orm

Submodules

• orm.bioreplicate
• orm.community
• orm.compartment
• orm.excel_file
• orm.experiment
• orm.experiment_compartment
• orm.measurement
• orm.measurement_context
• orm.measurement_technique
• orm.metabolite
• orm.modeling_request
• orm.modeling_result
• orm.orm_base
• orm.perturbation
• orm.project
• orm.project_user
• orm.strain
• orm.study
• orm.study_metabolite
• orm.study_user
• orm.submission
• orm.taxon
• orm.user

Classes

Bioreplicate
Community
Compartment
ExcelFile
Experiment
ExperimentCompartment
Measurement
MeasurementContext
MeasurementTechnique
Metabolite
ModelingRequest
ModelingResult
Perturbation
Project
ProjectUser
Strain
Study
StudyMetabolite
StudyUser
Submission
Taxon
User

Package Contents

class orm.Bioreplicate

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Bioreplicates'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

position: sqlalchemy.orm.Mapped[str]

biosampleUrl: sqlalchemy.orm.Mapped[str]

isControl: sqlalchemy.orm.Mapped[bool]

isBlank: sqlalchemy.orm.Mapped[bool]

calculationType: sqlalchemy.orm.Mapped[str]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

experimentId: sqlalchemy.orm.Mapped[int]

experiment: sqlalchemy.orm.Mapped[Experiment]

measurementContexts: sqlalchemy.orm.Mapped[List[MeasurementContext]]

measurements: sqlalchemy.orm.Mapped[List[Measurement]]

static find_for_study(db_session, study_id, name)

class orm.Community

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Communities'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

strainIds: sqlalchemy.orm.Mapped[sqlalchemy.types.JSON]

experiments: sqlalchemy.orm.Mapped[List[Experiment]]

get_strains(db_session)

class orm.Compartment

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Compartments'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

volume: sqlalchemy.orm.Mapped[decimal.Decimal]

pressure: sqlalchemy.orm.Mapped[decimal.Decimal]

stirringSpeed: sqlalchemy.orm.Mapped[decimal.Decimal]

stirringMode: sqlalchemy.orm.Mapped[str]

O2: sqlalchemy.orm.Mapped[decimal.Decimal]

CO2: sqlalchemy.orm.Mapped[decimal.Decimal]

H2: sqlalchemy.orm.Mapped[decimal.Decimal]

N2: sqlalchemy.orm.Mapped[decimal.Decimal]

inoculumConcentration: sqlalchemy.orm.Mapped[decimal.Decimal]

inoculumVolume: sqlalchemy.orm.Mapped[decimal.Decimal]

initialPh: sqlalchemy.orm.Mapped[decimal.Decimal]

initialTemperature: sqlalchemy.orm.Mapped[decimal.Decimal]

mediumName: sqlalchemy.orm.Mapped[str]

mediumUrl: sqlalchemy.orm.Mapped[str]

experimentCompartments: sqlalchemy.orm.Mapped[List[ExperimentCompartment]]

experiments: sqlalchemy.orm.Mapped[List[Experiment]]

measurementContexts: sqlalchemy.orm.Mapped[List[MeasurementContext]]

measurements: sqlalchemy.orm.Mapped[List[Measurement]]

property properties_description

class orm.ExcelFile

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'ExcelFiles'

id: sqlalchemy.orm.Mapped[int]

filename: sqlalchemy.orm.Mapped[str]

size: sqlalchemy.orm.Mapped[int]

content: sqlalchemy.orm.Mapped[bytes]

createdAt: sqlalchemy.orm.Mapped[datetime.datetime]

classmethod from_upload(uploaded_file)

property humanized_size

extract_sheets()

class orm.Experiment

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Experiments'

id: sqlalchemy.orm.Mapped[int]

publicId: sqlalchemy.orm.Mapped[str]

name: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

bioreplicates: sqlalchemy.orm.Mapped[List[Bioreplicate]]

communityId: sqlalchemy.orm.Mapped[int]

community: sqlalchemy.orm.Mapped[Community]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

cultivationMode: sqlalchemy.orm.Mapped[str]

experimentCompartments: sqlalchemy.orm.Mapped[List[ExperimentCompartment]]

compartments: sqlalchemy.orm.Mapped[List[Compartment]]

perturbations: sqlalchemy.orm.Mapped[List[Perturbation]]

