def test_control_of_licenses():
"""Test control of licenses."""
struct = orm.StructureData()
struct.source = {'license': 'GPL'}
struct.store()
folder = SandboxFolder()
export([struct],
file_format='folder',
writer_init={'folder': folder},
allowed_licenses=['GPL'])
# Folder should contain two files of metadata + nodes/
assert len(folder.get_content_list()) == 3
folder.erase(create_empty_folder=True)
assert len(folder.get_content_list()) == 0
export([struct],
file_format='folder',
writer_init={'folder': folder},
forbidden_licenses=['Academic'])
# Folder should contain two files of metadata + nodes/
assert len(folder.get_content_list()) == 3
with pytest.raises(LicensingException):
export([struct], file_format='null', allowed_licenses=['CC0'])
with pytest.raises(LicensingException):
export([struct], file_format='null', forbidden_licenses=['GPL'])
def cc_filter(license_):
return license_.startswith('CC')
def gpl_filter(license_):
return license_ == 'GPL'
def crashing_filter():
raise NotImplementedError('not implemented yet')
with pytest.raises(LicensingException):
export([struct], file_format='null', allowed_licenses=cc_filter)
with pytest.raises(LicensingException):
export([struct], file_format='null', forbidden_licenses=gpl_filter)
with pytest.raises(LicensingException):
export([struct], file_format='null', allowed_licenses=crashing_filter)
with pytest.raises(LicensingException):
export([struct],
file_format='null',
forbidden_licenses=crashing_filter)
class AbstractNode(object):
"""
Base class to map a node in the DB + its permanent repository counterpart.
Stores attributes starting with an underscore.
Caches files and attributes before the first save, and saves everything
only on store(). After the call to store(), in general attributes cannot
be changed, except for those listed in the self._updatable_attributes
tuple (empty for this class, can be extended in a subclass).
Only after storing (or upon loading from uuid) extras can be modified
and in this case they are directly set on the db.
In the plugin, also set the _plugin_type_string, to be set in the DB in
the 'type' field.
"""
class __metaclass__(ABCMeta):
"""
Some python black magic to set correctly the logger also in subclasses.
"""
def __new__(cls, name, bases, attrs):
newcls = ABCMeta.__new__(cls, name, bases, attrs)
newcls._logger = logging.getLogger(
'{:s}.{:s}'.format(attrs['__module__'], name))
# Note: the reverse logic (from type_string to name that can
# be passed to the plugin loader) is implemented in
# aiida.common.pluginloader.
prefix = "aiida.orm."
if attrs['__module__'].startswith(prefix):
# Strip aiida.orm.
# Append a dot at the end, always
newcls._plugin_type_string = "{}.{}.".format(
attrs['__module__'][len(prefix):], name)
# Make sure the pugin implementation match the import name.
# If you have implementation.django.calculation.job, we remove
# the first part to only get calculation.job.
if newcls._plugin_type_string.startswith('implementation.'):
newcls._plugin_type_string = \
'.'.join(newcls._plugin_type_string.split('.')[2:])
if newcls._plugin_type_string == 'node.Node.':
newcls._plugin_type_string = ''
newcls._query_type_string = get_query_type_string(
newcls._plugin_type_string
)
else:
raise InternalError("Class {} is not in a module under "
"aiida.orm. (module is {})".format(
name, attrs['__module__']))
return newcls
# Name to be used for the Repository section
_section_name = 'node'
# The name of the subfolder in which to put the files/directories
# added with add_path
_path_subfolder_name = 'path'
# A list of tuples, saying which attributes cannot be set at the same time
# See documentation in the set() method.
_set_incompatibilities = []
@staticmethod
def get_db_columns():
"""
This method returns a list with the column names and types of the table
corresponding to this class.
:return: a list with the names of the columns
"""
pass
@property
def logger(self):
"""
Get the logger of the Node object.
:return: Logger object
"""
return self._logger
@classmethod
@abstractmethod
def get_subclass_from_uuid(cls, uuid):
"""
Get a node object from the uuid, with the proper subclass of Node.
(if Node(uuid=...) is called, only the Node class is loaded).
:param uuid: a string with the uuid of the object to be loaded.
:return: the object of the proper subclass.
:raise: NotExistent: if there is no entry of the desired
object kind with the given uuid.
"""
pass
@classmethod
@abstractmethod
def get_subclass_from_pk(cls, pk):
"""
Get a node object from the pk, with the proper subclass of Node.
(integer primary key used in this database),
but loading the proper subclass where appropriate.
:param pk: a string with the pk of the object to be loaded.
:return: the object of the proper subclass.
:raise: NotExistent: if there is no entry of the desired
object kind with the given pk.
"""
pass
@property
def ctime(self):
"""
Return the creation time of the node.
"""
return self.dbnode.ctime
@property
def mtime(self):
"""
Return the modification time of the node.
