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How to find and query for data

An AiiDA database stores a graph of connected entities, which can be queried with the :class:`~aiida.orm.querybuilder.QueryBuilder` class.

Before starting to write a query, it helps to:

  • Know what you want to query for.
    In the language of databases, you need to tell the backend what entity you are looking for and optionally which of its properties you want to project.
    For example, you might be interested in the label of a calculation and the PKs of all its outputs.
  • Know the relationships between entities you are interested in.
    Nodes of an AiiDA graph (vertices) are connected with links (edges).
    A node can for example be either the input or output of another node, but also an ancestor or a descendant.
  • Know how you want to filter the results of your query.

Once you are clear about what you want and how you can get it, the :class:`~aiida.orm.querybuilder.QueryBuilder` will build an SQL-query for you.

There are two ways of using the :class:`~aiida.orm.querybuilder.QueryBuilder`:

  1. In the appender method, you construct your query step by step using the QueryBuilder.append() method.
  2. In the dictionary approach, you construct a dictionary that defines your query and pass it to the :class:`~aiida.orm.querybuilder.QueryBuilder`.

Both APIs provide the same functionality - the appender method may be more suitable for interactive use, e.g., in the verdi shell, whereas the dictionary method can be useful in scripting. In this section we will focus on the basics of the appender method. For more advanced queries or more details on the query dictionary, see the :ref:`topics section on advanced querying <topics:database:advancedquery>`.

Selecting entities

Using the append() method of the :class:`~aiida.orm.querybuilder.QueryBuilder`, you can query for the entities you are interested in. Suppose you want to query for calculation job nodes in your database:

from aiida.orm import QueryBuilder
qb = QueryBuilder()       # Instantiating instance. One instance -> one query
qb.append(CalcJobNode)    # Setting first vertex of path

If you are interested in instances of different classes, you can also pass an iterable of classes. However, they have to be of the same ORM-type (e.g. all have to be subclasses of :class:`~aiida.orm.nodes.node.Node`):

qb = QueryBuilder()       # Instantiating instance. One instance -> one query
qb.append([CalcJobNode, WorkChainNode]) # Setting first vertices of path, either WorkChainNode or Job.

Note

Processes have both a run-time :class:`~aiida.engine.processes.process.Process` that executes them and a :class:`~aiida.orm.nodes.node.Node` that stores their data in the database (see the :ref:`corresponding topics section<topics:processes:concepts:types>` for a detailed explanation). The :class:`~aiida.orm.querybuilder.QueryBuilder` allows you to pass either the :class:`~aiida.orm.nodes.node.Node` class (e.g. :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`) or the :class:`~aiida.engine.processes.process.Process` class (e.g. :class:`~aiida.engine.processes.calcjobs.calcjob.CalcJob`), which will automatically select the right entity for the query. Using either :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode` or :class:`~aiida.engine.processes.calcjobs.calcjob.CalcJob` will produce the same query results.

Retrieving results

Once you have appended the entity you want to query for to the :class:`~aiida.orm.querybuilder.QueryBuilder`, the next question is how to get the results. There are several ways to obtain data from a query:

qb = QueryBuilder()                 # Instantiating instance
qb.append(CalcJobNode)              # Setting first vertices of path

first_row = qb.first()              # Returns a list (!) of the results of the first row

all_results_d = qb.dict()           # Returns all results as a list of dictionaries

all_results_l = qb.all()            # Returns a list of lists

In case you are working with a large dataset, you can also return your query as a generator:

all_res_d_gen = qb.iterdict()       # Return a generator of dictionaries
                                    # of all results
all_res_l_gen = qb.iterall()        # Returns a generator of lists

This will retrieve the data in batches, and you can start working with the data before the query has completely finished. For example, you can iterate over the results of your query in a for loop:

for entry in qb.iterall():
    # do something with a single entry in the query result

Filters

Usually you do not want to query for all entities of a certain class, but rather filter the results based on certain properties. Suppose you do not want all :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode` data, but only those that are finished:

qb = QueryBuilder()                 # Initialize a QueryBuilder instance
qb.append(
    CalcJobNode,                    # Append a CalcJobNode
    filters={                       # Specify the filters:
        'attributes.process_state': 'finished',  # the process is finished
    },
)

