odML Tutorial

Author:Lyuba Zehl; based on work by Hagen Fritsch
Release:1.4
License:Creative Commons Attribution-ShareAlike 4.0 International License

odML (open metadata Markup Language)

odML (open metadata Markup Language) is a framework, proposed by Grewe et al. (2011), to organize and store experimental metadata in a human- and machine-readable, XML based format (odml). In this tutorial we will illustrate the conceptual design of the odML framework and show hands-on how you can generate your own odML metadata file collection. A well organized metadata management of your experiment is a key component to guarantee the reproducibility of your research and facilitate the provenance tracking of your analysis projects.

What are metadata and why are they needed?

Metadata are data about data. They describe the conditions under which the actual raw-data of an experimental study were acquired. The organization of such metadata and their accessibility may sound like a trivial task, and most laboratories developed their home-made solutions to keep track of their metadata. Most of these solutions, however, break down if data and metadata need to be shared within a collaboration, because implicit knowledge of what is important and how it is organized is often underestimated.

While maintaining the relation to the actual raw-data, odML can help to collect all metadata which are usually distributed over several files and formats, and to store them unitedly which facilitates sharing data and metadata.

Key features of odML
  • open, XML based language, to collect, store and share metadata
  • Machine- and human-readable
  • Python-odML library
  • Interactive odML-Editor

Structure of this tutorial

The scientific background of the possible user community of odML varies enormously (e.g. physics, informatics, mathematics, biology, medicine, psychology). Some users will be trained programmers, others probably have never learned a programming language.

To cover the different demands of all users, we provide a slow introduction to the odML framework that even allows programming beginners to learn the basic concepts. We will demonstrate how to generate an odML file and present more advanced possibilities of the Python-odML library (e.g., how to search for certain metadata or how to integrate existing terminologies).

At the end of this tutorial we will provide a few guidelines that will help you to create an odML file structure that is optimised for your individual experimental project and complements the special needs of your laboratory.

The code for the example odML files, which we use within this tutorial is part of the documentation package (see doc/example_odMLs/).

A summary of available odML terminologies and templates can be found at the G-Node odML terminology and odML template pages.


Download and Installation

The odML framework is an open source project of the German Neuroinformatics Node (G-Node, odML project website) of the International Neuroinformatics Coordination Facility (INCF). The source code for the Python-odML library is available on GitHub under the project name python-odml.

Dependencies

The Python-odML library (version 1.4+) runs under Python 3.6+.

Additionally, the Python-odML library depends on the lxml, pyyaml and rdflib python packages.

When the odML-Python library is installed via pip or the setup.py, these packages will be automatically downloaded and installed. Alternatively, they can be installed from the OS package manager.

On Ubuntu, the dependency packages are available as python-lxml, python-yaml and python-rdflib.

Note that on Ubuntu 14.04, the latter package additionally requires the installation of libxml2-dev, libxslt1-dev, and lib32z1-dev.

Python 2 has reached end of life. We will not keep any future versions of odml Python 2 compatible and also recommend using a Python version >= 3.6. If a Python version < 3.6 is a requirement, the following dependency needs to be installed as well:

The enum34 package with a pip installation or python-enum using the OS package manager.

Installation…

… via pip:

The simplest way to install the Python-odML library is from PyPI using pip:

$ pip install odml

The appropriate Python dependencies will be automatically downloaded and installed.

If you are not familiar with PyPI and pip, please have a look at the available online documentation.

… from source:

To download the Python-odML library please either use git and clone the repository from GitHub:

$ cd /home/usr/toolbox/
$ git clone https://github.com/G-Node/python-odml.git

… or if you don’t want to use git, download the ZIP file also provided on GitHub to your computer (e.g. as above on your home directory under a “toolbox” folder).

To install the Python-odML library, enter the corresponding directory and run:

$ cd /home/usr/toolbox/python-odml/
$ python setup.py install

Bugs & Questions

Should you find a behaviour that is likely a bug, please file a bug report at the github bug tracker.


