diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2317fa8c76086e9c5a9079daa5cbf31d74f4d088..e5498c05c7c663192919bd7b1a1ff27a6001c8de 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- TableImporter now accepts a `existing_columns` argument which demands that certain columns exist
### Changed ###
+
+- Name change: `caosdb` -> `linkahead`
- The converters and datatype arguments of TableImporter now may have keys for nonexisting columns
### Deprecated ###
diff --git a/CITATION.cff b/CITATION.cff
index 83f3a0b8fe6ff860e494351c6e903c6331668118..6aae9e3deb96898e814d7c0fa9068fc8bec74cd6 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -19,7 +19,7 @@ authors:
- family-names: Luther
given-names: Stefan
orcid: https://orcid.org/0000-0001-7214-8125
-title: CaosDB - Advanced User Tools
+title: LinkAhead - Advanced User Tools
version: 0.7.0
doi: 10.3390/data4020083
date-released: 2023-01-20
\ No newline at end of file
diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst
index 23e5fc4f6ddb666757fb9c79e192e07ffed8fb44..527aea98b1f6e51afb00193bcbd0cd05126c9105 100644
--- a/src/doc/concepts.rst
+++ b/src/doc/concepts.rst
@@ -1,6 +1,6 @@
-========================
-The concepts of pycaosdb
-========================
+===========================
+The concepts of pylinkahead
+===========================
Some text...
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 0de862860492d7e658901179dd79462751c2596c..622c37d4f2a2e909d2ac7a0f2b3dad6996306e92 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -14,7 +14,7 @@
#
# import os
# import sys
-# sys.path.insert(0, os.path.abspath('../caosdb'))
+# sys.path.insert(0, os.path.abspath('../linkahead'))
import sphinx_rtd_theme
@@ -190,7 +190,7 @@ epub_exclude_files = ['search.html']
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
"python": ("https://docs.python.org/", None),
- "caosdb-pylib": ("https://caosdb.gitlab.io/caosdb-pylib/", None),
+ "linkahead-pylib": ("https://linkahead.gitlab.io/linkahead-pylib/", None),
}
diff --git a/src/doc/crawler.rst b/src/doc/crawler.rst
index 14e19d81fc8659923722e56eab601a8812912337..43d47515d6f4202eb633e19ab5674b5fa59adf43 100644
--- a/src/doc/crawler.rst
+++ b/src/doc/crawler.rst
@@ -1,10 +1,10 @@
==============
-CaosDB Crawler
+LinkAhead Crawler
==============
-The `CaosDB
-crawler <https://gitlab.com/caosdb/caosdb-advanced-user-tools/blob/main/src/linkaheadadvancedtools/crawler.py>`__
-is a tool for the automated insertion or update of entities in CaosDB.
+The `LinkAhead
+crawler <https://gitlab.com/linkahead/linkahead-advanced-user-tools/blob/main/src/linkaheadadvancedtools/crawler.py>`__
+is a tool for the automated insertion or update of entities in LinkAhead.
Typically, a file structure is crawled, but other things can be crawled as well.
For example tables or HDF5 files.
@@ -14,7 +14,7 @@ Introduction
In simple terms, the crawler is a program that scans a directory
structure, identifies files that will be treated, and generates
-corresponding Entities in CaosDB, possibly filling meta data. During
+corresponding Entities in LinkAhead, possibly filling meta data. During
this process the crawler can also open files and derive content from
within, for example reading CSV tables and processing individual rows of
these tables.
@@ -32,7 +32,7 @@ is the following:
Technically, this behaviour can be adjusted to your needs using so
called CFood (pun intended! :-)) Python classes. More details on the
-different components of the CaosDB Crawler can be found in the
+different components of the LinkAhead Crawler can be found in the
`developers’ information <#extending-the-crawlers>`__ below.
In case you are happy with our suggestion of a standard crawler, feel
@@ -75,10 +75,10 @@ The crawler can be executed directly via a Python script (usually called
``crawl.py``). The script prints the progress and reports potential
problems. The exact behavior depends on your setup. However, you can
have a look at the example in the
-`tests <https://gitlab.indiscale.com/caosdb/src/caosdb-advanced-user-tools/-/blob/main/integrationtests/crawl.py>`__.
+`tests <https://gitlab.com/linkahead/linkahead-advanced-user-tools/-/blob/main/integrationtests/crawl.py>`__.
-.. Note:: The crawler depends on the CaosDB Python client, so make sure to install :doc:`pycaosdb
- <caosdb-pylib:getting_started>`.
+.. Note:: The crawler depends on the LinkAhead Python client, so make sure to install :doc:`pylinkahead
+ <linkahead-pylib:getting_started>`.
Call ``python3 crawl.py --help`` to see what parameters can be provided.
