db.schemas.legacy.models

emtellipro.db.schemas.legacy.models

This module contains all the ORM models, implemented using SQLAlchemy.

The attributes of each object are documented as being either ‘column’ or ‘dynamic’; ‘column’ means they’re actual columns in the database table, and ‘dynamic’ means they’re only convenience attributes created by the ORM to handle relationships.

Note that the actual data types used when creating tables depends on the SQL dialect used (i.e. which database it’s connected to). To check the exact data types, one can refer to SQLAlchemy’s documentation, or inspect the schema of the tables that were created using this tool.

NOTE: back-references may not always be documented.

Module Contents

Classes

NameDescription
BaseThe base of all tables.
AlembicVersionTable containg the alembic version. It’s defined here so that we can easily create and drop it along with all the other tables.
ProcessingDetailsTable containing details about the job submitted for processing.
DocumentMetadataTable containing arbitrary metadata for each document.
DocumentStructuredMetadataTable containing arbitrary metadata for each document.
DocumentTable containing details specific the the overall document that was processed.
DocumentSourceChunkTable containing chunks of source data.
OntologyVersionTable of ontology versions for each document.
EntityTable of entities stored in a specific document. The entity information is stored in different tables depending on entity type. The type_ column can be used along with the entity_id to determine which exact entity is referred to.
AssumedEntityTable containing assumed entities.
FoundEntityTable containing found entities.
FoundEntityMeasurementUnitTable containing the measurement units for a found entity
FoundEntityTypeTable containing the type_name information from found entities.
ConceptTable containing information about a specific column, with the primary keys being the concept_id and ontology.
FoundEntitySpanTable containging spans contained in found entities.
SentenceLocationTable containing sentence locations. It exists mainly as a link between the locations table and the spans.
SentenceLocationSpanTable containing sentence location spans
HeadingLocationTable containing heading locations. It exists mainly as a link between the locations table and the spans.
HeadingLocationSpanTable containing heading location spans
PageLocationTable containing page locations. It exists mainly as a link between the locations table and the spans.
PageLocationSpanTable containing page location spans
PageSectionTable containing links between pages and section, with a composite primary key of page_id and section_id.
RelationTable containing links to all the different kinds of relations. Use the type_ and relation_id fields to find the actual relation in one of the other *Relation tables.
LocationTable containing links to all the different kinds of locations. Use the type_ and location_id fields to find the actual location in one of the other *Location tables.
SectionLocationSpanTable containing sentence location span information.
ImageLinkRelationTable containing image link relation information.
FollowupRelationTable containign follow-up relation information.
ExperiencerRelationTable containing experience relation information.
MeasurementRelationTable containing measurement relations.
QualifierRelationTable containing qualifier relations.
MedicationRelationTable containing medication relations.
TemporalityRelationTable containing temporality relations.
ReportedEventRelationTable containing reported event relations.
AnatomicSiteRelationTable containing anatomic site relations.
SectionLocationTable containg section locations.
SentenceSectionTable containing links between sentences and section, with a composite primary key of sentence_id and section_id.
DocumentConceptAssociation table linking documents to concepts.
FoundEntityConceptAssociation table linking found entities to concepts.
FoundEntityLocationAssociation table linking found entities to locations.
ImageLinkRelationImageFindingAssociation table linking image link relations to entities specified as image findings.
ImageLinkRelationReferenceAssociation table linking image link relations to entities specified as references.
FollowupRelationProcedureAssociation table linking followup relations to entities specified as procedures.
FollowupRelationReasonAssociation table linking followup relations to entities specified as reasons.
MedicationRelationDosageAssociation table linking medication relations to entities specified as dosage
MedicationRelationFrequencyAssociation table linking medication relations to entities specified as frequency
MedicationRelationModeAssociation table linking medication relations to entities specified as mode
MedicationRelationQuantityAssociation table linking medication relations to entities specified as quantity
MedicationRelationRouteAssociation table linking medication relations to entities specified as route
MedicationRelationNecessityAssociation table linking medication relations to entities specified as route
MedicationRelationModifierAssociation table linking medication relations to entities specified as route
MedicationRelationDurationAssociation table linking medication relations to entities specified as duration
MedicationRelationIndicationAssociation table linking medication relations to entities specified as indication
MedicationRelationDatetimeAssociation table linking medication relations to entities specified as datetimes.
TemporalityRelationModifierAssociation table linking temporality relations to entities specified as modifiers
ReportedEventRelationToEntityAssociation table linking reported-event relations to entities which were recipients of the communication.
ReportedEventRelationFromEntityAssociation table linking reported-event relations to entities which were sources of the communication.
ReportedEventRelationMethodAssociation table linking reported-event relations to entities which were the methods of communication
ReportedEventRelationTimeExpressionAssociation table linking reported-event relations to entities which were the time expressions that indicate when the communication took place