Basic knowledge on odML

Before we start, it is important to know the basic structure of an odML file. Within an odML file metadata are grouped and stored in a hierarchical tree structure which consists of three basic odML objects.

Document:
  • description: root of the tree
  • parent: no parent
  • children: Section
Section:
  • description: branches of the tree
  • parent: Document or Section
  • children: Section and/or Property
Property:
  • description: leafs of the tree (contains metadata values)
  • parent: Section
  • children: none

Each of these odML objects has a certain set of attributes where the user can describe the object and its contents. Which attribute belongs to which object and what the attributes are used for is better explained in an example odML file (cf., “THGTTG.odml”).

A first look

If you want to get familiar with the concept behind the odML framework and how to handle odML files in Python, you can have a first look at the example odML file provided in the Python-odML library. For this you first need to run the python code (“thgttg.py”) to generate the example odML file (“THGTTG.odml”). When using the following commands, make sure you adapt the paths to the python-odml module to your own!:

$ cd /home/usr/.../python-odml
$ ls doc/example_odMLs
thgttg.py
$ python doc/example_odMLs/example_odMLs.py "/home/usr/.../python-odml"
$ ls doc/example_odMLs
THGTTG.odml  thgttg.py

Now open a Python shell within the Python-odML library directory, e.g. with IPython:

$ ipython

In the IPython shell, first import the odml package:

>>> import odml

Second, load the example odML file with the following command lines:

>>> to_load = './doc/example_odMLs/THGTTG.odml'
>>> odmlEX = odml.load(to_load)

If you open a Python shell outside of the Python-odML library directory, please adapt your Python-Path and the path to the “THGTTG.odml” file accordingly.

How you can access the different odML objects and their attributes once you loaded an odML file and how you can make use of the attributes is described in more detail in the following chapters for each odML object type (Document, Section, Property).

How you can create the different odML objects on your own and how to connect them to build your own metadata odML file will be described in later chapters. Further advanced functions you can use to navigate through your odML files, or to create an odML template file, or to make use of common odML terminologies provided via the G-Node repository can also be found later on in this tutorial.

But now, let us first have a look at the example odML file (THGTTG.odml)!

The Document

If you loaded the example odML file, let’s have a first look at the Document:

>>> print odmlEX
Document 42 {author = D. N. Adams, 2 sections}

As you can see, the printout gives you a short summary of the Document of the loaded example odML file.

The print out gives you already the following information about the odML file:

  • Document tells you that you are looking at an odML Document
  • 42 is the user defined version of this odML file
  • {...} provides author and number of attached sections
  • author states the author of the odML file, “D. N. Adams” in the example case
  • 2 sections tells you that this odML Document has 2 Section directly appended

Note that the Document printout tells you nothing about the depth of the complete tree structure, because it is not displaying the children of its directly attached Sections. It also does not display all Document attributes. In total, a Document has the following attributes:

author
  • Returns the author (returned as string) of an odML document.
date
  • Returns a user defined date. Could for example be used to state the date of the document creation or the date of the latest change.
document
  • Returns the current Document object.
parent
  • Returns the parent object (which is None for a Document).
repository
  • Returns the URL (returned as string) to a user defined repository of terminologies used in this Document. Could be the URL to the G-Node terminologies or to a user defined template.
version
  • Returns the user defined version (returned as string) of this odML file.
id
  • id is a UUID (universally unique identifier) that uniquely identifies the current document. If not otherwise specified, this id is automatically created and assigned.

Let’s check out all attributes with the following commands:

>>> print(odmlEX.author)
D. N. Adams
>>> print(odmlEX.date)
1979-10-12
>>> print(odmlEX.document)
Document 42 {author = D. N. Adams, 2 sections}
>>> print(odmlEX.parent)
None
>>> print(odmlEX.repository)
https://terminologies.g-node.org/v1.1/terminologies.xml
>>> print(odmlEX.version)
42

As expected for a Document, the attributes author and version match the information given in the Document printout, the document attribute just returns the Document, and the parent attribute is None.

