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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,250 +1,214 @@ | ||
| """ | ||
| Code to define the PaNOSC data model | ||
| TODO - Implement these using pydantic | ||
| """ | ||
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| from abc import ABC, abstractclassmethod, abstractmethod | ||
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| class PaNOSCAttribute(ABC): | ||
| from abc import ABC, abstractclassmethod | ||
| from datetime import datetime | ||
| from typing import List, Optional, Union | ||
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| from pydantic import ( | ||
| BaseModel, | ||
| Field, | ||
| root_validator, | ||
| StrictBool, | ||
| StrictFloat, | ||
| StrictInt, | ||
| StrictStr, | ||
| ) | ||
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| class PaNOSCAttribute(ABC, BaseModel): | ||
| @abstractclassmethod | ||
| def from_icat(self): | ||
| pass | ||
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| @abstractmethod | ||
| def to_icat(self): | ||
| pass | ||
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| class Affiliation(PaNOSCAttribute): | ||
| """Information about which facility a member is located at""" | ||
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| def __init__(self, id_, name=None, address=None, city=None, country=None): | ||
| # TODO - Inconsistency in data models regarding id and pid's | ||
| self.id = id_ | ||
| self.name = name | ||
| self.address = address | ||
| self.city = city | ||
| self.country = country | ||
| name: Optional[StrictStr] | ||
| id_: Optional[StrictStr] = Field(alias="id") | ||
| address: Optional[StrictStr] | ||
| city: Optional[StrictStr] | ||
| country: Optional[StrictStr] | ||
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| self.affiliations = None | ||
| members: Optional[List["Member"]] | ||
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
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| def to_icat(self): | ||
| pass | ||
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| class Dataset(PaNOSCAttribute): | ||
| """ | ||
| Information about an experimental run, including optional File, Sample, Instrument | ||
| and Technique | ||
| """ | ||
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| def __init__(self, pid, title, is_public, creation_date, size=None): | ||
| self.pid = pid # TODO - dataset.doi, field not filled out by ISIS | ||
| self.title = title # TODO - dataset.name, only ~1k of ISIS' 159k datasets aren't called "raw" | ||
| self.isPublic = is_public # Evaluate 3 years from date | ||
| self.creationDate = creation_date # TODO - dataset.startDate or creationDate? startDate is null on ISIS | ||
| self.size = size # TODO - Would require TopCAT request, but not mandatory | ||
| pid: StrictStr | ||
| title: StrictStr | ||
| is_public: StrictBool = Field(alias="isPublic") | ||
| creation_date: datetime = Field(alias="creationDate") | ||
| size: Optional[StrictInt] | ||
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| self.documents = Document() | ||
| self.techniques = Technique() | ||
| self.instrument = None | ||
| self.files = None | ||
| self.parameters = None | ||
| self.samples = None | ||
| documents: List["Document"] | ||
| techniques: List["Technique"] | ||
| instrument: Optional["Instrument"] | ||
| files: Optional[List["File"]] | ||
| parameters: Optional[List["Parameter"]] | ||
| samples: Optional[List["Sample"]] | ||
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
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| def to_icat(self): | ||
| pass | ||
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| class Document(PaNOSCAttribute): | ||
| """ | ||
| Proposal which includes the dataset or published paper which references the dataset | ||
| """ | ||
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| def __init__( | ||
| self, | ||
| pid, | ||
| is_public, | ||
| type_, | ||
| title, | ||
| summary=None, | ||
| doi=None, | ||
| start_date=None, | ||
| end_date=None, | ||
| release_date=None, | ||
| license_=None, | ||
| keywords=None, | ||
| ): | ||
| self.pid = pid # investigation.doi | ||
| self.isPublic = is_public # TODO - Evaluate 3 years of startDate or releaseDate | ||
| self.type = type_ # TODO - investigation.type.name | ||
| self.title = title # investigaton.name | ||
| self.summary = summary # investigation.summary | ||
| self.doi = doi # TODO - investigation.doi but we already use that for pid | ||
| self.startDate = start_date # investigation.startDate | ||
| self.endDate = end_date # investigation.endDate | ||
| self.releaseDate = release_date # investigation.releaseDate | ||
| self.license = license_ # Not stored in ICAT but not mandatory, ignore | ||
| self.keywords = keywords # TODO - Iterate through keywords.name? | ||
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| self.datasets = Dataset() | ||
| self.members = None | ||
| self.parameters = None | ||
| pid: StrictStr | ||
| is_public: StrictBool = Field(alias="isPublic") | ||
| type_: StrictStr = Field(alias="type") | ||
| title: StrictStr | ||
| summary: Optional[StrictStr] | ||
| doi: Optional[StrictStr] | ||
| start_date: Optional[datetime] = Field(alias="startDate") | ||
| end_date: Optional[datetime] = Field(alias="endDate") | ||
| release_date: Optional[datetime] = Field(alias="releaseDate") | ||
| license_: Optional[StrictStr] = Field(alias="license") | ||
| keywords: Optional[List[StrictStr]] | ||
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| datasets: List[Dataset] | ||
| members: Optional[List["Member"]] | ||
| parameters: Optional[List["Parameter"]] | ||
|
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
|
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| def to_icat(self): | ||
| pass | ||
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| class File(PaNOSCAttribute): | ||
| """Name of file and optionally location""" | ||
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| def __init__(self, id_, name, path=None, size=None): | ||
| self.id = id_ # datafile.id | ||
| self.name = name # datafile.name | ||
| self.path = path # datafile.location | ||
| self.size = size # datafile.fileSize | ||
| id_: StrictStr = Field(alias="id") | ||
| name: StrictStr | ||
| path: Optional[StrictStr] | ||
| size: Optional[StrictInt] | ||
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| self.dataset = Dataset() | ||
| dataset: Dataset | ||
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
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| def to_icat(self): | ||
| pass | ||
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| class Instrument(PaNOSCAttribute): | ||
| """Beam line where experiment took place""" | ||
