doc/tutorials/dataimport/index.rst
author Rémi Cardona <remi.cardona@logilab.fr>
Mon, 21 Sep 2015 18:28:10 +0200
changeset 10723 c5bedfdd1b22
parent 10496 e95b559a06a2
child 12556 d1c659d70368
permissions -rw-r--r--
[py3k] Don't encode URLs Python 3's urllib works with unicode objects.
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
8836
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     1
Importing relational data into a CubicWeb instance
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     2
==================================================
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     3
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     4
Introduction
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     5
~~~~~~~~~~~~
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     6
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     7
This tutorial explains how to import data from an external source (e.g. a collection of files) 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     8
into a CubicWeb cube instance.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
     9
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    10
First, once we know the format of the data we wish to import, we devise a 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    11
*data model*, that is, a CubicWeb (Yams) schema which reflects the way the data
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    12
is structured. This schema is implemented in the ``schema.py`` file.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    13
In this tutorial, we will describe such a schema for a particular data set, 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    14
the Diseasome data (see below).
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    15
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    16
Once the schema is defined, we create a cube and an instance. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    17
The cube is a specification of an application, whereas an instance 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    18
is the application per se. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    19
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    20
Once the schema is defined and the instance is created, the import can be performed, via
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    21
the following steps:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    22
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    23
1. Build a custom parser for the data to be imported. Thus, one obtains a Python
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    24
   memory representation of the data.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    25
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    26
2. Map the parsed data to the data model defined in ``schema.py``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    27
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    28
3. Perform the actual import of the data. This comes down to "populating"
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    29
   the data model with the memory representation obtained at 1, according to
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    30
   the mapping defined at 2.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    31
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    32
This tutorial illustrates all the above steps in the context of relational data
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    33
stored in the RDF format.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    34
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    35
More specifically, we describe the import of Diseasome_ RDF/OWL data.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    36
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    37
.. _Diseasome: http://datahub.io/dataset/fu-berlin-diseasome
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    38
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    39
Building a data model
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    40
~~~~~~~~~~~~~~~~~~~~~
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    41
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    42
The first thing to do when using CubicWeb for creating an application from scratch
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    43
is to devise a *data model*, that is, a relational representation of the problem to be
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    44
modeled or of the structure of the data to be imported. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    45
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    46
In such a schema, we define
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    47
an entity type (``EntityType`` objects) for each type of entity to import. Each such type
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    48
has several attributes. If the attributes are of known CubicWeb (Yams) types, viz. numbers,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    49
strings or characters, then they are defined as attributes, as e.g. ``attribute = Int()``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    50
for an attribute named ``attribute`` which is an integer. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    51
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    52
Each such type also has a set of
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    53
relations, which are defined like the attributes, except that they represent, in fact,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    54
relations between the entities of the type under discussion and the objects of a type which
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    55
is specified in the relation definition. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    56
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    57
For example, for the Diseasome data, we have two types of entities, genes and diseases.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    58
Thus, we create two classes which inherit from ``EntityType``::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    59
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    60
    class Disease(EntityType):
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    61
        # Corresponds to http://www.w3.org/2000/01/rdf-schema#label
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    62
        label = String(maxsize=512, fulltextindexed=True)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    63
        ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    64
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    65
        #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/associatedGene
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    66
        associated_genes = SubjectRelation('Gene', cardinality='**')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    67
        ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    68
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    69
        #Corresponds to 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/chromosomalLocation'
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    70
        chromosomal_location = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    71
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    72
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    73
    class Gene(EntityType):
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    74
        ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    75
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    76
In this schema, there are attributes whose values are numbers or strings. Thus, they are 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    77