As you learned in the beginning, Sections can be attached to a Document. They represent the next hierarchy level of an odML file. Let’s have a look which Sections were attached to the Document of our example odML file using the following command:

>>> print(odmlEX.sections)
[Section[4|2] {name = TheCrew, type = crew, id = ...},
 Section[1|7] {name = TheStarship, type = starship, id = ...}]

As expected from the Document printout our example contains two Sections. The printout and attributes of a Section are explained in the next chapter.

The Sections

There are several ways to access Sections. You can either call them by name or by index using either explicitly the function that returns the list of Sections (see last part of The Document chapter) or using again a short cut notation. Let’s test all the different ways to access a Section, by having a look at the first Section in the sections list attached to the Document in our example odML file:

>>> print(odmlEX.sections['TheCrew'])
Section[4|2] {name = TheCrew, type = crew, id = ...}
>>> print(odmlEX.sections[0])
Section[4|2] {name = TheCrew, type = crew, id = ...}
>>> print(odmlEX['TheCrew'])
Section[4|2] {name = TheCrew, type = crew, id = ...}
>>> print(odmlEX[0])
Section[4|2] {name = TheCrew, type = crew, id = ...}

In the following we will call Sections explicitly by their name using the short cut notation.

The printout of a Section is similar to the Document printout and gives you already the following information:

  • Section tells you that you are looking at an odML Section
  • [4|2] states that this Section has four Sections and two Properties directly attached to it
  • {...} provides name, type and id of the Section
  • name is the name of this Section, ‘TheCrew’ in the example case
  • type provides the type of the Section, ‘crew’ in the example case
  • id provides the uuid of the Section, the actual value has been omitted in the example to improve readability.

Note that the Section printout tells you nothing about the depth of a possible sub-Section tree below the directly attached ones. It also only lists the type of the Section as one of the Section attributes. In total, a Section can be defined by the following attributes:

name
  • Returns the name of this Section. Should indicate what kind of information can be found in this Section.
definition
  • Returns the definition of the content within this Section. Should describe what kind of information can be found in this Section.
document
  • Returns the Document to which this Section belongs to. Note that this attribute is set automatically for a Section and all its children when it is attached to a Document.
parent
  • Returns the parent to which this Section was directly attached to. Can be either a Document or another Section.
type
  • Returns the classification type which allows to connect related Sections due to a superior semantic context.
reference
  • Returns a reference that can be used to state the origin or source file of the metadata stored in the Properties that are grouped by this Section.
repository
  • Returns the URL (returned as string) to a user defined repository of terminologies used in this Document. Could be the URL to the G-Node terminologies or to a user defined template.
id
  • id is a UUID (universally unique identifiers) that uniquely identifies the current section. If not otherwise specified, this id is automatically created and assigned.

Let’s have a look at the attributes for the Section ‘TheCrew’:

>>> print(odmlEX['TheCrew'].name)
TheCrew
>>> print(odmlEX['TheCrew'].definition)
Information on the crew
>>> print(odmlEX['TheCrew'].document)
Document 42 {author = D. N. Adams, 2 sections}
>>> print(odmlEX['TheCrew'].parent)
Document 42 {author = D. N. Adams, 2 sections}
>>> print(odmlEX['TheCrew'].type)
crew
>>> print(odmlEX['TheCrew'].reference)
None
>>> print(odmlEX['TheCrew'].repository)
None
>>> print(odmlEX['TheCrew'].id)
6df940b5-b502-4749-8ad9-33d7432064f3

As expected for this Section, the name and type attribute match the information given in the Section printout, and the document and parent attributes return the same object, namely our example Document.