Functions

NameDescription
recreate_indexesRe-create all the full text search indexes.

Data

_supported_indexes_for _model_type_registry

API

emtellipro.db.schemas.legacy.models.Base

class emtellipro.db.schemas.legacy.models.Base

Bases: DeclarativeBase

Bases: sqlalchemy.orm.DeclarativeBase

The base of all tables.

Base.metadata
metadata

The MetaData instance specific to this base class.

Value: create_metadata(...)

Base.__tablename__
__tablename__()

emtellipro.db.schemas.legacy.models.AlembicVersion

class emtellipro.db.schemas.legacy.models.AlembicVersion

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containg the alembic version. It’s defined here so that we can easily create and drop it along with all the other tables.

AlembicVersion.__tablename__
__tablename__

Value: alembic_version

AlembicVersion.version_num
version_num

Value: Column(...)

AlembicVersion.__table_args__
__table_args__

Value: ()

emtellipro.db.schemas.legacy.models.ProcessingDetails

class emtellipro.db.schemas.legacy.models.ProcessingDetails

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing details about the job submitted for processing.

ProcessingDetails.id
id

Value: Column(...)

ProcessingDetails.job_id
job_id

Value: Column(...)

ProcessingDetails.submit_timestamp
submit_timestamp

Value: Column(...)

ProcessingDetails.task_id
task_id

Value: Column(...)

ProcessingDetails.engine_version
engine_version

Value: Column(...)

ProcessingDetails.sdk_version
sdk_version

Value: Column(...)

ProcessingDetails.sql_query
sql_query

Value: Column(...)

emtellipro.db.schemas.legacy.models.DocumentMetadata

class emtellipro.db.schemas.legacy.models.DocumentMetadata

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing arbitrary metadata for each document.

DocumentMetadata.id
id

Value: Column(...)

DocumentMetadata.document_id
document_id

Value: Column(...)

DocumentMetadata.document
document

Value: relationship(...)

DocumentMetadata.source_document_id
source_document_id

Value: Column(...)

DocumentMetadata.source_document_id_2
source_document_id_2

Value: Column(...)

DocumentMetadata.source_document_id_3
source_document_id_3

Value: Column(...)

DocumentMetadata.original_category
original_category

Value: Column(...)

DocumentMetadata.original_subcategory
original_subcategory

Value: Column(...)

DocumentMetadata.clinical_domain
clinical_domain

Value: Column(...)

DocumentMetadata.institution
institution

Value: Column(...)

DocumentMetadata.subject_id
subject_id

Value: Column(...)

DocumentMetadata.subject_id_2
subject_id_2

Value: Column(...)

DocumentMetadata.description
description

Value: Column(...)

DocumentMetadata.hadm_id
hadm_id

Value: Column(...)

DocumentMetadata.chartdate
chartdate

Value: Column(...)

DocumentMetadata.encounterdate
encounterdate

Value: Column(...)

DocumentMetadata.author_name
author_name

Value: Column(...)

DocumentMetadata.subject_name
subject_name

Value: Column(...)

DocumentMetadata.subject_dob
subject_dob

Value: Column(...)

DocumentMetadata.subject_gender
subject_gender

Value: Column(...)

DocumentMetadata.subject_address
subject_address

Value: Column(...)

DocumentMetadata.requestor
requestor

Value: Column(...)

