Importing relational data into a CubicWeb instance

==================================================

Introduction

~~~~~~~~~~~~

This tutorial explains how to import data from an external source (e.g. a collection of files) 

into a CubicWeb cube instance.

First, once we know the format of the data we wish to import, we devise a 

*data model*, that is, a CubicWeb (Yams) schema which reflects the way the data

is structured. This schema is implemented in the ``schema.py`` file.

In this tutorial, we will describe such a schema for a particular data set, 

the Diseasome data (see below).

Once the schema is defined, we create a cube and an instance. 

The cube is a specification of an application, whereas an instance 

is the application per se. 

Once the schema is defined and the instance is created, the import can be performed, via

the following steps:

1. Build a custom parser for the data to be imported. Thus, one obtains a Python

   memory representation of the data.

2. Map the parsed data to the data model defined in ``schema.py``.

3. Perform the actual import of the data. This comes down to "populating"

   the data model with the memory representation obtained at 1, according to

   the mapping defined at 2.

This tutorial illustrates all the above steps in the context of relational data

stored in the RDF format.

More specifically, we describe the import of Diseasome_ RDF/OWL data.

.. _Diseasome: http://datahub.io/dataset/fu-berlin-diseasome

Building a data model

~~~~~~~~~~~~~~~~~~~~~

The first thing to do when using CubicWeb for creating an application from scratch

is to devise a *data model*, that is, a relational representation of the problem to be

modeled or of the structure of the data to be imported. 

In such a schema, we define

an entity type (``EntityType`` objects) for each type of entity to import. Each such type

has several attributes. If the attributes are of known CubicWeb (Yams) types, viz. numbers,

strings or characters, then they are defined as attributes, as e.g. ``attribute = Int()``

for an attribute named ``attribute`` which is an integer. 

Each such type also has a set of

relations, which are defined like the attributes, except that they represent, in fact,

relations between the entities of the type under discussion and the objects of a type which

is specified in the relation definition. 

For example, for the Diseasome data, we have two types of entities, genes and diseases.

Thus, we create two classes which inherit from ``EntityType``::

    class Disease(EntityType):

        # Corresponds to http://www.w3.org/2000/01/rdf-schema#label

        label = String(maxsize=512, fulltextindexed=True)

        ...

        #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/associatedGene

        associated_genes = SubjectRelation('Gene', cardinality='**')

        ...

        #Corresponds to 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/chromosomalLocation'

        chromosomal_location = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)

    class Gene(EntityType):

        ...

In this schema, there are attributes whose values are numbers or strings. Thus, they are 

defined by using the CubicWeb / Yams primitive types, e.g., ``label = String(maxsize=12)``. 

These types can have several constraints or attributes, such as ``maxsize``. 

There are also relations, either between the entity types themselves, or between them

and a CubicWeb type, ``ExternalUri``. The latter defines a class of URI objects in 

CubicWeb. For instance, the ``chromosomal_location`` attribute is a relation between 

a ``Disease`` entity and an ``ExternalUri`` entity. The relation is marked by the CubicWeb /

Yams ``SubjectRelation`` method. The latter can have several optional keyword arguments, such as

``cardinality`` which specifies the number of subjects and objects related by the relation type 

specified. For example, the ``'?*'`` cardinality in the ``chromosomal_relation`` relation type says

that zero or more ``Disease`` entities are related to zero or one ``ExternalUri`` entities.

In other words, a ``Disease`` entity is related to at most one ``ExternalUri`` entity via the

``chromosomal_location`` relation type, and that we can have zero or more ``Disease`` entities in the

data base. 

For a relation between the entity types themselves, the ``associated_genes`` between a ``Disease``

entity and a ``Gene`` entity is defined, so that any number of ``Gene`` entities can be associated

to a ``Disease``, and there can be any number of ``Disease`` s if a ``Gene`` exists.

Of course, before being able to use the CubicWeb / Yams built-in objects, we need to import them::

    from yams.buildobjs import EntityType, SubjectRelation, String, Int

    from cubicweb.schemas.base import ExternalUri

Building a custom data parser

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The data we wish to import is structured in the RDF format,

as a text file containing a set of lines. 