You can apply multiple filters to one entity in a query. Say you are interested in all calculation jobs in your database that are finished and have exit_status == 0:

qb = QueryBuilder()                 # Initialize a QueryBuilder instance
qb.append(
    CalcJobNode,                    # Append a CalcJobNode
    filters={                       # Specify the filters:
        'attributes.process_state': 'finished',     # the process is finished AND
        'attributes.exit_status': 0                 # has exit_status == 0
    },
)

In case you want to query for calculation jobs that satisfy one of these conditions, you can use the or operator:

qb = QueryBuilder()
qb.append(
    CalcJobNode,
    filters={
        'or':[
            {'attributes.process_state': 'finished'},
            {'attributes.exit_status': 0}
        ]
    },
)

If we had written and instead of or in the example above, we would have performed the exact same query as the previous one, because and is the default behavior if you provide several filters as key-value pairs in a dictionary to the filters argument. In case you want all calculation jobs with state finished or excepted, you can also use the in operator:

qb = QueryBuilder()
qb.append(
    CalcJobNode,
    filters={
        'attributes.process_state': {'in': ['finished', 'excepted']}
    },
)

Operator negations

A filter can be turned into its associated negation by adding an exclamation mark, !, in front of the operator. So, to query for all calculation jobs that are not a finished or excepted state:

qb = QueryBuilder()
qb.append(
    CalcJobNode,
    filters={
        'attributes.process_state': {'!in': ['finished', 'excepted']}
    },
)

Note

The above rule applies to all operators. For example, you can check non-equality with !==, since this is the equality operator (==) with a negation prepended.

A complete list of all available operators can be found in the :ref:`advanced querying section<topics:database:advancedquery:tables:operators>`.

Relationships

It is possible to query for data based on its relationship to another entity in the database. Imagine you are not interested in the calculation jobs themselves, but in one of the outputs they create. You can build upon your initial query for all :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`'s in the database using the relationship of the output to the first step in the query:

qb = QueryBuilder()
qb.append(CalcJobNode, tag='calcjob')
qb.append(Int, with_incoming='calcjob')

In the first append call, we query for all :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`'s in the database, and tag this step with the unique identifier 'calcjob'. Next, we look for all Int nodes that are an output of the :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`'s found in the first step, using the with_incoming relationship argument. The Int node was created by the :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode` and as such has an incoming create link.

In the context of our query, we are building a path consisting of vertices (i.e. the entities we query for) connected by edges defined by the relationships between them. The complete set of all possible relationships you can use query for, as well as the entities that they connect to, can be found in the :ref:`advanced querying section<topics:database:advancedquery:tables:relationships>`.

Note

The tag identifier can be any alphanumeric string, it is simply a label used to refer to a previous vertex along the query path when defining a relationship.

Projections

By default, the :class:`~aiida.orm.querybuilder.QueryBuilder` returns the instances of the entities corresponding to the final append to the query path. For example:

qb = QueryBuilder()
qb.append(CalcJobNode, tag='calcjob')
qb.append(Int, with_incoming='calcjob')

The above code snippet will return all Int nodes that are outputs of any :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`. However, you can also project other entities in the path by adding project='*' to the corresponding append() call:

qb = QueryBuilder()
qb.append(CalcJobNode, tag='calcjob', project='*')
qb.append(Int, with_incoming='calcjob')

This will return all :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`'s that have an Int output node.