"""
return self.dbnode.mtime
@abstractmethod
def __int__(self):
"""
Convert the class to an integer. This is needed to allow querying
with Django. Be careful, though, not to pass it to a wrong field!
This only returns the local DB principal key (pk) value.
:return: the integer pk of the node or None if not stored.
"""
pass
@abstractmethod
def __init__(self, **kwargs):
"""
Initialize the object Node.
:param uuid: if present, the Node with given uuid is
loaded from the database.
(It is not possible to assign a uuid to a new Node.)
"""
self._to_be_stored = True
# Empty cache of input links in any case
self._inputlinks_cache = {}
@property
def is_stored(self):
"""
Return True if the node is stored, False otherwise.
"""
return not self._to_be_stored
def __repr__(self):
return '<{}: {}>'.format(self.__class__.__name__, str(self))
def __str__(self):
if not self.is_stored:
return "uuid: {} (unstored)".format(self.uuid)
else:
return "uuid: {} (pk: {})".format(self.uuid, self.pk)
def _init_internal_params(self):
"""
Set here the default values for this class; this method
is automatically called by the init.
:note: if you inherit this function, ALWAYS remember to
call super()._init_internal_params() as the first thing
in your inherited function.
"""
pass
@property
def _set_defaults(self):
"""
Default values to set in the __init__, if no value is explicitly provided
for the given key.
It is a dictionary, with k=v; if the key k is not provided to the __init__,
and a value is present here, this is set.
"""
return {}
@classmethod
@abstractmethod
def query(cls, *args, **kwargs):
"""
Map to the aiidaobjects manager of the DbNode, that returns
Node objects (or their subclasses) instead of DbNode entities.
# TODO: VERY IMPORTANT: the recognition of a subclass from the type
# does not work if the modules defining the subclasses are not
# put in subfolders.
# In the future, fix it either to make a cache and to store the
# full dependency tree, or save also the path.
"""
pass
def _set_with_defaults(self, **kwargs):
"""
Calls the set() method, but also adds the class-defined default
values (defined in the self._set_defaults attribute),
if they are not provided by the user.
:note: for the default values, also allow to define 'hidden' methods,
meaning that if a default value has a key "_state", it will not call
the function "set__state" but rather "_set_state".
This is not allowed, instead, for the standard set() method.
"""
self._set_internal(arguments=self._set_defaults, allow_hidden=True)
# Pass everything to 'set'
self.set(**kwargs)
def set(self, **kwargs):
"""
For each k=v pair passed as kwargs, call the corresponding
set_k(v) method (e.g., calling self.set(property=5, mass=2) will
call self.set_property(5) and self.set_mass(2).
Useful especially in the __init__.
:note: it uses the _set_incompatibilities list of the class to check
that we are not setting methods that cannot be set at the same time.
_set_incompatibilities must be a list of tuples, and each tuple
specifies the elements that cannot be set at the same time.
For instance, if _set_incompatibilities = [('property', 'mass')],
then the call self.set(property=5, mass=2) will raise a ValueError.
If a tuple has more than two values, it raises ValueError if *all*
keys are provided at the same time, but it does not give any error
if at least one of the keys is not present.
:note: If one element of _set_incompatibilities is a tuple with only
one element, this element will not be settable using this function
(and in particular,
:raise ValueError: if the corresponding set_k method does not exist
in self, or if the methods cannot be set at the same time.
"""
self._set_internal(arguments=kwargs, allow_hidden=False)
def _set_internal(self, arguments, allow_hidden=False):
"""
Works as self.set(), but takes a dictionary as the 'arguments' variable,
instead of reading it from the ``kwargs``; moreover, it allows to specify
allow_hidden to True. In this case, if a a key starts with and
underscore, as for instance ``_state``, it will not call
the function ``set__state`` but rather ``_set_state``.
"""
for incomp in self._set_incompatibilities:
if all(k in arguments.keys() for k in incomp):
if len(incomp) == 1:
raise ValueError("Cannot set {} directly when creating "
"the node or using the .set() method; "
"use the specific method instead.".format(
incomp[0]))
else:
raise ValueError("Cannot set {} at the same time".format(
" and ".join(incomp)))
for k, v in arguments.iteritems():
try:
if allow_hidden and k.startswith("_"):
method = getattr(self, '_set_{}'.format(k[1:]))
else:
method = getattr(self, 'set_{}'.format(k))
except AttributeError:
raise ValueError("Unable to set '{0}', no set_{0} method "
"found".format(k))
if not isinstance(method, collections.Callable):
raise ValueError("Unable to set '{0}', set_{0} is not "
"callable!".format(k))
method(v)
@property
def label(self):
"""
Get the label of the node.
:return: a string.
"""
return self.dbnode.label
@label.setter
def label(self, label):
"""
Set the label of the node.
:param label: a string
"""
self._update_db_label_field(label)
@abstractmethod
def _update_db_label_field(self, field_value):
"""
Update the label field acting directly on the DB
"""
pass
@property
def description(self):
"""
Get the description of the node.
