integrationtests/test_im_und_export.py

@@ -2,7 +2,7 @@
 import os
 from tempfile import TemporaryDirectory
 
-import caosdb as db
+import linkahead as db
 from caosadvancedtools.export_related import export_related_to
 from caosadvancedtools.import_from_xml import import_xml
 
@@ -19,7 +19,7 @@ if __name__ == "__main__":
     assert 0 == len(db.execute_query("FIND File which is stored at "
                                      "**/poster.pdf"))
     print("Importing stored elements")
-    import_xml(os.path.join(directory.name, "caosdb_data.xml"), interactive=False)
+    import_xml(os.path.join(directory.name, "linkahead_data.xml"), interactive=False)
 
     # The following tests the existence of some required entities.
     # However, this is not a full list.

integrationtests/test_json_schema_datamodel_parser.py

 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2022 IndiScale GmbH <info@indiscale.com>
 # Copyright (C) 2022 Florian Spreckelsen <f.spreckelsen@indiscale.com>
@@ -20,7 +20,7 @@
 
 import os
 
-import caosdb as db
+import linkahead as db
 from caosadvancedtools.models.parser import parse_model_from_json_schema
 
 

integrationtests/test_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>

integrationtests/test_table.py

 #!/usr/bin/env python3
 # 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
 #
@@ -20,7 +20,7 @@
 
 import logging
 
-import caosdb as db
+import linkahead as db
 import pandas as pd
 
 from caosadvancedtools.crawler import TableCrawler

integrationtests/test_yaml_parser.py

 # encoding: utf-8
 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2022 IndiScale GmbH <info@indiscale.com>
 # Copyright (C) 2022 Florian Spreckelsen <f.spreckelsen@indiscale.com>
@@ -19,7 +19,7 @@
 # with this program. If not, see <https://www.gnu.org/licenses/>.
 #
 
-import caosdb as db
+import linkahead as db
 from caosadvancedtools.models.parser import parse_model_from_string
 
 

integrationtests/update_analysis.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>
@@ -34,7 +34,7 @@ entities that where changed within a certain period of time.
 
 import sys
 
-import caosdb as db
+import linkahead as db
 from caosadvancedtools.serverside.generic_analysis import run
 
 

manual_tests/test_labfolder_import.py

 #!/usr/bin/env python3
 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (c) 2020 IndiScale GmbH
 # Copyright (c) 2020 Daniel Hornung <d.hornung@indiscale.com>

manual_tests/test_labfolder_retrieve.py

 #!/usr/bin/env python3
 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (c) 2020 IndiScale GmbH
 #

setup.py

@@ -149,7 +149,7 @@ def setup_package():
     metadata = dict(
         name='caosadvancedtools',
         version=get_version_info()[0],
-        description='advanced utilities for caosdb',
+        description='Advanced utilities for LinkAhead',
         long_description=long_description,
         long_description_content_type="text/markdown",
         author='Henrik tom Wörden',

src/caosadvancedtools/cache.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) 2020 Indiscale GmbH <info@indiscale.com>
 # Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
@@ -33,7 +33,7 @@ from abc import ABC, abstractmethod
 from copy import deepcopy
 from hashlib import sha256
 
-import caosdb as db
+import linkahead as db
 from lxml import etree
 
 

src/caosadvancedtools/cfood.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) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,9 +23,9 @@
 #
 # 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/>.
-""" 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
@@ -33,9 +33,9 @@ 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.
 """
 
@@ -45,10 +45,10 @@ 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,
-                               QueryNotUniqueError, TransactionError)
+import linkahead as db
+from linkahead.common.models import Entity
+from linkahead.exceptions import (BadQueryError, EmptyUniqueQueryError,
+                                  QueryNotUniqueError, TransactionError)
 
 from .datamodel_problems import DataModelProblems
 from .guard import global_guard as guard
@@ -65,7 +65,7 @@ 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:
@@ -81,7 +81,7 @@ 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.
 
     """
@@ -103,7 +103,7 @@ 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.
 
     """
 
@@ -120,7 +120,7 @@ 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
 
     """
@@ -140,7 +140,7 @@ def get_recordtype(name):
 class FileGuide(object):
     def access(self, path):
         """ should be replaced by a function that adds
-        a prefix to paths to allow to access caosdb files locally
+        a prefix to paths to allow to access LinkAhead files locally
 
         This default just returns the unchanged path.
         """

src/caosadvancedtools/cfoods/__init__.py

 #!/usr/bin/env python3
 
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (C) 2020 IndiScale GmbH <www.indiscale.com>
 # Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>

src/caosadvancedtools/cfoods/h5.py

@@ -34,7 +34,7 @@ Properties.
 
