openalea.vpltk.project package

Submodules

openalea.vpltk.project.configobj module

exception openalea.vpltk.project.configobj.ConfigObjError(message='', line_number=None, line='')

Bases: exceptions.SyntaxError

This is the base class for all errors that ConfigObj raises. It is a subclass of SyntaxError.

exception openalea.vpltk.project.configobj.NestingError(message='', line_number=None, line='')

Bases: openalea.vpltk.project.configobj.ConfigObjError

This error indicates a level of nesting that doesn’t match.

exception openalea.vpltk.project.configobj.ParseError(message='', line_number=None, line='')

Bases: openalea.vpltk.project.configobj.ConfigObjError

This error indicates that a line is badly written. It is neither a valid key = value line, nor a valid section marker line.

exception openalea.vpltk.project.configobj.DuplicateError(message='', line_number=None, line='')

Bases: openalea.vpltk.project.configobj.ConfigObjError

The keyword or section specified already exists.

exception openalea.vpltk.project.configobj.ConfigspecError(message='', line_number=None, line='')

Bases: openalea.vpltk.project.configobj.ConfigObjError

An error occured whilst parsing a configspec.

class openalea.vpltk.project.configobj.ConfigObj(infile=None, options=None, configspec=None, encoding=None, interpolation=True, raise_errors=False, list_values=True, create_empty=False, file_error=False, stringify=True, indent_type=None, default_encoding=None, unrepr=False, write_empty_values=False, _inspec=False)

Bases: openalea.vpltk.project.configobj.Section

An object to read, create, and write config files.

reload()

Reload a ConfigObj from file.

This method raises a ReloadError if the ConfigObj doesn’t have a filename attribute pointing to a file.

reset()

Clear ConfigObj instance and restore to ‘freshly created’ state.

validate(validator, preserve_errors=False, copy=False, section=None)

Test the ConfigObj against a configspec.

It uses the validator object from validate.py.

To run validate on the current ConfigObj, call:

test = config.validate(validator)

(Normally having previously passed in the configspec when the ConfigObj was created - you can dynamically assign a dictionary of checks to the configspec attribute of a section though).

It returns True if everything passes, or a dictionary of pass/fails (True/False). If every member of a subsection passes, it will just have the value True. (It also returns False if all members fail).

In addition, it converts the values from strings to their native types if their checks pass (and stringify is set).

If preserve_errors is True (False is default) then instead of a marking a fail with a False, it will preserve the actual exception object. This can contain info about the reason for failure. For example the VdtValueTooSmallError indicates that the value supplied was too small. If a value (or section) is missing it will still be marked as False.

You must have the validate module to use preserve_errors=True.

You can then use the flatten_errors function to turn your nested results dictionary into a flattened list of failures - useful for displaying meaningful error messages.

write(outfile=None, section=None)

Write the current ConfigObj as a file

tekNico: FIXME: use StringIO instead of real files

>>> filename = a.filename
>>> a.filename = 'test.ini'
>>> a.write()
>>> a.filename = filename
>>> a == ConfigObj('test.ini', raise_errors=True)
1
>>> import os
>>> os.remove('test.ini')

class openalea.vpltk.project.configobj.SimpleVal

Bases: object

A simple validator. Can be used to check that all members expected are present.

To use it, provide a configspec with all your members in (the value given will be ignored). Pass an instance of SimpleVal to the validate method of your ConfigObj. validate will return True if all members are present, or a dictionary with True/False meaning present/missing. (Whole missing sections will be replaced with False)

check(check, member, missing=False)

A dummy check method, always returns the value unchanged.

exception openalea.vpltk.project.configobj.InterpolationError(message='', line_number=None, line='')

Bases: openalea.vpltk.project.configobj.ConfigObjError

Base class for the two interpolation errors.

exception openalea.vpltk.project.configobj.InterpolationLoopError(option)

Bases: openalea.vpltk.project.configobj.InterpolationError

Maximum interpolation depth exceeded in string interpolation.

