repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.unique_identifier | def unique_identifier(self, purl):
"""
Set the unique identifier by looking through ``mods:identifier``
See `specs <https://ocr-d.github.io/mets#unique-id-for-the-document-processed>`_ for details.
"""
id_el = None
for t in IDENTIFIER_PRIORITY:
id_el = self._... | python | def unique_identifier(self, purl):
"""
Set the unique identifier by looking through ``mods:identifier``
See `specs <https://ocr-d.github.io/mets#unique-id-for-the-document-processed>`_ for details.
"""
id_el = None
for t in IDENTIFIER_PRIORITY:
id_el = self._... | Set the unique identifier by looking through ``mods:identifier``
See `specs <https://ocr-d.github.io/mets#unique-id-for-the-document-processed>`_ for details. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L72-L87 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.agents | def agents(self):
"""
List all `OcrdAgent </../../ocrd_models/ocrd_models.ocrd_agent.html>`_
"""
return [OcrdAgent(el_agent) for el_agent in self._tree.getroot().findall('mets:metsHdr/mets:agent', NS)] | python | def agents(self):
"""
List all `OcrdAgent </../../ocrd_models/ocrd_models.ocrd_agent.html>`_
"""
return [OcrdAgent(el_agent) for el_agent in self._tree.getroot().findall('mets:metsHdr/mets:agent', NS)] | List all `OcrdAgent </../../ocrd_models/ocrd_models.ocrd_agent.html>`_ | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L90-L94 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.add_agent | def add_agent(self, *args, **kwargs):
"""
Add an `OcrdAgent </../../ocrd_models/ocrd_models.ocrd_agent.html>`_ to the list of agents in the metsHdr.
"""
el_metsHdr = self._tree.getroot().find('.//mets:metsHdr', NS)
if el_metsHdr is None:
el_metsHdr = ET.Element(TAG_ME... | python | def add_agent(self, *args, **kwargs):
"""
Add an `OcrdAgent </../../ocrd_models/ocrd_models.ocrd_agent.html>`_ to the list of agents in the metsHdr.
"""
el_metsHdr = self._tree.getroot().find('.//mets:metsHdr', NS)
if el_metsHdr is None:
el_metsHdr = ET.Element(TAG_ME... | Add an `OcrdAgent </../../ocrd_models/ocrd_models.ocrd_agent.html>`_ to the list of agents in the metsHdr. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L96-L107 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.file_groups | def file_groups(self):
"""
List the ``USE`` attributes of all ``mets:fileGrp``.
"""
return [el.get('USE') for el in self._tree.getroot().findall('.//mets:fileGrp', NS)] | python | def file_groups(self):
"""
List the ``USE`` attributes of all ``mets:fileGrp``.
"""
return [el.get('USE') for el in self._tree.getroot().findall('.//mets:fileGrp', NS)] | List the ``USE`` attributes of all ``mets:fileGrp``. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L110-L114 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.find_files | def find_files(self, ID=None, fileGrp=None, pageId=None, mimetype=None, url=None, local_only=False):
"""
Search ``mets:file`` in this METS document.
Args:
ID (string) : ID of the file
fileGrp (string) : USE of the fileGrp to list files of
pageId (string) : ID... | python | def find_files(self, ID=None, fileGrp=None, pageId=None, mimetype=None, url=None, local_only=False):
"""
Search ``mets:file`` in this METS document.
Args:
ID (string) : ID of the file
fileGrp (string) : USE of the fileGrp to list files of
pageId (string) : ID... | Search ``mets:file`` in this METS document.
Args:
ID (string) : ID of the file
fileGrp (string) : USE of the fileGrp to list files of
pageId (string) : ID of physical page manifested by matching files
url (string) : @xlink:href of mets:Flocat of mets:file
... | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L116-L162 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.add_file_group | def add_file_group(self, fileGrp):
"""
Add a new ``mets:fileGrp``.
Arguments:
fileGrp (string): ``USE`` attribute of the new filegroup.
"""
el_fileSec = self._tree.getroot().find('mets:fileSec', NS)
if el_fileSec is None:
el_fileSec = ET.SubElemen... | python | def add_file_group(self, fileGrp):
"""
Add a new ``mets:fileGrp``.
Arguments:
fileGrp (string): ``USE`` attribute of the new filegroup.
"""
el_fileSec = self._tree.getroot().find('mets:fileSec', NS)
if el_fileSec is None:
el_fileSec = ET.SubElemen... | Add a new ``mets:fileGrp``.
Arguments:
fileGrp (string): ``USE`` attribute of the new filegroup. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L164-L178 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.add_file | def add_file(self, fileGrp, mimetype=None, url=None, ID=None, pageId=None, force=False, local_filename=None, **kwargs):
"""
Add a `OcrdFile </../../ocrd_models/ocrd_models.ocrd_file.html>`_.
Arguments:
fileGrp (string): Add file to ``mets:fileGrp`` with this ``USE`` attribute
... | python | def add_file(self, fileGrp, mimetype=None, url=None, ID=None, pageId=None, force=False, local_filename=None, **kwargs):
"""
Add a `OcrdFile </../../ocrd_models/ocrd_models.ocrd_file.html>`_.
Arguments:
fileGrp (string): Add file to ``mets:fileGrp`` with this ``USE`` attribute
... | Add a `OcrdFile </../../ocrd_models/ocrd_models.ocrd_file.html>`_.
Arguments:
fileGrp (string): Add file to ``mets:fileGrp`` with this ``USE`` attribute
mimetype (string):
url (string):
ID (string):
pageId (string):
force (boolean): Whethe... | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L180-L213 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.set_physical_page_for_file | def set_physical_page_for_file(self, pageId, ocrd_file, order=None, orderlabel=None):
"""
Create a new physical page
"""
# print(pageId, ocrd_file)
# delete any page mapping for this file.ID
for el_fptr in self._tree.getroot().findall(
'mets:structMap[@TY... | python | def set_physical_page_for_file(self, pageId, ocrd_file, order=None, orderlabel=None):
"""
Create a new physical page
"""
# print(pageId, ocrd_file)
# delete any page mapping for this file.ID
for el_fptr in self._tree.getroot().findall(
'mets:structMap[@TY... | Create a new physical page | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L224-L254 |
OCR-D/core | ocrd_models/ocrd_models/ocrd_mets.py | OcrdMets.get_physical_page_for_file | def get_physical_page_for_file(self, ocrd_file):
"""
Get the pageId for a ocrd_file
"""
ret = self._tree.getroot().xpath(
'/mets:mets/mets:structMap[@TYPE="PHYSICAL"]/mets:div[@TYPE="physSequence"]/mets:div[@TYPE="page"][./mets:fptr[@FILEID="%s"]]/@ID' %
ocrd_file... | python | def get_physical_page_for_file(self, ocrd_file):
"""
Get the pageId for a ocrd_file
"""
ret = self._tree.getroot().xpath(
'/mets:mets/mets:structMap[@TYPE="PHYSICAL"]/mets:div[@TYPE="physSequence"]/mets:div[@TYPE="page"][./mets:fptr[@FILEID="%s"]]/@ID' %
ocrd_file... | Get the pageId for a ocrd_file | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_models/ocrd_models/ocrd_mets.py#L256-L264 |
OCR-D/core | ocrd_validators/ocrd_validators/workspace_validator.py | WorkspaceValidator._validate | def _validate(self):
"""
Actual validation.
"""
try:
self._resolve_workspace()
if 'mets_unique_identifier' not in self.skip:
self._validate_mets_unique_identifier()
if 'mets_file_group_names' not in self.skip:
self._vali... | python | def _validate(self):
"""
Actual validation.
"""
try:
self._resolve_workspace()
if 'mets_unique_identifier' not in self.skip:
self._validate_mets_unique_identifier()
if 'mets_file_group_names' not in self.skip:
self._vali... | Actual validation. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_validators/ocrd_validators/workspace_validator.py#L66-L85 |
OCR-D/core | ocrd_validators/ocrd_validators/workspace_validator.py | WorkspaceValidator._resolve_workspace | def _resolve_workspace(self):
"""
Clone workspace from mets_url unless workspace was provided.
"""
if self.workspace is None:
self.workspace = self.resolver.workspace_from_url(self.mets_url, baseurl=self.src_dir, download=self.download)
self.mets = self.workspace.... | python | def _resolve_workspace(self):
"""
Clone workspace from mets_url unless workspace was provided.
"""
if self.workspace is None:
self.workspace = self.resolver.workspace_from_url(self.mets_url, baseurl=self.src_dir, download=self.download)
self.mets = self.workspace.... | Clone workspace from mets_url unless workspace was provided. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_validators/ocrd_validators/workspace_validator.py#L87-L93 |
OCR-D/core | ocrd_validators/ocrd_validators/workspace_validator.py | WorkspaceValidator._validate_pixel_density | def _validate_pixel_density(self):
"""
Validate image pixel density
See `spec <https://ocr-d.github.io/mets#pixel-density-of-images-must-be-explicit-and-high-enough>`_.
"""
for f in [f for f in self.mets.find_files() if f.mimetype.startswith('image/')]:
if not f.loca... | python | def _validate_pixel_density(self):
"""
Validate image pixel density
See `spec <https://ocr-d.github.io/mets#pixel-density-of-images-must-be-explicit-and-high-enough>`_.
