app.model.orm

• app.model.orm.bioreplicate
• app.model.orm.community
• app.model.orm.community_strain
• app.model.orm.compartment
• app.model.orm.custom_model
• app.model.orm.excel_file
• app.model.orm.experiment
• app.model.orm.experiment_compartment
• app.model.orm.measurement
• app.model.orm.measurement_context
• app.model.orm.measurement_technique
• app.model.orm.metabolite
• app.model.orm.modeling_result
• app.model.orm.orm_base
• app.model.orm.page_error
• app.model.orm.page_visit
• app.model.orm.page_visit_counter
• app.model.orm.perturbation
• app.model.orm.project
• app.model.orm.project_user
• app.model.orm.study
• app.model.orm.study_metabolite
• app.model.orm.study_strain
• app.model.orm.study_technique
• app.model.orm.study_user
• app.model.orm.submission
• app.model.orm.submission_backup
• app.model.orm.taxon
• app.model.orm.user
• app.model.orm.workspace
• app.model.orm.workspace_entry

Classes

Bioreplicate	A specific physical implementation of a particular experiment.
Community	A collection of strains measured in a particular study
CommunityStrain	Join table between Communities and StudyStrains
Compartment	The environment of a particular bioreplicate.
CustomModel	The description of a user-created model type.
ExcelFile	An uploaded excel file with measurement data
Experiment	An entity that describes the design of a particular experiment.
ExperimentCompartment	Join table between Experiments and Compartments
Measurement	A single observed measurement at a particular time point.
MeasurementContext	A collection of measurements of a particular subject with a particular technique.
MeasurementTechnique	The technique used for a particular set of measurements.
Metabolite	A metabolite record imported from ChEBI.
ModelingResult	The results of fitting a model onto a set of measurements.
PageError	A record of an error that occurred on a particular page, used for tracking
PageVisit	A record of a single visit of a page in the app, intended to be aggregated
PageVisitCounter	A record of a single visit of a page in the app, intended to be aggregated
Perturbation	The description of a change over time in a particular experiment's environment.
Project	A collection of studies.
ProjectUser	Join table between Projects and Users.
Study	The main container for a particular scientific study.
StudyMetabolite	Join table between Studies and Metabolites
StudyStrain	A microbial strain used in a particular study
StudyTechnique	A technique used within a study, parent to one or more MeasurementTechnique records
StudyUser	Join table between Studies and Users.
Submission	A temporary container for the data of a Study, uploaded by a particular User.
SubmissionBackup	A backup recording of a particular past submission
Taxon	A taxon record imported from NCBI.
User	A visitor to the site that is identified by ORCID.
Workspace	A space where users can upload data that is not linked to a study.
WorkspaceEntry	Data uploaded by a user that is not linked to a study.

Package Contents

class app.model.orm.Bioreplicate

Bases: app.model.orm.orm_base.OrmBase

A specific physical implementation of a particular experiment.

This would usually be a specific vessel or a connected combination of vessels (Compartment records). All bioreplicates of one particular experiment have the same experimental design. All measurements are made within the context of a bioreplicate.

__tablename__ = 'Bioreplicates'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

position: sqlalchemy.orm.Mapped[str]

biosampleUrl: sqlalchemy.orm.Mapped[str]

calculationType: sqlalchemy.orm.Mapped[str]

experimentId: sqlalchemy.orm.Mapped[str]

experiment: sqlalchemy.orm.Mapped[Experiment]

study: sqlalchemy.orm.Mapped[Study]

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

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

property externalId

For compatibility with other subjects of measurements. Always None, since a bioreplicate is not an external record.

get_df(db_session)

class app.model.orm.Community

Bases: app.model.orm.orm_base.OrmBase

A collection of strains measured in a particular study

__tablename__ = 'Communities'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

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

communityStrains: sqlalchemy.orm.Mapped[List[CommunityStrain]]

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

diff(other)

class app.model.orm.CommunityStrain

Bases: app.model.orm.orm_base.OrmBase

Join table between Communities and StudyStrains

__tablename__ = 'CommunityStrains'

id: sqlalchemy.orm.Mapped[int]

communityId: sqlalchemy.orm.Mapped[int]

strainId: sqlalchemy.orm.Mapped[int]

community: sqlalchemy.orm.Mapped[Community]

strain: sqlalchemy.orm.Mapped[StudyStrain]

class app.model.orm.Compartment

Bases: app.model.orm.orm_base.OrmBase

The environment of a particular bioreplicate.