measurementContexts: sqlalchemy.orm.Mapped[List[MeasurementContext]]

static generate_public_id(db_session)

class orm.ExperimentCompartment

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'ExperimentCompartments'

id: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[str]

experimentId: sqlalchemy.orm.Mapped[int]

compartmentId: sqlalchemy.orm.Mapped[int]

study: sqlalchemy.orm.Mapped[Study]

experiment: sqlalchemy.orm.Mapped[Experiment]

compartment: sqlalchemy.orm.Mapped[Compartment]

class orm.Measurement

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Measurements'

context_relationship

id: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

contextId: sqlalchemy.orm.Mapped[int]

context: sqlalchemy.orm.Mapped[MeasurementContext]

bioreplicate: sqlalchemy.orm.Mapped[Bioreplicate]

compartment: sqlalchemy.orm.Mapped[Compartment]

technique: sqlalchemy.orm.Mapped[MeasurementTechnique]

timeInSeconds: sqlalchemy.orm.Mapped[int]

value: sqlalchemy.orm.Mapped[decimal.Decimal]

std: sqlalchemy.orm.Mapped[decimal.Decimal]

timeInHours()

subjectId()

subjectType()

classmethod insert_from_csv_string(db_session, study, csv_string, subject_type)

class orm.MeasurementContext

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'MeasurementContexts'

id: sqlalchemy.orm.Mapped[int]

bioreplicateId: sqlalchemy.orm.Mapped[int]

bioreplicate: sqlalchemy.orm.Mapped[Bioreplicate]

compartmentId: sqlalchemy.orm.Mapped[int]

compartment: sqlalchemy.orm.Mapped[Compartment]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

techniqueId: sqlalchemy.orm.Mapped[int]

technique: sqlalchemy.orm.Mapped[MeasurementTechnique]

measurements: sqlalchemy.orm.Mapped[List[Measurement]]

modelingResults: sqlalchemy.orm.Mapped[List[ModelingResult]]

calculationType: sqlalchemy.orm.Mapped[str]

subjectId: sqlalchemy.orm.Mapped[str]

subjectType: sqlalchemy.orm.Mapped[str]

get_df(db_session)

get_chart_label(db_session)

get_subject(db_session)

class orm.MeasurementTechnique

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'MeasurementTechniques'

id: sqlalchemy.orm.Mapped[int]

type: sqlalchemy.orm.Mapped[str]

units: sqlalchemy.orm.Mapped[str]

subjectType: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

includeStd: sqlalchemy.orm.Mapped[bool]

metaboliteIds: sqlalchemy.orm.Mapped[sqlalchemy.JSON]

strainIds: sqlalchemy.orm.Mapped[sqlalchemy.JSON]

studyUniqueID: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

createdAt: sqlalchemy.orm.Mapped[datetime.datetime]

updatedAt: sqlalchemy.orm.Mapped[datetime.datetime]

measurementContexts: sqlalchemy.orm.Mapped[List[MeasurementContext]]

measurements: sqlalchemy.orm.Mapped[List[Measurement]]

__lt__(other)

property short_name

property long_name

property long_name_with_subject_type

property subject_short_name

property is_growth

get_bioreplicates(db_session)

get_subjects_for_bioreplicate(db_session, bioreplicate)

csv_column_name(subject_name=None)

get_grouped_contexts()

__str__()

class orm.Metabolite

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Metabolites'

id: sqlalchemy.orm.Mapped[int]

chebiId: sqlalchemy.orm.Mapped[str]

name: sqlalchemy.orm.Mapped[str]

averageMass: sqlalchemy.orm.Mapped[decimal.Decimal]

studyMetabolites: sqlalchemy.orm.Mapped[List[StudyMetabolite]]

__lt__(other)

static search_by_name(db_conn, term, page=1, per_page=10)

class orm.ModelingRequest

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'ModelingRequests'

id: sqlalchemy.orm.Mapped[int]

type: sqlalchemy.orm.Mapped[str]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

jobUuid: sqlalchemy.orm.Mapped[str]

state: sqlalchemy.orm.Mapped[str]

error: sqlalchemy.orm.Mapped[str]

createdAt: sqlalchemy.orm.Mapped[datetime.datetime]

updatedAt: sqlalchemy.orm.Mapped[datetime.datetime]

results: sqlalchemy.orm.Mapped[List[ModelingResult]]