"""
for f in [f for f in self.mets.find_files() if f.mimetype.startswith('image/')]:
if not f.loca... | Validate image pixel density
See `spec <https://ocr-d.github.io/mets#pixel-density-of-images-must-be-explicit-and-high-enough>`_. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_validators/ocrd_validators/workspace_validator.py#L104-L118 |
OCR-D/core | ocrd_validators/ocrd_validators/workspace_validator.py | WorkspaceValidator._validate_mets_file_group_names | def _validate_mets_file_group_names(self):
"""
Ensure ``USE`` attributes of ``mets:fileGrp`` conform to OCR-D naming schema..
See `spec <https://ocr-d.github.io/mets#file-group-use-syntax>`_.
"""
for fileGrp in self.mets.file_groups:
if not fileGrp.startswith(FILE_GR... | python | def _validate_mets_file_group_names(self):
"""
Ensure ``USE`` attributes of ``mets:fileGrp`` conform to OCR-D naming schema..
See `spec <https://ocr-d.github.io/mets#file-group-use-syntax>`_.
"""
for fileGrp in self.mets.file_groups:
if not fileGrp.startswith(FILE_GR... | Ensure ``USE`` attributes of ``mets:fileGrp`` conform to OCR-D naming schema..
See `spec <https://ocr-d.github.io/mets#file-group-use-syntax>`_. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_validators/ocrd_validators/workspace_validator.py#L120-L142 |
OCR-D/core | ocrd_validators/ocrd_validators/workspace_validator.py | WorkspaceValidator._validate_mets_files | def _validate_mets_files(self):
"""
Validate ``mets:file`` URLs are sane.
"""
if not self.mets.find_files():
self.report.add_error("No files")
for f in self.mets.find_files():
if f._el.get('GROUPID'): # pylint: disable=protected-access
self... | python | def _validate_mets_files(self):
"""
Validate ``mets:file`` URLs are sane.
"""
if not self.mets.find_files():
self.report.add_error("No files")
for f in self.mets.find_files():
if f._el.get('GROUPID'): # pylint: disable=protected-access
self... | Validate ``mets:file`` URLs are sane. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_validators/ocrd_validators/workspace_validator.py#L144-L160 |
OCR-D/core | ocrd_validators/ocrd_validators/workspace_validator.py | WorkspaceValidator._validate_page | def _validate_page(self):
"""
Run PageValidator on the PAGE-XML documents referenced in the METS.
"""
for ocrd_file in self.mets.find_files(mimetype=MIMETYPE_PAGE, local_only=True):
self.workspace.download_file(ocrd_file)
page_report = PageValidator.validate(ocrd_... | python | def _validate_page(self):
"""
Run PageValidator on the PAGE-XML documents referenced in the METS.
"""
for ocrd_file in self.mets.find_files(mimetype=MIMETYPE_PAGE, local_only=True):
self.workspace.download_file(ocrd_file)
page_report = PageValidator.validate(ocrd_... | Run PageValidator on the PAGE-XML documents referenced in the METS. | https://github.com/OCR-D/core/blob/57e68c578526cb955fd2e368207f5386c459d91d/ocrd_validators/ocrd_validators/workspace_validator.py#L162-L169 |
shtalinberg/django-actions-logger | actionslog/models.py | LogActionManager.create_log_action | def create_log_action(self, **kwargs):
"""
Helper method to create a new log entry.
This method automatically populates some fields when no explicit value is given.
:param instance: The model instance to log a change for.
:type instance: Model
:param kwargs: Field overrid... | python | def create_log_action(self, **kwargs):
"""
Helper method to create a new log entry.
This method automatically populates some fields when no explicit value is given.
:param instance: The model instance to log a change for.
:type instance: Model
:param kwargs: Field overrid... | Helper method to create a new log entry.
This method automatically populates some fields when no explicit value is given.
:param instance: The model instance to log a change for.
:type instance: Model
:param kwargs: Field overrides for the :py:class:`LogAction` object.
:return: T... | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/models.py#L28-L96 |
shtalinberg/django-actions-logger | actionslog/models.py | LogActionManager.get_for_objects | def get_for_objects(self, queryset):
"""
Get log entries for the objects in the specified queryset.
:param queryset: The queryset to get the log entries for.
:type queryset: QuerySet
:return: The LogAction objects for the objects in the given queryset.
:rtype: QuerySet
... | python | def get_for_objects(self, queryset):
"""
Get log entries for the objects in the specified queryset.
:param queryset: The queryset to get the log entries for.
:type queryset: QuerySet
:return: The LogAction objects for the objects in the given queryset.
:rtype: QuerySet
... | Get log entries for the objects in the specified queryset.
:param queryset: The queryset to get the log entries for.
:type queryset: QuerySet
:return: The LogAction objects for the objects in the given queryset.
:rtype: QuerySet | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/models.py#L114-L131 |
shtalinberg/django-actions-logger | actionslog/registry.py | ActionslogModelRegistry.register | def register(self, model, include_fields=[], exclude_fields=[]):
"""
Register a model with actionslog. Actionslog will then track mutations on this model's instances.
:param model: The model to register.
:type model: Model
:param include_fields: The fields to include. Implicitly... | python | def register(self, model, include_fields=[], exclude_fields=[]):
"""
Register a model with actionslog. Actionslog will then track mutations on this model's instances.
:param model: The model to register.
:type model: Model
:param include_fields: The fields to include. Implicitly... | Register a model with actionslog. Actionslog will then track mutations on this model's instances.
:param model: The model to register.
:type model: Model
:param include_fields: The fields to include. Implicitly excludes all other fields.
:type include_fields: list
:param exclude... | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/registry.py#L27-L45 |
shtalinberg/django-actions-logger | actionslog/diff.py | track_field | def track_field(field):
"""
Returns whether the given field should be tracked by Actionslog.
Untracked fields are many-to-many relations and relations to the Actionslog LogAction model.
:param field: The field to check.
:type field: Field
:return: Whether the given field should be tracked.
... | python | def track_field(field):
"""
Returns whether the given field should be tracked by Actionslog.
Untracked fields are many-to-many relations and relations to the Actionslog LogAction model.
:param field: The field to check.
:type field: Field
:return: Whether the given field should be tracked.
... | Returns whether the given field should be tracked by Actionslog.
Untracked fields are many-to-many relations and relations to the Actionslog LogAction model.
:param field: The field to check.
:type field: Field
:return: Whether the given field should be tracked.
:rtype: bool | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/diff.py#L8-L28 |
shtalinberg/django-actions-logger | actionslog/diff.py | model_instance_diff | def model_instance_diff(old, new):
"""
Calculates the differences between two model instances. One of the instances may be ``None`` (i.e., a newly
created model or deleted model). This will cause all fields with a value to have changed (from ``None``).
:param old: The old state of the model instance.
... | python | def model_instance_diff(old, new):
"""
Calculates the differences between two model instances. One of the instances may be ``None`` (i.e., a newly
created model or deleted model). This will cause all fields with a value to have changed (from ``None``).
:param old: The old state of the model instance.
... | Calculates the differences between two model instances. One of the instances may be ``None`` (i.e., a newly
created model or deleted model). This will cause all fields with a value to have changed (from ``None``).
:param old: The old state of the model instance.
:type old: Model
:param new: The new sta... | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/diff.py#L51-L116 |
shtalinberg/django-actions-logger | actionslog/middleware.py | ActionslogMiddleware.process_request | def process_request(self, request):
"""
Gets the current user from the request and prepares and connects a signal receiver with the user already
attached to it.
"""
# Initialize thread local storage
threadlocal.actionslog = {
'signal_duid': (self.__class__, ti... | python | def process_request(self, request):
"""
Gets the current user from the request and prepares and connects a signal receiver with the user already
attached to it.
"""
# Initialize thread local storage
threadlocal.actionslog = {
'signal_duid': (self.__class__, ti... | Gets the current user from the request and prepares and connects a signal receiver with the user already
attached to it. | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/middleware.py#L28-L46 |
shtalinberg/django-actions-logger | actionslog/middleware.py | ActionslogMiddleware.process_response | def process_response(self, request, response):
"""
Disconnects the signal receiver to prevent it from staying active.
"""
if hasattr(threadlocal, 'actionslog'):
pre_save.disconnect(sender=LogAction, dispatch_uid=threadlocal.actionslog['signal_duid'])
return response | python | def process_response(self, request, response):
"""
Disconnects the signal receiver to prevent it from staying active.
"""
if hasattr(threadlocal, 'actionslog'):
pre_save.disconnect(sender=LogAction, dispatch_uid=threadlocal.actionslog['signal_duid'])
return response | Disconnects the signal receiver to prevent it from staying active. | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/middleware.py#L48-L55 |
shtalinberg/django-actions-logger | actionslog/middleware.py | ActionslogMiddleware.process_exception | def process_exception(self, request, exception):
"""
Disconnects the signal receiver to prevent it from staying active in case of an exception.
"""
if hasattr(threadlocal, 'actionslog'):
pre_save.disconnect(sender=LogAction, dispatch_uid=threadlocal.actionslog['signal_duid'])... | python | def process_exception(self, request, exception):
"""
Disconnects the signal receiver to prevent it from staying active in case of an exception.
"""
if hasattr(threadlocal, 'actionslog'):
pre_save.disconnect(sender=LogAction, dispatch_uid=threadlocal.actionslog['signal_duid'])... | Disconnects the signal receiver to prevent it from staying active in case of an exception. | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/middleware.py#L57-L64 |
shtalinberg/django-actions-logger | actionslog/middleware.py | ActionslogMiddleware.set_user | def set_user(user, sender, instance, **kwargs):
"""
Signal receiver with an extra, required 'user' kwarg. This method becomes a real (valid) signal receiver when
it is curried with the user.
