mxcubecore.model.lims_session

Classes

Download(*, path, filename[, groupName])	Represents a downloadable file with metadata used to match pipeline references.
Instrument(*, name, id, instrumentScientists)	Represents a beamline.
Investigation(*, name, startDate, endDate, ...)	Represents an investigation and serves as a proposal to replace the Session class.
Lims(*[, name, description])	Represents a LIMS system.
LimsSessionManager(*[, active_session, ...])	Manages LIMS sessions and connected users.
LimsUser(*[, user_name, sessions])	Represents a user connected to MXCuBE.
Meta(*, page)	Metadata containing pagination details.
MetaPage(*, totalWithoutFilters, total, ...)	Pagination metadata.
Parameter(*, name, value, id, units)	Represents a generic parameter attached to entities like investigations, samples, or datasets.
Proposal(*[, proposal_id, person_id, type, ...])	Proposal with key identifying details.
Resource(*, _id, filename, file, fileType, ...)	Represents a resource, usually a file associated with a sample or
SampleInformation(*, _id, investigationId, ...)	Parameters metadata related to a sample, including a list of associated resources.
SampleSheet(*, id, name, investigation, ...)	Represents a description of a sample sheet as defined in user portals.
Session(*[, session_id, beamline_name, ...])	Represents an experiment in a specific time slot on a beamline for a proposal.

class mxcubecore.model.lims_session.Download(*, path: str, filename: str, groupName: str | None = None)

Bases: BaseModel

Represents a downloadable file with metadata used to match pipeline references.

Parameters:

• path (str) – Absolute file path to the downloaded file on the filesystem.

• filename (str) – Name of the file, used for matching with pipeline references.

• groupName (str | None) – Optional group identifier, used to match with search models. Can be None or a string such as ‘Group1’, ‘Group2’, etc.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'filename': FieldInfo(annotation=str, required=True, description="Name of the file (e.g., 'example.hkl')"), 'groupName': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description="Group name used for model matching (e.g., 'Group1')"), 'path': FieldInfo(annotation=str, required=True, description='Full path to the file on disk')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Instrument(*, name: str, id: int, instrumentScientists: List[Any])

Bases: BaseModel

Represents a beamline.

Parameters:

• name (str) – Name of the beamline.

• id (int) – Unique identifier of the beamline.

• instrumentScientists (List[Any]) – List of scientists associated with the instrument.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'id': FieldInfo(annotation=int, required=True), 'instrumentScientists': FieldInfo(annotation=List[Any], required=True), 'name': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Investigation(*, name: str, startDate: datetime, endDate: datetime, id: int, title: str, visitId: str, summary: str | None = '', parameters: Dict[str, Any], instrument: Instrument, investigationUsers: List[Any])

Bases: BaseModel

Represents an investigation and serves as a proposal to replace the Session class.

Parameters:

• name (str) – Name of the investigation.

• startDate (datetime) – Start date of the investigation.

• endDate (datetime) – End date of the investigation.

• id (int) – Unique identifier of the investigation.

• title (str) – Title of the investigation.

• visitId (str) – Identifier for the visit associated with the investigation.

• summary (str | None) – Summary description of the investigation.

• parameters (Dict[str, Any]) – Dictionary of investigation-specific parameters.

• instrument (Instrument) – Associated instrument for the investigation.

• investigationUsers (List[Any]) – List of users involved in the investigation.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'endDate': FieldInfo(annotation=datetime, required=True), 'id': FieldInfo(annotation=int, required=True), 'instrument': FieldInfo(annotation=Instrument, required=True), 'investigationUsers': FieldInfo(annotation=List[Any], required=True), 'name': FieldInfo(annotation=str, required=True), 'parameters': FieldInfo(annotation=Dict[str, Any], required=True), 'startDate': FieldInfo(annotation=datetime, required=True), 'summary': FieldInfo(annotation=Union[str, NoneType], required=False, default=''), 'title': FieldInfo(annotation=str, required=True), 'visitId': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Lims(*, name: str = '', description: str = '')

Bases: BaseModel

Represents a LIMS system.