_validate_type(key, value)

_validate_state(key, value)

property long_name

class orm.ModelingResult

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'ModelingResults'

id: sqlalchemy.orm.Mapped[int]

type: sqlalchemy.orm.Mapped[str]

requestId: sqlalchemy.orm.Mapped[int]

request: sqlalchemy.orm.Mapped[ModelingRequest]

measurementContextId: sqlalchemy.orm.Mapped[int]

measurementContext: sqlalchemy.orm.Mapped[MeasurementContext]

inputs: sqlalchemy.orm.Mapped[sqlalchemy.JSON]

fit: sqlalchemy.orm.Mapped[sqlalchemy.JSON]

coefficients: sqlalchemy.orm.Mapped[sqlalchemy.JSON]

state: sqlalchemy.orm.Mapped[str]

error: sqlalchemy.orm.Mapped[str]

rSummary: sqlalchemy.orm.Mapped[str]

createdAt: sqlalchemy.orm.Mapped[datetime.datetime]

updatedAt: sqlalchemy.orm.Mapped[datetime.datetime]

calculatedAt: sqlalchemy.orm.Mapped[datetime.datetime]

classmethod empty_coefficients(model_type)

classmethod empty_fit()

classmethod empty_inputs(model_type)

property model_name

_validate_type(key, value)

_validate_state(key, value)

generate_chart_df(measurements_df)

_predict(timepoints)

_predict_easy_linear(time)

_predict_logistic(time)

_predict_baranyi_roberts(time)

class orm.Perturbation

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Perturbations'

id: sqlalchemy.orm.Mapped[int]

description: sqlalchemy.orm.Mapped[str]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

experimentId: sqlalchemy.orm.Mapped[int]

experiment: sqlalchemy.orm.Mapped[Experiment]

startTimepoint: sqlalchemy.orm.Mapped[int]

removedCompartmentId: sqlalchemy.orm.Mapped[int]

addedCompartmentId: sqlalchemy.orm.Mapped[int]

oldCommunityId: sqlalchemy.orm.Mapped[int]

newCommunityId: sqlalchemy.orm.Mapped[int]

class orm.Project

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Projects'

projectUniqueID: sqlalchemy.orm.Mapped[str]

ownerUniqueID: sqlalchemy.orm.Mapped[str]

owner: sqlalchemy.orm.Mapped[User]

projectId: sqlalchemy.orm.Mapped[str]

projectName: sqlalchemy.orm.Mapped[str]

projectDescription: sqlalchemy.orm.Mapped[str]

projectUsers: sqlalchemy.orm.Mapped[List[ProjectUser]]

studies: sqlalchemy.orm.Mapped[List[Study]]

publicId()

uuid()

name()

property studyUuids

property managerUuids

static generate_public_id(db_session)

class orm.ProjectUser

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'ProjectUsers'

id: sqlalchemy.orm.Mapped[int]

projectUniqueID: sqlalchemy.orm.Mapped[str]

userUniqueID: sqlalchemy.orm.Mapped[str]

project: sqlalchemy.orm.Mapped[Project]

user: sqlalchemy.orm.Mapped[User]

class orm.Strain

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Strains'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

defined: sqlalchemy.orm.Mapped[bool]

NCBId: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

userUniqueID: sqlalchemy.orm.Mapped[str]

__lt__(other)

static find_for_study(db_conn, study_id, strain_name)

class orm.Study

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Studies'

owner_relationship

studyUniqueID: sqlalchemy.orm.Mapped[str]

ownerUniqueID: sqlalchemy.orm.Mapped[str]

owner: sqlalchemy.orm.Mapped[User]

studyId: sqlalchemy.orm.Mapped[str]

studyName: sqlalchemy.orm.Mapped[str]

studyDescription: sqlalchemy.orm.Mapped[str]

studyURL: sqlalchemy.orm.Mapped[str]

timeUnits: sqlalchemy.orm.Mapped[str]

projectUniqueID: sqlalchemy.orm.Mapped[str]

project: sqlalchemy.orm.Mapped[Project]

createdAt: sqlalchemy.orm.Mapped[datetime.datetime]

updatedAt: sqlalchemy.orm.Mapped[datetime.datetime]

publishableAt: sqlalchemy.orm.Mapped[datetime.datetime]

publishedAt: sqlalchemy.orm.Mapped[datetime.datetime]