exception openalea.vpltk.project.configobj.MissingInterpolationOption(option)

Bases: openalea.vpltk.project.configobj.InterpolationError

A value specified for interpolation was missing.

exception openalea.vpltk.project.configobj.RepeatSectionError(message='', line_number=None, line='')

Bases: openalea.vpltk.project.configobj.ConfigObjError

This error indicates additional sections in a section with a __many__ (repeated) section.

exception openalea.vpltk.project.configobj.ReloadError

Bases: exceptions.IOError

A ‘reload’ operation failed. This exception is a subclass of IOError.

exception openalea.vpltk.project.configobj.UnreprError(message='', line_number=None, line='')

Bases: openalea.vpltk.project.configobj.ConfigObjError

An error parsing in unrepr mode.

exception openalea.vpltk.project.configobj.UnknownType

Bases: exceptions.Exception

openalea.vpltk.project.configobj.flatten_errors(cfg, res, levels=None, results=None)

An example function that will turn a nested dictionary of results (as returned by ConfigObj.validate) into a flat list.

cfg is the ConfigObj instance being checked, res is the results dictionary returned by validate.

(This is a recursive function, so you shouldn’t use the levels or results arguments - they are used by the function.)

Returns a list of keys that failed. Each member of the list is a tuple:

([list of sections...], key, result)

If validate was called with preserve_errors=False (the default) then result will always be False.

list of sections is a flattened list of sections that the key was found in.

If the section was missing (or a section was expected and a scalar provided - or vice-versa) then key will be None.

If the value (or section) was missing then result will be False.

If validate was called with preserve_errors=True and a value was present, but failed the check, then result will be the exception object returned. You can use this as a string that describes the failure.

For example The value “3” is of the wrong type.

openalea.vpltk.project.configobj.get_extra_values(conf, _prepend=())

Find all the values and sections not in the configspec from a validated ConfigObj.

get_extra_values returns a list of tuples where each tuple represents either an extra section, or an extra value.

The tuples contain two values, a tuple representing the section the value is in and the name of the extra values. For extra values in the top level section the first member will be an empty tuple. For values in the ‘foo’ section the first member will be ('foo',). For members in the ‘bar’ subsection of the ‘foo’ section the first member will be ('foo', 'bar').

NOTE: If you call get_extra_values on a ConfigObj instance that hasn’t been validated it will return an empty list.

openalea.vpltk.project.loader module

class openalea.vpltk.project.loader.BGEOMLoader

Bases: openalea.vpltk.project.loader.ILoader

Specific loader that is used to manipulate PlantGL objects

default_name = 'BGEOMLoader'

input_format = '*.BGEOM'

load(filename)

Parameters:filename – filename to convert into python object Returns:a python object interpreted from string “text”

class openalea.vpltk.project.loader.CPickleLoader

Bases: openalea.vpltk.project.loader.ILoader

Specific loader that use cPickle.loads

default_name = 'CPickleLoader'

input_format = '*'

load(filename)

Parameters:filename – filename to convert into python object Returns:a python object interpreted from filename

class openalea.vpltk.project.loader.GenericLoader

Bases: object

Classical loader that read file

default_name = 'GenericLoader'

input_format = '*.py'

load(filename)

Parameters:filename – filename to convert into python object Returns:a python object interpreted from string “text”

class openalea.vpltk.project.loader.ILoader

Bases: object

Generic interface class for loaders

load(filename)

Parameters:filename – filename to convert into python object Returns:a python object

class openalea.vpltk.project.loader.PythonLoader

Bases: object

Classical loader that read file and try to eval object

default_name = 'PythonLoader'

input_format = '*.py'

load(filename)

Parameters:filename – filename to convert into python object Returns:a python object interpreted from string “text”

openalea.vpltk.project.loader.get_loader(name='GenericLoader')

openalea.vpltk.project.manager module

class openalea.vpltk.project.manager.ProjectManager

Bases: object

Object which manage projects: creation, loading, saving, searching, ...

