Skip to content

Commit

Permalink
output page index formatting
Browse files Browse the repository at this point in the history
  • Loading branch information
slobentanzer committed Apr 24, 2024
1 parent fc14271 commit 2d47b6a
Showing 1 changed file with 15 additions and 7 deletions.
22 changes: 15 additions & 7 deletions docs/output/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -9,20 +9,28 @@ and thus are open towards any output format for the knowledge representation. We
are currently working on other output formats, such as RDF, SQL, and ArangoDB,
and will update the documentation accordingly.

The used output format is specified via the ``dbms`` parameter in the ``biocypher_config.yaml`` (see the :ref:`config` for an example).
Currently supported are ``neo4j``, ``arangodb``, ``rdf``, ``postgres``, and ``sqlite``.
The used output format is specified via the ``dbms`` parameter in the
``biocypher_config.yaml`` (see the :ref:`config` for an example). Currently
supported are ``neo4j``, ``arangodb``, ``rdf``, ``postgres``, and ``sqlite``.

Furthermore you can specify whether to use the ``offline`` or ``online`` mode.
Furthermore, you can specify whether to use the ``offline`` or ``online`` mode.

- For the online mode set ``offline: false``. You need a running database instance and BioCypher will connect to this instance and directly writes the output to the database.
- For the offline mode set ``offline: true``. BioCypher will write the knowledge graph to files in a designated output folder (standard being ``biocypher-out/`` and the current datetime). Furthermore you can generate a bash script to insert the knowledge graph files into the specified ``dbms`` by running ``bc.write_import_call()``.
- For the online mode set ``offline: false``. You need a running database
instance and BioCypher will connect to this instance and directly writes the
output to the database.

- For the offline mode set ``offline: true``. BioCypher will write the knowledge
graph to files in a designated output folder (standard being ``biocypher-out/``
and the current datetime). Furthermore you can generate a bash script to insert
the knowledge graph files into the specified ``dbms`` by running
``bc.write_import_call()``.

.. caution::

The ``online`` mode is currently only supported for the ``neo4j`` database.


Details about the usage of the ``online`` and ``offline`` mode and the different supported output formats are described on the following pages:
Details about the usage of the ``online`` and ``offline`` mode and the different
supported output formats are described on the following pages:

.. toctree::
:maxdepth: 2
Expand Down

0 comments on commit 2d47b6a

Please sign in to comment.