There could be multiple of these within the same bioreplicate that form a single biological system, but can be measured separately.

One compartment may change to a different compartment due to a Perturbation.

In the future, this entity may be broken down into a separate “compartment” and “environment”.

__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]

dilutionRate: 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

diff(other)

class app.model.orm.CustomModel

Bases: app.model.orm.orm_base.OrmBase

The description of a user-created model type.

__tablename__ = 'CustomModels'

id: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[int]

study: sqlalchemy.orm.Mapped[Study]

name: sqlalchemy.orm.Mapped[str]

shortName: sqlalchemy.orm.Mapped[str]

url: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

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

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

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

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

property coefficientInfo

property fitInfo

class app.model.orm.ExcelFile

Bases: app.model.orm.orm_base.OrmBase

An uploaded excel file with measurement data

__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 app.model.orm.Experiment

Bases: app.model.orm.orm_base.OrmBase

An entity that describes the design of a particular experiment.

The specific measurements of an experiment are connected to its biological replicates (Bioreplicate), which are the concrete implementations of the experimental design.

A published study contains experiments with fixed publicId identifiers starting with the prefix “EMGDB”.

__tablename__ = 'Experiments'

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]]

get_df(db_session)

static generate_public_id(db_session)

class app.model.orm.ExperimentCompartment

Bases: app.model.orm.orm_base.OrmBase

Join table between Experiments and Compartments

__tablename__ = 'ExperimentCompartments'

id: sqlalchemy.orm.Mapped[int]

experimentId: sqlalchemy.orm.Mapped[str]

compartmentId: sqlalchemy.orm.Mapped[int]

experiment: sqlalchemy.orm.Mapped[Experiment]

compartment: sqlalchemy.orm.Mapped[Compartment]

class app.model.orm.Measurement

Bases: app.model.orm.orm_base.OrmBase

A single observed measurement at a particular time point.

A measurement may be an average of multiple technical replicates with a standard deviation. It may also be a “calculated” measurement from an average of multiple biological replicates. This information is encapsulated in a MeasurementContext, while this record mostly contains the time and recorded value.

__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)

class app.model.orm.MeasurementContext

Bases: app.model.orm.orm_base.OrmBase

A collection of measurements of a particular subject with a particular technique.

All connections between measurements and other entities are encapsulated here, so the individual Measurement objects can be packages of time and value alone.

__tablename__ = 'MeasurementContexts'

id: sqlalchemy.orm.Mapped[int]

bioreplicateId: sqlalchemy.orm.Mapped[int]

bioreplicate: sqlalchemy.orm.Mapped[Bioreplicate]

experiment: sqlalchemy.orm.Mapped[Experiment]

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[int]

subjectType: sqlalchemy.orm.Mapped[str]

subjectName: sqlalchemy.orm.Mapped[str]

subjectExternalId: sqlalchemy.orm.Mapped[str]

subjectTypeOrdering

property readyModelingResults

property publishedModelingResults

property units

get_df(db_session)

get_chart_label(model_name=None)

get_subject(db_session)

class app.model.orm.MeasurementTechnique

Bases: app.model.orm.orm_base.OrmBase

The technique used for a particular set of measurements.

__tablename__ = 'MeasurementTechniques'

id: sqlalchemy.orm.Mapped[int]

type: sqlalchemy.orm.Mapped[str]

cellType: sqlalchemy.orm.Mapped[str]

subjectType: sqlalchemy.orm.Mapped[str]

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

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

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

studyTechniqueId: sqlalchemy.orm.Mapped[int]

studyTechnique: sqlalchemy.orm.Mapped[StudyTechnique]

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

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

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

typeOrdering

subjectTypeOrdering

__lt__(other)

property units

property short_name

property long_name

property long_name_with_subject_type

property is_growth

property connectedExperimentIds

get_bioreplicates(db_session)

csv_column_name(subject_name=None)

get_grouped_contexts()

__str__()

class app.model.orm.Metabolite

Bases: app.model.orm.orm_base.OrmBase

A metabolite record imported from ChEBI.

This entity is independent from any particular study and it represents the general information about a metabolite.

__tablename__ = 'Metabolites'

id: sqlalchemy.orm.Mapped[int]

chebiId: sqlalchemy.orm.Mapped[str]

name: sqlalchemy.orm.Mapped[str]

definition: sqlalchemy.orm.Mapped[str]

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

massIsEstimation: sqlalchemy.orm.Mapped[bool]

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

__lt__(other)

property externalId

For compatibility with other subjects of measurements. The metabolite’s ChEBI id, e.g. “CHEBI:1234”

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

class app.model.orm.ModelingResult

Bases: app.model.orm.orm_base.OrmBase

The results of fitting a model onto a set of measurements.