defined by using the CubicWeb / Yams primitive types, e.g., ``label = String(maxsize=12)``. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    78
These types can have several constraints or attributes, such as ``maxsize``. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    79
There are also relations, either between the entity types themselves, or between them
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    80
and a CubicWeb type, ``ExternalUri``. The latter defines a class of URI objects in 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    81
CubicWeb. For instance, the ``chromosomal_location`` attribute is a relation between 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    82
a ``Disease`` entity and an ``ExternalUri`` entity. The relation is marked by the CubicWeb /
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    83
Yams ``SubjectRelation`` method. The latter can have several optional keyword arguments, such as
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    84
``cardinality`` which specifies the number of subjects and objects related by the relation type 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    85
specified. For example, the ``'?*'`` cardinality in the ``chromosomal_relation`` relation type says
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    86
that zero or more ``Disease`` entities are related to zero or one ``ExternalUri`` entities.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    87
In other words, a ``Disease`` entity is related to at most one ``ExternalUri`` entity via the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    88
``chromosomal_location`` relation type, and that we can have zero or more ``Disease`` entities in the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    89
data base. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    90
For a relation between the entity types themselves, the ``associated_genes`` between a ``Disease``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    91
entity and a ``Gene`` entity is defined, so that any number of ``Gene`` entities can be associated
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    92
to a ``Disease``, and there can be any number of ``Disease`` s if a ``Gene`` exists.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    93
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    94
Of course, before being able to use the CubicWeb / Yams built-in objects, we need to import them::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    95
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    96
    
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    97
    from yams.buildobjs import EntityType, SubjectRelation, String, Int
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    98
    from cubicweb.schemas.base import ExternalUri
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
    99
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   100
Building a custom data parser
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   101
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   102
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   103
The data we wish to import is structured in the RDF format,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   104
as a text file containing a set of lines. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   105
On each line, there are three fields. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   106
The first two fields are URIs ("Universal Resource Identifiers"). 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   107
The third field is either an URI or a string. Each field bares a particular meaning:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   108
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   109
- the leftmost field is an URI that holds the entity to be imported. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   110
  Note that the entities defined in the data model (i.e., in ``schema.py``) should 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   111
  correspond to the entities whose URIs are specified in the import file.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   112
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   113
- the middle field is an URI that holds a relation whose subject is the  entity 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   114
  defined by the leftmost field. Note that this should also correspond
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   115
  to the definitions in the data model.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   116
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   117
- the rightmost field is either an URI or a string. When this field is an URI, 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   118
  it gives the object of the relation defined by the middle field.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   119
  When the rightmost field is a string, the middle field is interpreted as an attribute
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   120
  of the subject (introduced by the leftmost field) and the rightmost field is
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   121
  interpreted as the value of the attribute.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   122
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   123
Note however that some attributes (i.e. relations whose objects are strings) 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   124
have their objects defined as strings followed by ``^^`` and by another URI;
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   125
we ignore this part.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   126
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   127
Let us show some examples:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   128
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   129
- of line holding an attribute definition:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   130
  ``<http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/CYP17A1> 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   131
  <http://www.w3.org/2000/01/rdf-schema#label> "CYP17A1" .``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   132
  The line contains the definition of the ``label`` attribute of an
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   133
  entity of type ``gene``. The value of ``label`` is '``CYP17A1``'.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   134
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   135
- of line holding a relation definition:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   136
  ``<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseases/1> 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   137
  <http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/associatedGene> 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   138
  <http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/HADH2> .``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   139
  The line contains the definition of the ``associatedGene`` relation between
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   140
  a ``disease`` subject entity identified by ``1`` and a ``gene`` object 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   141
  entity defined by ``HADH2``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   142
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   143
Thus, for parsing the data, we can (:note: see the ``diseasome_parser`` module):
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   144
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   145
1. define a couple of regular expressions for parsing the two kinds of lines, 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   146
   ``RE_ATTS`` for parsing the attribute definitions, and ``RE_RELS`` for parsing