:return: a string
"""
return self.dbnode.description
@description.setter
def description(self, desc):
"""
Set the description of the node
:param desc: a string
"""
self._update_db_description_field(desc)
@abstractmethod
def _update_db_description_field(self, field_value):
"""
Update the description of this node, acting directly at the DB level
"""
pass
def _validate(self):
"""
Check if the attributes and files retrieved from the DB are valid.
Raise a ValidationError if something is wrong.
Must be able to work even before storing: therefore, use the get_attr
and similar methods that automatically read either from the DB or
from the internal attribute cache.
For the base class, this is always valid. Subclasses will
reimplement this.
In the subclass, always call the super()._validate() method first!
"""
return True
def get_user(self):
"""
Get the user.
:return: a Django DbUser model object
"""
return self.dbnode.user
def _has_cached_links(self):
"""
Return True if there is at least one cached (input) link, that is a
link that is not stored yet in the database. False otherwise.
"""
return len(self._inputlinks_cache) != 0
def add_link_from(self, src, label=None, link_type=LinkType.UNSPECIFIED):
"""
Add a link to the current node from the 'src' node.
Both nodes must be a Node instance (or a subclass of Node)
:note: In subclasses, change only this. Moreover, remember to call
the super() method in order to properly use the caching logic!
:param src: the source object
:param str label: the name of the label to set the link from src.
Default = None.
:param link_type: The type of link, must be one of the enum values
from :class:`~aiida.common.links.LinkType`
"""
assert src, "You must provide a valid Node to link"
# Check that the label does not already exist
# This can happen also if both nodes are stored, e.g. if one first
# stores the output node and then the input node. Therefore I check
# it here.
if label in self._inputlinks_cache:
raise UniquenessError("Input link with name '{}' already present "
"in the internal cache".format(label))
# See if I am pointing to already saved nodes and I am already
# linking to a given node
if src.uuid in [_[0].uuid for _ in self._inputlinks_cache.values()]:
raise UniquenessError(
"A link from node with UUID={} and "
"the current node (UUID={}) already exists!".format(
src.uuid, self.uuid))
# Check if the source allows output links from this node
# (will raise ValueError if this is not the case)
src._linking_as_output(self, link_type)
# If both are stored, write directly on the DB
if self.is_stored and src.is_stored:
self._add_dblink_from(src, label, link_type)
else: # at least one is not stored: add to the internal cache
self._add_cachelink_from(src, label, link_type)
def _add_cachelink_from(self, src, label, link_type):
"""
Add a link in the cache.
"""
if label is None:
raise ModificationNotAllowed(
"Cannot store a link in the cache if "
"no explicit label is provided. You can avoid "
"to provide an input link name only if "
"both nodes are already stored: in this case, "
"the link will be directly stored in the DB "
"and a default name will be provided")
if label in self._inputlinks_cache:
raise UniquenessError("Input link with name '{}' already present "
"in the internal cache".format(label))
self._inputlinks_cache[label] = (src, link_type)
def _replace_link_from(self, src, label, link_type=LinkType.UNSPECIFIED):
"""
Replace an input link with the given label, or simply creates it
if it does not exist.
:note: In subclasses, change only this. Moreover, remember to call
the super() method in order to properly use the caching logic!
:param src: the source object
:param str label: the name of the label to set the link from src.
"""
# If both are stored, write directly on the DB
if self.is_stored and src.is_stored:
self._replace_dblink_from(src, label, link_type)
# If the link was in the local cache, remove it
# (this could happen if I first store the output node, then
# the input node.
try:
del self._inputlinks_cache[label]
except KeyError:
pass
else: # at least one is not stored: set in the internal cache
# See if I am pointing to already saved nodes and I am already
# linking to a given node
# It is similar to the 'add' method, but if I am replacing the
# same node, I will not complain (k!=label)
if src.uuid in [v[0].uuid for k, v in
self._inputlinks_cache.iteritems() if k != label]:
raise UniquenessError(
"A link from node with UUID={} and "
"the current node (UUID={}) already exists!".format(
src.uuid, self.uuid))
# I insert the link directly in the cache rather than calling
# _add_cachelink_from because this latter performs an undesired check
self._inputlinks_cache[label] = (src, link_type)
# self._add_cachelink_from(src, label, link_type)
def _remove_link_from(self, label):
"""
Remove from the DB the input link with the given label.
:note: In subclasses, change only this. Moreover, remember to call
the super() method in order to properly use the caching logic!
:note: No error is raised if the link does not exist.
:param str label: the name of the label to set the link from src.
:param link_type: The type of link, must be one of the enum values form
:class:`~aiida.common.links.LinkType`
"""
# Try to remove from the local cache, no problem if none is present
try:
del self._inputlinks_cache[label]
except KeyError:
pass
# If both are stored, remove also from the DB
if self.is_stored:
self._remove_dblink_from(label)
@abstractmethod
def _replace_dblink_from(self, src, label, link_type):
"""
Replace an input link with the given label and type, or simply creates
it if it does not exist.