"""
try:
app_label, model_name = settings.AUTH_USER_MODEL.split('.')
... | python | def set_user(user, sender, instance, **kwargs):
"""
Signal receiver with an extra, required 'user' kwarg. This method becomes a real (valid) signal receiver when
it is curried with the user.
"""
try:
app_label, model_name = settings.AUTH_USER_MODEL.split('.')
... | Signal receiver with an extra, required 'user' kwarg. This method becomes a real (valid) signal receiver when
it is curried with the user. | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/middleware.py#L67-L80 |
shtalinberg/django-actions-logger | actionslog/receivers.py | action_log_create | def action_log_create(sender, instance, created, **kwargs):
"""
Signal receiver that creates a log entry when a model instance is first saved to the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead.
"""
if created:
changes = mod... | python | def action_log_create(sender, instance, created, **kwargs):
"""
Signal receiver that creates a log entry when a model instance is first saved to the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead.
"""
if created:
changes = mod... | Signal receiver that creates a log entry when a model instance is first saved to the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead. | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/receivers.py#L9-L22 |
shtalinberg/django-actions-logger | actionslog/receivers.py | action_log_update | def action_log_update(sender, instance, **kwargs):
"""
Signal receiver that creates a log entry when a model instance is changed and saved to the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead.
"""
if instance.pk is not None:
... | python | def action_log_update(sender, instance, **kwargs):
"""
Signal receiver that creates a log entry when a model instance is changed and saved to the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead.
"""
if instance.pk is not None:
... | Signal receiver that creates a log entry when a model instance is changed and saved to the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead. | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/receivers.py#L25-L47 |
shtalinberg/django-actions-logger | actionslog/receivers.py | action_log_delete | def action_log_delete(sender, instance, **kwargs):
"""
Signal receiver that creates a log entry when a model instance is deleted from the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead.
"""
if instance.pk is not None:
changes ... | python | def action_log_delete(sender, instance, **kwargs):
"""
Signal receiver that creates a log entry when a model instance is deleted from the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead.
"""
if instance.pk is not None:
changes ... | Signal receiver that creates a log entry when a model instance is deleted from the database.
Direct use is discouraged, connect your model through :py:func:`actionslog.registry.register` instead. | https://github.com/shtalinberg/django-actions-logger/blob/2a7200bfb277ace47464a77b57aa475a9710271a/actionslog/receivers.py#L50-L63 |
a10networks/acos-client | acos_client/v21/axapi_http.py | HttpClient.request | def request(self, method, api_url, params={}, **kwargs):
"""Generate the API call to the device."""
LOG.debug("axapi_http: full url = %s", self.url_base + api_url)
LOG.debug("axapi_http: %s url = %s", method, api_url)
LOG.debug("axapi_http: params = %s", json.dumps(logutils.clean(params... | python | def request(self, method, api_url, params={}, **kwargs):
"""Generate the API call to the device."""
LOG.debug("axapi_http: full url = %s", self.url_base + api_url)
LOG.debug("axapi_http: %s url = %s", method, api_url)
LOG.debug("axapi_http: params = %s", json.dumps(logutils.clean(params... | Generate the API call to the device. | https://github.com/a10networks/acos-client/blob/14d1fff589650650c9a65047d54c6c8c1d6b75f2/acos_client/v21/axapi_http.py#L108-L173 |
a10networks/acos-client | acos_client/v30/license_manager.py | LicenseManager.create | def create(self, host_list=[], serial=None, instance_name=None, use_mgmt_port=False,
interval=None, bandwidth_base=None, bandwidth_unrestricted=None):
"""Creates a license manager entry
Keyword arguments:
instance_name -- license manager instance name
host_list -- list(di... | python | def create(self, host_list=[], serial=None, instance_name=None, use_mgmt_port=False,
interval=None, bandwidth_base=None, bandwidth_unrestricted=None):
"""Creates a license manager entry
Keyword arguments:
instance_name -- license manager instance name
host_list -- list(di... | Creates a license manager entry
Keyword arguments:
instance_name -- license manager instance name
host_list -- list(dict) a list of dictionaries of the format:
{'ip': '127.0.0.1', 'port': 443}
serial - (str) appliance serial number
use_mgmt_port - (bool) use manageme... | https://github.com/a10networks/acos-client/blob/14d1fff589650650c9a65047d54c6c8c1d6b75f2/acos_client/v30/license_manager.py#L34-L54 |
a10networks/acos-client | acos_client/v30/license_manager.py | LicenseManager.update | def update(self, host_list=[], serial=None, instance_name=None, use_mgmt_port=False,
interval=None, bandwidth_base=None, bandwidth_unrestricted=None):
"""Update a license manager entry
Keyword arguments:
instance_name -- license manager instance name
host_list -- list(dic... | python | def update(self, host_list=[], serial=None, instance_name=None, use_mgmt_port=False,
interval=None, bandwidth_base=None, bandwidth_unrestricted=None):
"""Update a license manager entry
Keyword arguments:
instance_name -- license manager instance name
host_list -- list(dic... | Update a license manager entry
Keyword arguments:
instance_name -- license manager instance name
host_list -- list(dict) a list of dictionaries of the format:
{'ip': '127.0.0.1', 'port': 443}
serial - (str) appliance serial number
use_mgmt_port - (bool) use managemen... | https://github.com/a10networks/acos-client/blob/14d1fff589650650c9a65047d54c6c8c1d6b75f2/acos_client/v30/license_manager.py#L56-L75 |
a10networks/acos-client | acos_client/v30/device_context.py | DeviceContext.switch | def switch(self, device_id, obj_slot_id):
"""Switching of device-context"""
payload = {
"device-context": self._build_payload(device_id, obj_slot_id)
}
return self._post(self.url_prefix, payload) | python | def switch(self, device_id, obj_slot_id):
"""Switching of device-context"""
payload = {
"device-context": self._build_payload(device_id, obj_slot_id)
}
return self._post(self.url_prefix, payload) | Switching of device-context | https://github.com/a10networks/acos-client/blob/14d1fff589650650c9a65047d54c6c8c1d6b75f2/acos_client/v30/device_context.py#L24-L30 |
a10networks/acos-client | acos_client/v30/route.py | RIB.create | def create(self, destination, mask, next_hops=[]):
"""Create route to {destination} {mask} using {next_hops} expressed as (gateway, distance)"""
payload = {
"rib": self._build_payload(destination, mask, next_hops)
}
return self._post(self.url_prefix, payload) | python | def create(self, destination, mask, next_hops=[]):
"""Create route to {destination} {mask} using {next_hops} expressed as (gateway, distance)"""
payload = {
"rib": self._build_payload(destination, mask, next_hops)
}
return self._post(self.url_prefix, payload) | Create route to {destination} {mask} using {next_hops} expressed as (gateway, distance) | https://github.com/a10networks/acos-client/blob/14d1fff589650650c9a65047d54c6c8c1d6b75f2/acos_client/v30/route.py#L25-L31 |
materialsproject/pymatgen-db | matgendb/creator.py | contains_vasp_input | def contains_vasp_input(dir_name):
"""
Checks if a directory contains valid VASP input.
Args:
dir_name:
Directory name to check.
Returns:
True if directory contains all four VASP input files (INCAR, POSCAR,
KPOINTS and POTCAR).
"""
for f in ["INCAR", "POSCAR... | python | def contains_vasp_input(dir_name):
"""
Checks if a directory contains valid VASP input.
Args:
dir_name:
Directory name to check.
Returns:
True if directory contains all four VASP input files (INCAR, POSCAR,
KPOINTS and POTCAR).
"""
for f in ["INCAR", "POSCAR... | Checks if a directory contains valid VASP input.
Args:
dir_name:
Directory name to check.
Returns:
True if directory contains all four VASP input files (INCAR, POSCAR,
KPOINTS and POTCAR). | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L692-L708 |
materialsproject/pymatgen-db | matgendb/creator.py | get_coordination_numbers | def get_coordination_numbers(d):
"""
Helper method to get the coordination number of all sites in the final
structure from a run.
Args:
d:
Run dict generated by VaspToDbTaskDrone.
Returns:
Coordination numbers as a list of dict of [{"site": site_dict,
"coordinat... | python | def get_coordination_numbers(d):
"""
Helper method to get the coordination number of all sites in the final
structure from a run.
Args:
d:
Run dict generated by VaspToDbTaskDrone.
Returns:
Coordination numbers as a list of dict of [{"site": site_dict,
"coordinat... | Helper method to get the coordination number of all sites in the final
structure from a run.
Args:
d:
Run dict generated by VaspToDbTaskDrone.
Returns:
Coordination numbers as a list of dict of [{"site": site_dict,
"coordination": number}, ...]. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L711-L734 |
materialsproject/pymatgen-db | matgendb/creator.py | get_uri | def get_uri(dir_name):
"""
Returns the URI path for a directory. This allows files hosted on
different file servers to have distinct locations.
Args:
dir_name:
A directory name.
Returns:
Full URI path, e.g., fileserver.host.com:/full/path/of/dir_name.
"""
fullpa... | python | def get_uri(dir_name):
"""
Returns the URI path for a directory. This allows files hosted on
different file servers to have distinct locations.
Args:
dir_name:
A directory name.
Returns:
Full URI path, e.g., fileserver.host.com:/full/path/of/dir_name.
"""
fullpa... | Returns the URI path for a directory. This allows files hosted on
different file servers to have distinct locations.
Args:
dir_name:
A directory name.