DocumentMetadata.document_summary
document_summary

Value: Column(...)

DocumentMetadata.predefined_names
predefined_names

The list of valid metadata columns in this table. This can be used to parse metadata out of other objects to determine what should go in this table vs. the DocumentStructuredMetadata table.

Value: ['author_name', 'chartdate', 'encounterdate', 'clinical_domain', 'description', 'document_summary', 'hadm_id', 'institution', 'original_category', 'original_subcategory', 'requestor', 'source_document_id', 'source_document_id_2', 'source_document_id_3', 'subject_address', 'subject_dob', 'subject_gender', 'subject_id', 'subject_id_2', 'subject_name']

DocumentMetadata.__table_args__
__table_args__

Value: ()

DocumentMetadata.parse_dates
parse_dates(
metadata, parse_dates = False
)

Optionally parse dates in the metadata. This also converts empty strings to None.

Parameters:

metadata

a metadata dictionary

parse_dates

whether to actually parse the dates in the metadata dict. Parsing dates is only relevant for certain database types.

emtellipro.db.schemas.legacy.models.DocumentStructuredMetadata

class emtellipro.db.schemas.legacy.models.DocumentStructuredMetadata

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing arbitrary metadata for each document.

DocumentStructuredMetadata.id
id

Value: Column(...)

DocumentStructuredMetadata.document_id
document_id

Value: Column(...)

DocumentStructuredMetadata.document
document

Value: relationship(...)

DocumentStructuredMetadata.key
key

Value: Column(...)

DocumentStructuredMetadata.value
value

Value: Column(...)

emtellipro.db.schemas.legacy.models.Document

class emtellipro.db.schemas.legacy.models.Document

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing details specific the the overall document that was processed.

Document.id
id

Value: Column(...)

Document.category
category

Value: Column(...)

Document.subcategory
subcategory

Value: Column(...)

Document.filename
filename

Value: Column(...)

Document.section_label
section_label

Value: Column(...)

Document.text
text

Value: Column(...)

Document.json_representation
json_representation

Value: Column(...)

Document.processing_status
processing_status

Value: Column(...)

Document.processing_details_id
processing_details_id

Value: Column(...)

Document.source_type
source_type

Value: Column(...)

Document.source_path
source_path

Value: Column(...)

Document.source_size
source_size

Value: Column(...)

Document.processing_details
processing_details

Value: relationship(...)

Document.concepts
concepts

Value: relationship(...)

Document.entities
entities

Value: relationship(...)

Document.relations
relations

Value: relationship(...)

Document.locations
locations

Value: relationship(...)

Document.ontology_versions
ontology_versions

Value: relationship(...)

emtellipro.db.schemas.legacy.models.DocumentSourceChunk

class emtellipro.db.schemas.legacy.models.DocumentSourceChunk

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing chunks of source data.

This is useful for storing the original PDF data if you’ve extracted the text from it and have used the plaintext for processing.

DocumentSourceChunk.document_id
document_id

Value: Column(...)

DocumentSourceChunk.offset
offset

Value: Column(...)

DocumentSourceChunk.data
data

Value: Column(...)

emtellipro.db.schemas.legacy.models.OntologyVersion

class emtellipro.db.schemas.legacy.models.OntologyVersion

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table of ontology versions for each document.

OntologyVersion.document_id
document_id

Value: Column(...)

OntologyVersion.ontology
ontology

Value: Column(...)

OntologyVersion.release_version
release_version

Value: Column(...)

OntologyVersion.document
document

Value: relationship(...)

emtellipro.db.schemas.legacy.models.Entity

class emtellipro.db.schemas.legacy.models.Entity

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table of entities stored in a specific document. The entity information is stored in different tables depending on entity type. The type_ column can be used along with the entity_id to determine which exact entity is referred to.

Entity.id
id

Value: Column(...)

Entity.type_
type_

Value: Column(...)

Entity.document_id
document_id

Value: Column(...)

Entity.entity_id
entity_id

Value: Column(...)

Entity.entity
property entity

The actual *Entity instance this relation references.

emtellipro.db.schemas.legacy.models.AssumedEntity

class emtellipro.db.schemas.legacy.models.AssumedEntity

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing assumed entities.

