All nodes in an AiiDA provenance graph inherit from the
Among those are the
Data class, the
ProcessNode class representing computations that transform data, and the
Code class representing executables (and file collections that are used by calculations).
A node can store information in attributes.
Since AiiDA guarantees a certain level of provenance, these attributes become immutable as soon as the node is stored.
This means that as soon as a node is stored, any attempt to alter its attributes, changing its value or deleting it altogether, shall be met with a raised exception.
Certain subclasses of nodes need to adapt this behavior however, as for example in the case of the
ProcessNode class (see calculation updatable attributes), but since the immutability of stored nodes is a core concept of AiiDA, this behavior is nonetheless enforced on the node level.
This guarantees that any subclasses of the Node class will respect this behavior unless it is explicitly overriden.
clean_value()takes a value and returns an object which can be serialized for storage in the database. Such an object must be able to be subsequently deserialized without changing value. If a simple datatype is passed (integer, float, etc.), a check is performed to see if it has a value of
inf, as these cannot be stored. Otherwise, if a list, tuple, dictionary, etc., is passed, this check is performed for each value it contains. This is done recursively, automatically handling the case of nested objects. It is important to note that iterable type objects are converted to lists during this process, and mappings are converted to normal dictionaries. For efficiency reasons, the cleaning of attribute values is delayed to the last moment possible. This means that for an unstored node, new attributes are not cleaned but simply set in the cache of the underlying database model. When the node is then stored, all attributes are cleaned in one fell swoop and if successful the values are flushed to the database. Once a node is stored, there no longer is such a cache and so the attribute values are cleaned straight away for each call. The same mechanism holds for the cleaning of the values of extras.
Node methods & properties¶
In the following sections, the most important methods and properties of the
Node class will be described.
Node subclasses organization¶
Node class has two important attributes:
_plugin_type_stringcharacterizes the class of the object.
_query_type_stringcharacterizes the class and all its subclasses (by pointing to the package or Python file that contain the class).
The convention for all the
Node subclasses is that if a
class B is inherited by a
class A then there should be a package
aiida/orm that has a file
__init__.py and a
B.py in that directory (or a
B package with the corresponding
An example of this is the
ArrayData and the
ArrayData is placed in
KpointsData which inherits from
ArrayData is placed in
This is an implicit & quick way to check the inheritance of the
General purpose methods¶
__init__(): Will construct a new unstored
Node. Note that this cannot be used to load an existing node from the database.
computer()returns the computer associated to this node.
user()returns the user that created the node.
uuid()returns the universally unique identifier (UUID) of the node.
Node can be annotated with labels, description and comments.
The following methods can be used for the management of these properties.
labelreturns the label of the node. It can also be used to change the label, e.g.
mynode.label = "new label".
description: returns the description of the node (more detailed than the label). It can also be used to change the description, e.g.
mynode.description = "new description".
Folder objects represent directories on the disk (virtual or not) where extra information for the node are stored.
These folders can be temporary or permanent.
Store & deletion¶
store_all()stores all the input
nodes, then it stores the current
nodeand in the end, it stores the cached input links.
verify_are_parents_stored()checks that the parents are stored.
store()method checks that the
nodedata is valid, then check if
node’s parents are stored, then moves the contents of the temporary folder to the repository folder and in the end, it stores in the database the information that are in the cache. The latter happens with a database transaction. In case this transaction fails, then the data transfered to the repository folder are moved back to the temporary folder.
Folder and its subclasses to add an abstraction layer between the functions and methods working directly on the file-system and AiiDA.
This is particularly useful when we want to easily change between different folder options (temporary, permanent etc) and storage options (plain local directories, compressed files, remote files & directories etc).
This is the main class of the available
Apart from the abstraction provided to the OS operations needed by AiiDA, one of its main features is that it can restrict all the available operations within a given folder limit.
The available methods are:
get_subfolder()returns the subfolder matching the given name
get_content_list()returns the contents matching a pattern.
create_symlink()creates a symlink pointing the given location inside the
create_file_from_filelike()creates a file from the given contents.
open()opens a file in the
folder_limit()returns the limit under which the creation of files/folders is restrained.
exists()returns true or false depending whether a folder exists or not.
isfile()and py:meth:~aiida.common.folders.Folder.isdir return true or false depending on the existence of the given file/folder.
Objects of this class correspond to the repository folders.