Returns:
Full URI path, e.g., fileserver.host.com:/full/path/of/dir_name. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L737-L754 |
materialsproject/pymatgen-db | matgendb/creator.py | VaspToDbTaskDrone.assimilate | def assimilate(self, path):
"""
Parses vasp runs. Then insert the result into the db. and return the
task_id or doc of the insertion.
Returns:
If in simulate_mode, the entire doc is returned for debugging
purposes. Else, only the task_id of the inserted doc is re... | python | def assimilate(self, path):
"""
Parses vasp runs. Then insert the result into the db. and return the
task_id or doc of the insertion.
Returns:
If in simulate_mode, the entire doc is returned for debugging
purposes. Else, only the task_id of the inserted doc is re... | Parses vasp runs. Then insert the result into the db. and return the
task_id or doc of the insertion.
Returns:
If in simulate_mode, the entire doc is returned for debugging
purposes. Else, only the task_id of the inserted doc is returned. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L169-L187 |
materialsproject/pymatgen-db | matgendb/creator.py | VaspToDbTaskDrone.get_task_doc | def get_task_doc(self, path):
"""
Get the entire task doc for a path, including any post-processing.
"""
logger.info("Getting task doc for base dir :{}".format(path))
files = os.listdir(path)
vasprun_files = OrderedDict()
if "STOPCAR" in files:
#Stoppe... | python | def get_task_doc(self, path):
"""
Get the entire task doc for a path, including any post-processing.
"""
logger.info("Getting task doc for base dir :{}".format(path))
files = os.listdir(path)
vasprun_files = OrderedDict()
if "STOPCAR" in files:
#Stoppe... | Get the entire task doc for a path, including any post-processing. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L202-L241 |
materialsproject/pymatgen-db | matgendb/creator.py | VaspToDbTaskDrone.post_process | def post_process(self, dir_name, d):
"""
Simple post-processing for various files other than the vasprun.xml.
Called by generate_task_doc. Modify this if your runs have other
kinds of processing requirements.
Args:
dir_name:
The dir_name.
... | python | def post_process(self, dir_name, d):
"""
Simple post-processing for various files other than the vasprun.xml.
Called by generate_task_doc. Modify this if your runs have other
kinds of processing requirements.
Args:
dir_name:
The dir_name.
... | Simple post-processing for various files other than the vasprun.xml.
Called by generate_task_doc. Modify this if your runs have other
kinds of processing requirements.
Args:
dir_name:
The dir_name.
d:
Current doc generated. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L299-L395 |
materialsproject/pymatgen-db | matgendb/creator.py | VaspToDbTaskDrone.process_killed_run | def process_killed_run(self, dir_name):
"""
Process a killed vasp run.
"""
fullpath = os.path.abspath(dir_name)
logger.info("Processing Killed run " + fullpath)
d = {"dir_name": fullpath, "state": "killed", "oszicar": {}}
for f in os.listdir(dir_name):
... | python | def process_killed_run(self, dir_name):
"""
Process a killed vasp run.
"""
fullpath = os.path.abspath(dir_name)
logger.info("Processing Killed run " + fullpath)
d = {"dir_name": fullpath, "state": "killed", "oszicar": {}}
for f in os.listdir(dir_name):
... | Process a killed vasp run. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L397-L479 |
materialsproject/pymatgen-db | matgendb/creator.py | VaspToDbTaskDrone.process_vasprun | def process_vasprun(self, dir_name, taskname, filename):
"""
Process a vasprun.xml file.
"""
vasprun_file = os.path.join(dir_name, filename)
if self.parse_projected_eigen and (self.parse_projected_eigen != 'final' or \
taskname == self.runs[-1]):
... | python | def process_vasprun(self, dir_name, taskname, filename):
"""
Process a vasprun.xml file.
"""
vasprun_file = os.path.join(dir_name, filename)
if self.parse_projected_eigen and (self.parse_projected_eigen != 'final' or \
taskname == self.runs[-1]):
... | Process a vasprun.xml file. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L481-L511 |
materialsproject/pymatgen-db | matgendb/creator.py | VaspToDbTaskDrone.generate_doc | def generate_doc(self, dir_name, vasprun_files):
"""
Process aflow style runs, where each run is actually a combination of
two vasp runs.
"""
try:
fullpath = os.path.abspath(dir_name)
# Defensively copy the additional fields first. This is a MUST.
... | python | def generate_doc(self, dir_name, vasprun_files):
"""
Process aflow style runs, where each run is actually a combination of
two vasp runs.
"""
try:
fullpath = os.path.abspath(dir_name)
# Defensively copy the additional fields first. This is a MUST.
... | Process aflow style runs, where each run is actually a combination of
two vasp runs. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L513-L587 |
materialsproject/pymatgen-db | matgendb/creator.py | VaspToDbTaskDrone.get_valid_paths | def get_valid_paths(self, path):
"""
There are some restrictions on the valid directory structures:
1. There can be only one vasp run in each directory. Nested directories
are fine.
2. Directories designated "relax1", "relax2" are considered to be 2
parts of an afl... | python | def get_valid_paths(self, path):
"""
There are some restrictions on the valid directory structures:
1. There can be only one vasp run in each directory. Nested directories
are fine.
2. Directories designated "relax1", "relax2" are considered to be 2
parts of an afl... | There are some restrictions on the valid directory structures:
1. There can be only one vasp run in each directory. Nested directories
are fine.
2. Directories designated "relax1", "relax2" are considered to be 2
parts of an aflow style run.
3. Directories containing vasp ... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/creator.py#L589-L606 |
materialsproject/pymatgen-db | matgendb/vv/util.py | total_size | def total_size(o, handlers={}, verbose=False, count=False):
"""Returns the approximate memory footprint an object and all of its contents.
Automatically finds the contents of the following builtin containers and
their subclasses: tuple, list, deque, dict, set and frozenset.
To search other containers,... | python | def total_size(o, handlers={}, verbose=False, count=False):
"""Returns the approximate memory footprint an object and all of its contents.
Automatically finds the contents of the following builtin containers and
their subclasses: tuple, list, deque, dict, set and frozenset.
To search other containers,... | Returns the approximate memory footprint an object and all of its contents.
Automatically finds the contents of the following builtin containers and
their subclasses: tuple, list, deque, dict, set and frozenset.
To search other containers, add handlers to iterate over their contents:
handlers = {... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/util.py#L44-L84 |
materialsproject/pymatgen-db | matgendb/vv/util.py | args_kvp_nodup | def args_kvp_nodup(s):
"""Parse argument string as key=value pairs separated by commas.
:param s: Argument string
:return: Parsed value
:rtype: dict
:raises: ValueError for format violations or a duplicated key.
"""
if s is None:
return {}
d = {}
for item in [e.strip() for e... | python | def args_kvp_nodup(s):
"""Parse argument string as key=value pairs separated by commas.
:param s: Argument string
:return: Parsed value
:rtype: dict
:raises: ValueError for format violations or a duplicated key.
"""
if s is None:
return {}
d = {}
for item in [e.strip() for e... | Parse argument string as key=value pairs separated by commas.
:param s: Argument string
:return: Parsed value
:rtype: dict
:raises: ValueError for format violations or a duplicated key. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/util.py#L210-L235 |
materialsproject/pymatgen-db | matgendb/vv/util.py | JsonWalker.walk | def walk(self, o):
"""Walk a dict & transform.
"""
if isinstance(o, dict):
d = o if self._dx is None else self._dx(o)
return {k: self.walk(v) for k, v in d.items()}
elif isinstance(o, list):
return [self.walk(v) for v in o]
else:
re... | python | def walk(self, o):
"""Walk a dict & transform.
"""
if isinstance(o, dict):
d = o if self._dx is None else self._dx(o)
return {k: self.walk(v) for k, v in d.items()}
elif isinstance(o, list):
return [self.walk(v) for v in o]
else:
re... | Walk a dict & transform. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/util.py#L140-L149 |
materialsproject/pymatgen-db | matgendb/vv/util.py | JsonWalker.dict_expand | def dict_expand(o):
"""Expand keys in a dict with '.' in them into
sub-dictionaries, e.g.
{'a.b.c': 'foo'} ==> {'a': {'b': {'c': 'foo'}}}
"""
r = {}
for k, v in o.items():
if isinstance(k, str):
k = k.replace('$', '_')
if "." in k:... | python | def dict_expand(o):
"""Expand keys in a dict with '.' in them into
sub-dictionaries, e.g.
{'a.b.c': 'foo'} ==> {'a': {'b': {'c': 'foo'}}}
"""
r = {}
for k, v in o.items():
if isinstance(k, str):
k = k.replace('$', '_')
if "." in k:... | Expand keys in a dict with '.' in them into
sub-dictionaries, e.g.
{'a.b.c': 'foo'} ==> {'a': {'b': {'c': 'foo'}}} | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/util.py#L161-L181 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | TrackedQueryEngine.collection_name | def collection_name(self, value):
"""Switch to another collection.
Note that you may have to set the aliases and default properties if the
schema of the new collection differs from the current collection.
"""
self._collection_name = value
self._mongo_coll = self.db[value]... | python | def collection_name(self, value):
"""Switch to another collection.
Note that you may have to set the aliases and default properties if the
schema of the new collection differs from the current collection.
"""
self._collection_name = value
self._mongo_coll = self.db[value]... | Switch to another collection.
Note that you may have to set the aliases and default properties if the
schema of the new collection differs from the current collection. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L128-L136 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | TrackedCollection.tracked_find | def tracked_find(self, *args, **kwargs):
"""Replacement for regular ``find()``.
