records_that_reference_ids,

src/caosadvancedtools/scifolder/withreadme.py

@@ -22,7 +22,7 @@ import logging
 import os
 from dataclasses import dataclass
 
-import caosdb as db
+import linkahead 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

src/caosadvancedtools/serverside/examples/example_script.py

@@ -2,7 +2,7 @@
 # encoding: utf-8
 #
 # ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
 # Copyright (C) 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
@@ -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 caosadvancedtools.cfood import assure_property_is
@@ -68,18 +68,18 @@ 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.
     """
 
-    caosdb_config = db.configuration.get_config()
+    linkahead_config = db.configuration.get_config()
     text = """Dear Curator,
 The following changes where done automatically.
 
 {changes}
     """.format(changes="\n".join(changes))
     try:
-        fro = caosdb_config["advancedtools"]["automated_updates.from_mail"]
+        fro = linkahead_config["advancedtools"]["automated_updates.from_mail"]
     except KeyError:
         logger.error("Server Configuration is missing a setting for "
                      "sending mails. The administrator should check "

src/caosadvancedtools/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__)
 

src/caosadvancedtools/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):
@@ -165,7 +165,7 @@ def recordtype_is_child_of(rt, parent):
     Parameters
     ----------
 
-    rt : caosdb.Entity
+    rt : linkahead.Entity
         The child RecordType.
     parent : str or int
         The parent's name or id.
@@ -193,7 +193,7 @@ def init_data_model(entities):
     Parameters
     ----------
 
-    entities : iterable of caosdb.Entity
+    entities : iterable of linkahead.Entity
         The data model entities which are to be checked for existence.
 
     Raises
@@ -339,7 +339,7 @@ def send_mail(from_addr, to, subject, body, cc=None, bcc=None,
               send_mail_bin=None):
     """ Send an email via the configured send_mail client.
 
-    The relevant options in the pycaosdb.ini are:
+    The relevant options in the pylinkahead.ini are:
 
         [Misc]
         sendmail = ...
@@ -365,8 +365,8 @@ def send_mail(from_addr, to, subject, body, cc=None, bcc=None,
     ------
     subprocess.CalledProcessError
         If the sendmail client returned with a non-zero code.
-    caosdb.ConfigurationException
-        If the caosdb configuration has no `Misc.sendmail` configured while the
+    linkahead.ConfigurationException
+        If the linkahead configuration has no `Misc.sendmail` configured while the
         `send_mail_bin` parameter is None.
     """
 
@@ -389,14 +389,14 @@ def send_mail(from_addr, to, subject, body, cc=None, bcc=None,
     if send_mail_bin is not None:
         sendmail = send_mail_bin
     else:
-        caosdb_config = db.configuration.get_config()
+        linkahead_config = db.configuration.get_config()
 
-        if "Misc" not in caosdb_config or "sendmail" not in caosdb_config["Misc"]:
+        if "Misc" not in linkahead_config or "sendmail" not in linkahead_config["Misc"]:
             err_msg = ("No sendmail executable configured. "
                        "Please configure `Misc.sendmail` "
-                       "in your pycaosdb.ini.")
+                       "in your pylinkahead.ini.")
             raise db.ConfigurationError(err_msg)
-        sendmail = caosdb_config["Misc"]["sendmail"]
+        sendmail = linkahead_config["Misc"]["sendmail"]
 
     # construct sendmail command
     # options explained (from `man sendmail`):
@@ -438,7 +438,7 @@ def get_file_via_download(ent, logger=logging.getLogger(__name__)):
     try:
         # TODO remove the following treatment of size=0 when the
         # following issue is resolved:
-        # https://gitlab.com/caosdb/caosdb-server/-/issues/107
+        # https://gitlab.com/linkahead/linkahead-server/-/issues/107
 
         if ent.size > 0:
             val_file = ent.download()
@@ -450,7 +450,7 @@ 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