embargoExpiresAt: sqlalchemy.orm.Mapped[datetime.datetime]

studyUsers: sqlalchemy.orm.Mapped[List[StudyUser]]

experiments: sqlalchemy.orm.Mapped[List[Experiment]]

strains: sqlalchemy.orm.Mapped[List[Strain]]

communities: sqlalchemy.orm.Mapped[List[Community]]

compartments: sqlalchemy.orm.Mapped[List[Compartment]]

measurementTechniques: sqlalchemy.orm.Mapped[List[MeasurementTechnique]]

measurementContexts: sqlalchemy.orm.Mapped[List[MeasurementContext]]

modelingRequests: sqlalchemy.orm.Mapped[List[ModelingRequest]]

experimentCompartments: sqlalchemy.orm.Mapped[List[ExperimentCompartment]]

bioreplicates: sqlalchemy.orm.Mapped[List[Bioreplicate]]

perturbations: sqlalchemy.orm.Mapped[List[Perturbation]]

measurements: sqlalchemy.orm.Mapped[List[Measurement]]

modelingResults: sqlalchemy.orm.Mapped[List[ModelingResult]]

studyMetabolites: sqlalchemy.orm.Mapped[List[StudyMetabolite]]

metabolites: sqlalchemy.orm.Mapped[List[Metabolite]]

uuid()

publicId()

name()

description()

isPublished()

isPublishable()

visible_to_user(user)

manageable_by_user(user)

find_last_submission(db_session)

property managerUuids

publish()

static generate_public_id(db_session)

class orm.StudyMetabolite

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'StudyMetabolites'

id: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[str]

chebi_id: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

metabolite: sqlalchemy.orm.Mapped[Metabolite]

class orm.StudyUser

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'StudyUsers'

id: sqlalchemy.orm.Mapped[int]

studyUniqueID: sqlalchemy.orm.Mapped[str]

userUniqueID: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

user: sqlalchemy.orm.Mapped[User]

class orm.Submission

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Submissions'

id: sqlalchemy.orm.Mapped[int]

projectUniqueID: sqlalchemy.orm.Mapped[str]

studyUniqueID: sqlalchemy.orm.Mapped[str]

project: sqlalchemy.orm.Mapped[Project | None]

study: sqlalchemy.orm.Mapped[Study | None]

userUniqueID: sqlalchemy.orm.Mapped[str]

user: sqlalchemy.orm.Mapped[User]

studyDesign: sqlalchemy.orm.Mapped[sqlalchemy.types.JSON]

dataFileId: sqlalchemy.orm.Mapped[int]

dataFile: sqlalchemy.orm.Mapped[ExcelFile | None]

createdAt: sqlalchemy.orm.Mapped[datetime.datetime]

updatedAt: sqlalchemy.orm.Mapped[datetime.datetime]

property completed_step_count

build_techniques()

class orm.Taxon

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Taxa'

id: sqlalchemy.orm.Mapped[int]

ncbiId: sqlalchemy.orm.Mapped[str]

name: sqlalchemy.orm.Mapped[str]

property short_name

static search_by_name(db_conn, term, page=1, per_page=10)

class orm.User

Bases: app.model.orm.orm_base.OrmBase

__tablename__ = 'Users'

owner_relationship

id: sqlalchemy.orm.Mapped[int]

uuid: sqlalchemy.orm.Mapped[str]

orcidId: sqlalchemy.orm.Mapped[str]

orcidToken: sqlalchemy.orm.Mapped[str]

name: sqlalchemy.orm.Mapped[str]

isAdmin: sqlalchemy.orm.Mapped[bool]

createdAt: sqlalchemy.orm.Mapped[datetime.datetime]

updatedAt: sqlalchemy.orm.Mapped[datetime.datetime]

lastLoginAt: sqlalchemy.orm.Mapped[datetime.datetime]

ownedProjects: sqlalchemy.orm.Mapped[List[Project]]

ownedStudies: sqlalchemy.orm.Mapped[List[Study]]

submissions: sqlalchemy.orm.Mapped[List[Submission]]

studyUsers: sqlalchemy.orm.Mapped[List[StudyUser]]

managedStudies: sqlalchemy.orm.Mapped[List[Study]]

projectUsers: sqlalchemy.orm.Mapped[List[ProjectUser]]

managedProjects: sqlalchemy.orm.Mapped[List[Project]]

property orcidUrl