emtellipro_db package

Submodules

emtellipro_db.exc module

This module contains exceptions raised within the emtellipro_db module

exception emtellipro_db.exc.EmtelliproDBException

Bases: Exception

Base exception which is subclassed by more specific exceptions

exception emtellipro_db.exc.MissingFullTextSupport

Bases: emtellipro_db.exc.EmtelliproDBException

Raised when SQL Server is missing full-text support

emtellipro_db.models module

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.

class emtellipro_db.models.AssumedEntity(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing assumed entities.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

document

instance of Document

Type: dynamic

document_id

uuid foreign key pointing to document.id

Type: column

id

uuid primary key

Type: column

value

unicode string of max length 255

Type: column

class emtellipro_db.models.Concept(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

concept_id

unicode string of max length 255, part of primary key

Type: column

description

unicode text

Type: column

documents

list of Document objects containing this concept

Type: dynamic

found_entities

list of FoundEntity objects containing this concept

Type: dynamic

ontology

unicode string of max length 255, part of primary key

Type: column

class emtellipro_db.models.Document(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

category

unicode string of max length 255

Type: column

concepts

list of Concept objects found in this document

Type: dynamic

entities

list of Entity objects found in this document

Type: dynamic

filename

unicode text field

Type: column

id

uuid primary key

Type: column

json_representation

unicode text field, containing the JSON returned by the server for this document

Type: column

locations

list of Location objects found in this document

Type: dynamic

processing_details

instance of ProcessingDetails which is associated with this document

Type: dynamic

processing_details_id

uuid foreign key pointing to processingdetails.id

Type: column

processing_status

unicode string of max length 255

Type: column

relations

list of Relation objects found in this document

Type: dynamic

section_label

unicode text field

Type: column

subcategory

unicode string of max length 255

Type: column

text

unicode text field, containing the document text or NULL if it was not saved

Type: column

class emtellipro_db.models.DocumentConcept(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking documents to concepts.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

concept_id

unicode string of max length 255, foreign key pointing to concept.concept_id, part of primary key

Type: column

concept_ontology

unicode string of max length 255, foreign key pointing to concept.ontology, part of primary key

Type: column

document_id

uuid foreign key pointing to document.id, part of primary key.

Type: column

class emtellipro_db.models.DocumentMetadata(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing arbitrary metadata for each document.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

author_name

author name

Type: column

chartdate

chart date

Type: column

description

description

Type: column

document

instance of Document

Type: dynamic

document_id

uuid foreign key pointing to document.id

Type: column

hadm_id

hadm ID

Type: column

id

uuid primary key

Type: column

institution

institution

Type: column

original_category

unicode string of max length 255

Type: column

original_subcategory

unicode string of max length 255

Type: column

static parse_dates(metadata, parse_dates=False)

Optionally parse dates in the metadata.

Parameters

metadata (dict) – a metadata dictionary
parse_dates (bool) – whether to actually parse the dates in the metadata dict. Parsing dates is only relevant for certain database types.

requestor

requestor

Type: column

source_document_id

the primary key of the document in the source database

Type: column

subject_dob

date of birth of subject

Type: column

subject_gender

subject gender

Type: column

subject_id

subject ID

Type: column

subject_name

subject name

Type: column

class emtellipro_db.models.DocumentStructuredMetadata(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing arbitrary metadata for each document.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

document

instance of Document

Type: dynamic

document_id

uuid foreign key pointing to document.id

Type: column

id

uuid primary key

Type: column

key

unicode text field

Type: column

value

unicode text field

Type: column

class emtellipro_db.models.Entity(**kwargs)

Bases: sqlalchemy.orm.decl_api.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.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

document_id

uuid foreign key pointing to document.id

Type: column

entity_id

uuid reffering to the id column of one of the *Entity tables.

Type: column

id

uuid primary key

Type: column

type_

unicode string of max length 255, describing the type of the entity.