"""
_log.info("tracked_find.begin")
# if tracking is off, just call find (ie do nothing)
if self._tracking_off:
_log.info("tracked_find.end, tracking=off")
return self._coll_fi... | python | def tracked_find(self, *args, **kwargs):
"""Replacement for regular ``find()``.
"""
_log.info("tracked_find.begin")
# if tracking is off, just call find (ie do nothing)
if self._tracking_off:
_log.info("tracked_find.end, tracking=off")
return self._coll_fi... | Replacement for regular ``find()``. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L179-L199 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | Mark.update | def update(self):
"""Update the position of the mark in the collection.
:return: this object, for chaining
:rtype: Mark
"""
rec = self._c.find_one({}, {self._fld: 1}, sort=[(self._fld, -1)], limit=1)
if rec is None:
self._pos = self._empty_pos()
elif ... | python | def update(self):
"""Update the position of the mark in the collection.
:return: this object, for chaining
:rtype: Mark
"""
rec = self._c.find_one({}, {self._fld: 1}, sort=[(self._fld, -1)], limit=1)
if rec is None:
self._pos = self._empty_pos()
elif ... | Update the position of the mark in the collection.
:return: this object, for chaining
:rtype: Mark | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L249-L265 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | Mark.as_dict | def as_dict(self):
"""Representation as a dict for JSON serialization.
"""
return {self.FLD_OP: self._op.name,
self.FLD_MARK: self._pos,
self.FLD_FLD: self._fld} | python | def as_dict(self):
"""Representation as a dict for JSON serialization.
"""
return {self.FLD_OP: self._op.name,
self.FLD_MARK: self._pos,
self.FLD_FLD: self._fld} | Representation as a dict for JSON serialization. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L274-L279 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | Mark.from_dict | def from_dict(cls, coll, d):
"""Construct from dict
:param coll: Collection for the mark
:param d: Input
:type d: dict
:return: new instance
:rtype: Mark
"""
return Mark(collection=coll, operation=Operation[d[cls.FLD_OP]],
pos=d[cls.FL... | python | def from_dict(cls, coll, d):
"""Construct from dict
:param coll: Collection for the mark
:param d: Input
:type d: dict
:return: new instance
:rtype: Mark
"""
return Mark(collection=coll, operation=Operation[d[cls.FLD_OP]],
pos=d[cls.FL... | Construct from dict
:param coll: Collection for the mark
:param d: Input
:type d: dict
:return: new instance
:rtype: Mark | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L284-L294 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | Mark.query | def query(self):
"""A mongdb query expression to find all records with higher values
for this mark's fields in the collection.
:rtype: dict
"""
q = {}
for field, value in self._pos.items():
if value is None:
q.update({field: {'$exists': True}}... | python | def query(self):
"""A mongdb query expression to find all records with higher values
for this mark's fields in the collection.
:rtype: dict
"""
q = {}
for field, value in self._pos.items():
if value is None:
q.update({field: {'$exists': True}}... | A mongdb query expression to find all records with higher values
for this mark's fields in the collection.
:rtype: dict | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L297-L309 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | CollectionTracker.create | def create(self):
"""Create tracking collection.
Does nothing if tracking collection already exists.
"""
if self._track is None:
self._track = self.db[self.tracking_collection_name] | python | def create(self):
"""Create tracking collection.
Does nothing if tracking collection already exists.
"""
if self._track is None:
self._track = self.db[self.tracking_collection_name] | Create tracking collection.
Does nothing if tracking collection already exists. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L348-L353 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | CollectionTracker.save | def save(self, mark):
"""Save a position in this collection.
:param mark: The position to save
:type mark: Mark
:raises: DBError, NoTrackingCollection
"""
self._check_exists()
obj = mark.as_dict()
try:
# Make a 'filter' to find/update existing... | python | def save(self, mark):
"""Save a position in this collection.
:param mark: The position to save
:type mark: Mark
:raises: DBError, NoTrackingCollection
"""
self._check_exists()
obj = mark.as_dict()
try:
# Make a 'filter' to find/update existing... | Save a position in this collection.
:param mark: The position to save
:type mark: Mark
:raises: DBError, NoTrackingCollection | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L355-L371 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | CollectionTracker.retrieve | def retrieve(self, operation, field=None):
"""Retrieve a position in this collection.
:param operation: Name of an operation
:type operation: :class:`Operation`
:param field: Name of field for sort order
:type field: str
:return: The position for this operation
:... | python | def retrieve(self, operation, field=None):
"""Retrieve a position in this collection.
:param operation: Name of an operation
:type operation: :class:`Operation`
:param field: Name of field for sort order
:type field: str
:return: The position for this operation
:... | Retrieve a position in this collection.
:param operation: Name of an operation
:type operation: :class:`Operation`
:param field: Name of field for sort order
:type field: str
:return: The position for this operation
:rtype: Mark
:raises: NoTrackingCollection | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L373-L388 |
materialsproject/pymatgen-db | matgendb/builders/incr.py | CollectionTracker._get | def _get(self, operation, field):
"""Get tracked position for a given operation and field."""
self._check_exists()
query = {Mark.FLD_OP: operation.name,
Mark.FLD_MARK + "." + field: {"$exists": True}}
return self._track.find_one(query) | python | def _get(self, operation, field):
"""Get tracked position for a given operation and field."""
self._check_exists()
query = {Mark.FLD_OP: operation.name,
Mark.FLD_MARK + "." + field: {"$exists": True}}
return self._track.find_one(query) | Get tracked position for a given operation and field. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/incr.py#L390-L395 |
materialsproject/pymatgen-db | matgendb/vv/diff.py | Differ.diff | def diff(self, c1, c2, only_missing=False, only_values=False, allow_dup=False):
"""Perform a difference between the 2 collections.
The first collection is treated as the previous one, and the second
is treated as the new one.
Note: this is not 'big data'-ready; we assume all the records... | python | def diff(self, c1, c2, only_missing=False, only_values=False, allow_dup=False):
"""Perform a difference between the 2 collections.
The first collection is treated as the previous one, and the second
is treated as the new one.
Note: this is not 'big data'-ready; we assume all the records... | Perform a difference between the 2 collections.
The first collection is treated as the previous one, and the second
is treated as the new one.
Note: this is not 'big data'-ready; we assume all the records can fit in memory.
:param c1: Collection (1) config file, or QueryEngine object
... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/diff.py#L70-L219 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.collection_name | def collection_name(self, value):
"""Switch to another collection.
Note that you may have to set the aliases and default properties if the
schema of the new collection differs from the current collection.
"""
self._collection_name = value
self.collection = self.db[value] | python | def collection_name(self, value):
"""Switch to another collection.
Note that you may have to set the aliases and default properties if the
schema of the new collection differs from the current collection.
"""
self._collection_name = value
self.collection = self.db[value] | Switch to another collection.
Note that you may have to set the aliases and default properties if the
schema of the new collection differs from the current collection. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L151-L157 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.set_aliases_and_defaults | def set_aliases_and_defaults(self, aliases_config=None,
default_properties=None):
"""
Set the alias config and defaults to use. Typically used when
switching to a collection with a different schema.
Args:
aliases_config:
An al... | python | def set_aliases_and_defaults(self, aliases_config=None,
default_properties=None):
"""
Set the alias config and defaults to use. Typically used when
switching to a collection with a different schema.
Args:
aliases_config:
An al... | Set the alias config and defaults to use. Typically used when
switching to a collection with a different schema.
Args:
aliases_config:
An alias dict to use. Defaults to None, which means the default
aliases defined in "aliases.json" is used. See constructor
... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L175-L205 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.get_entries_in_system | def get_entries_in_system(self, elements, inc_structure=False,
optional_data=None, additional_criteria=None):
"""
Gets all entries in a chemical system, e.g. Li-Fe-O will return all
Li-O, Fe-O, Li-Fe, Li-Fe-O compounds.
.. note::
The get_entrie... | python | def get_entries_in_system(self, elements, inc_structure=False,
optional_data=None, additional_criteria=None):
"""
Gets all entries in a chemical system, e.g. Li-Fe-O will return all
Li-O, Fe-O, Li-Fe, Li-Fe-O compounds.
.. note::
The get_entrie... | Gets all entries in a chemical system, e.g. Li-Fe-O will return all
Li-O, Fe-O, Li-Fe, Li-Fe-O compounds.
.. note::
The get_entries_in_system and get_entries methods should be used
with care. In essence, all entries, GGA, GGA+U or otherwise,
are returned. The data... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L220-L261 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.get_entries | def get_entries(self, criteria, inc_structure=False, optional_data=None):
"""
Get ComputedEntries satisfying a particular criteria.
.. note::
The get_entries_in_system and get_entries methods should be used
with care. In essence, all entries, GGA, GGA+U or otherwise,
... | python | def get_entries(self, criteria, inc_structure=False, optional_data=None):
"""
Get ComputedEntries satisfying a particular criteria.
.. note::
The get_entries_in_system and get_entries methods should be used
with care. In essence, all entries, GGA, GGA+U or otherwise,
... | Get ComputedEntries satisfying a particular criteria.
.. note::
The get_entries_in_system and get_entries methods should be used
with care. In essence, all entries, GGA, GGA+U or otherwise,
are returned. The dataset is very heterogeneous and not
directly compa... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L263-L327 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine._parse_criteria | def _parse_criteria(self, criteria):
"""
Internal method to perform mapping of criteria to proper mongo queries
using aliases, as well as some useful sanitization. For example, string
formulas such as "Fe2O3" are auto-converted to proper mongo queries of
{"Fe":2, "O":3}.