:note: this function should not be called directly; it acts directly on
the database.
:param str src: the source object.
:param str label: the label of the link from src to the current Node
:param link_type: The type of link, must be one of the enum values form
:class:`~aiida.common.links.LinkType`
"""
pass
@abstractmethod
def _remove_dblink_from(self, label):
"""
Remove from the DB the input link with the given label.
:note: this function should not be called directly; it acts directly on
the database.
:note: No checks are done to verify that the link actually exists.
:param str label: the label of the link from src to the current Node
:param link_type: The type of link, must be one of the enum values form
:class:`~aiida.common.links.LinkType`
"""
pass
@abstractmethod
def _add_dblink_from(self, src, label=None, link_type=LinkType.UNSPECIFIED):
"""
Add a link to the current node from the 'src' node.
Both nodes must be a Node instance (or a subclass of Node)
:note: this function should not be called directly; it acts directly on
the database.
:param src: the source object
:param str label: the name of the label to set the link from src.
Default = None.
"""
pass
def _linking_as_output(self, dest, link_type):
"""
Raise a ValueError if a link from self to dest is not allowed.
Implement in subclasses.
:param dest: the destination output Node
:return: a boolean (True)
"""
return True
def get_inputs_dict(self, only_in_db=False, link_type=None):
"""
Return a dictionary where the key is the label of the input link, and
the value is the input node.
:param only_in_db: If true only get stored links, not cached
:param link_type: Only get inputs of this link type, if None then
returns all inputs of all link types.
:return: a dictionary {label:object}
"""
return dict(
self.get_inputs(
also_labels=True, only_in_db=only_in_db, link_type=link_type))
def get_outputs_dict(self, link_type=None):
"""
Return a dictionary where the key is the label of the output link, and
the value is the input node.
As some Nodes (Datas in particular) can have more than one output with
the same label, all keys have the name of the link with appended the pk
of the node in output.
The key without pk appended corresponds to the oldest node.
:return: a dictionary {linkname:object}
"""
all_outputs = self.get_outputs(also_labels=True, link_type=link_type)
all_linknames = [i[0] for i in all_outputs]
linknames_set = list(set(all_linknames))
# prepare a new output list
new_outputs = {}
# first add the defaults
for irreducible_linkname in linknames_set:
this_elements = [i[1] for i in all_outputs if i[0] == irreducible_linkname]
# select the oldest element
last_element = sorted(this_elements, key=lambda x: x.ctime)[0]
# for this one add the default value
new_outputs[irreducible_linkname] = last_element
# now for everyone append the string with the pk
for i in this_elements:
new_outputs[irreducible_linkname + "_{}".format(i.pk)] = i
return new_outputs
@abstractmethod
def get_inputs(self, node_type=None, also_labels=False, only_in_db=False,
link_type=None):
"""
Return a list of nodes that enter (directly) in this node
:param node_type: If specified, should be a class, and it filters only
elements of that specific type (or a subclass of 'type')
:param also_labels: If False (default) only return a list of input nodes.
If True, return a list of tuples, where each tuple has the
following format: ('label', Node), with 'label' the link label,
and Node a Node instance or subclass
:param only_in_db: Return only the inputs that are in the database,
ignoring those that are in the local cache. Otherwise, return
all links.
:param link_type: Only get inputs of this link type, if None then
returns all inputs of all link types.
"""
pass
@abstractmethod
def get_outputs(self, type=None, also_labels=False, link_type=None):
"""
Return a list of nodes that exit (directly) from this node
:param type: if specified, should be a class, and it filters only
elements of that specific type (or a subclass of 'type')
:param also_labels: if False (default) only return a list of input nodes.
If True, return a list of tuples, where each tuple has the
following format: ('label', Node), with 'label' the link label,
and Node a Node instance or subclass
:param link_type: Only return outputs connected by links of this type.
"""
pass
def get_computer(self):
"""
Get the computer associated to the node.
:return: the Computer object or None.
"""
from aiida.orm.computer import Computer
if self.dbnode.dbcomputer is None:
return None
else:
return Computer(dbcomputer=self.dbnode.dbcomputer)
@abstractmethod
def set_computer(self, computer):
"""
Set the computer to be used by the node.
Note that the computer makes sense only for some nodes: Calculation,
RemoteData, ...
:param computer: the computer object
"""
# TODO: probably this method should be in the base class, and
# check for the type
pass
@abstractmethod
def _set_attr(self, key, value):
"""
Set a new attribute to the Node (in the DbAttribute table).
:param str key: key name
:param value: its value
:raise ModificationNotAllowed: if such attribute cannot be added (e.g.
because the node was already stored, and the attribute is not listed
as updatable).
:raise ValidationError: if the key is not valid (e.g. it contains the
separator symbol).