Type: column

class emtellipro_db.models.ExperiencerRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing experience relation information.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

experienced

Entity instance

Type: dynamic

experienced_id

uuid foreign key pointing to entity.id

Type: column

experiencer

Entity instance

Type: dynamic

experiencer_id

uuid foreign key pointing to entity.id

Type: column

id

uuid primary key

Type: column

polarity

unicode string of max lenght 255

Type: column

class emtellipro_db.models.FollowupRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containign follow-up relation information.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

id

uuid primary key

Type: column

polarity

unicode string of max length 255

Type: column

procedures

Entity instance

Type: dynamic

reasons

Entity instance

Type: dynamic

time_expression

Entity instance

Type: dynamic

time_expression_id

uuid foreign key pointing to entity.id

Type: column

class emtellipro_db.models.FollowupRelationProcedure(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking followup relations to entities specified as procedures.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

uuid foreign key pointing to entity.id, part of primary key

Type: column

followup_id

uuid foreign key pointing to followuprelation.id, part of primary key

Type: column

class emtellipro_db.models.FollowupRelationReason(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking followup relations to entities specified as reasons.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

uuid foreign key pointing to entity.id, part of primary key

Type: column

followup_id

uuid foreign key pointing to followuprelation.id, part of primary key

Type: column

class emtellipro_db.models.FoundEntity(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing found entities.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

concepts

list of Concept instances associated with this entity

Type: dynamic

document

instance of Document

Type: dynamic

document_id

uuid foreign key pointing to document.id

Type: column

guidance

unicode text field

Type: column

id

uuid primary key

Type: column

known_ambiguity

unicode text field

Type: column

locations

list of Location objects associated with this entity

Type: dynamic

measurement_units

list of FoundEntityMeasurementUnit objects assocated with this entity

Type: dynamic

polarity

unicode string of max length 255

Type: column

question_status

unicode text field

Type: column

section_name

unicode text field

Type: column

spans

list of FoundEntitySpan objects associated with this entity

Type: dynamic

type_names

list of FoundEntityType objects associated with this entity

Type: dynamic

uncertainty

unicode string of max length 255

Type: column

class emtellipro_db.models.FoundEntityConcept(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking found entities to concepts.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

concept_id

unicode string of max length 255, foreign key pointing to concept.concept_id, part of primary key

Type: column

concept_ontology

unicode string of max length 255, foreign key pointing to concept.ontology, part of primary key

Type: column

found_entity_id

uuid foreign key pointing to foundentity.id, part of primary key

Type: column

class emtellipro_db.models.FoundEntityLocation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking found entities to locations.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

found_entity_id

uuid foreign key pointing to foundentity.id, part of primary key

Type: column

location_id

uuid foreign key pointing to location.id, part of primary key

Type: column

class emtellipro_db.models.FoundEntityMeasurementUnit(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing the measurement units for a found entity

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

found_entity_id

uuid foreign key pointing to foundentity.id

Type: column

id

uuid primary key

Type: column

text

unicode string of max length 255

Type: column

class emtellipro_db.models.FoundEntitySpan(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containging spans contained in found entities.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

end

integer end position

Type: column

found_entity_id

uuid foreign key pointing to foundentity.id

Type: column

id

uuid primary key

Type: column

start

integer start position

Type: column

text

unicode text contained in this span

Type: column

class emtellipro_db.models.FoundEntityType(**kwargs)

Bases: sqlalchemy.orm.decl_api.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.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

found_entity_id

uuid foreign key pointing to foundentity.id

Type: column

ontology

unicode string of max length 255

Type: column

type_name

unicode string of max length 255

Type: column

class emtellipro_db.models.GUID(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

Platform-independent GUID type.

Uses PostgreSQL’s UUID type, otherwise uses CHAR(36), storing as stringified hex values.

impl: alias of sqlalchemy.sql.sqltypes.Integer

load_dialect_impl(dialect)

Return the data type implementation based on the dialect used.