@@ -90,11 +90,11 @@ Typically, an invocation looks like:
.. Note:: For trying out the above mentioned example crawler from the integration tests,
make sure that the ``extroot`` directory in the ``integrationtests`` folder is used as
- CaosDB's extroot directory, and call the crawler indirectly via ``./test.sh``.
+ LinkAhead's extroot directory, and call the crawler indirectly via ``./test.sh``.
In this case ``/someplace/`` identifies the path to be crawled **within
-CaosDB's file system**. You can browse the CaosDB file system by
-opening the WebUI of your CaosDB instance and clicking on “File System”.
+LinkAhead's file system**. You can browse the LinkAhead file system by
+opening the WebUI of your LinkAhead instance and clicking on “File System”.
In the backend, ``crawl.py`` starts a CQL query
``FIND File WHICH IS STORED AT /someplace/**`` and crawls the resulting
@@ -114,18 +114,18 @@ function ``loadFiles`` contained in the package:
::
- python3 -m linkaheadadvancedtools.loadFiles /opt/caosdb/mnt/extroot
+ python3 -m linkaheadadvancedtools.loadFiles /opt/linkahead/mnt/extroot
-``/opt/caosdb/mnt/extroot`` is the root of the file system to be crawled
-as seen by the CaosDB server (The actual path may vary. This is the used
-in the LinkAhead distribution of CaosDB). In this case the root file
-system as seen from within the CaosDB docker process is used.
+``/opt/linkahead/mnt/extroot`` is the root of the file system to be crawled
+as seen by the LinkAhead server (The actual path may vary. This is the used
+in the LinkAhead distribution of LinkAhead). In this case the root file
+system as seen from within the LinkAhead docker process is used.
-You can provide a ``.caosdbignore`` file as a commandline option to the above
+You can provide a ``.linkaheadignore`` file as a commandline option to the above
loadFiles command. The syntax of that file is the same as for `gitignore
<https://git-scm.com/docs/gitignore>`_ files. Note, that you can have additional
-``.caosdbignore`` files at lower levels which are appended to the current ignore
+``.linkaheadignore`` files at lower levels which are appended to the current ignore
file and have an effect of the respective subtree.
@@ -168,15 +168,15 @@ It should be independent of other data and define the following methods:
updated on the Server must be in ``AbstractCFood.to_be_updated`` after this call.
As hinted above, the main feature of an ``identifiable`` is its fingerprinting ability: it has
-sufficient properties to identify an existing Record in CaosDB so that the CFood can decide which
+sufficient properties to identify an existing Record in LinkAhead so that the CFood can decide which
Records should be updated by the Crawler instead of inserting a new one. Obviously, this allows the
-Crawler to run twice on the same file structure without duplicating the data in CaosDB.
+Crawler to run twice on the same file structure without duplicating the data in LinkAhead.
-An ``identifiable`` is a Python :py:class:`~caosdb.common.models.Record` object with the features to
-identify the correct Record in CaosDB. This object is used to create a query in order to determine
+An ``identifiable`` is a Python :py:class:`~linkahead.common.models.Record` object with the features to
+identify the correct Record in LinkAhead. This object is used to create a query in order to determine
whether the Record exists. If the Record does not exist, the ``identifiable`` is used to insert the
Record. Thus, after this step the Crawler guarantees that a Record with the features of the
-``identifiable`` exists in CaosDB (either previously existing or newly created).
+``identifiable`` exists in LinkAhead (either previously existing or newly created).
An example: An experiment might be uniquely identified by the date when it was conducted and a
@@ -208,13 +208,13 @@ In short, the Crawler interacts with the available CFoods in the following way:
#. ``cfood.create_identifiables()`` As described :ref:`above<c-food-introduction>`, create
identifiables.
- #. All the identifiables in ``cfood.identifiables`` are searched for existence in the CaosDB
+ #. All the identifiables in ``cfood.identifiables`` are searched for existence in the LinkAhead
instance, and inserted if they do not exist.
#. ``cfood.update_identifiables()`` As described :ref:`above<c-food-introduction>`, update the
identifiables if their content needs to change.
- #. All the identifiables in ``cfood.to_be_updated`` are synced to the CaosDB instance.
+ #. All the identifiables in ``cfood.to_be_updated`` are synced to the LinkAhead instance.
The following sketch aims to visualize this procedure.
@@ -223,11 +223,11 @@ The following sketch aims to visualize this procedure.
Sketch of how the Crawler uses the CFoods to process objects. Of the four identifiables
(fingerprints) on the right, only the second does not exist yet and is thus inserted in the
second step. Only the identifiables number 2 and 4 have new or changed content, so only these
- are synced to CaosDB in the last step.