To see which Sections are directly attached to the Section ‘TheCrew’ again use the following command:

>>> print(odmlEX['TheCrew'].sections)
[Section[0|5] {name = Arthur Philip Dent, type = crew/person, id = ...},
 Section[0|5] {name = Zaphod Beeblebrox, type = crew/person, id = ...},
 Section[0|5] {name = Tricia Marie McMillan, type = crew/person, id = ...},
 Section[0|5] {name = Ford Prefect, type = crew/person, id = ...}]

Or, for accessing these sub-Sections:

>>> print(odmlEX['TheCrew'].sections['Ford Prefect'])
Section[0|5] {name = Ford Prefect, type = crew/person, id = ...}
>>> print(odmlEX['TheCrew'].sections[3])
Section[0|5] {name = Ford Prefect, type = crew/person, id = ...}
>>> print(odmlEX['TheCrew']['Ford Prefect'])
Section[0|5] {name = Ford Prefect, type = crew/person, id = ...}
>>> print(odmlEX['TheCrew'][3])
Section[0|5] {name = Ford Prefect, type = crew/person, id = ...}

As you learned, besides sub-Sections, a Section can also have Properties attached. Let’s see which Properties are attached to the Section ‘TheCrew’:

>>> print(odmlEX['TheCrew'].properties)
[Property: {name = NameCrewMembers},
 Property: {name = NoCrewMembers}]

The printout and attributes of a Property are explained in the next chapter.

The Properties

Properties need to be called explicitly via the properties function of a Section. You can then either call a Property by name or by index:

>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'])
Property: {name = NoCrewMembers}
>>> print(odmlEX['TheCrew'].properties[1])
Property: {name = NoCrewMembers}

In the following we will only call Properties explicitly by their name.

The Property printout is reduced and only gives you information about the following:

  • Property tells you that you are looking at an odML Property
  • {...} provides the name of the Property
  • NoCrewMembers is the name of this Property

Note that the Property printout tells you nothing about the number of Values, and very little about the Property attributes. In total, a Property can be defined by the following attributes:

name
  • Returns the name of the Property. Should indicate what kind of metadata are stored in this Property.
definition
  • Returns the definition of this Property. Should describe what kind of metadata are stored in this Property.
document
  • Returns the Document to which the parent Section of this Property belongs to. Note that this attribute is set automatically for a Section and all its children when it is attached to a Document.
parent
  • Returns the parent Section to which this Property was attached to.
values
  • Returns the metadata of this Property. Can be either a single metadata or multiple, but homogeneous metadata (all with the same dtype, unit and uncertainty). For this reason, the output is always provided as a list.
dtype
  • Returns the odml data type of the stored metadata.
unit
  • Returns the unit of the stored metadata.
uncertainty
  • recommended
  • Can be used to specify the uncertainty of the given metadata value.
reference
  • Returns a reference that can be used to state an external definition of the metadata value.
dependency
  • optional
  • A name of another Property within the same section, which this property depends on.
dependency_value
  • optional
  • Value of the other Property specified in the ‘dependency’ attribute on which this Property depends on.
value_origin
  • A reference to state the origin of the metadata value e.g. a file name.

Let’s check which attributes were defined for the Property ‘NoCrewMembers’:

>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].name)
NoCrewMembers
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].definition)
Number of crew members
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].document)
Document 42 {author = D. N. Adams, 2 sections}
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].values)
[4]
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].dtype)
int
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].unit)
None
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].uncertainty)
1
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].reference)
The Hitchhiker's guide to the Galaxy (novel)
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].dependency)
None
>>> print(odmlEX['TheCrew'].properties['NoCrewMembers'].dependency_value)
None

As mentioned the values attribute of a Property can only contain multiple metadata when they have the same dtype and unit, as it is the case for the Property ‘NameCrewMembers’:

>>> print(odmlEX['TheCrew'].properties['NameCrewMembers'].values)
['Arthur Philip Dent',
 'Zaphod Beeblebrox',
 'Tricia Marie McMillan',
 'Ford Prefect']
>>> print(odmlEX['TheCrew'].properties['NameCrewMembers'].dtype)
person
>>> print(odmlEX['TheCrew'].properties['NameCrewMembers'].unit)
None

NOTE: property.values will always return a copy! Any direct changes to the returned list will have no affect on the actual Property values. If you want to make changes to a Property value, either use the append, extend and remove methods or assign a new value list to the property.