... | python | def _parse_criteria(self, criteria):
"""
Internal method to perform mapping of criteria to proper mongo queries
using aliases, as well as some useful sanitization. For example, string
formulas such as "Fe2O3" are auto-converted to proper mongo queries of
{"Fe":2, "O":3}.
... | Internal method to perform mapping of criteria to proper mongo queries
using aliases, as well as some useful sanitization. For example, string
formulas such as "Fe2O3" are auto-converted to proper mongo queries of
{"Fe":2, "O":3}.
If 'criteria' is None, returns an empty dict. Putting th... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L329-L362 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.ensure_index | def ensure_index(self, key, unique=False):
"""Wrapper for pymongo.Collection.ensure_index
"""
return self.collection.ensure_index(key, unique=unique) | python | def ensure_index(self, key, unique=False):
"""Wrapper for pymongo.Collection.ensure_index
"""
return self.collection.ensure_index(key, unique=unique) | Wrapper for pymongo.Collection.ensure_index | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L364-L367 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.query | def query(self, properties=None, criteria=None, distinct_key=None,
**kwargs):
"""
Convenience method for database access. All properties and criteria
can be specified using simplified names defined in Aliases. You can
use the supported_properties property to get the list ... | python | def query(self, properties=None, criteria=None, distinct_key=None,
**kwargs):
"""
Convenience method for database access. All properties and criteria
can be specified using simplified names defined in Aliases. You can
use the supported_properties property to get the list ... | Convenience method for database access. All properties and criteria
can be specified using simplified names defined in Aliases. You can
use the supported_properties property to get the list of supported
properties.
Results are returned as an iterator of dicts to ensure memory and cpu
... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L369-L417 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine._parse_properties | def _parse_properties(self, properties):
"""Make list of properties into 2 things:
(1) dictionary of { 'aliased-field': 1, ... } for a mongodb query eg. {''}
(2) dictionary, keyed by aliased field, for display
"""
props = {}
# TODO: clean up prop_dict?
prop_dict =... | python | def _parse_properties(self, properties):
"""Make list of properties into 2 things:
(1) dictionary of { 'aliased-field': 1, ... } for a mongodb query eg. {''}
(2) dictionary, keyed by aliased field, for display
"""
props = {}
# TODO: clean up prop_dict?
prop_dict =... | Make list of properties into 2 things:
(1) dictionary of { 'aliased-field': 1, ... } for a mongodb query eg. {''}
(2) dictionary, keyed by aliased field, for display | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L419-L449 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.query_one | def query_one(self, *args, **kwargs):
"""Return first document from :meth:`query`, with same parameters.
"""
for r in self.query(*args, **kwargs):
return r
return None | python | def query_one(self, *args, **kwargs):
"""Return first document from :meth:`query`, with same parameters.
"""
for r in self.query(*args, **kwargs):
return r
return None | Return first document from :meth:`query`, with same parameters. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L451-L456 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.get_structure_from_id | def get_structure_from_id(self, task_id, final_structure=True):
"""
Returns a structure from the database given the task id.
Args:
task_id:
The task_id to query for.
final_structure:
Whether to obtain the final or initial structure. Defaul... | python | def get_structure_from_id(self, task_id, final_structure=True):
"""
Returns a structure from the database given the task id.
Args:
task_id:
The task_id to query for.
final_structure:
Whether to obtain the final or initial structure. Defaul... | Returns a structure from the database given the task id.
Args:
task_id:
The task_id to query for.
final_structure:
Whether to obtain the final or initial structure. Defaults to
True. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L458-L478 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.from_config | def from_config(config_file, use_admin=False):
"""
Initialize a QueryEngine from a JSON config file generated using mgdb
init.
Args:
config_file:
Filename of config file.
use_admin:
If True, the admin user and password in the confi... | python | def from_config(config_file, use_admin=False):
"""
Initialize a QueryEngine from a JSON config file generated using mgdb
init.
Args:
config_file:
Filename of config file.
use_admin:
If True, the admin user and password in the confi... | Initialize a QueryEngine from a JSON config file generated using mgdb
init.
Args:
config_file:
Filename of config file.
use_admin:
If True, the admin user and password in the config file is
used. Otherwise, the readonly_user and pa... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L485-L509 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryEngine.get_dos_from_id | def get_dos_from_id(self, task_id):
"""
Overrides the get_dos_from_id for the MIT gridfs format.
"""
args = {'task_id': task_id}
fields = ['calculations']
structure = self.get_structure_from_id(task_id)
dosid = None
for r in self.query(fields, args):
... | python | def get_dos_from_id(self, task_id):
"""
Overrides the get_dos_from_id for the MIT gridfs format.
"""
args = {'task_id': task_id}
fields = ['calculations']
structure = self.get_structure_from_id(task_id)
dosid = None
for r in self.query(fields, args):
... | Overrides the get_dos_from_id for the MIT gridfs format. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L517-L549 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryResults._wrapper | def _wrapper(self, func):
"""
This function wraps all callable objects returned by self.__getattr__.
If the result is a cursor, wrap it into a QueryResults object
so that you can invoke postprocess functions in self._pproc
"""
def wrapped(*args, **kwargs):
ret... | python | def _wrapper(self, func):
"""
This function wraps all callable objects returned by self.__getattr__.
If the result is a cursor, wrap it into a QueryResults object
so that you can invoke postprocess functions in self._pproc
"""
def wrapped(*args, **kwargs):
ret... | This function wraps all callable objects returned by self.__getattr__.
If the result is a cursor, wrap it into a QueryResults object
so that you can invoke postprocess functions in self._pproc | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L574-L586 |
materialsproject/pymatgen-db | matgendb/query_engine.py | QueryResults._mapped_result | def _mapped_result(self, r):
"""Transform/map a result.
"""
# Apply result_post funcs for pulling out sandbox properties
for func in self._pproc:
func(r)
# If we haven't asked for specific properties, just return object
if not self._prop_dict:
resu... | python | def _mapped_result(self, r):
"""Transform/map a result.
"""
# Apply result_post funcs for pulling out sandbox properties
for func in self._pproc:
func(r)
# If we haven't asked for specific properties, just return object
if not self._prop_dict:
resu... | Transform/map a result. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/query_engine.py#L623-L640 |
materialsproject/pymatgen-db | matgendb/builders/schema.py | add_schemas | def add_schemas(path, ext="json"):
"""Add schemas from files in 'path'.
:param path: Path with schema files. Schemas are named by their file,
with the extension stripped. e.g., if path is "/tmp/foo",
then the schema in "/tmp/foo/bar.json" will be named "bar".
:type path: s... | python | def add_schemas(path, ext="json"):
"""Add schemas from files in 'path'.
:param path: Path with schema files. Schemas are named by their file,
with the extension stripped. e.g., if path is "/tmp/foo",
then the schema in "/tmp/foo/bar.json" will be named "bar".
:type path: s... | Add schemas from files in 'path'.
:param path: Path with schema files. Schemas are named by their file,
with the extension stripped. e.g., if path is "/tmp/foo",
then the schema in "/tmp/foo/bar.json" will be named "bar".
:type path: str
:param ext: File extension that ide... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/schema.py#L55-L78 |
materialsproject/pymatgen-db | matgendb/builders/schema.py | load_schema | def load_schema(file_or_fp):
"""Load schema from file.
:param file_or_fp: File name or file object
:type file_or_fp: str, file
:raise: IOError if file cannot be opened or read, ValueError if
file is not valid JSON or JSON is not a valid schema.
"""
fp = open(file_or_fp, 'r') if isin... | python | def load_schema(file_or_fp):
"""Load schema from file.
:param file_or_fp: File name or file object
:type file_or_fp: str, file
:raise: IOError if file cannot be opened or read, ValueError if
file is not valid JSON or JSON is not a valid schema.
"""
fp = open(file_or_fp, 'r') if isin... | Load schema from file.
:param file_or_fp: File name or file object
:type file_or_fp: str, file
:raise: IOError if file cannot be opened or read, ValueError if
file is not valid JSON or JSON is not a valid schema. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/schema.py#L93-L104 |
materialsproject/pymatgen-db | matgendb/builders/schema.py | Schema.json_schema | def json_schema(self, **add_keys):
"""Convert our compact schema representation to the standard, but more verbose,
JSON Schema standard.
Example JSON schema: http://json-schema.org/examples.html
Core standard: http://json-schema.org/latest/json-schema-core.html
:param add_keys:... | python | def json_schema(self, **add_keys):
"""Convert our compact schema representation to the standard, but more verbose,
JSON Schema standard.
Example JSON schema: http://json-schema.org/examples.html
Core standard: http://json-schema.org/latest/json-schema-core.html
:param add_keys:... | Convert our compact schema representation to the standard, but more verbose,
JSON Schema standard.
Example JSON schema: http://json-schema.org/examples.html
Core standard: http://json-schema.org/latest/json-schema-core.html
:param add_keys: Key, default value pairs to add in,
... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/schema.py#L180-L193 |
materialsproject/pymatgen-db | matgendb/builders/schema.py | Schema._build_schema | def _build_schema(self, s):
"""Recursive schema builder, called by `json_schema`.
"""
w = self._whatis(s)
if w == self.IS_LIST:
w0 = self._whatis(s[0])
js = {"type": "array",
"items": {"type": self._jstype(w0, s[0])}}
elif w == self.IS_DI... | python | def _build_schema(self, s):
"""Recursive schema builder, called by `json_schema`.