However, in many cases we are not interested in the entities themselves, but rather their PK, UUID, attributes or some other piece of information stored by the entity. This can be achieved by providing the corresponding column to the project keyword argument:

qb = QueryBuilder()
qb.append(CalcJobNode, tag='calcjob')
qb.append(Int, with_incoming='calcjob', project='id')

In the above example, executing the query returns all PK's of the Int nodes which are outputs of all :class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`'s in the database. Moreover, you can project more than one piece of information for one vertex by providing a list:

qb = QueryBuilder()
qb.append(CalcJobNode, tag='calcjob')
qb.append(Int, with_incoming='calcjob', project=['id', 'attributes.value'])

For the query above, qb.all() will return a list of lists, for which each element corresponds to one entity and contains two items: the PK of the Int node and its value. Finally, you can project information for multiple vertices along the query path:

qb = QueryBuilder()
qb.append(CalcJobNode, tag='calcjob', project='*')
qb.append(Int, with_incoming='calcjob', project=['id', 'attributes.value'])

All projections must start with one of the columns of the entities in the database, or project the instances themselves using '*'. Examples of columns we have encountered so far are id, uuid and attributes. If the column is a dictionary, you can expand the dictionary values using a dot notation, as we have done in the previous example to obtain the attributes.value. This can be used to project the values of nested dictionaries as well.

Note

Be aware that for consistency, QueryBuilder.all() / iterall() always returns a list of lists, even if you only project one property of a single entity. Use QueryBuilder.all(flat=True) to return the query result as a flat list in this case.

As mentioned in the beginning, this section provides only a brief introduction to the :class:`~aiida.orm.querybuilder.QueryBuilder`'s basic functionality. To learn about more advanced queries, please see :ref:`the corresponding topics section<topics:database:advancedquery>`.

Shortcuts

The :class:`~aiida.orm.querybuilder.QueryBuilder` is the generic way of querying for data in AiiDA. For certain common queries, shortcuts have been added to the AiiDA python API to save you a couple of lines of code.

Incoming and outgoing links

The provenance graph in AiiDA is a :ref:`directed graph <topics:provenance:concepts>`. The vertices of the graph are the nodes, and the edges that connect them are called links. Since the graph is directed, any node can have incoming and outgoing links that connect it to neighboring nodes.

To discover the neighbors of a given node, you can use the methods :meth:`~aiida.orm.nodes.links.NodeLinks.get_incoming` and :meth:`~aiida.orm.nodes.links.NodeLinks.get_outgoing`. They have the exact same interface but will return the neighbors connected to the current node with a link coming into it or with links going out of it, respectively. For example, for a given node, to inspect all the neighboring nodes from which a link is incoming to the node:

node.get_incoming()

This will return an instance of the :class:`~aiida.orm.utils.links.LinkManager`. From that manager, you can request the results in a specific format. If you are only interested in the neighboring nodes themselves, you can call the :class:`~aiida.orm.utils.links.LinkManager.all_nodes` method:

node.get_incoming().all_nodes()

This will return a list of :class:`~aiida.orm.nodes.node.Node` instances that correspond to the nodes that are neighbors of node, where the link is going towards node. Calling the :meth:`~aiida.orm.utils.links.LinkManager.all` method of the manager instead will return a list of :class:`~aiida.orm.utils.links.LinkTriple` named tuples. These tuples contain, in addition to the neighboring node, also the link label and the link type with which they are connected to the origin node. For example, to list all the neighbors of a node from which a link is incoming:

for link_triple in node.get_incoming().all():
    print(link_triple.node, link_triple.link_type, link_triple.link_label)

Note that the :class:`~aiida.orm.utils.links.LinkManager` provides many convenience methods to get information from the neigboring nodes, such as :meth:`~aiida.orm.utils.links.LinkManager.all_link_labels` if you only need the list of link labels.

The :meth:`~aiida.orm.nodes.links.NodeLinks.get_incoming` and :meth:`~aiida.orm.nodes.links.NodeLinks.get_outgoing` methods accept various arguments that allow one to filter what neighboring nodes should be matched:

  • node_class: accepts a subclass of :class:`~aiida.orm.nodes.node.Node`, only neighboring nodes with a class that matches this will be returned
  • link_type: accepts a value of :class:`~aiida.common.links.LinkType`, only neighboring nodes that are linked with this link type will be returned
  • link_label_filter: accepts a string expression (with optional wildcards using the syntax of SQL LIKE patterns, see below), only neighboring nodes that are linked with a link label that matches the pattern will be returned