Parameters:

• name (str) – Unique identifier for the LIMS (e.g., “ispyb”, “icat”).

• description (str) – Free text providing a short description of the LIMS.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'description': FieldInfo(annotation=str, required=False, default=''), 'name': FieldInfo(annotation=str, required=False, default='')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.LimsSessionManager(*, active_session: Session | None = None, sessions: List[Session] | None = [], users: Dict[str, LimsUser] | None = {})

Bases: BaseModel

Manages LIMS sessions and connected users.

Parameters:

• active_session (Session | None) – The current active session, if any.

• sessions (List[Session] | None) – List of selectable sessions determined based on connected users.

• users (Dict[str, LimsUser] | None) – Dictionary of currently connected users.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'active_session': FieldInfo(annotation=Union[Session, NoneType], required=False, default=None), 'sessions': FieldInfo(annotation=Union[List[Session], NoneType], required=False, default=[]), 'users': FieldInfo(annotation=Union[Dict[str, LimsUser], NoneType], required=False, default={})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.LimsUser(*, user_name: str = '', sessions: List[Session] | None = [])

Bases: BaseModel

Represents a user connected to MXCuBE.

Parameters:

• user_name (str) – Identifier for the user, typically their login name.

• sessions (List[Session] | None) – List of sessions the user is allowed to collect data from.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'sessions': FieldInfo(annotation=Union[List[Session], NoneType], required=False, default=[]), 'user_name': FieldInfo(annotation=str, required=False, default='')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Meta(*, page: MetaPage)

Bases: BaseModel

Metadata containing pagination details.

Parameters:

page (MetaPage) – Pagination details.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'page': FieldInfo(annotation=MetaPage, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.MetaPage(*, totalWithoutFilters: int, total: int, totalPages: int, currentPage: int)

Bases: BaseModel

Pagination metadata.

Parameters:

• totalWithoutFilters (int) – Total count of items without filters applied.

• total (int) – Total count of items with filters applied.

• totalPages (int) – Total number of pages available.

• currentPage (int) – Current page number.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'currentPage': FieldInfo(annotation=int, required=True), 'total': FieldInfo(annotation=int, required=True), 'totalPages': FieldInfo(annotation=int, required=True), 'totalWithoutFilters': FieldInfo(annotation=int, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Parameter(*, name: str, value: str, id: int, units: str)

Bases: BaseModel

Represents a generic parameter attached to entities like investigations, samples, or datasets.

Parameters:

• name (str) – Name of the parameter.

• value (str) – Value assigned to the parameter.

• id (int) – Unique identifier of the parameter.

• units (str) – Measurement units, if applicable.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'id': FieldInfo(annotation=int, required=True), 'name': FieldInfo(annotation=str, required=True), 'units': FieldInfo(annotation=str, required=True), 'value': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Proposal(*, proposal_id: str = '', person_id: str = '', type: str = '', code: str = '', number: str = '', title: str = '')

Bases: BaseModel

Proposal with key identifying details.

Parameters:

• proposal_id (str) – Unique identifier for the proposal.

• person_id (str) – Identifier of the person associated.

• type (str) – Type/category of the proposal (e.g., “MX”).

• code (str) – Specific code associated with the proposal e.g., “IH-LS”.

• number (str) – Proposal number; may be sequential or unique (uniqueness may depend on the combination of code and number)

• title (str) – Title of the proposal

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'code': FieldInfo(annotation=str, required=False, default=''), 'number': FieldInfo(annotation=str, required=False, default=''), 'person_id': FieldInfo(annotation=str, required=False, default=''), 'proposal_id': FieldInfo(annotation=str, required=False, default=''), 'title': FieldInfo(annotation=str, required=False, default=''), 'type': FieldInfo(annotation=str, required=False, default='')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Resource(*, _id: str, filename: str, file: str, fileType: str, createdAt: datetime, updatedAt: datetime, groupName: str | None = None)

Bases: BaseModel

Represents a resource, usually a file associated with a sample or

investigation.