AssumedEntity.id
id

Value: Column(...)

AssumedEntity.value
value

Value: Column(...)

AssumedEntity.document_id
document_id

Value: Column(...)

AssumedEntity.document
document

Value: relationship(...)

emtellipro.db.schemas.legacy.models.FoundEntity

class emtellipro.db.schemas.legacy.models.FoundEntity

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing found entities.

FoundEntity.id
id

Value: Column(...)

FoundEntity.polarity
polarity

Value: Column(...)

FoundEntity.section_name
section_name

Value: Column(...)

FoundEntity.uncertainty
uncertainty

Value: Column(...)

FoundEntity.known_ambiguity
known_ambiguity

Value: Column(...)

FoundEntity.question_status
question_status

Value: Column(...)

FoundEntity.guidance
guidance

Value: Column(...)

FoundEntity.experiencer
experiencer

Value: Column(...)

FoundEntity.factuality
factuality

Value: Column(...)

FoundEntity.heading_status
heading_status

Value: Column(...)

FoundEntity.text
text

Value: Column(...)

FoundEntity.start
start

Value: Column(...)

FoundEntity.document_id
document_id

Value: Column(...)

FoundEntity.document
document

Value: relationship(...)

FoundEntity.concepts
concepts

Value: relationship(...)

FoundEntity.locations
locations

Value: relationship(...)

FoundEntity.spans
spans

Value: relationship(...)

FoundEntity.type_names
type_names

Value: relationship(...)

FoundEntity.measurement_units
measurement_units

Value: relationship(...)

emtellipro.db.schemas.legacy.models.FoundEntityMeasurementUnit

class emtellipro.db.schemas.legacy.models.FoundEntityMeasurementUnit

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing the measurement units for a found entity

FoundEntityMeasurementUnit.id
id

Value: Column(...)

FoundEntityMeasurementUnit.found_entity_id
found_entity_id

Value: Column(...)

FoundEntityMeasurementUnit.text
text

Value: Column(...)

emtellipro.db.schemas.legacy.models.FoundEntityType

class emtellipro.db.schemas.legacy.models.FoundEntityType

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing the type_name information from found entities.

Note that all 3 columns form the primary key since there is a unique type name per ontology per found entity.

FoundEntityType.found_entity_id
found_entity_id

Value: Column(...)

FoundEntityType.ontology
ontology

Value: Column(...)

FoundEntityType.type_name
type_name

Value: Column(...)

emtellipro.db.schemas.legacy.models.Concept

class emtellipro.db.schemas.legacy.models.Concept

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing information about a specific column, with the primary keys being the concept_id and ontology.

Concept.concept_id
concept_id

Value: Column(...)

Concept.ontology
ontology

Value: Column(...)

Concept.description
description

Value: Column(...)

Concept.documents
documents

Value: relationship(...)

Concept.found_entities
found_entities

Value: relationship(...)

emtellipro.db.schemas.legacy.models.FoundEntitySpan

class emtellipro.db.schemas.legacy.models.FoundEntitySpan

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containging spans contained in found entities.

FoundEntitySpan.id
id

Value: Column(...)

FoundEntitySpan.start
start

Value: Column(...)

FoundEntitySpan.end
end

Value: Column(...)

FoundEntitySpan.text
text

Value: Column(...)

FoundEntitySpan.found_entity_id
found_entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.SentenceLocation

class emtellipro.db.schemas.legacy.models.SentenceLocation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing sentence locations. It exists mainly as a link between the locations table and the spans.

SentenceLocation.id
id

Value: Column(...)

SentenceLocation.text
text

Value: Column(...)

SentenceLocation.spans
spans

Value: relationship(...)

SentenceLocation.sections
sections

Value: relationship(...)

emtellipro.db.schemas.legacy.models.SentenceLocationSpan

class emtellipro.db.schemas.legacy.models.SentenceLocationSpan

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing sentence location spans

SentenceLocationSpan.id
id

Value: Column(...)

SentenceLocationSpan.start
start

Value: Column(...)