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   147
   the relation definitions.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   148
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   149
2. define a function that iterates through the lines of the file and retrieves
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   150
   (``yield`` s) a (subject, relation, object) tuple for each line.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   151
   We called it ``_retrieve_structure`` in the ``diseasome_parser`` module.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   152
   The function needs the file name and the types for which information
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   153
   should be retrieved.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   154
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   155
Alternatively, instead of hand-making the parser, one could use the RDF parser provided
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   156
in the ``dataio`` cube.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   157
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   158
.. XXX To further study and detail the ``dataio`` cube usage.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   159
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   160
Once we get to have the (subject, relation, object) triples, we need to map them into
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   161
the data model.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   162
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   163
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   164
Mapping the data to the schema
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   165
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   166
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   167
In the case of diseasome data, we can just define two dictionaries for mapping
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   168
the names of the relations as extracted by the parser, to the names of the relations
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   169
as defined in the ``schema.py`` data model. In the ``diseasome_parser`` module 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   170
they are called ``MAPPING_ATTS`` and ``MAPPING_RELS``. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   171
Given that the relation and attribute names are given in CamelCase in the original data,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   172
mappings are necessary if we follow the PEP08 when naming the attributes in the data model.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   173
For example, the RDF relation ``chromosomalLocation`` is mapped into the schema relation 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   174
``chromosomal_location``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   175
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   176
Once these mappings have been defined, we just iterate over the (subject, relation, object)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   177
tuples provided by the parser and we extract the entities, with their attributes and relations.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   178
For each entity, we thus have a dictionary with two keys, ``attributes`` and ``relations``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   179
The value associated to the ``attributes`` key is a dictionary containing (attribute: value) 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   180
pairs, where "value" is a string, plus the ``cwuri`` key / attribute holding the URI of 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   181
the entity itself.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   182
The value associated to the ``relations`` key is a dictionary containing (relation: value)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   183
pairs, where "value" is an URI.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   184
This is implemented in the ``entities_from_rdf`` interface function of the module 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   185
``diseasome_parser``. This function provides an iterator on the dictionaries containing
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   186
the ``attributes`` and ``relations`` keys for all entities.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   187
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   188
However, this is a simple case. In real life, things can get much more complicated, and the 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   189
mapping can be far from trivial, especially when several data sources (which can follow 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   190
different formatting and even structuring conventions) must be mapped into the same data model.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   191
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   192
Importing the data
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   193
~~~~~~~~~~~~~~~~~~
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   194
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   195
The data import code should be placed in a Python module. Let us call it 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   196
``diseasome_import.py``. Then, this module should be called via
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   197
``cubicweb-ctl``, as follows::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   198
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   199
    cubicweb-ctl shell diseasome_import.py -- <other arguments e.g. data file>
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   200
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   201
In the import module, we should use a *store* for doing the import.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   202
A store is an object which provides three kinds of methods for
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   203
importing data:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   204
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   205
- a method for importing the entities, along with the values
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   206
  of their attributes.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   207
- a method for importing the relations between the entities.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   208
- a method for committing the imports to the database.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   209
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   210
In CubicWeb, we have four stores:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   211
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   212
1. ``ObjectStore`` base class for the stores in CubicWeb.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   213
   It only provides a skeleton for all other stores and
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   214
   provides the means for creating the memory structures
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   215
   (dictionaries) that hold the entities and the relations
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   216
   between them.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   217
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   218
2. ``RQLObjectStore``: store which uses the RQL language for performing
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   219
   database insertions and updates. It relies on all the CubicWeb hooks 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   220
   machinery, especially for dealing with security issues (database access
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   221
   permissions).