It is a singleton.

clear()

Clear the list of projects.

close(project_name=None, project_path=None)

TODO:not yet implemented

create(project_name, project_path=None)

Create new project and return it.

Use:

>>> project1 = project_manager.create('project1')
>>> project2 = project_manager.create('project2', '/path/to/project')

Parameters:

• project_name – name of project to create (str)
• project_path – path where project will be saved. By default, project_path is the user path of all projects ($HOME/.openalea/projects/).

Returns:

Project

default()

Returns:a default empty project

discover()

Discover projects from your disk and put them in self.projects.

Projects are not loaded, only metadata are.

Use:

>>> project_manager.discover()
>>> print project_manager.projects

To discover new projects, you can add path into self.find_links

project_manager.find_links.append('path/to/search/projects')
project_manager.discover()

get_current()

Returns:

current active project

Use:

>>> project = project_manager.get_current()

instance = None

load(project_name, project_path=None)

Load existing project

Use:

>>> project1 = project_manager.load('project1')
>>> project2 = project_manager.load('project2', '/path/to/project')

Parameters:

• project_name – name of project to load. Must be a string.
• project_path – path of project to load. Must be a path (see module path.py). By default, the path is the openaelea.core.settings.get_project_dir() ($HOME/.openalea/projects/).

Returns:

Project

load_default()

Load default project if it exists, else create it.

Returns:the default loaded project

search(*args, **kwargs)

Search a specific project that match filters.

Use:

>>> project_manager.search(name="*mtg*", author="*Godin*")

TODO:

not implemented yet

openalea.vpltk.project.manager.main()

openalea.vpltk.project.project module

The Project is a structure which permit to manage different objects.

It store metadata (name, author, description, version, license, ...) and data (src, models, images, ...).

You have here the default architecture of the project named “project_name”, stored in your computer.

/project_name

oaproject.cfg (Configuration file) /src (Files sources, Script Python, LPy...) /control (Control, like color map or curve) /scene (scene, scene 3D) /cache (Intermediary saved objects) /data (Data files like images, .dat, ...) /startup (Preprocessing scripts) .py (Preprocessing scripts) *import.py (Libs and packages to import in preprocessing)

use:

project1 = Project(project_name="mynewproj", project_path="/path/to/proj")
project1.start()
project1.add(category="src", name"hello.py", value="print 'Hello World'")
project1.author = "John Doe"
project1.description = "This project is used to said hello to everyone"
project1.save()

class openalea.vpltk.project.project.Project(project_name, project_path, icon='', author='OpenAlea Consortium', author_email='', description='', long_description='', citation='', url='', dependencies=, []license='CeCILL-C', version='0.1')

Bases: object

add(category, name, value)

Add an object in the project

Parameters:

• category – type of object to add (“src”, “control”, “scene”, ...)
• name – filename of the object to add (path or str)
• value – to add (string)

See also

get() remove()

add_script(name, script)

Add a src in the project

Deprecated:

replace by add() method

Parameters:

• name – filename of the src to add (path or str)
• script – to add (string)

See also

add()

author

author_email

cache

citation

control

create()

Do the same thing that import method.

See also

start() load() load_manifest()

data

dependencies

description

doc

get(category, name)

Search an object inside project and return it.

Parameters:

• category – category of object to get
• name – name of object to get

Returns:

object named name in the category category if it exists. Else, None.

Use:

>>> get(category="src", name="myscript.py")

See also

add()

get_scene()

Returns:self.scene (dict)

icon

is_project()

Returns:True

is_script()

Returns:False

license

load()

Realize a total loading of project (contrary to load_manifest()).

1. Load manifest load_manifest()
2. Read data files listed in manifest and fill project object.

See also

start() load_manifest()

load_manifest()

Partially load a project from a manifest file.