Parameters:

• id (str) – The unique identifier for the resource. The key “_id” is used in JSON and mapped to “id” in the class.

• filename (str) – The name of the file associated with the resource.

• file (str) – The URL or path pointing to the actual file or resource content.

• fileType (str) – The type of the file (e.g., “pdb”, “hkl”, etc.).

• createdAt (datetime) – The timestamp representing when the resource was created.

• updatedAt (datetime) – The timestamp representing when the resource was last updated.

• groupName (Optional[str]) – The optional group name associated with the resource (default is None).

• _id (str) –

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'createdAt': FieldInfo(annotation=datetime, required=True), 'file': FieldInfo(annotation=str, required=True), 'fileType': FieldInfo(annotation=str, required=True), 'filename': FieldInfo(annotation=str, required=True), 'groupName': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'id': FieldInfo(annotation=str, required=True, alias='_id', alias_priority=2), 'updatedAt': FieldInfo(annotation=datetime, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.SampleInformation(*, _id: str, investigationId: int, sampleId: int, createdAt: datetime, updatedAt: datetime, resources: List[Resource])

Bases: BaseModel

Parameters metadata related to a sample, including a list of associated resources.

Parameters:

• id (str) – The unique identifier for the sample. The key “_id” is used in JSON and mapped to “id” in the class.

• investigationId (int) – The unique identifier of the investigation this sample is associated with.

• sampleId (int) – The unique identifier for the sample in ICAT. Most of the cases this represents the protein itself

• createdAt (datetime) – The timestamp representing when the sample information was created.

• updatedAt (datetime) – The timestamp representing when the sample information was last updated.

• resources (List[Resource]) – A list of Resource objects associated with this sample information.

• _id (str) –

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'createdAt': FieldInfo(annotation=datetime, required=True), 'id': FieldInfo(annotation=str, required=True, alias='_id', alias_priority=2), 'investigationId': FieldInfo(annotation=int, required=True), 'resources': FieldInfo(annotation=List[Resource], required=True), 'sampleId': FieldInfo(annotation=int, required=True), 'updatedAt': FieldInfo(annotation=datetime, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.SampleSheet(*, id: int, name: str, investigation: Investigation, modTime: datetime, parameters: List[Parameter], datasets: List[Any], meta: Meta)

Bases: BaseModel

Represents a description of a sample sheet as defined in user portals.

Parameters:

• id (int) – Unique identifier for the sample sheet.

• name (str) – Name of the sample sheet, often corresponding to the protein’s name.

• investigation (Investigation) – Investigation associated with the sample sheet.

• modTime (datetime) – Last modification time of the sample sheet.

• parameters (List[Parameter]) – Generic list of parameters, dependent on the user portal.

• datasets (List[Any]) – List of datasets collected for this sample.

• meta (Meta) – Pagination metadata.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'datasets': FieldInfo(annotation=List[Any], required=True), 'id': FieldInfo(annotation=int, required=True), 'investigation': FieldInfo(annotation=Investigation, required=True), 'meta': FieldInfo(annotation=Meta, required=True), 'modTime': FieldInfo(annotation=datetime, required=True), 'name': FieldInfo(annotation=str, required=True), 'parameters': FieldInfo(annotation=List[Parameter], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class mxcubecore.model.lims_session.Session(*, session_id: str = '', beamline_name: str = '', start_date: str = '', start_time: str = '', end_date: str = '', end_time: str = '', title: str = '', code: str = '', number: str = '', proposal_id: str = '', proposal_name: str = '', comments: str | None = '', start_datetime: datetime = None, end_datetime: datetime | None = None, actual_start_date: str = '', actual_start_time: str = '', actual_end_date: str = '', actual_end_time: str = '', nb_shifts: str = '', scheduled: str = '', is_rescheduled: bool = False, is_scheduled_beamline: bool = False, is_scheduled_time: bool = False, user_portal_URL: str | None = None, data_portal_URL: str | None = None, logbook_URL: str | None = None, volume: str | None = None, dataset_count: str | None = None, sample_count: str | None = None)

Bases: BaseModel

Represents an experiment in a specific time slot on a beamline for a proposal.