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   222
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   223
2. ``NoHookRQLObjectStore``: store which uses the RQL language for
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   224
   performing database insertions and updates, but for which 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   225
   all hooks are deactivated. This implies that 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   226
   certain checks with respect to the CubicWeb / Yams schema 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   227
   (data model) are not performed. However, all SQL queries 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   228
   obtained from the RQL ones are executed in a sequential
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   229
   manner, one query per inserted entity.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   230
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   231
4. ``SQLGenObjectStore``: store which uses the SQL language directly. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   232
   It inserts entities either sequentially, by executing an SQL query 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   233
   for each entity, or directly by using one PostGRES ``COPY FROM`` 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   234
   query for a set of similarly structured entities. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   235
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   236
For really massive imports (millions or billions of entities), there
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   237
is a cube ``dataio`` which contains another store, called 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   238
``MassiveObjectStore``. This store is similar to ``SQLGenObjectStore``,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   239
except that anything related to CubicWeb is bypassed. That is, even the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   240
CubicWeb EID entity identifiers are not handled. This store is the fastest,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   241
but has a slightly different API from the other four stores mentioned above.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   242
Moreover, it has an important limitation, in that it doesn't insert inlined [#]_
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   243
relations in the database. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   244
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   245
.. [#] An inlined relation is a relation defined in the schema
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   246
       with the keyword argument ``inlined=True``. Such a relation
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   247
       is inserted in the database as an attribute of the entity
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   248
       whose subject it is.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   249
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   250
In the following section we will see how to import data by using the stores
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   251
in CubicWeb's ``dataimport`` module.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   252
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   253
Using the stores in ``dataimport``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   254
++++++++++++++++++++++++++++++++++
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   255
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   256
``ObjectStore`` is seldom used in real life for importing data, since it is
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   257
only the base store for the other stores and it doesn't perform an actual
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   258
import of the data. Nevertheless, the other three stores, which import data,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   259
are based on ``ObjectStore`` and provide the same API.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   260
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   261
All three stores ``RQLObjectStore``, ``NoHookRQLObjectStore`` and
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   262
``SQLGenObjectStore`` provide exactly the same API for importing data, that is
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   263
entities and relations, in an SQL database. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   264
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   265
Before using a store, one must import the ``dataimport`` module and then initialize 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   266
the store, with the current ``session`` as a parameter::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   267
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   268
    import cubicweb.dataimport as cwdi
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   269
    ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   270
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   271
    store = cwdi.RQLObjectStore(session)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   272
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   273
Each such store provides three methods for data import:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   274
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   275
#. ``create_entity(Etype, **attributes)``, which allows us to add
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   276
   an entity of the Yams type ``Etype`` to the database. This entity's attributes
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   277
   are specified in the ``attributes`` dictionary. The method returns the entity 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   278
   created in the database. For example, we add two entities,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   279
   a person, of ``Person`` type, and a location, of ``Location`` type::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   280
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   281
        person = store.create_entity('Person', name='Toto', age='18', height='190')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   282
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   283
        location = store.create_entity('Location', town='Paris', arrondissement='13')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   284
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   285
#. ``relate(subject_eid, r_type, object_eid)``, which allows us to add a relation
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   286
   of the Yams type ``r_type`` to the database. The relation's subject is an entity
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   287
   whose EID is ``subject_eid``; its object is another entity, whose EID is 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   288
   ``object_eid``.  For example [#]_::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   289
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   290
        store.relate(person.eid(), 'lives_in', location.eid(), **kwargs)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   291
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   292
   ``kwargs`` is only used by the ``SQLGenObjectStore``'s ``relate`` method and is here
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   293
   to allow us to specify the type of the subject of the relation, when the relation is
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   294
   defined as inlined in the schema. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   295
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   296
.. [#] The ``eid`` method of an entity defined via ``create_entity`` returns
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   297
       the entity identifier as assigned by CubicWeb when creating the entity.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   298
       This only works for entities defined via the stores in the CubicWeb's
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   299
       ``dataimport`` module.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   300
10496
e95b559a06a2 [doc] more fixes of warnings/errors in doc build
David Douard <david.douard@logilab.fr>
parents: 8927
diff changeset
   301
   The keyword argument that is understood by ``SQLGenObjectStore`` is called 
8836
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   302
   ``subjtype`` and holds the type of the subject entity. For the example considered here,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   303
   this comes to having [#]_::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   304
8927
885dea8f16a0 [cubicweb/doc] Replace dc_type() by cw_etype
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents: 8836
diff changeset
   305
        store.relate(person.eid(), 'lives_in', location.eid(), subjtype=person.cw_etype)
8836
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   306
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   307
   If ``subjtype`` is not specified, then the store tries to infer the type of the subject.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   308
   However, this doesn't always work, e.g. when there are several possible subject types
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   309
   for a given relation type. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   310
8927
885dea8f16a0 [cubicweb/doc] Replace dc_type() by cw_etype
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents: 8836
diff changeset
   311
.. [#] The ``cw_etype`` attribute of an entity defined via ``create_entity`` holds
8836
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   312
       the type of the entity just created. This only works for entities defined via
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   313
       the stores in the CubicWeb's ``dataimport`` module. In the example considered
8927
885dea8f16a0 [cubicweb/doc] Replace dc_type() by cw_etype
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents: 8836
diff changeset
   314
       here, ``person.cw_etype`` holds ``'Person'``.