"""
pass
@abstractmethod
def _del_attr(self, key):
"""
Delete an attribute.
:param key: attribute to delete.
:raise AttributeError: if key does not exist.
:raise ModificationNotAllowed: if the Node was already stored.
"""
pass
def _del_all_attrs(self):
"""
Delete all attributes associated to this node.
:raise ModificationNotAllowed: if the Node was already stored.
"""
# I have to convert the attrs in a list, because the list will change
# while deleting elements
for attr_name in list(self.attrs()):
self._del_attr(attr_name)
@abstractmethod
def get_attr(self, key, default=_NO_DEFAULT):
"""
Get the attribute.
:param key: name of the attribute
:param default: if no attribute key is found, returns default
:return: attribute value
:raise AttributeError: If no attribute is found and there is no default
"""
pass
@abstractmethod
def set_extra(self, key, value, exclusive=False):
"""
Immediately sets an extra of a calculation, in the DB!
No .store() to be called. Can be used *only* after saving.
:param key: key name
:param value: key value
:param exclusive: (default=False).
If exclusive is True, it raises a UniquenessError if an Extra with
the same name already exists in the DB (useful e.g. to "lock" a
node and avoid to run multiple times the same computation on it).
:raise UniquenessError: if extra already exists and exclusive is True.
"""
pass
def set_extras(self, the_dict):
"""
Immediately sets several extras of a calculation, in the DB!
No .store() to be called.
Can be used *only* after saving.
:param the_dict: a dictionary of key:value to be set as extras
"""
try:
for key, value in the_dict.iteritems():
self.set_extra(key, value)
except AttributeError:
raise AttributeError("set_extras takes a dictionary as argument")
@abstractmethod
def reset_extras(self, new_extras):
"""
Deletes existing extras and creates new ones.
:param new_extras: dictionary with new extras
:return: nothing, an exceptions is raised in several circumnstances
"""
pass
@abstractmethod
def get_extra(self, key, *args):
"""
Get the value of a extras, reading directly from the DB!
Since extras can be added only after storing the node, this
function is meaningful to be called only after the .store() method.
:param key: key name
:param value: if no attribute key is found, returns value
:return: the key value
:raise ValueError: If more than two arguments are passed to get_extra
"""
pass
@abstractmethod
def get_extras(self):
"""
Get the value of extras, reading directly from the DB!
Since extras can be added only after storing the node, this
function is meaningful to be called only after the .store() method.
:return: the dictionary of extras ({} if no extras)
"""
pass
@abstractmethod
def del_extra(self, key):
"""
Delete a extra, acting directly on the DB!
The action is immediately performed on the DB.
Since extras can be added only after storing the node, this
function is meaningful to be called only after the .store() method.
:param str key: key name
:raise: AttributeError: if key starts with underscore
:raise: ModificationNotAllowed: if the node is not stored yet
"""
pass
@abstractmethod
def extras(self):
"""
Get the keys of the extras.
:return: a list of strings
"""
pass
@abstractmethod
def iterextras(self):
"""
Iterator over the extras, returning tuples (key, value)
:todo: verify that I am not creating a list internally
"""
pass
@abstractmethod
def iterattrs(self):
"""
Iterator over the attributes, returning tuples (key, value)
:todo: optimize! At the moment, the call is very slow because it is
also calling attr.getvalue() for each attribute, that has to
perform complicated queries to rebuild the object.
:param bool also_updatable: if False, does not iterate over
attributes that are updatable
"""
pass
@abstractmethod
def get_attrs(self):
"""
Return a dictionary with all attributes of this node.
"""
pass
@abstractmethod
def attrs(self):
"""
Returns the keys of the attributes.
:return: a list of strings
"""
# Note: I "duplicate" the code from iterattrs, rather than
# calling iterattrs from here, because iterattrs is slow on each call
# since it has to call .getvalue(). To improve!
pass
@abstractmethod
def add_comment(self, content, user=None):
"""
Add a new comment.
:param content: string with comment
"""
pass
@abstractmethod
def get_comments(self, pk=None):
"""
Return a sorted list of comment values, one for each comment associated
to the node.
:param pk: integer or list of integers. If it is specified, returns the
comment values with desired pks. (pk refers to DbComment.pk)
:return: the list of comments, sorted by pk; each element of the
list is a dictionary, containing (pk, email, ctime, mtime, content)
"""
pass
@abstractmethod
def _get_dbcomments(self, pk=None):
"""
Return a sorted list of DbComment associated with the Node.
:param pk: integer or list of integers. If it is specified, returns the
comment values with desired pks. (pk refers to DbComment.pk)
:return: the list of DbComment, sorted by pk.
"""
pass
@abstractmethod
def _update_comment(self, new_field, comment_pk, user):
"""
Function called by verdi comment update
"""
pass
@abstractmethod
def _remove_comment(self, comment_pk, user):
"""
Function called by verdi comment remove
"""
pass
@abstractmethod
def _increment_version_number_db(self):
"""
This function increments the version number in the DB.