This class is maintained for legacy purposes because ISPyB relies on it.

Parameters:

• session_id (str) – Unique identifier for the experiment, dependent on the LIMS.

• beamline_name (str) – Name of the beamline where the experiment is scheduled.

• start_date (str) – Official start date (format: YYYYMMDD).

• start_time (str) – Official start time.

• end_date (str) – Official end date (format: YYYYMMDD).

• end_time (str) – Official end time.

• title (str) – Title of the proposal associated with the session.

• code (str) – Code associated with the proposal.

• number (str) – Proposal number.

• proposal_id (str) – Unique identifier of the proposal.

• proposal_name (str) – Name of the proposal.

• comments (str | None) – Optional comments about the session.

• start_datetime (datetime) – Start datetime of the session.

• end_datetime (datetime | None) – End datetime of the session

• actual_start_date (str) – Start date if the session was rescheduled.

• actual_start_time (str) – Start time if the session was rescheduled.

• actual_end_date (str) – End date if the session was rescheduled.

• actual_end_time (str) – End time if the session was rescheduled.

• nb_shifts (str) – Number of shifts allocated to the session (typically 8h)

• scheduled (str) – if the session is officially scheduled and approved.

• is_rescheduled (bool) – if the session was rescheduled in time or beamline.

• is_scheduled_beamline (bool) – if the session is scheduled on the current bm

• is_scheduled_time (bool) – if the session is currently active.

• user_portal_URL (str | None) – Optional link to the session page in the User Portal.

• data_portal_URL (str | None) – link to the data portal or LIMS.

• logbook_URL (str | None) – Optional link to the session page in the logbook.

• volume (str | None) – Optional volume (in bytes) of data produced.

• dataset_count (str | None) – Optional number of datasets collected.

• sample_count (str | None) – Optional number of samples collected.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'actual_end_date': FieldInfo(annotation=str, required=False, default=''), 'actual_end_time': FieldInfo(annotation=str, required=False, default=''), 'actual_start_date': FieldInfo(annotation=str, required=False, default=''), 'actual_start_time': FieldInfo(annotation=str, required=False, default=''), 'beamline_name': FieldInfo(annotation=str, required=False, default=''), 'code': FieldInfo(annotation=str, required=False, default=''), 'comments': FieldInfo(annotation=Union[str, NoneType], required=False, default=''), 'data_portal_URL': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'dataset_count': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'end_date': FieldInfo(annotation=str, required=False, default=''), 'end_datetime': FieldInfo(annotation=Union[datetime, NoneType], required=False, default_factory=<lambda>), 'end_time': FieldInfo(annotation=str, required=False, default=''), 'is_rescheduled': FieldInfo(annotation=bool, required=False, default=False), 'is_scheduled_beamline': FieldInfo(annotation=bool, required=False, default=False), 'is_scheduled_time': FieldInfo(annotation=bool, required=False, default=False), 'logbook_URL': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'nb_shifts': FieldInfo(annotation=str, required=False, default=''), 'number': FieldInfo(annotation=str, required=False, default=''), 'proposal_id': FieldInfo(annotation=str, required=False, default=''), 'proposal_name': FieldInfo(annotation=str, required=False, default=''), 'sample_count': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'scheduled': FieldInfo(annotation=str, required=False, default=''), 'session_id': FieldInfo(annotation=str, required=False, default=''), 'start_date': FieldInfo(annotation=str, required=False, default=''), 'start_datetime': FieldInfo(annotation=datetime, required=False, default_factory=builtin_function_or_method), 'start_time': FieldInfo(annotation=str, required=False, default=''), 'title': FieldInfo(annotation=str, required=False, default=''), 'user_portal_URL': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'volume': FieldInfo(annotation=Union[str, NoneType], required=False, default=None)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.