8836
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   315
    
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   316
   All the other stores but ``SQLGenObjectStore`` ignore the ``kwargs`` parameters.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   317
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   318
#. ``flush()``, which allows us to perform the actual commit into the database, along
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   319
   with some cleanup operations. Ideally, this method should be called as often as 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   320
   possible, that is after each insertion in the database, so that database sessions
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   321
   are kept as atomic as possible. In practice, we usually call this method twice: 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   322
   first, after all the entities have been created, second, after all relations have
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   323
   been created. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   324
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   325
   Note however that before each commit the database insertions
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   326
   have to be consistent with the schema. Thus, if, for instance,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   327
   an entity has an attribute defined through a relation (viz.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   328
   a ``SubjectRelation``) with a ``"1"`` or ``"+"`` object 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   329
   cardinality, we have to create the entity under discussion,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   330
   the object entity of the relation under discussion, and the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   331
   relation itself, before committing the additions to the database.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   332
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   333
   The ``flush`` method is simply called as::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   334
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   335
        store.flush().
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   336
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   337
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   338
Using the ``MassiveObjectStore`` in the ``dataio`` cube
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   339
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   340
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   341
This store, available in the ``dataio`` cube, allows us to
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   342
fully dispense with the CubicWeb import mechanisms and hence
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   343
to interact directly with the database server, via SQL queries.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   344
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   345
Moreover, these queries rely on PostGreSQL's ``COPY FROM`` instruction
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   346
to create several entities in a single query. This brings tremendous 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   347
performance improvements with respect to the RQL-based data insertion
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   348
procedures.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   349
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   350
However, the API of this store is slightly different from the API of
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   351
the stores in CubicWeb's ``dataimport`` module.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   352
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   353
Before using the store, one has to import the ``dataio`` cube's 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   354
``dataimport`` module, then initialize the store by giving it the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   355
``session`` parameter::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   356
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   357
    from cubes.dataio import dataimport as mcwdi
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   358
    ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   359
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   360
    store = mcwdi.MassiveObjectStore(session)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   361
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   362
The ``MassiveObjectStore`` provides six methods for inserting data
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   363
into the database:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   364
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   365
#. ``init_rtype_table(SubjEtype, r_type, ObjEtype)``, which specifies the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   366
   creation of the tables associated to the relation types in the database.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   367
   Each such table has three column, the type of the subject entity, the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   368
   type of the relation (that is, the name of the attribute in the subject
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   369
   entity which is defined via the relation), and the type of the object
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   370
   entity. For example::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   371
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   372
        store.init_rtype_table('Person', 'lives_in', 'Location')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   373
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   374
   Please note that these tables can be created before the entities, since
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   375
   they only specify their types, not their unique identifiers.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   376
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   377
#. ``create_entity(Etype, **attributes)``, which allows us to add new entities,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   378
   whose attributes are given in the ``attributes`` dictionary. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   379
   Please note however that, by default, this method does *not* return 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   380
   the created entity. The method is called, for example, as in::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   381
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   382
        store.create_entity('Person', name='Toto', age='18', height='190', 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   383
                            uri='http://link/to/person/toto_18_190')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   384
        store.create_entity('Location', town='Paris', arrondissement='13',
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   385
                            uri='http://link/to/location/paris_13')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   386
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   387
   In order to be able to link these entities via the relations when needed,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   388
   we must provide ourselves a means for uniquely identifying the entities.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   389
   In general, this is done via URIs, stored in attributes like ``uri`` or
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   390
   ``cwuri``. The name of the attribute is irrelevant as long as its value is
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   391
   unique for each entity.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   392
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   393
#. ``relate_by_iid(subject_iid, r_type, object_iid)`` allows us to actually 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   394
   relate the entities uniquely identified by ``subject_iid`` and 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   395
   ``object_iid`` via a relation of type ``r_type``. For example::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   396
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   397
        store.relate_by_iid('http://link/to/person/toto_18_190',
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   398
                            'lives_in',
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   399
                            'http://link/to/location/paris_13')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   400
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   401
   Please note that this method does *not* work for inlined relations!