On each line, there are three fields. 

The first two fields are URIs ("Universal Resource Identifiers"). 

The third field is either an URI or a string. Each field bares a particular meaning:

- the leftmost field is an URI that holds the entity to be imported. 

  Note that the entities defined in the data model (i.e., in ``schema.py``) should 

  correspond to the entities whose URIs are specified in the import file.

- the middle field is an URI that holds a relation whose subject is the  entity 

  defined by the leftmost field. Note that this should also correspond

  to the definitions in the data model.

- the rightmost field is either an URI or a string. When this field is an URI, 

  it gives the object of the relation defined by the middle field.

  When the rightmost field is a string, the middle field is interpreted as an attribute

  of the subject (introduced by the leftmost field) and the rightmost field is

  interpreted as the value of the attribute.

Note however that some attributes (i.e. relations whose objects are strings) 

have their objects defined as strings followed by ``^^`` and by another URI;

we ignore this part.

Let us show some examples:

- of line holding an attribute definition:

  ``<http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/CYP17A1> 

  <http://www.w3.org/2000/01/rdf-schema#label> "CYP17A1" .``

  The line contains the definition of the ``label`` attribute of an

  entity of type ``gene``. The value of ``label`` is '``CYP17A1``'.

- of line holding a relation definition:

  ``<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseases/1> 

  <http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/associatedGene> 

  <http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/HADH2> .``

  The line contains the definition of the ``associatedGene`` relation between

  a ``disease`` subject entity identified by ``1`` and a ``gene`` object 

  entity defined by ``HADH2``.

Thus, for parsing the data, we can (:note: see the ``diseasome_parser`` module):

1. define a couple of regular expressions for parsing the two kinds of lines, 

   ``RE_ATTS`` for parsing the attribute definitions, and ``RE_RELS`` for parsing

   the relation definitions.

2. define a function that iterates through the lines of the file and retrieves

   (``yield`` s) a (subject, relation, object) tuple for each line.

   We called it ``_retrieve_structure`` in the ``diseasome_parser`` module.

   The function needs the file name and the types for which information

   should be retrieved.

Alternatively, instead of hand-making the parser, one could use the RDF parser provided

in the ``dataio`` cube.

.. XXX To further study and detail the ``dataio`` cube usage.

Once we get to have the (subject, relation, object) triples, we need to map them into

the data model.

Mapping the data to the schema

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In the case of diseasome data, we can just define two dictionaries for mapping

the names of the relations as extracted by the parser, to the names of the relations

as defined in the ``schema.py`` data model. In the ``diseasome_parser`` module 

they are called ``MAPPING_ATTS`` and ``MAPPING_RELS``. 

Given that the relation and attribute names are given in CamelCase in the original data,

mappings are necessary if we follow the PEP08 when naming the attributes in the data model.

For example, the RDF relation ``chromosomalLocation`` is mapped into the schema relation 

``chromosomal_location``.

Once these mappings have been defined, we just iterate over the (subject, relation, object)

tuples provided by the parser and we extract the entities, with their attributes and relations.

For each entity, we thus have a dictionary with two keys, ``attributes`` and ``relations``.

The value associated to the ``attributes`` key is a dictionary containing (attribute: value) 

pairs, where "value" is a string, plus the ``cwuri`` key / attribute holding the URI of 

the entity itself.

The value associated to the ``relations`` key is a dictionary containing (relation: value)

pairs, where "value" is an URI.

This is implemented in the ``entities_from_rdf`` interface function of the module 

``diseasome_parser``. This function provides an iterator on the dictionaries containing

the ``attributes`` and ``relations`` keys for all entities.

However, this is a simple case. In real life, things can get much more complicated, and the 

mapping can be far from trivial, especially when several data sources (which can follow 

different formatting and even structuring conventions) must be mapped into the same data model.