+ are synced to LinkAhead in the last step.
.. note:: **Practical hint:** After the call to
:py:meth:`~linkaheadadvancedtools.cfood.AbstractCFood.create_identifiables`, the Crawler
- guarantees that an ``Experiment`` with those properties exists in CaosDB. In the call to
+ guarantees that an ``Experiment`` with those properties exists in LinkAhead. In the call to
:py:meth:`~linkaheadadvancedtools.cfood.AbstractCFood.update_identifiables`, further properties
might be added to this Record, e.g. references to data files that were recorded in that
experiment or to the person that did the experiment.
@@ -241,7 +241,7 @@ Let’s look at the following Example:
>>> # Example CFood
>>> from linkaheadadvancedtools.cfood import AbstractFileCFood, assure_has_property
- >>> import caosdb as db
+ >>> import linkahead as db
>>>
>>> class ExampleCFood(AbstractFileCFood):
... @staticmethod
@@ -333,7 +333,7 @@ In the ``crawl.py`` file, you should set this appropriately:
>>> fileguide.access = lambda path: "/main/data/" + path
-This prefixes all paths that are used in CaosDB with “/main/data/”. In
+This prefixes all paths that are used in LinkAhead with “/main/data/”. In
CFoods, files can then be accessed using the fileguide as follows:
.. code:: python
@@ -342,16 +342,16 @@ CFoods, files can then be accessed using the fileguide as follows:
# do stuff
pass
-Changing data in CaosDB
+Changing data in LinkAhead
-----------------------
As described above, a Record matching the identifiable will be inserted
if no such Record existed before. This is typically unproblematic.
However, what if existing Records need to be modified? Many
manipulations have the potential of overwriting changes in made in
-CaosDB. Thus, unless the data being crawled is a single source of truth
-for the information in CaosDB (and changes to the respective data in
-CaosDB should thus not be possible) changes have to be done with some
+LinkAhead. Thus, unless the data being crawled is a single source of truth
+for the information in LinkAhead (and changes to the respective data in
+LinkAhead should thus not be possible) changes have to be done with some
considerations.
Use the functions ``assure_has_xyz`` defined in the :py:mod:`cfood module <.cfood>` to
@@ -374,10 +374,10 @@ function, a security level can be given.
... interactive=False) # the crawler runs without asking intermediate questions
>>> c.crawl(security_level=INSERT)
-This assures that every manipulation of data in CaosDB that is done via the functions provided by
+This assures that every manipulation of data in LinkAhead that is done via the functions provided by
the :py:class:`~linkaheadadvancedtools.guard` class is checked against the provided security level:
-- ``RETRIEVE``: allows only to retrieve data from CaosDB. No manipulation is allowed
+- ``RETRIEVE``: allows only to retrieve data from LinkAhead. No manipulation is allowed
- ``INSERT``: allows only to insert new entities and the manipulation of those newly inserted ones
- ``UPDATE``: allows all manipulations
@@ -390,7 +390,7 @@ If you provide the ``to_be_updated`` member variable of CFoods to those
``assure...`` functions, the crawler provides another convenient
feature: When an update is prevented due to the security level, the
update is saved and can be subsequently be authorized. If the crawler
-runs on the CaosDB server, it will try to send a mail which allows to
+runs on the LinkAhead server, it will try to send a mail which allows to
authorize the change. If it runs as a local script it will notify you
that there are unauthorized changes and provide a code with which the
crawler can be started to authorize the change.
@@ -404,7 +404,7 @@ shows how a set of CFoods can be defined to deal with a complex file structure.
You can find detailed information on files need to be structured `here
<https://gitlab.com/salexan/check-sfs/-/blob/f-software/filesystem_structure.md>`__ and the source
-code of the CFoods `here <https://gitlab.com/caosdb/caosdb-advanced-user-tools>`__.
+code of the CFoods `here <https://gitlab.com/linkahead/linkahead-advanced-user-tools>`__.