This should be called every time you need to increment the version
(e.g. on adding a extra or attribute).
:note: Do not manually increment the version number, because if
two different threads are adding/changing an attribute concurrently,
the version number would be incremented only once.
"""
pass
@abstractmethod
def copy(self):
"""
Return a copy of the current object to work with, not stored yet.
This is a completely new entry in the DB, with its own UUID.
Works both on stored instances and with not-stored ones.
Copies files and attributes, but not the extras.
Does not store the Node to allow modification of attributes.
:return: an object copy
"""
pass
@property
@abstractmethod
def uuid(self):
"""
:return: a string with the uuid
"""
pass
@property
@abstractmethod
def pk(self):
"""
:return: the principal key (the ID) as an integer, or None if the
node was not stored yet
"""
pass
@property
@abstractmethod
def id(self):
"""
:return: the principal key (the ID) as an integer, or None if the
node was not stored yet
"""
pass
@property
@abstractmethod
def dbnode(self):
"""
:return: the corresponding DbNode object.
"""
# I also update the internal _dbnode variable, if it was saved
# from aiida.backends.djsite.db.models import DbNode
# if not self._to_be_stored:
# self._dbnode = DbNode.objects.get(pk=self._dbnode.pk)
pass
@property
def _repository_folder(self):
"""
Get the permanent repository folder.
Use preferentially the folder property.
:return: the permanent RepositoryFolder object
"""
return self._repo_folder
@property
def folder(self):
"""
Get the folder associated with the node,
whether it is in the temporary or the permanent repository.
:return: the RepositoryFolder object.
"""
if not self.is_stored:
return self._get_temp_folder()
else:
return self._repository_folder
@property
def _get_folder_pathsubfolder(self):
"""
Get the subfolder in the repository.
:return: a Folder object.
"""
return self.folder.get_subfolder(
self._path_subfolder_name, reset_limit=True)
def get_folder_list(self, subfolder='.'):
"""
Get the the list of files/directory in the repository of the object.
:param subfolder: get the list of a subfolder
:return: a list of strings.
"""
return self._get_folder_pathsubfolder.get_subfolder(subfolder).get_content_list()
def _get_temp_folder(self):
"""
Get the folder of the Node in the temporary repository.
:return: a SandboxFolder object mapping the node in the repository.
"""
# I create the temp folder only at is first usage
if self._temp_folder is None:
self._temp_folder = SandboxFolder() # This is also created
# Create the 'path' subfolder in the Sandbox
self._get_folder_pathsubfolder.create()
return self._temp_folder
def remove_path(self, path):
"""
Remove a file or directory from the repository directory.
Can be called only before storing.
:param str path: relative path to file/directory.
"""
if self.is_stored:
raise ModificationNotAllowed(
"Cannot delete a path after storing the node")
if os.path.isabs(path):
raise ValueError("The destination path in remove_path "
"must be a relative path")
self._get_folder_pathsubfolder.remove_path(path)
def add_path(self, src_abs, dst_path):
"""
Copy a file or folder from a local file inside the repository directory.
If there is a subpath, folders will be created.
Copy to a cache directory if the entry has not been saved yet.
:param str src_abs: the absolute path of the file to copy.
:param str dst_filename: the (relative) path on which to copy.
:todo: in the future, add an add_attachment() that has the same
meaning of a extras file. Decide also how to store. If in two
separate subfolders, remember to reset the limit.
"""
if self.is_stored:
raise ModificationNotAllowed(
"Cannot insert a path after storing the node")
if not os.path.isabs(src_abs):
raise ValueError("The source path in add_path must be absolute")
if os.path.isabs(dst_path):
raise ValueError("The destination path in add_path must be a"
"filename without any subfolder")
self._get_folder_pathsubfolder.insert_path(src_abs, dst_path)
def get_abs_path(self, path=None, section=None):
"""
Get the absolute path to the folder associated with the
Node in the AiiDA repository.
:param str path: the name of the subfolder inside the section. If None
returns the abspath of the folder. Default = None.
:param section: the name of the subfolder ('path' by default).
:return: a string with the absolute path
For the moment works only for one kind of files, 'path' (internal files)
"""
if path is None:
return self.folder.abspath
if section is None:
section = self._path_subfolder_name
# TODO: For the moment works only for one kind of files,
# 'path' (internal files)
if os.path.isabs(path):
raise ValueError("The path in get_abs_path must be relative")
return self.folder.get_subfolder(section,
reset_limit=True).get_abs_path(path, check_existence=True)
@abstractmethod
def store_all(self, with_transaction=True):
"""
Store the node, together with all input links, if cached, and also the
linked nodes, if they were not stored yet.
:parameter with_transaction: if False, no transaction is used. This
is meant to be used ONLY if the outer calling function has already
a transaction open!