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   402
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   403
#. ``convert_relations(SubjEtype, r_type, ObjEtype, subj_iid_attribute,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   404
   obj_iid_attribute)``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   405
   allows us to actually insert
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   406
   the relations in the database. At one call of this method, one inserts
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   407
   all the relations of type ``rtype`` between entities of given types.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   408
   ``subj_iid_attribute`` and ``object_iid_attribute`` are the names
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   409
   of the attributes which store the unique identifiers of the entities,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   410
   as assigned by the user. These names can be identical, as long as
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   411
   their values are unique. For example, for inserting all relations
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   412
   of type ``lives_in`` between ``People`` and ``Location`` entities,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   413
   we write::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   414
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   415
        store.convert_relations('Person', 'lives_in', 'Location', 'uri', 'uri')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   416
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   417
#. ``flush()`` performs the actual commit in the database. It only needs 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   418
   to be called after ``create_entity`` and ``relate_by_iid`` calls. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   419
   Please note that ``relate_by_iid`` does *not* perform insertions into
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   420
   the database, hence calling ``flush()`` for it would have no effect.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   421
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   422
#. ``cleanup()`` performs database cleanups, by removing temporary tables.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   423
   It should only be called at the end of the import.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   424
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   425
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   426
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   427
.. XXX to add smth on the store's parameter initialization.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   428
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   429
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   430
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   431
Application to the Diseasome data
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   432
+++++++++++++++++++++++++++++++++
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   433
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   434
Import setup
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   435
############
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   436
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   437
We define an import function, ``diseasome_import``, which does basically four things:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   438
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   439
#. creates and initializes the store to be used, via a line such as::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   440
    
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   441
        store = cwdi.SQLGenObjectStore(session)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   442
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   443
   where ``cwdi`` is the imported ``cubicweb.dataimport`` or 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   444
   ``cubes.dataio.dataimport``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   445
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   446
#. calls the diseasome parser, that is, the ``entities_from_rdf`` function in the 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   447
   ``diseasome_parser`` module and iterates on its result, in a line such as::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   448
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   449
        for entity, relations in parser.entities_from_rdf(filename, ('gene', 'disease')):
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   450
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   451
   where ``parser`` is the imported ``diseasome_parser`` module, and ``filename`` is the 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   452
   name of the file containing the data (with its path), e.g. ``../data/diseasome_dump.nt``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   453
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   454
#. creates the entities to be inserted in the database; for Diseasome, there are two 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   455
   kinds of entities:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   456
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   457
   #. entities defined in the data model, viz. ``Gene`` and ``Disease`` in our case.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   458
   #. entities which are built in CubicWeb / Yams, viz. ``ExternalUri`` which define
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   459
      URIs.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   460
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   461
   As we are working with RDF data, each entity is defined through a series of URIs. Hence,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   462
   each "relational attribute" [#]_ of an entity is defined via an URI, that is, in CubicWeb
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   463
   terms, via an ``ExternalUri`` entity. The entities are created, in the loop presented above,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   464
   as such::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   465
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   466
        ent = store.create_entity(etype, **entity)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   467
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   468
   where ``etype`` is the appropriate entity type, either ``Gene`` or ``Disease``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   469
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   470
.. [#] By "relational attribute" we denote an attribute (of an entity) which
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   471
       is defined through a relation, e.g. the ``chromosomal_location`` attribute
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   472
       of ``Disease`` entities, which is defined through a relation between a
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   473
       ``Disease`` and an ``ExternalUri``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   474
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   475
   The ``ExternalUri`` entities are as many as URIs in the data file. For them, we define a unique
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   476
   attribute, ``uri``, which holds the URI under discussion::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   477
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   478
        extu = store.create_entity('ExternalUri', uri="http://path/of/the/uri")
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   479
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   480
#. creates the relations between the entities. We have relations between:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   481