Sources
=======
diff --git a/src/doc/images/crawler_fingerprint.svg b/src/doc/images/crawler_fingerprint.svg
index ee57b4af85a197d0b4d649f2be2e8c223a4d8cc5..305fc3277255bb25f26121bc8e165ced59d956af 100644
--- a/src/doc/images/crawler_fingerprint.svg
+++ b/src/doc/images/crawler_fingerprint.svg
@@ -633,7 +633,7 @@
id="tspan6473"
x="89.143967"
y="95.349686"
- style="font-size:3.88055563px;stroke-width:0.26458332">CaosDB-Server</tspan></text>
+ style="font-size:3.88055563px;stroke-width:0.26458332">LinkAhead-Server</tspan></text>
<image
width="20.404667"
height="25.484667"
diff --git a/src/doc/images/crawler_flow_sketch.svg b/src/doc/images/crawler_flow_sketch.svg
index 0714573ca692a8698ef2d4a1f7519af0da03292d..ba6a82d38225917171fbc5c3bd73b8d19d1ac793 100644
--- a/src/doc/images/crawler_flow_sketch.svg
+++ b/src/doc/images/crawler_flow_sketch.svg
@@ -909,7 +909,7 @@
x="212.41925"
y="197.43471"
style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:4.23333311px;font-family:monospace;-inkscape-font-specification:monospace;stroke-width:0.26458332"
- id="tspan88248">-crawler.push_identifiables_to_CaosDB()</tspan></tspan></text>
+ id="tspan88248">-crawler.push_identifiables_to_LinkAhead()</tspan></tspan></text>
</g>
<g
id="g44584"
diff --git a/src/doc/index.rst b/src/doc/index.rst
index 6999d27f769d766a4640916e6e3e38596d3359f0..62158834ce618a088b65f2fb92c786fbce2828ec 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -1,7 +1,7 @@
Welcome to linkaheadadvancedtools' documentation!
============================================
-Welcome to the advanced Python tools for CaosDB!
+Welcome to the advanced Python tools for LinkAhead!
This documentation helps you to :doc:`get started<getting_started>`, explains the most important
@@ -13,7 +13,7 @@ This documentation helps you to :doc:`get started<getting_started>`, explains th
Getting started <README_SETUP>
Concepts <concepts>
- The Caosdb Crawler <crawler>
+ The LinkAhead Crawler <crawler>
YAML data model specification <yaml_interface>
_apidoc/modules
diff --git a/src/doc/yaml_interface.rst b/src/doc/yaml_interface.rst
index e0152772ed29dbc8927eabcaef81358a11ba3904..51eb44fc95a8c3de108eaf6c2d277288373da68f 100644
--- a/src/doc/yaml_interface.rst
+++ b/src/doc/yaml_interface.rst
@@ -4,10 +4,10 @@
===============================
The ``linkaheadadvancedtools`` library features the possibility to create and update
-CaosDB models using a simplified definition in YAML format.
+LinkAhead models using a simplified definition in YAML format.
Let's start with an example taken from `model.yml
-<https://gitlab.indiscale.com/caosdb/src/caosdb-advanced-user-tools/-/blob/dev/unittests/model.yml>`__
+<https://gitlab.com/linkahead/linkahead-advanced-user-tools/-/blob/dev/unittests/model.yml>`__
in the library sources.
.. code-block:: yaml
@@ -57,9 +57,9 @@ This example defines 3 ``RecordTypes``:
``Textfile``.
-One major advantage of using this interface (in contrast to the standard python interface) is that properties can be defined and added to record types "on-the-fly". E.g. the three lines for ``firstName`` as sub entries of ``Person`` have two effects on CaosDB:
+One major advantage of using this interface (in contrast to the standard python interface) is that properties can be defined and added to record types "on-the-fly". E.g. the three lines for ``firstName`` as sub entries of ``Person`` have two effects on LinkAhead:
-- A new property with name ``firstName``, datatype ``TEXT`` and description ``first name`` is inserted (or updated, if already present) into CaosDB.
+- A new property with name ``firstName``, datatype ``TEXT`` and description ``first name`` is inserted (or updated, if already present) into LinkAhead.
- The new property is added as a recommended property to record type ``Person``.
Any further occurrences of ``firstName`` in the yaml file will reuse the definition provided for ``Person``.
@@ -70,7 +70,7 @@ Note the difference between the three property declarations of ``LabbookEntry``:
- ``responsible``: This defines and adds a property with name "responsible" to ``LabbookEntry`, which has a datatype ``Person``. ``Person`` is defined above.
- ``firstName``: This defines and adds a property with the standard data type ``TEXT`` to record type ``Person``.
-If the data model depends on record types or properties which already exist in CaosDB, those can be
+If the data model depends on record types or properties which already exist in LinkAhead, those can be
added using the ``extern`` keyword: ``extern`` takes a list of previously defined names.
@@ -78,7 +78,7 @@ added using the ``extern`` keyword: ``extern`` takes a list of previously define
Datatypes
=========
-You can use any data type understood by CaosDB as datatype attribute in the yaml model.
+You can use any data type understood by LinkAhead as datatype attribute in the yaml model.
List attributes are a bit special:
@@ -126,7 +126,7 @@ You can use the yaml parser directly in python as follows:
This creates a DataModel object containing all entities defined in the yaml file.
You can then use the functions from linkaheadadvancedtools.models.data_model.DataModel to synchronize
-the model with a CaosDB instance, e.g.:
+the model with a LinkAhead instance, e.g.:
.. code-block:: python