This means UUID for postgresql, UNIQUEIDENTIFIER for MSSQL, and CHAR(36) everywhere else.

class emtellipro_db.models.ImageLinkRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing image link relation information.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

id

uuid primary key

Type: column

image_findings

list of Entity objects which were the image findings

Type: dynamic

references

list of Entity objects which were the image references

Type: dynamic

class emtellipro_db.models.ImageLinkRelationImageFinding(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

uuid foreign key pointing to entity.id, part of primary key

Type: column

imagelink_id

uuid foreign key pointing to imagelinkrelation.id, part of primary key

Type: column

class emtellipro_db.models.ImageLinkRelationReference(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

uuid foreign key pointing to entity.id, part of primary key

Type: column

imagelink_id

uuid foreign key pointing to imagelinkrelation.id, part of primary key

Type: column

class emtellipro_db.models.Location(**kwargs)

Bases: sqlalchemy.orm.decl_api.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.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

document_id

uuid foreign key pointing to document.id

Type: column

id

uuid primary key

Type: column

location_id

uuid referring to the id column of another *Location table

Type: column

type_

unicode string of max length 255, containing the type of location

Type: column

class emtellipro_db.models.MeasurementRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing measurement relations.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

id

uuid primary key

Type: column

subject

Entity instance

Type: dynamic

subject_id

uuid foreign key pointing to entity.id

Type: column

value

Entity instance

Type: dynamic

value_id

uuid foreign key pointing to entity.id

Type: column

class emtellipro_db.models.MedicationRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing medication relations.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

date_times

list of Entity objects which are datetimes

Type: dynamic

dosages

list of Entity objects which were dosages

Type: dynamic

drug

Entity instance

Type: dynamic

drug_entity_id

uuid foreign key pointing to entity.id

Type: column

durations

list of Entity objects which were durations

Type: dynamic

frequencies

list of Entity objects which were frequencies

Type: dynamic

id

uuid primary key

Type: column

indications

list of Entity objects which were indications

Type: dynamic

modes

list of Entity objects which were modes

Type: dynamic

modifiers

list of Entity objects which were modifier

Type: dynamic

necessities

list of Entity objects which were necessities

Type: dynamic

quantities

list of Entity objects which were quantities

Type: dynamic

routes

list of Entity objects which were routes

Type: dynamic

class emtellipro_db.models.MedicationRelationDatetime(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as datetimes.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

GUID() foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationDosage(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as dosage

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

uuid foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationDuration(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as duration

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationFrequency(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as frequency

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationIndication(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as indication

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationMode(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as mode

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationModifier(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as route

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationNecessity(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as route

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationQuantity(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as quantity

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.MedicationRelationRoute(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking medication relations to entities specified as route

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

GUID() foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

medication_id

uuid foreign key pointing to medicationrelation.id, part of primary key

Type: column

class emtellipro_db.models.OntologyVersion(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table of ontology versions for each document.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

document

instance of Document

Type: dynamic

document_id

uuid foreign key pointing to document.id

Type: column

ontology

unicode string of max length 255, part of primary key

Type: column

release_version

unicode string of max length 255

Type: column

class emtellipro_db.models.ProcessingDetails(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing details about the job submitted for processing.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

engine_version

the engine version, if provided

Type: column

id

uuid primary key

Type: column

job_id

a user-provided (or generated) string ID for the overall processing job. This is different than the task ID which is generated by the server and which is per-shard. Max length is 255.

Type: column

sdk_version

the SDK version

Type: column

submit_timestamp

a datetime field

Type: column

task_id

unicode string of max length 255, generated by the server

Type: column

class emtellipro_db.models.QualifierRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing qualifier relations.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

id

uuid primary key

Type: column

qualifier

Entity instance

Type: dynamic

qualifier_id

uuid foreign key pointing to entity.id

Type: column

qualifier_type

unicode string of max length 255

Type: column

qualifies

Entity instance

Type: dynamic

qualifies_id

uuid foreign key pointing to entity.id

Type: column

class emtellipro_db.models.Relation(**kwargs)