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   482
   #. entities defined in the schema, e.g. between ``Disease`` and ``Gene``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   483
      entities, such as the ``associated_genes`` relation defined for 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   484
      ``Disease`` entities.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   485
   #. entities defined in the schema and ``ExternalUri`` entities, such as ``gene_id``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   486
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   487
   The way relations are added to the database depends on the store: 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   488
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   489
   - for the stores in the CubicWeb ``dataimport`` module, we only use 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   490
     ``store.relate``, in 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   491
     another loop, on the relations (that is, a 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   492
     loop inside the preceding one, mentioned at step 2)::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   493
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   494
        for rtype, rels in relations.iteritems():
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   495
            ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   496
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   497
            store.relate(ent.eid(), rtype, extu.eid(), **kwargs)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   498
        
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   499
     where ``kwargs`` is a dictionary designed to accommodate the need for specifying
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   500
     the type of the subject entity of the relation, when the relation is inlined and
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   501
     ``SQLGenObjectStore`` is used. For example::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   502
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   503
            ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   504
            store.relate(ent.eid(), 'chromosomal_location', extu.eid(), subjtype='Disease')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   505
   
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   506
   - for the ``MassiveObjectStore`` in the ``dataio`` cube's ``dataimport`` module, 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   507
     the relations are created in three steps:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   508
     
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   509
     #. first, a table is created for each relation type, as in::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   510
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   511
            ...
8927
885dea8f16a0 [cubicweb/doc] Replace dc_type() by cw_etype
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents: 8836
diff changeset
   512
            store.init_rtype_table(ent.cw_etype, rtype, extu.cw_etype)
8836
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   513
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   514
        which comes down to lines such as::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   515
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   516
            store.init_rtype_table('Disease', 'associated_genes', 'Gene')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   517
            store.init_rtype_table('Gene', 'gene_id', 'ExternalUri')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   518
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   519
     #. second, the URI of each entity will be used as its identifier, in the 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   520
        ``relate_by_iid`` method, such as::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   521
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   522
            disease_uri = 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseases/3'
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   523
            gene_uri = '<http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/HSD3B2'
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   524
            store.relate_by_iid(disease_uri, 'associated_genes', gene_uri)
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   525
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   526
     #. third, the relations for each relation type will be added to the database, 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   527
        via the ``convert_relations`` method, such as in::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   528
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   529
            store.convert_relations('Disease', 'associated_genes', 'Gene', 'cwuri', 'cwuri')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   530
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   531
        and::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   532
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   533
            store.convert_relations('Gene', 'hgnc_id', 'ExternalUri', 'cwuri', 'uri')
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   534
            
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   535
        where ``cwuri`` and ``uri`` are the attributes which store the URIs of the entities
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   536
        defined in the data model, and of the ``ExternalUri`` entities, respectively.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   537
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   538
#. flushes all relations and entities::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   539
    
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   540
    store.flush()
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   541
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   542
   which performs the actual commit of the inserted entities and relations in the database.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   543
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   544
If the ``MassiveObjectStore`` is used, then a cleanup of temporary SQL tables should be performed
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   545
at the end of the import::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   546
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   547
    store.cleanup()
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   548
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   549
Timing benchmarks
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   550
#################
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   551
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   552
In order to time the import script, we just decorate the import function with the ``timed``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   553
decorator::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   554
    
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   555
    from logilab.common.decorators import timed
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   556
    ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   557
    
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   558
    @timed
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   559
    def diseasome_import(session, filename):
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   560
        ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   561
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   562
After running the import function as shown in the "Importing the data" section, we obtain two time measurements::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   563
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   564
    diseasome_import clock: ... / time: ...