Printing overviews to navigate the contents of an odML document

The odML entities Property, Section and Document feature a method that allows to print a tree-like representation of all child entities to get an overview of the file structure.

>>> MYodML.pprint()
>>> sec = MYodML['TheCrew']
>>> sec.pprint()
>>> prop = odmlEX['TheCrew'].properties['NameCrewMembers']
>>> prop.pprint()

Generating an odML-file

After getting familiar with the different odML objects and their attributes, you will now learn how to generate your own odML file by reproducing some parts of the example THGTTG.odml.

We will show you first how to create the different odML objects with their attributes. Please note that some attributes are obligatory, some are recommended and others are optional when creating the corresponding odML objects. A few are automatically generated in the process of creating an odML file. Furthermore, all attributes of an odML object can be edited at any time.

If you opened a new IPython shell, please import first again the odml package:

>>> import odml

Create a document

Let’s start by creating the Document. Note that none of the Document attributes are obligatory:

>>> MYodML = odml.Document()

You can check if your new Document contains actually what you created by using some of the commands you learned before:

>>> MYodML
>>> Document None {author = None, 0 sections}

As you can see, we created an “empty” Document where the version and the author attributes are not defined and no section is yet attached. You will learn how to create and add a Section to a Document in the next chapter. Let’s focus here on defining the Document attributes:

>>> MYodML.author = 'D. N. Adams'
>>> MYodML.version = 42

For the date attribute you require a datetime object as entry. For this reason, you need to first import the Python package datetime:

>>> import datetime as dt

Now, let’s define the date attribute of the Document:

>>> MYodML.date = dt.date(1979, 10, 12)

Next, let us also add a repository attribute. Exemplary, we can import the Python package os to extract the absolute path to our previously used example odML file and add this as repository:

>>> import os
>>> url2odmlEX = 'file:///' + os.path.abspath(to_load)
>>> MYodML.repository = url2odmlEX

The document and parent attribute are automatically set and should not be fiddled with.

Check if your new Document actually contains all attributes now:

>>> print(MYodML.author)
D. N. Adams
>>> print(MYodML.date)
1979-10-12
>>> print(MYodML.document)
Document 42 {author = D. N. Adams, 0 sections}
>>> print(MYodML.parent)
None
>>> print(MYodML.repository)
file:///home/usr/.../python-odml/doc/example_odMLs/THGTTG.odml
>>> print(MYodML.version)
42

Note that you can also define all attributes when first creating a Document:

>>> MYodML = odml.Document(author='D. N. Adams',
                           version=42,
                           date=dt.date(1979, 10, 12),
                           repository=url2odmlEX)

Our newly created Document is, though, still “empty”, because it does not contain Sections yet. Let’s change this!

Create a section

We now create a Section by reproducing the Section “TheCrew” of the example odML file from the beginning:

>>> sec1 = odml.Section(name="TheCrew",
                       definition="Information on the crew",
                       type="crew")

Note that only the attribute name is obligatory. The attributes definition and type are recommended, but could be either not defined at all or defined later on.

Let us now attach this Section to our previously generated Document. With this, the attribute document and parent of our new Section are automatically updated:

>>> MYodML.append(sec1)

>>> print(MYodML)
Document 42 {author = D. N. Adams, 1 sections}
>>> print(MYodML.sections)
[Section[0|0] {name = TheCrew, type = crew, id = ...}]

>>> print(sec1.document)
Document 42 {author = D. N. Adams, 1 sections}
>>> print(sec1.parent)
Document 42 {author = D. N. Adams, 1 sections}

It is also possible to connect a Section directly to a parent object. Let’s try this with the next Section we create:

>>> sec2 = odml.Section(name="Arthur Philip Dent",
                        definition="Information on Arthur Dent",
                        type="crew/person",
                        parent=sec1)