SentenceLocationSpan.end
end

Value: Column(...)

SentenceLocationSpan.sentence_location_id
sentence_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.HeadingLocation

class emtellipro.db.schemas.legacy.models.HeadingLocation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing heading locations. It exists mainly as a link between the locations table and the spans.

HeadingLocation.id
id

Value: Column(...)

HeadingLocation.text
text

Value: Column(...)

HeadingLocation.section_location_id
section_location_id

Value: Column(...)

HeadingLocation.spans
spans

Value: relationship(...)

HeadingLocation.section
section

Value: relationship(...)

emtellipro.db.schemas.legacy.models.HeadingLocationSpan

class emtellipro.db.schemas.legacy.models.HeadingLocationSpan

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing heading location spans

HeadingLocationSpan.id
id

Value: Column(...)

HeadingLocationSpan.start
start

Value: Column(...)

HeadingLocationSpan.end
end

Value: Column(...)

HeadingLocationSpan.heading_location_id
heading_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.PageLocation

class emtellipro.db.schemas.legacy.models.PageLocation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing page locations. It exists mainly as a link between the locations table and the spans.

PageLocation.id
id

Value: Column(...)

PageLocation.text
text

Value: Column(...)

PageLocation.page_index
page_index

Value: Column(...)

PageLocation.spans
spans

Value: relationship(...)

PageLocation.sections
sections

Value: relationship(...)

emtellipro.db.schemas.legacy.models.PageLocationSpan

class emtellipro.db.schemas.legacy.models.PageLocationSpan

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing page location spans

PageLocationSpan.id
id

Value: Column(...)

PageLocationSpan.start
start

Value: Column(...)

PageLocationSpan.end
end

Value: Column(...)

PageLocationSpan.page_location_id
page_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.PageSection

class emtellipro.db.schemas.legacy.models.PageSection

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links between pages and section, with a composite primary key of page_id and section_id.

PageSection.page_id
page_id

Value: Column(...)

PageSection.section_id
section_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.Relation

class emtellipro.db.schemas.legacy.models.Relation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links to all the different kinds of relations. Use the type_ and relation_id fields to find the actual relation in one of the other *Relation tables.

Relation.id
id

Value: Column(...)

Relation.type_
type_

Value: Column(...)

Relation.document_id
document_id

Value: Column(...)

Relation.relation_id
relation_id

Value: Column(...)

Relation.relation
property relation

The actual *Relation instance this relation references.

emtellipro.db.schemas.legacy.models.Location

class emtellipro.db.schemas.legacy.models.Location

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links to all the different kinds of locations. Use the type_ and location_id fields to find the actual location in one of the other *Location tables.

Location.id
id

Value: Column(...)

Location.type_
type_

Value: Column(...)

Location.document_id
document_id

Value: Column(...)

Location.location_id
location_id

Value: Column(...)

Location.location
property location

The actual *Location instance this relation references.

emtellipro.db.schemas.legacy.models.SectionLocationSpan

class emtellipro.db.schemas.legacy.models.SectionLocationSpan

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing sentence location span information.

SectionLocationSpan.id
id

Value: Column(...)

SectionLocationSpan.start
start

Value: Column(...)

SectionLocationSpan.end
end

Value: Column(...)

SectionLocationSpan.section_location_id
section_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ImageLinkRelation

class emtellipro.db.schemas.legacy.models.ImageLinkRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing image link relation information.

ImageLinkRelation.id
id

Value: Column(...)

ImageLinkRelation.image_findings
image_findings

Value: relationship(...)

ImageLinkRelation.references
references

Value: relationship(...)

ImageLinkRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.FollowupRelation

class emtellipro.db.schemas.legacy.models.FollowupRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containign follow-up relation information.

FollowupRelation.id
id

Value: Column(...)

FollowupRelation.polarity
polarity

Value: Column(...)

FollowupRelation.time_expression_id
time_expression_id

Value: Column(...)

FollowupRelation.time_expression
time_expression

Value: relationship(...)

FollowupRelation.procedures
procedures

Value: relationship(...)