"""
pass
@abstractmethod
def _store_input_nodes(self):
"""
Find all input nodes, and store them, checking that they do not
have unstored inputs in turn.
:note: this function stores all nodes without transactions; always
call it from within a transaction!
"""
pass
@abstractmethod
def _check_are_parents_stored(self):
"""
Check if all parents are already stored, otherwise raise.
:raise ModificationNotAllowed: if one of the input nodes in not already
stored.
"""
# Preliminary check to verify that inputs are stored already
pass
@abstractmethod
def _store_cached_input_links(self, with_transaction=True):
"""
Store all input links that are in the local cache, transferring them
to the DB.
:note: This can be called only if all parents are already stored.
:note: Links are stored only after the input nodes are stored. Moreover,
link storage is done in a transaction, and if one of the links
cannot be stored, an exception is raised and *all* links will remain
in the cache.
:note: This function can be called only after the node is stored.
After that, it can be called multiple times, and nothing will be
executed if no links are still in the cache.
:parameter with_transaction: if False, no transaction is used. This
is meant to be used ONLY if the outer calling function has already
a transaction open!
"""
pass
@abstractmethod
def store(self, with_transaction=True):
"""
Store a new node in the DB, also saving its repository directory
and attributes.
After being called attributes cannot be
changed anymore! Instead, extras can be changed only AFTER calling
this store() function.
:note: After successful storage, those links that are in the cache, and
for which also the parent node is already stored, will be
automatically stored. The others will remain unstored.
:parameter with_transaction: if False, no transaction is used. This
is meant to be used ONLY if the outer calling function has already
a transaction open!
"""
# TODO: This needs to be generalized, allowing for flexible methods
# for storing data and its attributes.
pass
def __del__(self):
"""
Called only upon real object destruction from memory
I just try to remove junk, whenever possible; do not trust
too much this function!
"""
if getattr(self, '_temp_folder', None) is not None:
self._temp_folder.erase()
@property
def out(self):
"""
Traverse the graph of the database.
Returns a databaseobject, linked to the current node, by means of the linkname.
Example:
B = A.out.results: Returns the object B, with link from A to B, with linkname parameters
"""
return NodeOutputManager(self)
@property
def inp(self):
"""
Traverse the graph of the database.
Returns a databaseobject, linked to the current node, by means of the linkname.
Example:
B = A.inp.parameters: returns the object (B), with link from B to A, with linkname parameters
C= A.inp: returns an InputManager, an object that is meant to be accessed as the previous example
"""
return NodeInputManager(self)
@abstractproperty
def has_children(self):
"""
Property to understand if children are attached to the node
:return: a boolean
"""
# use the transitive closure
pass
@abstractproperty
def has_parents(self):
"""
Property to understand if parents are attached to the node
:return: a boolean
"""
# use the transitive closure
pass
@combomethod
def querybuild(self_or_cls, **kwargs):
"""
Instantiates and
:returns: a QueryBuilder instance.
The QueryBuilder's path has one vertice so far, namely this class.
Additional parameters (e.g. filters or a label),
can be passes as keyword arguments.
:param label: Label to give
:param filters: filters to apply
:param project: projections
This class is a comboclass (see :func:`~aiida.common.utils.combomethod`)
therefore the method can be called as class or instance method.
If called as an instance method, adds a filter on the id.
"""
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm import Node as AiidaNode
isclass = kwargs.pop('isclass')
qb = QueryBuilder()
if isclass:
qb.append(self_or_cls, **kwargs)
else:
filters = kwargs.pop('filters', {})
filters.update({'id': self_or_cls.pk})
qb.append(self_or_cls.__class__, filters=filters, **kwargs)
return qb
class ReaderJsonBase(ArchiveReaderAbstract):
"""A reader base for the JSON compressed formats."""
FILENAME_DATA = 'data.json'
FILENAME_METADATA = 'metadata.json'
REPO_FOLDER = NODES_EXPORT_SUBFOLDER
def __init__(self,
filename: str,
sandbox_in_repo: bool = False,
**kwargs: Any):
"""A reader for JSON compressed archives.
:param filename: the filename (possibly including the absolute path)
of the file on which to export.
:param sandbox_in_repo: Create the temporary uncompressed folder within the aiida repository
"""
super().__init__(filename, **kwargs)
self._metadata = None
self._data = None
# a temporary folder used to extract the file tree
self._sandbox: Optional[SandboxFolder] = None
self._sandbox_in_repo = sandbox_in_repo
@property
def file_format_verbose(self) -> str:
raise NotImplementedError()
@property
def compatible_export_version(self) -> str:
return EXPORT_VERSION
def __enter__(self):
super().__enter__()
self._sandbox = SandboxFolder(self._sandbox_in_repo)
return self
def __exit__(self, exctype: Optional[Type[BaseException]],
excinst: Optional[BaseException],
exctb: Optional[TracebackType]):
self._sandbox.erase() # type: ignore
self._sandbox = None
self._metadata = None
self._data = None
super().__exit__(exctype, excinst, exctb)
def _get_metadata(self):
"""Retrieve the metadata JSON."""
raise NotImplementedError()
def _get_data(self):
"""Retrieve the data JSON."""
raise NotImplementedError()
def _extract(self, *, path_prefix: str, callback: Callable[[str, Any],
None]):
"""Extract repository data to a temporary folder.