The measurements are represented by a ModelingContext and the results of the calculation are stored in the params field. The state of the record describes the status of the job that runs the calculations.

__tablename__ = 'ModelingResults'

id: sqlalchemy.orm.Mapped[int]

type: sqlalchemy.orm.Mapped[str]

measurementContextId: sqlalchemy.orm.Mapped[int]

measurementContext: sqlalchemy.orm.Mapped[MeasurementContext]

study: sqlalchemy.orm.Mapped[Study]

workspaceEntryId: sqlalchemy.orm.Mapped[int]

workspaceEntry: sqlalchemy.orm.Mapped[WorkspaceEntry]

customModelId: sqlalchemy.orm.Mapped[int]

customModel: sqlalchemy.orm.Mapped[CustomModel]

params: 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]

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

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

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

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

classmethod empty_params(model_type)

isPublished()

property info

property model_name

property short_model_name

property model_url

property model_description

property model_params

property target

property units

get_chart_label()

generate_chart_df(measurements_df=None)

update_model_params(form)

visible_to_user(user)

class app.model.orm.PageError

Bases: app.model.orm.orm_base.OrmBase

A record of an error that occurred on a particular page, used for tracking unseen problems in the application in production.

__tablename__ = 'PageErrors'

id: sqlalchemy.orm.Mapped[int]

fullPath: sqlalchemy.orm.Mapped[str]

uuid: sqlalchemy.orm.Mapped[str]

userId: sqlalchemy.orm.Mapped[int]

traceback: sqlalchemy.orm.Mapped[str]

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

class app.model.orm.PageVisit

Bases: app.model.orm.orm_base.OrmBase

A record of a single visit of a page in the app, intended to be aggregated into counts and deleted on a regular basis.

__tablename__ = 'PageVisits'

id: sqlalchemy.orm.Mapped[int]

path: sqlalchemy.orm.Mapped[str]

query: sqlalchemy.orm.Mapped[str]

referrer: sqlalchemy.orm.Mapped[str]

ip: sqlalchemy.orm.Mapped[str]

country: sqlalchemy.orm.Mapped[str]

userAgent: sqlalchemy.orm.Mapped[str]

uuid: sqlalchemy.orm.Mapped[str]

isUser: sqlalchemy.orm.Mapped[bool]

isAdmin: sqlalchemy.orm.Mapped[bool]

isBot: sqlalchemy.orm.Mapped[bool]

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

property parsedQuery

class app.model.orm.PageVisitCounter

Bases: app.model.orm.orm_base.OrmBase

A record of a single visit of a page in the app, intended to be aggregated into counts and deleted on a regular basis.

__tablename__ = 'PageVisitCounters'

id: sqlalchemy.orm.Mapped[int]

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

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

totalVisitCount: sqlalchemy.orm.Mapped[int]

totalBotVisitCount: sqlalchemy.orm.Mapped[int]

totalVisitorCount: sqlalchemy.orm.Mapped[int]

totalUserCount: sqlalchemy.orm.Mapped[int]

totalApiVisitCount: sqlalchemy.orm.Mapped[int]

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

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

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

class app.model.orm.Perturbation

Bases: app.model.orm.orm_base.OrmBase

The description of a change over time in a particular experiment’s environment.

A perturbation is described by the addition or removal of a Compartment to the experiment or by the change from one Community to another.

This may be changed in the future as we collect more studies with perturbations.

__tablename__ = 'Perturbations'

id: sqlalchemy.orm.Mapped[int]

description: sqlalchemy.orm.Mapped[str]

experimentId: sqlalchemy.orm.Mapped[str]

experiment: sqlalchemy.orm.Mapped[Experiment]

study: sqlalchemy.orm.Mapped[Study]

startTimeInSeconds: sqlalchemy.orm.Mapped[int]

endTimeInSeconds: sqlalchemy.orm.Mapped[int]

removedCompartmentId: sqlalchemy.orm.Mapped[int]

addedCompartmentId: sqlalchemy.orm.Mapped[int]

oldCommunityId: sqlalchemy.orm.Mapped[int]

newCommunityId: sqlalchemy.orm.Mapped[int]

oldCommunity: sqlalchemy.orm.Mapped[Community | None]

newCommunity: sqlalchemy.orm.Mapped[Community | None]

removedCompartment: sqlalchemy.orm.Mapped[Compartment | None]

addedCompartment: sqlalchemy.orm.Mapped[Compartment | None]

startTimeInHours()

endTimeInHours()

class app.model.orm.Project

Bases: app.model.orm.orm_base.OrmBase

A collection of studies.