Bases: sqlalchemy.orm.decl_api.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.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

document_id

uuid foreign key pointing to document.id

Type: column

id

uuid primary key

Type: column

relation_id

uuid referring to the id column of another *Relation table

Type: column

type_

unicode string of max length 255, containing the type of the relation

Type: column

class emtellipro_db.models.ReportedEventRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing reported event relations.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

category

unicode string of max length 255

Type: column

from_entities

list of Entity objects

Type: dynamic

id

uuid/integer primary key

Type: column

methods

list of Entity objects

Type: dynamic

polarity

unicode string of max length 255

Type: column

subject

Entity instance

Type: dynamic

subject_id

foreign key poinging to entity.id

Type: column

time_expressions

list of Entity objects

Type: dynamic

to_entities

list of Entity objects

Type: dynamic

class emtellipro_db.models.ReportedEventRelationFromEntity(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

foreign key pointing to entity.id, part of primary key

Type: column

reported_event_id

foreign key pointing to reportedeventrelation.id, part of primary key

Type: column

class emtellipro_db.models.ReportedEventRelationMethod(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

foreign key pointing to entity.id, part of primary key

Type: column

reported_event_id

foreign key pointing to reportedeventrelation.id, part of primary key

Type: column

class emtellipro_db.models.ReportedEventRelationTimeExpression(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

foreign key pointing to entity.id, part of primary key

Type: column

reported_event_id

foreign key pointing to reportedeventrelation.id, part of primary key

Type: column

class emtellipro_db.models.ReportedEventRelationToEntity(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

foreign key pointing to entity.id, part of primary key

Type: column

reported_event_id

foreign key pointing to reportedeventrelation.id, part of primary key

Type: column

class emtellipro_db.models.SectionLocation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containg section locations.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

children

list of SectionLocation objects

Type: dynamic

id

uuid primary key

Type: column

level

integer

Type: column

name

unicode string of max length 255

Type: column

parent_id

uuid foreign key pointing to this table

Type: column

spans

list of SectionLocationSpan objects

Type: dynamic

text

entire text of the section

Type: column

class emtellipro_db.models.SectionLocationSpan(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing sentence location span information.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

end

integer end position

Type: column

id

uuid primary key

Type: column

section_location_id

uuid foreign key pointing to sectionlocation.id

Type: column

start

integer start position

Type: column

class emtellipro_db.models.SentenceLocation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

id

uuid primary key

Type: column

spans

list of SentenceLocationSpan objects

Type: dynamic

text

entire text of the sentence

Type: column

class emtellipro_db.models.SentenceLocationSpan(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing sentence location spans

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

end

integer end position

Type: column

id

uuid primary key

Type: column

sentence_location_id

uuid foreign key pointing to sentencelocation.id

Type: column

start

integer start position

Type: column

class emtellipro_db.models.SentenceSection(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

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

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

section

SectionLocation instance

Type: dynamic

section_id

uuid foreign key pointing to sectionlocation.id, part of primary key

Type: column

sentence

SentenceLocation instance

Type: dynamic

sentence_id

uuid foreign key pointing to sentencelocation.id, part of primary key.

Type: column

class emtellipro_db.models.TemporalityRelation(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Table containing temporality relations.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

category

unicode string of max length 255

Type: column

id

uuid primary key

Type: column

modifiers

list of Entity objects which were modifiers

Type: dynamic

polarity

unicode string of max length 255

Type: column

subject

Entity instance

Type: dynamic

subject_id

foreign key pointing to entity.id

Type: column

temporal_entity

Entity instance

Type: dynamic

temporal_entity_id

foreign key pointing to entity.id

Type: column

class emtellipro_db.models.TemporalityRelationModifier(**kwargs)

Bases: sqlalchemy.orm.decl_api.Base

Association table linking temporality relations to entities specified as modifiers

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entity_id

foreign key pointing to entity.id, part of primary key

Type: column

id

uuid primary key

Type: column

temporality_id

foreign key pointing to temporalityrelation.id, part of primary key

Type: column

class emtellipro_db.models.UnicodeLongText(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

This is a semi-custom type which is used to allow compiling UnicodeText as LONGTEXT on MySQL. It’ll compile using the default dialect implementations for other databases.

impl: alias of sqlalchemy.sql.sqltypes.UnicodeText

class emtellipro_db.models.XUnicode(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

A custom Unicode type which is identical to SQLAlchemy’s Unicode type, except it skips processing the result from the driver.