Importing the data

~~~~~~~~~~~~~~~~~~

The data import code should be placed in a Python module. Let us call it 

``diseasome_import.py``. Then, this module should be called via

``cubicweb-ctl``, as follows::

    cubicweb-ctl shell diseasome_import.py -- <other arguments e.g. data file>

In the import module, we should use a *store* for doing the import.

A store is an object which provides three kinds of methods for

importing data:

- a method for importing the entities, along with the values

  of their attributes.

- a method for importing the relations between the entities.

- a method for committing the imports to the database.

In CubicWeb, we have four stores:

1. ``ObjectStore`` base class for the stores in CubicWeb.

   It only provides a skeleton for all other stores and

   provides the means for creating the memory structures

   (dictionaries) that hold the entities and the relations

   between them.

2. ``RQLObjectStore``: store which uses the RQL language for performing

   database insertions and updates. It relies on all the CubicWeb hooks 

   machinery, especially for dealing with security issues (database access

   permissions).

2. ``NoHookRQLObjectStore``: store which uses the RQL language for

   performing database insertions and updates, but for which 

   all hooks are deactivated. This implies that 

   certain checks with respect to the CubicWeb / Yams schema 

   (data model) are not performed. However, all SQL queries 

   obtained from the RQL ones are executed in a sequential

   manner, one query per inserted entity.

4. ``SQLGenObjectStore``: store which uses the SQL language directly. 

   It inserts entities either sequentially, by executing an SQL query 

   for each entity, or directly by using one PostGRES ``COPY FROM`` 

   query for a set of similarly structured entities. 

For really massive imports (millions or billions of entities), there

is a cube ``dataio`` which contains another store, called 

``MassiveObjectStore``. This store is similar to ``SQLGenObjectStore``,

except that anything related to CubicWeb is bypassed. That is, even the

CubicWeb EID entity identifiers are not handled. This store is the fastest,

but has a slightly different API from the other four stores mentioned above.

Moreover, it has an important limitation, in that it doesn't insert inlined [#]_

relations in the database. 

.. [#] An inlined relation is a relation defined in the schema

       with the keyword argument ``inlined=True``. Such a relation

       is inserted in the database as an attribute of the entity

       whose subject it is.

In the following section we will see how to import data by using the stores

in CubicWeb's ``dataimport`` module.

Using the stores in ``dataimport``

++++++++++++++++++++++++++++++++++

``ObjectStore`` is seldom used in real life for importing data, since it is

only the base store for the other stores and it doesn't perform an actual

import of the data. Nevertheless, the other three stores, which import data,

are based on ``ObjectStore`` and provide the same API.

All three stores ``RQLObjectStore``, ``NoHookRQLObjectStore`` and

``SQLGenObjectStore`` provide exactly the same API for importing data, that is

entities and relations, in an SQL database. 

Before using a store, one must import the ``dataimport`` module and then initialize 

the store, with the current ``session`` as a parameter::

    import cubicweb.dataimport as cwdi

    ...

    store = cwdi.RQLObjectStore(session)

Each such store provides three methods for data import:

#. ``create_entity(Etype, **attributes)``, which allows us to add

   an entity of the Yams type ``Etype`` to the database. This entity's attributes

   are specified in the ``attributes`` dictionary. The method returns the entity 

   created in the database. For example, we add two entities,

   a person, of ``Person`` type, and a location, of ``Location`` type::

        person = store.create_entity('Person', name='Toto', age='18', height='190')

        location = store.create_entity('Location', town='Paris', arrondissement='13')

#. ``relate(subject_eid, r_type, object_eid)``, which allows us to add a relation

   of the Yams type ``r_type`` to the database. The relation's subject is an entity

   whose EID is ``subject_eid``; its object is another entity, whose EID is 

   ``object_eid``.  For example [#]_::

        store.relate(person.eid(), 'lives_in', location.eid(), **kwargs)

   ``kwargs`` is only used by the ``SQLGenObjectStore``'s ``relate`` method and is here

   to allow us to specify the type of the subject of the relation, when the relation is

   defined as inlined in the schema. 

.. [#] The ``eid`` method of an entity defined via ``create_entity`` returns