It has a fixed publicId identifier starting with the prefix “PMGDB”.

__tablename__ = 'Projects'

publicId: sqlalchemy.orm.Mapped[str]

uuid: sqlalchemy.orm.Mapped[str]

ownerUuid: sqlalchemy.orm.Mapped[str]

owner: sqlalchemy.orm.Mapped[User]

name: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

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

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

property studyUuids

property managerUuids

static generate_public_id(db_session)

class app.model.orm.ProjectUser

Bases: app.model.orm.orm_base.OrmBase

Join table between Projects and Users.

The users recorded in this table have the ability to manage a particular project, add studies to it.

__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 app.model.orm.Study

Bases: app.model.orm.orm_base.OrmBase

The main container for a particular scientific study.

Updates to experiments and measurements can only be done by issuing a Submission to update a particular study. Access control over the individual experiments is also done at the study level.

It has a fixed publicId identifier starting with the prefix “SMGDB”.

__tablename__ = 'Studies'

owner_relationship

publicId: sqlalchemy.orm.Mapped[str]

uuid: sqlalchemy.orm.Mapped[str]

ownerUuid: sqlalchemy.orm.Mapped[str]

owner: sqlalchemy.orm.Mapped[User]

name: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

url: sqlalchemy.orm.Mapped[str]

licenseUrl: sqlalchemy.orm.Mapped[str]

timeUnits: sqlalchemy.orm.Mapped[str]

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

authorCache: sqlalchemy.orm.Mapped[str]

projectUuid: 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[StudyStrain]]

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

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

studyTechniques: sqlalchemy.orm.Mapped[List[StudyTechnique]]

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

customModels: sqlalchemy.orm.Mapped[List[CustomModel]]

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

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

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

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

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

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

lastSubmissionId: sqlalchemy.orm.Mapped[int]

lastSubmission: sqlalchemy.orm.Mapped[Submission]

isPublished()

property nameWithId

property isPublishable

property managerUuids

visible_to_user(user)

manageable_by_user(user)

get_model_info_list()

find_last_submission(db_session)

fetch_grouped_measurement_subjects(db_session)

fetch_experiment_ids_by_measurement_subject(db_session)

publish(db_session)

get_cc_code()

If the license URL is to a Creative Commons license, get the corresponding code to render the appropriate image.

static generate_public_id(db_session)

class app.model.orm.StudyMetabolite

Bases: app.model.orm.orm_base.OrmBase

Join table between Studies and Metabolites

__tablename__ = 'StudyMetabolites'

id: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[str]

chebiId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

metabolite: sqlalchemy.orm.Mapped[Metabolite]

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

class app.model.orm.StudyStrain

Bases: app.model.orm.orm_base.OrmBase

A microbial strain used in a particular study

__tablename__ = 'StudyStrains'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

defined: sqlalchemy.orm.Mapped[bool]

ncbiId: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

userUniqueID: sqlalchemy.orm.Mapped[str]

taxon: sqlalchemy.orm.Mapped[Taxon]

communityStrains: sqlalchemy.orm.Mapped[List[CommunityStrain]]

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

__lt__(other)

isUnknown()

notUnknown()

property externalId

For compatibility with other subjects of measurements. The strain’s (or parent strain’s) NCBI id, e.g. “NCBI:1234”

class app.model.orm.StudyTechnique

Bases: app.model.orm.orm_base.OrmBase

A technique used within a study, parent to one or more MeasurementTechnique records

__tablename__ = 'StudyTechniques'

id: sqlalchemy.orm.Mapped[int]

type: sqlalchemy.orm.Mapped[str]

subjectType: sqlalchemy.orm.Mapped[str]

units: sqlalchemy.orm.Mapped[str]

includeStd: sqlalchemy.orm.Mapped[bool]

includeUnknown: sqlalchemy.orm.Mapped[bool]

label: sqlalchemy.orm.Mapped[str]

description: sqlalchemy.orm.Mapped[str]

studyId: sqlalchemy.orm.Mapped[str]

study: sqlalchemy.orm.Mapped[Study]

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

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

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

typeOrdering

subjectTypeOrdering

property is_growth

property short_name

property short_name_with_units

property short_name_with_subject_type

property long_name

property long_name_with_subject_type

class app.model.orm.StudyUser

Bases: app.model.orm.orm_base.OrmBase

Join table between Studies and Users.