RepositoryFolder specific methods are:
__init__()initializes the object with the necessary folder names and limits.
get_topdir()returns the top directory.
section()returns the section to which the
folderbelongs. This can be for the moment only
subfolder()returns the subfolder within the section/uuid folder.
uuid()the UUID of the corresponding
Navigating inputs and outputs¶
NodeLinksManagercan be used to quickly go from a node to a neighboring node. For example:
In : # Let's load a node with a specific pk In : c = load_node(139168) In : c Out: <CpCalculation: uuid: 49084dcf-c708-4422-8bcf-808e4c3382c2 (pk: 139168)> In : # Let's traverse the inputs of this node. In : # By typing c.inputs.<TAB> we get all the input links In : c.inputs. c.inputs.code c.inputs.parent_calc_folder c.inputs.pseudo_O c.inputs.settings c.inputs.parameters c.inputs.pseudo_Ba c.inputs.pseudo_Ti c.inputs.structure In : # We may follow any of these links to access other nodes. For example, let's follow the parent_calc_folder In : c.inputs.parent_calc_folder Out: <RemoteData: uuid: becb4894-c50c-4779-b84f-713772eaceff (pk: 139118)> In : # Let's assign to r the node reached by the parent_calc_folder link In : r = c.inputs.parent_calc_folder In : r.inputs.__dir__() Out: ['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__format__', '__getattr__', '__getattribute__', '__getitem__', '__hash__', '__init__', '__iter__', '__module__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', u'remote_folder']
.outputsmanager both for
WorkflowNodework in the same way (see below).
ProcessNode class is a subclass of the
Node class, which means that its attributes become immutable once stored.
However, for a
Calculation to be runnable it needs to be stored, but that would mean that its state, which is stored in an attribute can no longer be updated.
To solve this issue the
Sealable mixin is introduced.
This mixin can be used for subclasses of
Node that need to have updatable attributes even after the node has been stored in the database.
The mixin defines the
_updatable_attributes tuple, which defines the attributes that are considered to be mutable even when the node is stored.
It also allows the node to be sealed, after which even the updatable attributes become immutable.
Deprecated features, renaming, and adding new methods¶
In case a method is renamed or removed, this is the procedure to follow:
(If you want to rename) move the code to the new function name. Then, in the docstring, add something like:
.. versionadded:: 0.7 Renamed from OLDMETHODNAME
Don’t remove directly the old function, but just change the code to use the new function, and add in the docstring:
.. deprecated:: 0.7 Use :meth:`NEWMETHODNAME` instead.
Moreover, at the beginning of the function, add something like:
import warnings # If we call this DeprecationWarning, pycharm will properly strike out the function from aiida.common.warnings import AiidaDeprecationWarning as DeprecationWarning # pylint: disable=redefined-builtin warnings.warn("<Deprecation warning here - MAKE IT SPECIFIC TO THIS DEPRECATION, as it will be shown only once per different message>", DeprecationWarning) # <REST OF THE FUNCTION HERE>
(of course replace the parts between
< >symbols with the correct strings).
The advantage of the method above is:
pycharm will still show the method crossed out
AiidaDeprecationWarningdoes not inherit from
DeprecationWarning, so it will not be “hidden” by python
User can disable our warnings (and only those) by using AiiDA properties with:
verdi config warnings.showdeprecations False
Changing the config.json structure¶
In general, changes to
config.json should be avoided if possible.
However, if there is a need to modify it, the following procedure should be used to create a migration:
Determine whether the change will be backwards-compatible. This means that an older version of AiiDA will still be able to run with the new
config.jsonstructure. It goes without saying that it’s preferable to change
config.jsonin a backwards-compatible way.
aiida/manage/configuration/migrations/migrations.py, increase the
CURRENT_CONFIG_VERSIONby one. If the change is not backwards-compatible, set
OLDEST_COMPATIBLE_CONFIG_VERSIONto the same value.
Write a function which transforms the old config dict into the new version. It is possible that you need user input for the migration, in which case this should also be handled in that function.
Add an entry in
_MIGRATION_LOOKUPwhere the key is the version before the migration, and the value is a
ConfigMigrationis constructed from your migration function, and the hard-coded values of
OLDEST_COMPATIBLE_CONFIG_VERSION. If these values are not hard-coded, the migration will break as soon as the values are changed again.
Add tests for the migration, in
aiida/backends/tests/manage/configuration/migrations/test_migrations.py. You can add two types of tests:
Tests that run the entire migration, using the
check_and_migrate_configfunction. Make sure to run it with
store=False, otherwise it will overwrite your
config.jsonfile. For these tests, you will have to update the reference files.
Tests that run a single step in the migration, using the
ConfigMigration.applymethod. This can be used if you need to test different edge cases of the migration.
There are examples for both types of tests.
Daemon and signal handling¶
While the AiiDA daemon is running, interrupt signals (
SIGTERM) are captured so that the daemon can shut down gracefully.
This is implemented using Python’s
signal module, as shown in the following dummy example:
import signal def print_foo(*args): print('foo') signal.signal(signal.SIGINT, print_foo)
You should be aware of this while developing code which runs in the daemon.
In particular, it’s important when creating subprocesses.
When a signal is sent, the whole process group receives that signal.
As a result, the subprocess can be killed even though the Python main process captures the signal.
This can be avoided by creating a new process group for the subprocess, meaning that it will not receive the signal.
To do this, you need to pass
preexec_fn=os.setsid to the
import os import subprocess print(subprocess.check_output('sleep 3; echo bar', preexec_fn=os.setsid))
When dropping python 2.7 support,
preexec_fn=os.setsid should be replaced
by the thread safe
start_new_session=True introduced in python 3.2.