FollowupRelation.reasons
reasons

Value: relationship(...)

FollowupRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.ExperiencerRelation

class emtellipro.db.schemas.legacy.models.ExperiencerRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing experience relation information.

ExperiencerRelation.id
id

Value: Column(...)

ExperiencerRelation.polarity
polarity

Value: Column(...)

ExperiencerRelation.experiencer_id
experiencer_id

Value: Column(...)

ExperiencerRelation.experienced_id
experienced_id

Value: Column(...)

ExperiencerRelation.experiencer
experiencer

Value: relationship(...)

ExperiencerRelation.experienced
experienced

Value: relationship(...)

ExperiencerRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.MeasurementRelation

class emtellipro.db.schemas.legacy.models.MeasurementRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing measurement relations.

MeasurementRelation.id
id

Value: Column(...)

MeasurementRelation.subject_id
subject_id

Value: Column(...)

MeasurementRelation.value_id
value_id

Value: Column(...)

MeasurementRelation.subject
subject

Value: relationship(...)

MeasurementRelation.value
value

Value: relationship(...)

MeasurementRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.QualifierRelation

class emtellipro.db.schemas.legacy.models.QualifierRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing qualifier relations.

QualifierRelation.id
id

Value: Column(...)

QualifierRelation.qualifier_type
qualifier_type

Value: Column(...)

QualifierRelation.qualifier_id
qualifier_id

Value: Column(...)

QualifierRelation.qualifies_id
qualifies_id

Value: Column(...)

QualifierRelation.qualifier
qualifier

Value: relationship(...)

QualifierRelation.qualifies
qualifies

Value: relationship(...)

QualifierRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelation

class emtellipro.db.schemas.legacy.models.MedicationRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing medication relations.

MedicationRelation.id
id

Value: Column(...)

MedicationRelation.drug_entity_id
drug_entity_id

Value: Column(...)

MedicationRelation.drug
drug

Value: relationship(...)

MedicationRelation.dosages
dosages

Value: relationship(...)

MedicationRelation.frequencies
frequencies

Value: relationship(...)

MedicationRelation.modes
modes

Value: relationship(...)

MedicationRelation.quantities
quantities

Value: relationship(...)

MedicationRelation.routes
routes

Value: relationship(...)

MedicationRelation.necessities
necessities

Value: relationship(...)

MedicationRelation.modifiers
modifiers

Value: relationship(...)

MedicationRelation.durations
durations

Value: relationship(...)

MedicationRelation.indications
indications

Value: relationship(...)

MedicationRelation.date_times
date_times

Value: relationship(...)

MedicationRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.TemporalityRelation

class emtellipro.db.schemas.legacy.models.TemporalityRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing temporality relations.

TemporalityRelation.id
id

Value: Column(...)

TemporalityRelation.polarity
polarity

Value: Column(...)

TemporalityRelation.category
category

Value: Column(...)

TemporalityRelation.temporal_entity_id
temporal_entity_id

Value: Column(...)

TemporalityRelation.subject_id
subject_id

Value: Column(...)

TemporalityRelation.temporal_entity
temporal_entity

Value: relationship(...)

TemporalityRelation.subject
subject

Value: relationship(...)

TemporalityRelation.modifiers
modifiers

Value: relationship(...)

TemporalityRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelation

class emtellipro.db.schemas.legacy.models.ReportedEventRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing reported event relations.

ReportedEventRelation.id
id

Value: Column(...)

ReportedEventRelation.polarity
polarity

Value: Column(...)

ReportedEventRelation.category
category

Value: Column(...)

ReportedEventRelation.subject_id
subject_id

Value: Column(...)

ReportedEventRelation.subject
subject

Value: relationship(...)

ReportedEventRelation.to_entities
to_entities

Value: relationship(...)

ReportedEventRelation.from_entities
from_entities

Value: relationship(...)

ReportedEventRelation.methods
methods

Value: relationship(...)

ReportedEventRelation.time_expressions
time_expressions

Value: relationship(...)

ReportedEventRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.AnatomicSiteRelation

class emtellipro.db.schemas.legacy.models.AnatomicSiteRelation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing anatomic site relations.