Snowflake’s Python db connector supports unicode natively, but doesn’t define the Unicode type.

impl: alias of sqlalchemy.sql.sqltypes.Unicode

result_processor(dialect, coltype)

Provide a result value processing function for the given Dialect.

This is the method that fulfills the TypeEngine contract for bound value conversion which normally occurs via the _types.TypeEngine.result_processor() method.

Note

User-defined subclasses of _types.TypeDecorator should not implement this method, and should instead implement _types.TypeDecorator.process_result_value() so that the “inner” processing provided by the implementing type is maintained.

Parameters

dialect – Dialect instance in use.
coltype – A SQLAlchemy data type

class emtellipro_db.models.XUnicodeText(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

A custom UnicodeText type which is identical to SQLAlchemy’s UnicodeText type, except it skips processing the result from the driver.

Snowflake’s Python db connector supports unicode natively, but doesn’t define the Unicode type.

impl: alias of sqlalchemy.sql.sqltypes.UnicodeText

result_processor(dialect, coltype)

Provide a result value processing function for the given Dialect.

This is the method that fulfills the TypeEngine contract for bound value conversion which normally occurs via the _types.TypeEngine.result_processor() method.

Note

User-defined subclasses of _types.TypeDecorator should not implement this method, and should instead implement _types.TypeDecorator.process_result_value() so that the “inner” processing provided by the implementing type is maintained.

Parameters

dialect – Dialect instance in use.
coltype – A SQLAlchemy data type

emtellipro_db.models.recreate_indexes(connection)

Re-create all the 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

emtellipro_db.rowtypes module

This module contains enums that define the values of the type_ columns in the tables that have them.

class emtellipro_db.rowtypes.EntityRowType(value)

Bases: enum.Enum

Enumeration of valid values for the type_ column in the entity table.

class emtellipro_db.rowtypes.LocationRowType(value)

Bases: enum.Enum

Enumeration of valid values for the type_ column in the location table.

class emtellipro_db.rowtypes.RelationRowType(value)

Bases: enum.Enum

Enumeration of valid values for the type_ column in the relation table.

emtellipro_db.save module

This module contains code for saving all models to a database.

emtellipro_db.save.exec_insert(conn, cls, values, fill_in_defaults=False)

Execute INSERT statements for the given table, using the provided values.

Parameters

conn – SQLAlchemy Connection object
cls – The Model class representing the table to insert into
values (list) – list of dictionaries containing the values to be inserted; these must all have the same set of keys, unless fill_in_defaults is enabled.
fill_in_defaults (bool) – if True, fill in None for missing keys in values. When inserting multiple values, they must all have the same set of keys to match the list of columns in the INSERT; if values come from variable JSON objects, this constraint may not hold, so you can use this parameter to add the missing keys with values of None.

emtellipro_db.save.exec_insert_default_returning_id(conn, cls): For these tables, there are no columns other than the ID, so we have no values to insert.

emtellipro_db.save.save_doc(session, annotated_doc, filename, concepts_created, original_doc, job_id, job_timestamp, task_id, metadata, store_doc_text=False, store_json=False, store_sections_and_sentences=False, processing_details_rows=None, engine_version=None): Saves an annotated document to a database.

emtellipro_db.save.save_multiple(docs, job_id, job_timestamp, task_id, engine, store_json, store_sections_and_sentences, engine_version, processing_details_id=None)

Save multiple documents at once

Parameters: docs – list of dictionaries with keys: {‘annotated_doc’, ‘metadata’, ‘filename’, ‘original_doc’}

emtellipro_db.save.save_relation_argument_association(connection, *, relations, relation_ids, entities, table, argument, rel_column): This is a generic argument association saving method for the relations which have many-to-many relationships between the relation and arguments of the same type.

Module contents

This is a package for storing data returned by the Emtellipro API through the SDK to a database.

USAGE

For usage information, run

emtellipro-db-client –help