       the entity identifier as assigned by CubicWeb when creating the entity.

       This only works for entities defined via the stores in the CubicWeb's

       ``dataimport`` module.

   ``subjtype`` and holds the type of the subject entity. For the example considered here,

   this comes to having [#]_::

        store.relate(person.eid(), 'lives_in', location.eid(), subjtype=person.cw_etype)

   If ``subjtype`` is not specified, then the store tries to infer the type of the subject.

   However, this doesn't always work, e.g. when there are several possible subject types

   for a given relation type. 

.. [#] The ``cw_etype`` attribute of an entity defined via ``create_entity`` holds

       the type of the entity just created. This only works for entities defined via

       the stores in the CubicWeb's ``dataimport`` module. In the example considered

       here, ``person.cw_etype`` holds ``'Person'``.

   All the other stores but ``SQLGenObjectStore`` ignore the ``kwargs`` parameters.

#. ``flush()``, which allows us to perform the actual commit into the database, along

   with some cleanup operations. Ideally, this method should be called as often as 

   possible, that is after each insertion in the database, so that database sessions

   are kept as atomic as possible. In practice, we usually call this method twice: 

   first, after all the entities have been created, second, after all relations have

   been created. 

   Note however that before each commit the database insertions

   have to be consistent with the schema. Thus, if, for instance,

   an entity has an attribute defined through a relation (viz.

   a ``SubjectRelation``) with a ``"1"`` or ``"+"`` object 

   cardinality, we have to create the entity under discussion,

   the object entity of the relation under discussion, and the

   relation itself, before committing the additions to the database.

   The ``flush`` method is simply called as::

        store.flush().

Using the ``MassiveObjectStore`` in the ``dataio`` cube

+++++++++++++++++++++++++++++++++++++++++++++++++++++++

This store, available in the ``dataio`` cube, allows us to

fully dispense with the CubicWeb import mechanisms and hence

to interact directly with the database server, via SQL queries.

Moreover, these queries rely on PostGreSQL's ``COPY FROM`` instruction

to create several entities in a single query. This brings tremendous 

performance improvements with respect to the RQL-based data insertion

procedures.

However, the API of this store is slightly different from the API of

the stores in CubicWeb's ``dataimport`` module.

Before using the store, one has to import the ``dataio`` cube's 

``dataimport`` module, then initialize the store by giving it the

``session`` parameter::

    from cubes.dataio import dataimport as mcwdi

    ...

    store = mcwdi.MassiveObjectStore(session)

The ``MassiveObjectStore`` provides six methods for inserting data

into the database:

#. ``init_rtype_table(SubjEtype, r_type, ObjEtype)``, which specifies the

   creation of the tables associated to the relation types in the database.

   Each such table has three column, the type of the subject entity, the

   type of the relation (that is, the name of the attribute in the subject

   entity which is defined via the relation), and the type of the object

   entity. For example::

        store.init_rtype_table('Person', 'lives_in', 'Location')

   Please note that these tables can be created before the entities, since

   they only specify their types, not their unique identifiers.

#. ``create_entity(Etype, **attributes)``, which allows us to add new entities,

   whose attributes are given in the ``attributes`` dictionary. 

   Please note however that, by default, this method does *not* return 

   the created entity. The method is called, for example, as in::

        store.create_entity('Person', name='Toto', age='18', height='190', 

                            uri='http://link/to/person/toto_18_190')

        store.create_entity('Location', town='Paris', arrondissement='13',

                            uri='http://link/to/location/paris_13')

   In order to be able to link these entities via the relations when needed,

   we must provide ourselves a means for uniquely identifying the entities.

   In general, this is done via URIs, stored in attributes like ``uri`` or

   ``cwuri``. The name of the attribute is irrelevant as long as its value is

   unique for each entity.

#. ``relate_by_iid(subject_iid, r_type, object_iid)`` allows us to actually 

   relate the entities uniquely identified by ``subject_iid`` and 

   ``object_iid`` via a relation of type ``r_type``. For example::