>>> print(sec2)
Section[0|0] {name = Arthur Philip Dent, type = crew/person, id = ...}

>>> print(sec2.document)
Document 42 {author = D. N. Adams, 1 sections}
>>> print(sec2.parent)
[Section[1|0] {name = TheCrew, type = crew, id = ...}

Note that all of our created Sections do not contain any Properties yet. Let’s see if we can change this…

Create a Property:

Let’s create our first Property:

>>> prop1 = odml.Property(name="Gender",
                          definition="Sex of the subject",
                          values="male")

Note that again, only the name attribute is obligatory for creating a Property. The remaining attributes can be defined later on, or are automatically generated in the process.

If a value is defined, but the dtype is not, as it is the case for our example above, the dtype is deduced automatically:

>>> print(prop1.dtype)
string

Generally, you can use the following odML data types to describe the format of the stored metadata:

dtype required data examples
odml.DType.int or ‘int’ 42
odml.DType.float or ‘float’ 42.0
odml.DType.boolean or ‘boolean’ True or False
odml.DType.string or ‘string’ ‘Earth’
odml.DType.date or ‘date’ dt.date(1979, 10, 12)
odml.DType.datetime or ‘datetime’ dt.datetime(1979, 10, 12, 11, 11, 11)
odml.DType.time or ‘time’ dt.time(11, 11, 11)
odml.DType.person or ‘person’ ‘Zaphod Beeblebrox’
odml.DType.text or ‘text’ ‘any text containing n linebreaks’
odml.DType.url or ‘url’ https://en.wikipedia.org/wiki/Earth
odml.DType.tuple “(39.12; 67.19)” cf. usage note below

The available types are implemented in the ‘odml.dtypes’ Module. Note that the last four data types, if not defined, cannot be deduced, but are instead always interpreted as string.

If we append now our new Property to the previously created sub-Section ‘Arthur Philip Dent’, the Property will also inherit the document attribute and automatically update its parent attribute:

>>> MYodML['TheCrew']['Arthur Philip Dent'].append(prop1)

>>> print(prop1.document)
Document 42 {author = D. N. Adams, 1 sections}
>>> print(prop1.parent)
Section[0|1] {name = Arthur Philip Dent, type = crew/person, id = ...}

Next, let us create a Property with multiple metadata entries:

>>> prop2 = odml.Property(name="NameCrewMembers",
                          definition="List of crew members names",
                          values=["Arthur Philip Dent",
                                  "Zaphod Beeblebrox",
                                  "Tricia Marie McMillan",
                                  "Ford Prefect"],
                          dtype=odml.DType.person)

As you learned before, in such a case the metadata entries must be homogeneous! That means they have to be of the same dtype, unit, and uncertainty (here odml.DType.person, None, and None, respectively).

To further build up our odML file, let us attach now this new Property to the previously created Section ‘TheCrew’:

>>> MYodML['TheCrew'].append(prop2)

Note that it is also possible to add a metadata entry later on:

>>> prop2.append("Blind Passenger")
>>> print(MYodML['TheCrew'].properties['NameCrewMembers'].values)
['Arthur Philip Dent',
 'Zaphod Beeblebrox',
 'Tricia Marie McMillan',
 'Ford Prefect',
 'Blind Passenger']

The tuple datatype you might have noticed in the dtype table above has to be specially handled. It is intended to enforce a specific number of data points for each value entry. This is useful in case of 2D or 3D data, where all data points always have to be present for each entry. The dtype itself has to contain the number corresponding to the required value data points. For the value data points themselves, they have to be enclosed by brackets and separated by a semicolon.

>>> pixel_prop = odml.Property(name="pixel map")
>>> pixel_prop.dtype = "2-tuple"
>>> pixel_prop.values = ["(1; 2)", "(3; 4)"]
>>> voxel_prop = odml.Property(name="voxel map")
>>> voxel_prop.dtype = "3-tuple"
>>> voxel_prop.values = "(1; 2; 3)"

Please note, that inconsistent tuple values will raise an error:

>>> tprop = odml.Property(name="tuple fail")
>>> tprop.dtype = "3-tuple"
>>> tprop.values = ["(1; 2)"]

Printing the XML-representation of an odML file:

Although the XML-representation of an odML file is a bit hard to read, it is sometimes helpful to check, especially during a generation process, how the hierarchical structure of the odML file looks like.