"""
w = self._whatis(s)
if w == self.IS_LIST:
w0 = self._whatis(s[0])
js = {"type": "array",
"items": {"type": self._jstype(w0, s[0])}}
elif w == self.IS_DI... | Recursive schema builder, called by `json_schema`. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/schema.py#L195-L214 |
materialsproject/pymatgen-db | matgendb/builders/schema.py | Schema._jstype | def _jstype(self, stype, sval):
"""Get JavaScript name for given data type, called by `_build_schema`.
"""
if stype == self.IS_LIST:
return "array"
if stype == self.IS_DICT:
return "object"
if isinstance(sval, Scalar):
return sval.jstype
... | python | def _jstype(self, stype, sval):
"""Get JavaScript name for given data type, called by `_build_schema`.
"""
if stype == self.IS_LIST:
return "array"
if stype == self.IS_DICT:
return "object"
if isinstance(sval, Scalar):
return sval.jstype
... | Get JavaScript name for given data type, called by `_build_schema`. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/schema.py#L216-L227 |
materialsproject/pymatgen-db | matgendb/builders/util.py | get_schema_dir | def get_schema_dir(db_version=1):
"""Get path to directory with schemata.
:param db_version: Version of the database
:type db_version: int
:return: Path
:rtype: str
"""
v = str(db_version)
return os.path.join(_top_dir, '..', 'schemata', 'versions', v) | python | def get_schema_dir(db_version=1):
"""Get path to directory with schemata.
:param db_version: Version of the database
:type db_version: int
:return: Path
:rtype: str
"""
v = str(db_version)
return os.path.join(_top_dir, '..', 'schemata', 'versions', v) | Get path to directory with schemata.
:param db_version: Version of the database
:type db_version: int
:return: Path
:rtype: str | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/util.py#L36-L45 |
materialsproject/pymatgen-db | matgendb/builders/util.py | get_schema_file | def get_schema_file(db_version=1, db="mg_core", collection="materials"):
"""Get file with appropriate schema.
:param db_version: Version of the database
:type db_version: int
:param db: Name of database, e.g. 'mg_core'
:type db: str
:param collection: Name of collection, e.g. 'materials'
:t... | python | def get_schema_file(db_version=1, db="mg_core", collection="materials"):
"""Get file with appropriate schema.
:param db_version: Version of the database
:type db_version: int
:param db: Name of database, e.g. 'mg_core'
:type db: str
:param collection: Name of collection, e.g. 'materials'
:t... | Get file with appropriate schema.
:param db_version: Version of the database
:type db_version: int
:param db: Name of database, e.g. 'mg_core'
:type db: str
:param collection: Name of collection, e.g. 'materials'
:type collection: str
:return: File with schema
:rtype: file
:raise: I... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/util.py#L48-L64 |
materialsproject/pymatgen-db | matgendb/dbconfig.py | get_settings | def get_settings(infile):
"""Read settings from input file.
:param infile: Input file for JSON settings.
:type infile: file or str path
:return: Settings parsed from file
:rtype: dict
"""
settings = yaml.load(_as_file(infile))
if not hasattr(settings, 'keys'):
raise ValueError("... | python | def get_settings(infile):
"""Read settings from input file.
:param infile: Input file for JSON settings.
:type infile: file or str path
:return: Settings parsed from file
:rtype: dict
"""
settings = yaml.load(_as_file(infile))
if not hasattr(settings, 'keys'):
raise ValueError("... | Read settings from input file.
:param infile: Input file for JSON settings.
:type infile: file or str path
:return: Settings parsed from file
:rtype: dict | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbconfig.py#L135-L155 |
materialsproject/pymatgen-db | matgendb/dbconfig.py | auth_aliases | def auth_aliases(d):
"""Interpret user/password aliases.
"""
for alias, real in ((USER_KEY, "readonly_user"),
(PASS_KEY, "readonly_password")):
if alias in d:
d[real] = d[alias]
del d[alias] | python | def auth_aliases(d):
"""Interpret user/password aliases.
"""
for alias, real in ((USER_KEY, "readonly_user"),
(PASS_KEY, "readonly_password")):
if alias in d:
d[real] = d[alias]
del d[alias] | Interpret user/password aliases. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbconfig.py#L157-L164 |
materialsproject/pymatgen-db | matgendb/dbconfig.py | normalize_auth | def normalize_auth(settings, admin=True, readonly=True, readonly_first=False):
"""Transform the readonly/admin user and password to simple user/password,
as expected by QueryEngine. If return value is true, then
admin or readonly password will be in keys "user" and "password".
:param settings: Connecti... | python | def normalize_auth(settings, admin=True, readonly=True, readonly_first=False):
"""Transform the readonly/admin user and password to simple user/password,
as expected by QueryEngine. If return value is true, then
admin or readonly password will be in keys "user" and "password".
:param settings: Connecti... | Transform the readonly/admin user and password to simple user/password,
as expected by QueryEngine. If return value is true, then
admin or readonly password will be in keys "user" and "password".
:param settings: Connection settings
:type settings: dict
:param admin: Check for admin password
:p... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbconfig.py#L166-L207 |
materialsproject/pymatgen-db | matgendb/vv/report.py | Emailer.send | def send(self, text, fmt):
"""Send the email message.
:param text: The text to send
:type text: str
:param fmt: The name of the format of the text
:type fmt: str
:return: Number of recipients it was sent to
:rtype: int
"""
main_fmt, sub_fmt = fmt.... | python | def send(self, text, fmt):
"""Send the email message.
:param text: The text to send
:type text: str
:param fmt: The name of the format of the text
:type fmt: str
:return: Number of recipients it was sent to
:rtype: int
"""
main_fmt, sub_fmt = fmt.... | Send the email message.
:param text: The text to send
:type text: str
:param fmt: The name of the format of the text
:type fmt: str
:return: Number of recipients it was sent to
:rtype: int | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/report.py#L376-L414 |
materialsproject/pymatgen-db | matgendb/vv/report.py | DiffFormatter.result_subsets | def result_subsets(self, rs):
"""Break a result set into subsets with the same keys.
:param rs: Result set, rows of a result as a list of dicts
:type rs: list of dict
:return: A set with distinct keys (tuples), and a dict, by these tuples, of max. widths for each column
"""
... | python | def result_subsets(self, rs):
"""Break a result set into subsets with the same keys.
:param rs: Result set, rows of a result as a list of dicts
:type rs: list of dict
:return: A set with distinct keys (tuples), and a dict, by these tuples, of max. widths for each column
"""
... | Break a result set into subsets with the same keys.
:param rs: Result set, rows of a result as a list of dicts
:type rs: list of dict
:return: A set with distinct keys (tuples), and a dict, by these tuples, of max. widths for each column | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/report.py#L449-L465 |
materialsproject/pymatgen-db | matgendb/vv/report.py | DiffFormatter.ordered_cols | def ordered_cols(self, columns, section):
"""Return ordered list of columns, from given columns and the name of the section
"""
columns = list(columns) # might be a tuple
fixed_cols = [self.key]
if section.lower() == "different":
fixed_cols.extend([Differ.CHANGED_MAT... | python | def ordered_cols(self, columns, section):
"""Return ordered list of columns, from given columns and the name of the section
"""
columns = list(columns) # might be a tuple
fixed_cols = [self.key]
if section.lower() == "different":
fixed_cols.extend([Differ.CHANGED_MAT... | Return ordered list of columns, from given columns and the name of the section | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/report.py#L467-L476 |
materialsproject/pymatgen-db | matgendb/vv/report.py | DiffFormatter.sort_rows | def sort_rows(self, rows, section):
"""Sort the rows, as appropriate for the section.
:param rows: List of tuples (all same length, same values in each position)
:param section: Name of section, should match const in Differ class
:return: None; rows are sorted in-place
"""
... | python | def sort_rows(self, rows, section):
"""Sort the rows, as appropriate for the section.
:param rows: List of tuples (all same length, same values in each position)
:param section: Name of section, should match const in Differ class
:return: None; rows are sorted in-place
"""
... | Sort the rows, as appropriate for the section.
:param rows: List of tuples (all same length, same values in each position)
:param section: Name of section, should match const in Differ class
:return: None; rows are sorted in-place | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/report.py#L478-L492 |
materialsproject/pymatgen-db | matgendb/vv/report.py | DiffJsonFormatter.document | def document(self, result):
"""Build dict for MongoDB, expanding result keys as we go.
"""
self._add_meta(result)
walker = JsonWalker(JsonWalker.value_json, JsonWalker.dict_expand)
r = walker.walk(result)
return r | python | def document(self, result):
"""Build dict for MongoDB, expanding result keys as we go.
"""
self._add_meta(result)
walker = JsonWalker(JsonWalker.value_json, JsonWalker.dict_expand)
r = walker.walk(result)
return r | Build dict for MongoDB, expanding result keys as we go. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/report.py#L530-L536 |
materialsproject/pymatgen-db | matgendb/vv/report.py | DiffHtmlFormatter.format | def format(self, result):
"""Generate HTML report.
:return: Report body
:rtype: str
"""
css = "\n".join(self.css)
content = "{}{}".format(self._header(), self._body(result))
if self._email:
text = """<!DOCTYPE html>
<html>
<div... | python | def format(self, result):
"""Generate HTML report.
:return: Report body
:rtype: str
"""
css = "\n".join(self.css)
content = "{}{}".format(self._header(), self._body(result))
if self._email:
text = """<!DOCTYPE html>
<html>
<div... | Generate HTML report.
:return: Report body
:rtype: str | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/report.py#L595-L615 |
materialsproject/pymatgen-db | matgendb/vv/report.py | DiffTextFormatter.format | def format(self, result):
"""Generate plain text report.