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| def __init__(self, id_, name, facility): | ||
| self.id = id_ # instrument.id | ||
| self.name = name # instrument.name | ||
| self.facility = facility # TODO - instrument.facility.name or fullName | ||
| pid: StrictStr | ||
| name: StrictStr | ||
| facility: StrictStr | ||
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| self.datasets = None | ||
| datasets: Optional[List[Dataset]] | ||
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
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| def to_icat(self): | ||
| pass | ||
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| class Member(PaNOSCAttribute): | ||
| """Proposal team member or paper co-author""" | ||
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| def __init__(self, role=None): | ||
| self.role = role # investigationUser.role | ||
| id_: StrictStr = Field(alias="id") | ||
| role: Optional[StrictStr] = Field(alias="role") | ||
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| self.person = Person() | ||
| self.affiliations = None | ||
| document: Document | ||
| person: Optional["Person"] | ||
| affiliation: Optional[Affiliation] | ||
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
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| def to_icat(self): | ||
| pass | ||
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| class Parameter(PaNOSCAttribute): | ||
| """ | ||
| Scalar measurement with value and units. | ||
| Note: a parameter is either related to a dataset or a document, but not both. | ||
| """ | ||
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| def __init__(self, name, value, unit=None): | ||
| self.name = name # investigationParameter.type.name | ||
| """ | ||
| Value can be a number or a string so either field can be used, ICAT also has | ||
| dateTimeValue which we could check and convert into a string if there's no | ||
| stringValue or numericValue | ||
| """ | ||
| self.value = value # investigationParameter.numericValue or stringValue | ||
| self.unit = unit # TODO - investigationParameter.type.units or unitsFullName. In ISIS, units is just "None", full name is null | ||
| id_: StrictStr = Field(alias="id") | ||
| name: StrictStr | ||
| value: Union[StrictFloat, StrictInt, StrictStr] | ||
| unit: Optional[StrictStr] | ||
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| dataset: Optional[Dataset] | ||
| document: Optional[Document] | ||
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| @root_validator(skip_on_failure=True) | ||
| def validate_dataset_and_document(cls, values): # noqa: B902, N805 | ||
| if values["dataset"] is None and values["document"] is None: | ||
| raise TypeError("must have a dataset or document") | ||
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| if values["dataset"] is not None and values["document"] is not None: | ||
| # TODO - Should an exception be raised here instead? | ||
| values["Document"] = None | ||
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| return values | ||
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
|
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| def to_icat(self): | ||
| pass | ||
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| class Person(PaNOSCAttribute): | ||
| """Human who carried out experiment""" | ||
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| def __init__( | ||
| self, | ||
| id_, | ||
| full_name, | ||
| orcidid=None, | ||
| researcher_id=None, | ||
| first_name=None, | ||
| last_name=None, | ||
| ): | ||
| # TODO - anon doesn't have permissions to query users on ISIS, has to be on an include | ||
| self.id = id_ # user.id | ||
| self.full_name = full_name # user.fullName | ||
| self.orcidid = orcidid # user.orcidId | ||
| self.researcherId = researcher_id # TODO - not sure, not mandatory, keep blank? | ||
| # TODO - These can be null on ISIS data? | ||
| self.firstName = first_name # user.givenName | ||
| self.lastName = last_name # user.familyName | ||
| id_: StrictStr = Field(alias="id") | ||
| full_name: StrictStr = Field(alias="fullName") | ||
| orcid: Optional[StrictStr] | ||
| researcher_id: Optional[StrictStr] = Field(alias="researcherId") | ||
| first_name: Optional[StrictStr] = Field(alias="firstName") | ||
| last_name: Optional[StrictStr] = Field(alias="lastName") | ||
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| members: Optional[List[Member]] | ||
|
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
|
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| def to_icat(self): | ||
| pass | ||
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| class Sample(PaNOSCAttribute): | ||
| """Extract of material used in the experiment""" | ||
|
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| def __init__(self, name, pid=None, description=None): | ||
| self.name = name # sample.name | ||
| self.pid = pid # TODO - sample.pid, seems to be null on ISIS | ||
| # parameters will be a list, description isn't mandatory, maybe just leave? | ||
| self.description = description # TODO - sample.parameters.type.description | ||
| name: StrictStr | ||
| pid: StrictStr | ||
| description: Optional[StrictStr] | ||
|
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| self.datasets = None | ||
| datasets: Optional[List[Dataset]] | ||
|
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
|
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| def to_icat(self): | ||
| pass | ||
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|
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| class Technique(PaNOSCAttribute): | ||
| """Common name of scientific method used""" | ||
|
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| def __init__(self, pid, name): | ||
| self.pid = pid | ||
| self.name = name | ||
| pid: StrictStr | ||
| name: StrictStr | ||
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| datasets: Optional[List[Dataset]] | ||
|
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| @classmethod | ||
| def from_icat(cls): | ||
| pass | ||
|
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| def to_icat(self): | ||
| pass | ||
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| # The below models reference other models that may not be defined during their | ||
| # creation so their references have to manually be updated to lead to the actual | ||
| # models or else an exception will be raised. This can be done with the help of | ||
| # the postponed annotations via the future import together with the | ||
| # `update_forward_refs` method, only after all related models are declared. | ||
| Affiliation.update_forward_refs() | ||
| Dataset.update_forward_refs() | ||
| Document.update_forward_refs() | ||
| Member.update_forward_refs() |
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