Let’s have a look at the XML-representation of our small odML file we just generated:

>>> print(odml.tools.xmlparser.XMLWriter(MYodML))
<odML version="1.1">
  <date>1979-10-12</date>
  <section>
    <definition>Information on the crew</definition>
    <property>
      <definition>List of crew members names</definition>
      <name>NameCrewMembers</name>
      <type>person</type>
      <value>[Arthur Philip Dent,Zaphod Beeblebrox,Tricia Marie McMillan,Ford Prefect,Blind Passenger&#13;]</value>
    </property>
    <name>TheCrew</name>
    <section>
      <definition>Information on Arthur Dent</definition>
      <property>
        <definition>Sex of the subject</definition>
        <name>Gender</name>
        <type>string</type>
        <value>[male&#13;]</value>
      </property>
      <name>Arthur Philip Dent</name>
      <type>crew/person</type>
    </section>
    <type>crew</type>
  </section>
  <version>42</version>
  <repository>file:///home/usr/Projects/toolbox/python-odml/doc/example_odMLs/THGTTG.odml</repository>
  <author>D. N. Adams</author>
</odML>

Saving an odML file:

You can save your odML file using the following command:

>>> save_to = '/home/usr/toolbox/python-odml/doc/example_odMLs/myodml.odml'
>>> odml.save(MYodML, save_to)

By default, every odML file will be saved using the XML file format. Note, that you can also choose to save an odML Document using the JSON or the YAML file format as well, specifying the corresponding option in the command.

>>> save_to = '/home/usr/toolbox/python-odml/doc/example_odMLs/myodml.json'
>>> odml.save(MYodML, save_to, "JSON")
>>> save_to = '/home/usr/toolbox/python-odml/doc/example_odMLs/myodml.yaml'
>>> odml.save(MYodML, save_to, "YAML")

Loading an odML file:

You already learned how to load the example odML file. Here just as a reminder you can try to reload your own saved odML file:

>>> my_reloaded_odml = odml.load(save_to)

Again, the load function by default assumes, that an odML file was saved using the XML format. If it was saved in either JSON or YAML, add the appropriate format option when loading the document:

>>> my_reloaded_odml_json = odml.load(save_to, "JSON")
>>> my_reloaded_odml_yaml = odml.load(save_to, "YAML")

Advanced Value features

Data type conversions

After creating a Property with metadata, the data type can be changed and the format of the corresponding entry will be converted to the new data type, if the new type is valid for the given metadata:

>>> test_dtype_conv = odml.Property('p', values=1.0)
>>> print(test_dtype_conv.values)
[1.0]
>>> print(test_dtype_conv.dtype)
float
>>> test_dtype_conv.dtype = odml.DType.int
>>> print(test_dtype_conv.values)
[1]
>>> print(test_dtype_conv.dtype)
int

If the conversion is invalid, a ValueError is raised.

Also note, that during such a process metadata loss may occur, if a float is converted to integer and then back to float:

>>> test_dtype_conv = odml.Property('p', values=42.42)
>>> print(test_dtype_conv.values)
[42.42]
>>> test_dtype_conv.dtype = odml.DType.int
>>> test_dtype_conv.dtype = odml.DType.float
>>> print(test_dtype_conv.values)
[42.0]

Terminologies

odML supports terminologies that are data structure templates for typical use cases. Sections can have a repository attribute. As repositories can be inherited, the current applicable one can be obtained using the odml.section.BaseSection.get_repository method.

To see whether an object has a terminology equivalent, use the odml.property.BaseProperty.get_terminology_equivalent method, which returns the corresponding object of the terminology.