AnatomicSiteRelation.id
id

Value: Column(...)

AnatomicSiteRelation.site_id
site_id

Value: Column(...)

AnatomicSiteRelation.situated_entity_id
situated_entity_id

Value: Column(...)

AnatomicSiteRelation.site
site

Value: relationship(...)

AnatomicSiteRelation.situated_entity
situated_entity

Value: relationship(...)

AnatomicSiteRelation.confidence
confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.SectionLocation

class emtellipro.db.schemas.legacy.models.SectionLocation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containg section locations.

SectionLocation.id
id

Value: Column(...)

SectionLocation.name
name

Value: Column(...)

SectionLocation.level
level

Value: Column(...)

SectionLocation.parent_id
parent_id

Value: Column(...)

SectionLocation.text
text

Value: Column(...)

SectionLocation.children
children

Value: relationship(...)

SectionLocation.spans
spans

Value: relationship(...)

SectionLocation.pages
pages

Value: relationship(...)

SectionLocation.sentences
sentences

Value: relationship(...)

emtellipro.db.schemas.legacy.models.SentenceSection

class emtellipro.db.schemas.legacy.models.SentenceSection

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links between sentences and section, with a composite primary key of sentence_id and section_id.

SentenceSection.sentence_id
sentence_id

Value: Column(...)

SentenceSection.section_id
section_id

Value: Column(...)

SentenceSection.sentence
sentence

Value: relationship(...)

SentenceSection.section
section

Value: relationship(...)

emtellipro.db.schemas.legacy.models.DocumentConcept

class emtellipro.db.schemas.legacy.models.DocumentConcept

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking documents to concepts.

DocumentConcept.document_id
document_id

Value: Column(...)

DocumentConcept.concept_id
concept_id

Value: Column(...)

DocumentConcept.concept_ontology
concept_ontology

Value: Column(...)

DocumentConcept.__table_args__
__table_args__

Value: ()

emtellipro.db.schemas.legacy.models.FoundEntityConcept

class emtellipro.db.schemas.legacy.models.FoundEntityConcept

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking found entities to concepts.

FoundEntityConcept.found_entity_id
found_entity_id

Value: Column(...)

FoundEntityConcept.concept_id
concept_id

Value: Column(...)

FoundEntityConcept.concept_ontology
concept_ontology

Value: Column(...)

FoundEntityConcept.confidence
confidence

Value: Column(...)

FoundEntityConcept.__table_args__
__table_args__

Value: ()

emtellipro.db.schemas.legacy.models.FoundEntityLocation

class emtellipro.db.schemas.legacy.models.FoundEntityLocation

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking found entities to locations.

FoundEntityLocation.found_entity_id
found_entity_id

Value: Column(...)

FoundEntityLocation.location_id
location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ImageLinkRelationImageFinding

class emtellipro.db.schemas.legacy.models.ImageLinkRelationImageFinding

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking image link relations to entities specified as image findings.

imagelink_id

Value: Column(...)

ImageLinkRelationImageFinding.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ImageLinkRelationReference

class emtellipro.db.schemas.legacy.models.ImageLinkRelationReference

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking image link relations to entities specified as references.

imagelink_id

Value: Column(...)

ImageLinkRelationReference.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.FollowupRelationProcedure

class emtellipro.db.schemas.legacy.models.FollowupRelationProcedure

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking followup relations to entities specified as procedures.

FollowupRelationProcedure.followup_id
followup_id

Value: Column(...)

FollowupRelationProcedure.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.FollowupRelationReason

class emtellipro.db.schemas.legacy.models.FollowupRelationReason

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking followup relations to entities specified as reasons.

FollowupRelationReason.followup_id
followup_id

Value: Column(...)

FollowupRelationReason.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationDosage

class emtellipro.db.schemas.legacy.models.MedicationRelationDosage

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as dosage

MedicationRelationDosage.id
id

Value: Column(...)

MedicationRelationDosage.medication_id
medication_id

Value: Column(...)

MedicationRelationDosage.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationFrequency

class emtellipro.db.schemas.legacy.models.MedicationRelationFrequency

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as frequency

MedicationRelationFrequency.id
id

Value: Column(...)