:return: Report body
:rtype: str
"""
m = self.meta
lines = ['-' * len(self.TITLE),
self.TITLE,
'-' * len(self.TITLE),
"Compared: {db1} <-> {db2}".format(**m),
... | python | def format(self, result):
"""Generate plain text report.
:return: Report body
:rtype: str
"""
m = self.meta
lines = ['-' * len(self.TITLE),
self.TITLE,
'-' * len(self.TITLE),
"Compared: {db1} <-> {db2}".format(**m),
... | Generate plain text report.
:return: Report body
:rtype: str | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/vv/report.py#L689-L725 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | create_query_engine | def create_query_engine(config, clazz):
"""Create and return new query engine object from the
given `DBConfig` object.
:param config: Database configuration
:type config: dbconfig.DBConfig
:param clazz: Class to use for creating query engine. Should
act like query_engine.QueryEngi... | python | def create_query_engine(config, clazz):
"""Create and return new query engine object from the
given `DBConfig` object.
:param config: Database configuration
:type config: dbconfig.DBConfig
:param clazz: Class to use for creating query engine. Should
act like query_engine.QueryEngi... | Create and return new query engine object from the
given `DBConfig` object.
:param config: Database configuration
:type config: dbconfig.DBConfig
:param clazz: Class to use for creating query engine. Should
act like query_engine.QueryEngine.
:type clazz: class
:return: New que... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L244-L259 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | ConfigGroup.add_path | def add_path(self, path, pattern="*.json"):
"""Add configuration file(s)
in `path`. The path can be a single file or a directory.
If path is a directory, then `pattern`
(Unix glob-style) will be used to get a list of all config
files in the directory.
The name given to e... | python | def add_path(self, path, pattern="*.json"):
"""Add configuration file(s)
in `path`. The path can be a single file or a directory.
If path is a directory, then `pattern`
(Unix glob-style) will be used to get a list of all config
files in the directory.
The name given to e... | Add configuration file(s)
in `path`. The path can be a single file or a directory.
If path is a directory, then `pattern`
(Unix glob-style) will be used to get a list of all config
files in the directory.
The name given to each file is the database name
and collection na... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L41-L69 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | ConfigGroup.add | def add(self, name, cfg, expand=False):
"""Add a configuration object.
:param name: Name for later retrieval
:param cfg: Configuration object
:param expand: Flag for adding sub-configs for each sub-collection.
See discussion in method doc.
:return: self, f... | python | def add(self, name, cfg, expand=False):
"""Add a configuration object.
:param name: Name for later retrieval
:param cfg: Configuration object
:param expand: Flag for adding sub-configs for each sub-collection.
See discussion in method doc.
:return: self, f... | Add a configuration object.
:param name: Name for later retrieval
:param cfg: Configuration object
:param expand: Flag for adding sub-configs for each sub-collection.
See discussion in method doc.
:return: self, for chaining
:raises: CreateQueryEngineError... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L71-L84 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | ConfigGroup.expand | def expand(self, name):
"""Expand config for `name` by adding a sub-configuration for every
dot-separated collection "below" the given one (or all, if none given).
For example, for a database 'mydb' with collections
['spiderman.amazing', 'spiderman.spectacular', 'spiderman2']
... | python | def expand(self, name):
"""Expand config for `name` by adding a sub-configuration for every
dot-separated collection "below" the given one (or all, if none given).
For example, for a database 'mydb' with collections
['spiderman.amazing', 'spiderman.spectacular', 'spiderman2']
... | Expand config for `name` by adding a sub-configuration for every
dot-separated collection "below" the given one (or all, if none given).
For example, for a database 'mydb' with collections
['spiderman.amazing', 'spiderman.spectacular', 'spiderman2']
and a configuration
{... | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L86-L108 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | ConfigGroup._expand | def _expand(self, name):
"""Perform real work of `expand()` function."""
cfg = self._d[name]
if cfg.collection is None:
base_coll = ''
else:
base_coll = cfg.collection + self.SEP
qe = self._get_qe(name, cfg)
coll, db = qe.collection, qe.db
... | python | def _expand(self, name):
"""Perform real work of `expand()` function."""
cfg = self._d[name]
if cfg.collection is None:
base_coll = ''
else:
base_coll = cfg.collection + self.SEP
qe = self._get_qe(name, cfg)
coll, db = qe.collection, qe.db
... | Perform real work of `expand()` function. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L110-L126 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | ConfigGroup.uncache | def uncache(self, name):
"""Remove all created query engines that match `name` from
the cache (this disconnects from MongoDB, which is the point).
:param name: Name used for :meth:`add`, or pattern
:return: None
"""
delme = []
if self._is_pattern(name):
... | python | def uncache(self, name):
"""Remove all created query engines that match `name` from
the cache (this disconnects from MongoDB, which is the point).
:param name: Name used for :meth:`add`, or pattern
:return: None
"""
delme = []
if self._is_pattern(name):
... | Remove all created query engines that match `name` from
the cache (this disconnects from MongoDB, which is the point).
:param name: Name used for :meth:`add`, or pattern
:return: None | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L128-L145 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | ConfigGroup.set_prefix | def set_prefix(self, prefix=None):
"""Set prefix to use as a namespace for item lookup.
A dot (.) will be automatically added to the given string.
:param prefix: Prefix, or None to unset
:return: None
"""
if prefix is None:
self._pfx = None
else:
... | python | def set_prefix(self, prefix=None):
"""Set prefix to use as a namespace for item lookup.
A dot (.) will be automatically added to the given string.
:param prefix: Prefix, or None to unset
:return: None
"""
if prefix is None:
self._pfx = None
else:
... | Set prefix to use as a namespace for item lookup.
A dot (.) will be automatically added to the given string.
:param prefix: Prefix, or None to unset
:return: None | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L184-L194 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | ConfigGroup._get_qe | def _get_qe(self, key, obj):
"""Instantiate a query engine, or retrieve a cached one.
"""
if key in self._cached:
return self._cached[key]
qe = create_query_engine(obj, self._class)
self._cached[key] = qe
return qe | python | def _get_qe(self, key, obj):
"""Instantiate a query engine, or retrieve a cached one.
"""
if key in self._cached:
return self._cached[key]
qe = create_query_engine(obj, self._class)
self._cached[key] = qe
return qe | Instantiate a query engine, or retrieve a cached one. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L206-L213 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | RegexDict.re_keys | def re_keys(self, pattern):
"""Find keys matching `pattern`.
:param pattern: Regular expression
:return: Matching keys or empty list
:rtype: list
"""
if not pattern.endswith("$"):
pattern += "$"
expr = re.compile(pattern)
return list(filter(ex... | python | def re_keys(self, pattern):
"""Find keys matching `pattern`.
:param pattern: Regular expression
:return: Matching keys or empty list
:rtype: list
"""
if not pattern.endswith("$"):
pattern += "$"
expr = re.compile(pattern)
return list(filter(ex... | Find keys matching `pattern`.
:param pattern: Regular expression
:return: Matching keys or empty list
:rtype: list | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L224-L234 |
materialsproject/pymatgen-db | matgendb/dbgroup.py | RegexDict.re_get | def re_get(self, pattern):
"""Return values whose key matches `pattern`
:param pattern: Regular expression
:return: Found values, as a dict.
"""
return {k: self[k] for k in self.re_keys(pattern)} | python | def re_get(self, pattern):
"""Return values whose key matches `pattern`
:param pattern: Regular expression
:return: Found values, as a dict.
"""
return {k: self[k] for k in self.re_keys(pattern)} | Return values whose key matches `pattern`
:param pattern: Regular expression
:return: Found values, as a dict. | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/dbgroup.py#L236-L242 |
materialsproject/pymatgen-db | matgendb/builders/examples/copy_builder.py | CopyBuilder.get_items | def get_items(self, source=None, target=None, crit=None):
"""Copy records from source to target collection.
:param source: Input collection
:type source: QueryEngine
:param target: Output collection
:type target: QueryEngine
:param crit: Filter criteria, e.g. "{ 'flag': ... | python | def get_items(self, source=None, target=None, crit=None):
"""Copy records from source to target collection.
:param source: Input collection
:type source: QueryEngine
:param target: Output collection
:type target: QueryEngine
:param crit: Filter criteria, e.g. "{ 'flag': ... | Copy records from source to target collection.
:param source: Input collection
:type source: QueryEngine
:param target: Output collection
:type target: QueryEngine
:param crit: Filter criteria, e.g. "{ 'flag': True }".
:type crit: dict | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/examples/copy_builder.py#L28-L44 |
materialsproject/pymatgen-db | matgendb/builders/core.py | parse_fn_docstring | def parse_fn_docstring(fn):
"""Get parameter and return types from function's docstring.
Docstrings must use this format::
:param foo: What is foo
:type foo: int
:return: What is returned
:rtype: double
:return: A map of names, each with keys 'type' and 'desc'.
:rtype: tup... | python | def parse_fn_docstring(fn):
"""Get parameter and return types from function's docstring.
Docstrings must use this format::
:param foo: What is foo
:type foo: int
:return: What is returned
:rtype: double
:return: A map of names, each with keys 'type' and 'desc'.
:rtype: tup... | Get parameter and return types from function's docstring.
Docstrings must use this format::
:param foo: What is foo
:type foo: int
:return: What is returned
:rtype: double
:return: A map of names, each with keys 'type' and 'desc'.
:rtype: tuple(dict) | https://github.com/materialsproject/pymatgen-db/blob/02e4351c2cea431407644f49193e8bf43ed39b9a/matgendb/builders/core.py#L45-L80 |
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