The users recorded in this table have the ability to manage a particular study, to update it, or to reuse its components in other uploads.

__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 app.model.orm.Submission

Bases: app.model.orm.orm_base.OrmBase

A temporary container for the data of a Study, uploaded by a particular User.

The study design is stored in a JSON field, built up over several steps in a frontend form. The study measurements are stored in an uploaded excel file. Both of these are processed to create individual entities that are accessible to the public.

__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.JSON]

dataFileId: sqlalchemy.orm.Mapped[int]

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

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

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

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

changelogText: sqlalchemy.orm.Mapped[sqlalchemy.String]

isPublished()

property completedStepCount

build_techniques()

export_data(message, timestamp=None)

class app.model.orm.SubmissionBackup

Bases: app.model.orm.orm_base.OrmBase

A backup recording of a particular past submission

__tablename__ = 'SubmissionBackups'

id: sqlalchemy.orm.Mapped[int]

projectId: sqlalchemy.orm.Mapped[int]

studyId: sqlalchemy.orm.Mapped[int]

userUuid: sqlalchemy.orm.Mapped[str]

dataFileId: sqlalchemy.orm.Mapped[int]

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

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

class app.model.orm.Taxon

Bases: app.model.orm.orm_base.OrmBase

A taxon record imported from NCBI.

This entity is independent from any particular study and it represents the general information about a specific taxon.

__tablename__ = 'Taxa'

id: sqlalchemy.orm.Mapped[int]

ncbiId: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

studyStrains: sqlalchemy.orm.Mapped[List[StudyStrain]]

property short_name

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

class app.model.orm.User

Bases: app.model.orm.orm_base.OrmBase

A visitor to the site that is identified by ORCID.

Every project and study need to be owned by a specific user and may be editable by other users. This ensures a trace for who uploaded a particular study in case moderation or editing is needed.

__tablename__ = 'Users'

owner_relationship

id: sqlalchemy.orm.Mapped[int]

uuid: sqlalchemy.orm.Mapped[str]

orcidId: sqlalchemy.orm.Mapped[str]

orcidToken: sqlalchemy.orm.Mapped[str]

apiKey: 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]]

workspaces: sqlalchemy.orm.Mapped[List[Workspace]]

property orcidUrl

__str__()

class app.model.orm.Workspace

Bases: app.model.orm.orm_base.OrmBase

A space where users can upload data that is not linked to a study.

The actual data instances are in `WorkspaceEntry` records. This is a container for them that is linked to a specific user with a specific name. It can be made public or kept private (the default).

__tablename__ = 'Workspaces'

id: sqlalchemy.orm.Mapped[int]

name: sqlalchemy.orm.Mapped[str]

userId: sqlalchemy.orm.Mapped[int]

user: sqlalchemy.orm.Mapped[User]

entries: sqlalchemy.orm.Mapped[List[WorkspaceEntry]]

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

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

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

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

property uploadedEntries

property apiEntries

isPublished()

visible_to_user(user)

manageable_by_user(user)

class app.model.orm.WorkspaceEntry

Bases: app.model.orm.orm_base.OrmBase

Data uploaded by a user that is not linked to a study.

This data is meant to be shown on a user’s dashboard, or attached to a study post-upload. It could be observational measurements, or it could be modeling results.

__tablename__ = 'WorkspaceEntries'

id: sqlalchemy.orm.Mapped[int]

label: sqlalchemy.orm.Mapped[str]

data: sqlalchemy.orm.Mapped[str]

sourceType: sqlalchemy.orm.Mapped[Literal['upload', 'api']]

dataType: sqlalchemy.orm.Mapped[Literal['measurement', 'model', 'other']]

subjectType: sqlalchemy.orm.Mapped[Literal['community', 'strain', 'metabolite']]

subjectId: sqlalchemy.orm.Mapped[int]

units: sqlalchemy.orm.Mapped[str]

workspaceId: sqlalchemy.orm.Mapped[int]

workspace: sqlalchemy.orm.Mapped[Workspace]

user: sqlalchemy.orm.Mapped[User]

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

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

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

classmethod from_upload(df, workspace, metadata={}, include_error=False)

Construct workspace entry records from the data in a CSV file.

The first column will be parsed as time values, every other column will be considered to represent measurements. If `include_error` is truthy, columns will be parsed as pairs of value and error measurements.

property isGrowth

property canBeModeled

property readyModelingResults

get_df(db_session=None)

get_chart_label(model_name=None)