MedicationRelationFrequency.medication_id
medication_id

Value: Column(...)

MedicationRelationFrequency.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationMode

class emtellipro.db.schemas.legacy.models.MedicationRelationMode

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as mode

MedicationRelationMode.id
id

Value: Column(...)

MedicationRelationMode.medication_id
medication_id

Value: Column(...)

MedicationRelationMode.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationQuantity

class emtellipro.db.schemas.legacy.models.MedicationRelationQuantity

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as quantity

MedicationRelationQuantity.id
id

Value: Column(...)

MedicationRelationQuantity.medication_id
medication_id

Value: Column(...)

MedicationRelationQuantity.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationRoute

class emtellipro.db.schemas.legacy.models.MedicationRelationRoute

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as route

MedicationRelationRoute.id
id

Value: Column(...)

MedicationRelationRoute.medication_id
medication_id

Value: Column(...)

MedicationRelationRoute.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationNecessity

class emtellipro.db.schemas.legacy.models.MedicationRelationNecessity

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as route

MedicationRelationNecessity.id
id

Value: Column(...)

MedicationRelationNecessity.medication_id
medication_id

Value: Column(...)

MedicationRelationNecessity.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationModifier

class emtellipro.db.schemas.legacy.models.MedicationRelationModifier

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as route

MedicationRelationModifier.id
id

Value: Column(...)

MedicationRelationModifier.medication_id
medication_id

Value: Column(...)

MedicationRelationModifier.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationDuration

class emtellipro.db.schemas.legacy.models.MedicationRelationDuration

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as duration

MedicationRelationDuration.id
id

Value: Column(...)

MedicationRelationDuration.medication_id
medication_id

Value: Column(...)

MedicationRelationDuration.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationIndication

class emtellipro.db.schemas.legacy.models.MedicationRelationIndication

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as indication

MedicationRelationIndication.id
id

Value: Column(...)

MedicationRelationIndication.medication_id
medication_id

Value: Column(...)

MedicationRelationIndication.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationDatetime

class emtellipro.db.schemas.legacy.models.MedicationRelationDatetime

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as datetimes.

MedicationRelationDatetime.id
id

Value: Column(...)

MedicationRelationDatetime.medication_id
medication_id

Value: Column(...)

MedicationRelationDatetime.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.TemporalityRelationModifier

class emtellipro.db.schemas.legacy.models.TemporalityRelationModifier

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking temporality relations to entities specified as modifiers

TemporalityRelationModifier.id
id

Value: Column(...)

TemporalityRelationModifier.temporality_id
temporality_id

Value: Column(...)

TemporalityRelationModifier.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationToEntity

class emtellipro.db.schemas.legacy.models.ReportedEventRelationToEntity

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were recipients of the communication.

ReportedEventRelationToEntity.reported_event_id
reported_event_id

Value: Column(...)

ReportedEventRelationToEntity.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationFromEntity

class emtellipro.db.schemas.legacy.models.ReportedEventRelationFromEntity

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were sources of the communication.

ReportedEventRelationFromEntity.reported_event_id
reported_event_id

Value: Column(...)

ReportedEventRelationFromEntity.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationMethod

class emtellipro.db.schemas.legacy.models.ReportedEventRelationMethod

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were the methods of communication

ReportedEventRelationMethod.reported_event_id
reported_event_id

Value: Column(...)

ReportedEventRelationMethod.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationTimeExpression

class emtellipro.db.schemas.legacy.models.ReportedEventRelationTimeExpression

Bases: Base

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were the time expressions that indicate when the communication took place

ReportedEventRelationTimeExpression.reported_event_id
reported_event_id

Value: Column(...)

ReportedEventRelationTimeExpression.entity_id
entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.recreate_indexes

emtellipro.db.schemas.legacy.models.recreate_indexes(connection)

Re-create all the full text search indexes.

This is normally executed by the migrate and create-db commands

Parameters:

connection

this is an SQLAlchemy connection object

Returns:

number of indexes created