1. Read manifest file (oaproject.cfg).
2. Load metadata inside project from manifest.
3. Load filenames of data files inside project from manifest.
4. Not load data ! If you want to load data, please use load().

Warning:load metadata and list of filenames but does not load files

See also

save_manifest() load()

long_description

name

ns

remove(category, name)

Remove an object in the project

Remove nothing on disk.

Parameters:

• category – category of object to remove (“src”, “control”, “scene”, ...) (str)
• name – filename of the src to remove (path or str)

remove_script(name)

Add a src in the project

Remove nothing on disk.

Deprecated:replace by remove() method Parameters:name – filename of the src to remove (path or str)

See also

remove()

rename(category, old_name, new_name)

Rename a src, a scene or a control in the project. If category is project, rename the entire project.

Parameters:

• category – Can be “src”, “control”, “scene” or “project” (str)
• old_name – current name of thing to rename (str)
• new_name – future name of thing to rename (str)

run_src(name)

Try to run the source file named name into current shell

save()

Save project on disk.

1. Save data files.
2. Save metadata and list on previously saved data into a manifest file (oaproject.cfg).

See also

save_manifest()

save_manifest()

Save a manifest file on disk. His name is “oaproject.cfg”.

It contains list of files that are inside project (manifest) and metadata (author, version, ...).

See also

load_manifest()

scene

src

start()

1. load() objects into project.
2. Import startup.
3. Run preprocessing.

See also

load() load_manifest()

startup

url

use_ipython()

Returns:True if project is instaciated with a shell IPython. Else, return False.

version

openalea.vpltk.project.saver module

class openalea.vpltk.project.saver.BGEOMSaver

Bases: object

Specific loader that is used to manipulate PlantGL objects

default_name = 'BGEOMSaver'

output_format = '*.BGEOM'

save(obj, filename)

Store obj into filename

class openalea.vpltk.project.saver.CPickleSaver

Bases: object

Specific saver that use cPickle.dump

default_name = 'CPickleSaver'

output_format = '*'

save(obj, filename)

Store obj into filename

class openalea.vpltk.project.saver.GenericSaver

Bases: object

Classical saver that write str(obj) into file

default_name = 'GenericSaver'

output_format = '*.py'

save(obj, filename)

Store str(obj) into filename

class openalea.vpltk.project.saver.ISaver

Bases: object

Generic interface class for savers

save(obj, filename)

openalea.vpltk.project.saver.get_saver(name='GenericSaver')

Module contents

Project and Project Manager Quick Start

You can work directly on project:

project1 = Project(project_name="mynewproj", project_path="/path/to/proj")

project1.rename("project", "mynewproj", "hello_project")
project1.import()
project1.authors = "OpenAlea Consortium and John Doe"
project1.description = "Test project concept with numpy"
project1.long_description = '''This project import numpy.
Then, it create and display a numpy eye.
We use it to test concept of Project.''

project1.add(category="scripts", name"hello.py", value="print 'Hello World'")
project1.description = "This project is used to said hello to everyone"

project1.add("startup", "begin_numpy.py", "import numpy as np")
project1.add("scripts", "eye.py", "print np.eye(2)")
project1.rename("scripts", "eye.py", "eye_numpy.py")

project1.save()

Or, you can create or load a project thanks to the project manager.

from openalea.vpltk.project.manager import ProjectManager
# Instanciate ProjectManager
project_manager = ProjectManager()
# Discover available projects
project_manager.discover()
print project_manager.projects

# Create project in default directory or in specific one
p1 = project_manager.create('project1')
p2 = project_manager.create('project2', '/path/to/project')
# Load project from default directory or in specific one
p3 = project_manager.load('project3')
p4 = project_manager.load('project4', '/path/to/project')

# Load
project2 = project_manager.load("numpy_project")
# Run startup
project2.import()
# Run script
project2.run_script("eye_numpy.py")

To search projects that are not located inside default directories:

project_manager.find_links.append('path/to/search/projects')
project_manager.discover()
print project_manager.projects