:param path_prefix: Only extract paths starting with this prefix.
:param callback: a callback to report on the process, ``callback(action, value)``,
with the following callback signatures:
- ``callback('init', {'total': <int>, 'description': <str>})``,
to signal the start of a process, its total iterations and description
- ``callback('update', <int>)``,
to signal an update to the process and the number of iterations to progress
:raises TypeError: if parameter types are not respected
"""
raise NotImplementedError()
@property
def export_version(self) -> str:
metadata = self._get_metadata()
if 'export_version' not in metadata:
raise CorruptArchive('export_version missing from metadata.json')
return metadata['export_version']
@property
def metadata(self) -> ArchiveMetadata:
metadata = self._get_metadata()
export_parameters = metadata.get('export_parameters', {})
output = {
'export_version':
metadata['export_version'],
'aiida_version':
metadata['aiida_version'],
'all_fields_info':
metadata['all_fields_info'],
'unique_identifiers':
metadata['unique_identifiers'],
'graph_traversal_rules':
export_parameters.get('graph_traversal_rules', None),
'entities_starting_set':
export_parameters.get('entities_starting_set', None),
'include_comments':
export_parameters.get('include_comments', None),
'include_logs':
export_parameters.get('include_logs', None),
'conversion_info':
metadata.get('conversion_info', [])
}
try:
return ArchiveMetadata(**output)
except TypeError as error:
raise CorruptArchive(f'Metadata invalid: {error}')
def entity_count(self, name: str) -> int:
data = self._get_data().get('export_data', {}).get(name, {})
return len(data)
@property
def link_count(self) -> int:
return len(self._get_data()['links_uuid'])
def iter_entity_fields(
self,
name: str,
fields: Optional[Tuple[str, ...]] = None
) -> Iterator[Tuple[int, Dict[str, Any]]]:
if name not in self.entity_names:
raise ValueError(f'Unknown entity name: {name}')
data = self._get_data()['export_data'].get(name, {})
if name == NODE_ENTITY_NAME:
# here we merge in the attributes and extras before yielding
attributes = self._get_data().get('node_attributes', {})
extras = self._get_data().get('node_extras', {})
for pk, all_fields in data.items():
if pk not in attributes:
raise CorruptArchive(
f'Unable to find attributes info for Node with Pk={pk}'
)
if pk not in extras:
raise CorruptArchive(
f'Unable to find extra info for Node with Pk={pk}')
all_fields = {
**all_fields,
**{
'attributes': attributes[pk],
'extras': extras[pk]
}
}
if fields is not None:
all_fields = {
k: v
for k, v in all_fields.items() if k in fields
}
yield int(pk), all_fields
else:
for pk, all_fields in data.items():
if fields is not None:
all_fields = {
k: v
for k, v in all_fields.items() if k in fields
}
yield int(pk), all_fields
def iter_node_uuids(self) -> Iterator[str]:
for _, fields in self.iter_entity_fields(NODE_ENTITY_NAME,
fields=('uuid', )):
yield fields['uuid']
def iter_group_uuids(self) -> Iterator[Tuple[str, Set[str]]]:
group_uuids = self._get_data()['groups_uuid']
for _, fields in self.iter_entity_fields(GROUP_ENTITY_NAME,
fields=('uuid', )):
key = fields['uuid']
yield key, set(group_uuids.get(key, set()))
def iter_link_data(self) -> Iterator[dict]:
for value in self._get_data()['links_uuid']:
yield value
def iter_node_repos(
self,
uuids: Iterable[str],
callback: Callable[[str, Any], None] = null_callback,
) -> Iterator[Folder]:
path_prefixes = [
os.path.join(self.REPO_FOLDER, export_shard_uuid(uuid))
for uuid in uuids
]
if not path_prefixes:
return
self.assert_within_context()
assert self._sandbox is not None # required by mypy
# unarchive the common folder if it does not exist
common_prefix = os.path.commonpath(path_prefixes)
if not self._sandbox.get_subfolder(common_prefix).exists():
self._extract(path_prefix=common_prefix, callback=callback)
callback(
'init', {
'total': len(path_prefixes),
'description': 'Iterating node repositories'
})
for uuid, path_prefix in zip(uuids, path_prefixes):
callback('update', 1)
subfolder = self._sandbox.get_subfolder(path_prefix)
if not subfolder.exists():
raise CorruptArchive(
f'Unable to find the repository folder for Node with UUID={uuid} in the exported file'
)
yield subfolder