As an example:

node.get_incoming(node_class=Data, link_type=LinkType.INPUT_CALC, link_label_filter='output%node_').all_nodes()

will return only neighboring data nodes that are linked to the node with a link of type LinkType.INPUT_CALC and where the link label matches the pattern 'output%node_'. Reminder on the syntax of SQL LIKE patterns: the % character matches any string of zero or more characters, while the _ character matches exactly one character. These two special characters can be escaped by prepending them with a backslash (note that when putting a backslash in a Python string you have to escape the backslash itself, so you will need two backslashes: e.g., to match exactly a link label a_b you need to pass link_label_filter='a\\_b').

Inputs and outputs of processes

The :meth:`~aiida.orm.nodes.links.NodeLinks.get_incoming` and :meth:`~aiida.orm.nodes.links.NodeLinks.get_outgoing` methods, described in the :ref:`previous section <how-to:query:shortcuts:incoming-outgoing>`, can be used to access all neighbors from a certain node and provide advanced filtering options. However, often one doesn't need this expressivity and simply wants to retrieve all neighboring nodes with a syntax that is as succint as possible. A prime example is to retrieve the inputs or outputs of :ref:`a process <topics:processes:concepts>`. Instead of using :meth:`~aiida.orm.nodes.links.NodeLinks.get_incoming` and :meth:`~aiida.orm.nodes.links.NodeLinks.get_outgoing`, to get the inputs and outputs of a process_node one can do:

inputs = process_node.inputs
outputs = process_node.outputs

These properties do not return the actual inputs and outputs directly, but instead return an instance of :class:`~aiida.orm.utils.managers.NodeLinksManager`. The reason is because through the manager, the inputs or outputs are accessible through their link label (that, for inputs and outputs of processes, is unique) and can be tab-completed. For example, if the process_node has an output with the label result, it can be retrieved as:

process_node.outputs.result

The inputs or outputs can also be accessed through key dereferencing:

process_node.outputs['result']

If there is no neighboring output with the given link label, a :class:`~aiida.common.exceptions.NotExistentAttributeError` or :class:`~aiida.common.exceptions.NotExistentKeyError` will be raised, respectively.

Note

The inputs and outputs properties are only defined for :class:`~aiida.orm.nodes.process.process.ProcessNode`'s. This means that you cannot chain these calls, because an input or output of a process node is guaranteed to be a :class:`~aiida.orm.Data` node, which does not have inputs or outputs.

Creator, caller and called

Similar to the inputs and outputs properties of process nodes, there are some more properties that make exploring the provenance graph easier:

Note

Using the creator and inputs properties, one can easily move up the provenance graph. For example, starting from some data node that represents the result of a long workflow, one can move up the provenance graph to find an initial input node of interest: result.creator.inputs.some_input.creator.inputs.initial_input.

Calculation job results

:class:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode`'s provide the :meth:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode.res` property, that can give easy access to the results of the calculation job. The requirement is that the :class:`~aiida.engine.processes.calcjobs.calcjob.CalcJob` class that produced the node, defines a default output node in its spec. This node should be a :class:`~aiida.orm.nodes.data.dict.Dict` output that will always be created. An example is the :class:`~aiida.calculations.templatereplacer.TemplatereplacerCalculation` plugin, that has the output_parameters output that is specified as its default output node.

The :meth:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode.res` property will give direct easy access to all the keys within this dictionary output. For example, the following:

list(node.res)

will return a list of all the keys in the output node. Individual keys can then be accessed through attribute dereferencing:

node.res.some_key

In an interactive shell, the available keys are also tab-completed. If you type node.res. followed by the tab key twice, a list of the available keys is printed.

Note

The :meth:`~aiida.orm.nodes.process.calculation.calcjob.CalcJobNode.res` property is really just a shortcut to quickly and easily access an attribute of the default output node of a calculation job. For example, if the default output node link label is output_parameters, then node.res.some_key is exactly equivalent to node.outputs.output_parameters.dict.some_key. That is to say, when using res, one is accessing attributes of one of the output nodes, and not of the calculation job node itself.