 from copy import deepcopy
 
-import caosdb as db
+import linkahead as db
 import h5py
 import numpy as np
 from caosadvancedtools.cfood import fileguide
@@ -45,7 +45,7 @@ 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
@@ -168,7 +168,7 @@ class H5CFood(AbstractFileCFood):
         self.to_be_inserted = db.Container()
         self.insert_missing_structure(self.structure)
 
-        # TODO this is a workaround due to the fact that the caosdb library
+        # TODO this is a workaround due to the fact that the linkahead library
         # changes the objects in the Container if it is inserted. The graph
         # structure is flattened. I.e. references to other entity objects are
         # replaced with their IDs. However this code depends on this graph.

src/caosadvancedtools/collect_datamodel.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
@@ -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
 

src/caosadvancedtools/converter/labfolder_api.py

 #!/usr/bin/env python3
 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (c) 2020 IndiScale GmbH
 # Copyright (c) 2020 Daniel Hornung <d.hornung@indiscale.com>
@@ -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
 
 

src/caosadvancedtools/converter/labfolder_export.py

 #!/usr/bin/env python3
 #
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead project.
 #
 # Copyright (c) 2020 IndiScale GmbH
 # Copyright (c) 2020 Daniel Hornung <d.hornung@indiscale.com>
@@ -25,7 +25,7 @@ import os
 
 from bs4 import BeautifulSoup
 
-import caosdb as db
+import linkahead as db
 
 RERUN = False
 # crawler = Crawler()

src/caosadvancedtools/crawler.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
@@ -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.
 
@@ -512,16 +512,16 @@ ____________________\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
 
         """
         from xml.sax.saxutils import escape
 
-        caosdb_config = db.configuration.get_config()
-        if ("advancedtools" in caosdb_config and "crawler.customcssfile" in
-                caosdb_config["advancedtools"]):
-            cssfile = caosdb_config["advancedtools"]["crawler.customcssfile"]
+        linkahead_config = db.configuration.get_config()
+        if ("advancedtools" in linkahead_config and "crawler.customcssfile" in
+                linkahead_config["advancedtools"]):
+            cssfile = linkahead_config["advancedtools"]["crawler.customcssfile"]
         else:
             cssfile = None
         # TODO move path related stuff to sss_helper
@@ -584,11 +584,11 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
     </script>
 </body>
 </html>
-""".format(url=caosdb_config["Connection"]["url"],
+""".format(url=linkahead_config["Connection"]["url"],
            rid=run_id,
            changes=escape("\n".join(changes)),
            customcssfile='<link rel="stylesheet" href="{url}/webinterface/css/{customcssfile}"/>'.format(
-               url=caosdb_config["Connection"]["url"], customcssfile=cssfile) if cssfile else "",
+               url=linkahead_config["Connection"]["url"], customcssfile=cssfile) if cssfile else "",
            path=path)
 
         if "SHARED_DIR" in os.environ:
@@ -611,11 +611,11 @@ ____________________\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
         """
 
-        caosdb_config = db.configuration.get_config()
+        linkahead_config = db.configuration.get_config()
         text = """Dear Curator,
 there where changes that need your authorization. Please check the following
 carefully and if the changes are ok, click on the following link:
@@ -623,12 +623,12 @@ carefully and if the changes are ok, click on the following link:
 {url}/Shared/{filename}
 
 {changes}
-        """.format(url=caosdb_config["Connection"]["url"],
+        """.format(url=linkahead_config["Connection"]["url"],
                    filename=filename,
                    changes="\n".join(changes))
         try:
-            fro = caosdb_config["advancedtools"]["crawler.from_mail"]
-            to = caosdb_config["advancedtools"]["crawler.to_mail"]
+            fro = linkahead_config["advancedtools"]["crawler.from_mail"]
+            to = linkahead_config["advancedtools"]["crawler.to_mail"]
         except KeyError:
             logger.error("Server Configuration is missing a setting for "
                          "sending mails. The administrator should check "
@@ -646,11 +646,11 @@ 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 = []
@@ -699,7 +699,7 @@ 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
@@ -735,7 +735,7 @@ 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.

src/caosadvancedtools/datainconsistency.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 Indiscale GmbH <info@indiscale.com>
 # Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>

src/caosadvancedtools/datamodel_problems.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) 2020 Indiscale GmbH <info@indiscale.com>
 # Copyright (C) 2020 Florian Sprckelsen <f.spreckelsen@indiscale.com>
@@ -27,10 +27,10 @@ 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,
-                               TransactionError,
-                               UnqualifiedParentsError,
-                               UnqualifiedPropertiesError)
+from linkahead.exceptions import (EntityDoesNotExistError,
+                                  TransactionError,
+                                  UnqualifiedParentsError,
+                                  UnqualifiedPropertiesError)
 
 
 class DataModelProblems(object):

src/caosadvancedtools/example_cfood.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
@@ -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