        store.relate_by_iid('http://link/to/person/toto_18_190',

                            'lives_in',

                            'http://link/to/location/paris_13')

   Please note that this method does *not* work for inlined relations!

#. ``convert_relations(SubjEtype, r_type, ObjEtype, subj_iid_attribute,

   obj_iid_attribute)``

   allows us to actually insert

   the relations in the database. At one call of this method, one inserts

   all the relations of type ``rtype`` between entities of given types.

   ``subj_iid_attribute`` and ``object_iid_attribute`` are the names

   of the attributes which store the unique identifiers of the entities,

   as assigned by the user. These names can be identical, as long as

   their values are unique. For example, for inserting all relations

   of type ``lives_in`` between ``People`` and ``Location`` entities,

   we write::

        store.convert_relations('Person', 'lives_in', 'Location', 'uri', 'uri')

#. ``flush()`` performs the actual commit in the database. It only needs 

   to be called after ``create_entity`` and ``relate_by_iid`` calls. 

   Please note that ``relate_by_iid`` does *not* perform insertions into

   the database, hence calling ``flush()`` for it would have no effect.

#. ``cleanup()`` performs database cleanups, by removing temporary tables.

   It should only be called at the end of the import.

.. XXX to add smth on the store's parameter initialization.

Application to the Diseasome data

+++++++++++++++++++++++++++++++++

Import setup

############

We define an import function, ``diseasome_import``, which does basically four things:

#. creates and initializes the store to be used, via a line such as::

        store = cwdi.SQLGenObjectStore(session)

   where ``cwdi`` is the imported ``cubicweb.dataimport`` or 

   ``cubes.dataio.dataimport``.

#. calls the diseasome parser, that is, the ``entities_from_rdf`` function in the 

   ``diseasome_parser`` module and iterates on its result, in a line such as::

        for entity, relations in parser.entities_from_rdf(filename, ('gene', 'disease')):

   where ``parser`` is the imported ``diseasome_parser`` module, and ``filename`` is the 

   name of the file containing the data (with its path), e.g. ``../data/diseasome_dump.nt``.

#. creates the entities to be inserted in the database; for Diseasome, there are two 

   kinds of entities:

   #. entities defined in the data model, viz. ``Gene`` and ``Disease`` in our case.

   #. entities which are built in CubicWeb / Yams, viz. ``ExternalUri`` which define

      URIs.

   As we are working with RDF data, each entity is defined through a series of URIs. Hence,

   each "relational attribute" [#]_ of an entity is defined via an URI, that is, in CubicWeb

   terms, via an ``ExternalUri`` entity. The entities are created, in the loop presented above,

   as such::

        ent = store.create_entity(etype, **entity)

   where ``etype`` is the appropriate entity type, either ``Gene`` or ``Disease``.

.. [#] By "relational attribute" we denote an attribute (of an entity) which

       is defined through a relation, e.g. the ``chromosomal_location`` attribute

       of ``Disease`` entities, which is defined through a relation between a

       ``Disease`` and an ``ExternalUri``.

   The ``ExternalUri`` entities are as many as URIs in the data file. For them, we define a unique

   attribute, ``uri``, which holds the URI under discussion::

        extu = store.create_entity('ExternalUri', uri="http://path/of/the/uri")

#. creates the relations between the entities. We have relations between:

   #. entities defined in the schema, e.g. between ``Disease`` and ``Gene``

      entities, such as the ``associated_genes`` relation defined for 

      ``Disease`` entities.

   #. entities defined in the schema and ``ExternalUri`` entities, such as ``gene_id``.

   The way relations are added to the database depends on the store: 

   - for the stores in the CubicWeb ``dataimport`` module, we only use 

     ``store.relate``, in 

     another loop, on the relations (that is, a 

     loop inside the preceding one, mentioned at step 2)::

        for rtype, rels in relations.iteritems():

            ...

            store.relate(ent.eid(), rtype, extu.eid(), **kwargs)

     where ``kwargs`` is a dictionary designed to accommodate the need for specifying

     the type of the subject entity of the relation, when the relation is inlined and

     ``SQLGenObjectStore`` is used. For example::

            ...

            store.relate(ent.eid(), 'chromosomal_location', extu.eid(), subjtype='Disease')

   - for the ``MassiveObjectStore`` in the ``dataio`` cube's ``dataimport`` module,