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   565
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   566
Here, the meanings of these measurements are [#]_:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   567
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   568
- ``clock`` is the time spent by CubicWeb, on the server side (i.e. hooks and data pre- / post-processing on SQL 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   569
  queries),
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   570
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   571
- ``time`` is the sum between ``clock`` and the time spent in PostGreSQL.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   572
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   573
.. [#] The meanings of the ``clock`` and ``time`` measurements, when using the ``@timed``
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   574
       decorators, were taken from `a blog post on massive data import in CubicWeb`_.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   575
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   576
.. _a blog post on massive data import in CubicWeb: http://www.cubicweb.org/blogentry/2116712
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   577
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   578
The import function is put in an import module, named ``diseasome_import`` here. The module is called
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   579
directly from the CubicWeb shell, as follows::
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   580
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   581
    cubicweb-ctl shell diseasome_instance diseasome_import.py \
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   582
    -- -df diseasome_import_file.nt -st StoreName
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   583
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   584
The module accepts two arguments:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   585
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   586
- the data file, introduced by ``-df [--datafile]``, and
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   587
- the store, introduced by ``-st [--store]``.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   588
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   589
The timings (in seconds) for different stores are given in the following table, for 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   590
importing 4213 ``Disease`` entities and 3919 ``Gene`` entities with the import module
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   591
just described:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   592
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   593
+--------------------------+------------------------+--------------------------------+------------+
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   594
| Store                    | CubicWeb time (clock)  | PostGreSQL time (time - clock) | Total time |
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   595
+==========================+========================+================================+============+
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   596
| ``RQLObjectStore``       | 225.98                 | 62.05                          | 288.03     |
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   597
+--------------------------+------------------------+--------------------------------+------------+
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   598
| ``NoHookRQLObjectStore`` | 62.73                  | 51.38                          | 114.11     |
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   599
+--------------------------+------------------------+--------------------------------+------------+
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   600
| ``SQLGenObjectStore``    | 20.41                  | 11.03                          | 31.44      |
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   601
+--------------------------+------------------------+--------------------------------+------------+
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   602
| ``MassiveObjectStore``   | 4.84                   | 6.93                           | 11.77      |
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   603
+--------------------------+------------------------+--------------------------------+------------+
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   604
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   605
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   606
Conclusions
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   607
~~~~~~~~~~~
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   608
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   609
In this tutorial we have seen how to import data in a CubicWeb application instance. We have first seen how to
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   610
create a schema, then how to create a parser of the data and a mapping of the data to the schema.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   611
Finally, we have seen four ways of importing data into CubicWeb.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   612
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   613
Three of those are integrated into CubicWeb, namely the ``RQLObjectStore``, ``NoHookRQLObjectStore`` and
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   614
``SQLGenObjectStore`` stores, which have a common API:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   615
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   616
- ``RQLObjectStore`` is by far the slowest, especially its time spent on the 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   617
  CubicWeb side, and so it should be used only for small amounts of 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   618
  "sensitive" data (i.e. where security is a concern).
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   619
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   620
- ``NoHookRQLObjectStore`` slashes by almost four the time spent on the CubicWeb side, 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   621
  but is also quite slow; on the PostGres side it is as slow as the previous store. 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   622
  It should be used for data where security is not a concern,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   623
  but consistency (with the data model) is.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   624
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   625
- ``SQLGenObjectStore`` slashes by three the time spent on the CubicWeb side and by five the time 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   626
  spent on the PostGreSQL side. It should be used for relatively great amounts of data, where
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   627
  security and data consistency are not a concern. Compared to the previous store, it has the
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   628
  disadvantage that, for inlined relations, we must specify their subjects' types.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   629
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   630
For really huge amounts of data there is a fourth store, ``MassiveObjectStore``, available
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   631
from the ``dataio`` cube. It provides a blazing performance with respect to all other stores:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   632
it is almost 25 times faster than ``RQLObjectStore`` and almost three times faster than 
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   633
``SQLGenObjectStore``. However, it has a few usage caveats that should be taken into account:
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   634
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   635
#. it cannot insert relations defined as inlined in the schema,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   636
#. no security or consistency check is performed on the data,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   637
#. its API is slightly different from the other stores.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   638
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   639
Hence, this store should be used when security and data consistency are not a concern,
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   640
and there are no inlined relations in the schema.
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   641
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   642
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   643
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   644
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   645
8a57802d40d3 [cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff changeset
   646