api.admin

Submodules

• api.admin.actions
• api.admin.models

Package Contents

Classes

ReportErrorModelAdminMixin	Mixin to catch all errors in the Django Admin and map them to user-visible errors.
DatasetAdmin	Mixin to catch all errors in the Django Admin and map them to user-visible errors.
ProjectAnnotateEntitiesAdmin
ProjectGroupAdmin
AnnotatedEntityAdmin
ConceptDBAdmin
VocabularyAdmin
ModelPackAdmin
MetaCATModelAdmin
MetaAnnotationAdmin
DocumentAdmin
ExportedProjectAdmin
ProjectMetricsAdmin
AnnotatedEntity
MetaAnnotation
EntityRelation
Document
ConceptDB
ModelPack
Vocabulary
MetaCATModel
Dataset
DatasetForm
ProjectFields
Project
Entity
Relation
MetaTaskValue
MetaTask
ProjectAnnotateEntitiesFields	Abstract class for all model fields for ProjectAnnotateEntities models.
ProjectAnnotateEntities	Class for any single ProjectAnnotateEntities model fields that should not be inherited by ProjectGroup
ProjectGroup	Abstract class for all model fields for ProjectAnnotateEntities models.
ExportedProject
ProjectMetrics
AnnotatedEntity
MetaAnnotation
EntityRelation
Document
ConceptDB
ModelPack
ConceptDB
Vocabulary
MetaCATModel
Dataset
DatasetForm
Document
ProjectFields
Project
Entity
Relation
EntityRelation
AnnotatedEntity
MetaTaskValue
MetaTask
ProjectAnnotateEntitiesFields	Abstract class for all model fields for ProjectAnnotateEntities models.
ProjectAnnotateEntities	Class for any single ProjectAnnotateEntities model fields that should not be inherited by ProjectGroup
ProjectGroup	Abstract class for all model fields for ProjectAnnotateEntities models.
MetaAnnotation
ExportedProject
ProjectMetrics

Functions

drop_collection(cdb_model)
import_all_concepts(cdb, cdb_model)
clear_cdb_cnf_addons(cdb, cdb_id)
reset_project(modeladmin, request, queryset)
download_without_text(modeladmin, request, queryset)
download_without_text_with_doc_names(modeladmin, ...)
download_projects_without_text(projects, with_doc_name)
download(modeladmin, request, queryset)
download_projects_with_text(projects)
retrieve_project_data(projects)	A function to convert a list of projects and:
clone_projects(modeladmin, request, queryset)
dataset_document_counts(dataset)
_reset_cdb_filters(id)
import_concepts_from_cdb(cdb_model_id)
reset_cdb_filters(modeladmin, request, queryset)
import_concepts(modeladmin, request, queryset)
delete_indexed_concepts(modeladmin, request, queryset)
remove_all_documents(modeladmin, request, queryset)
auto_delete_cdb_file_on_delete(sender, instance, **kwargs)
auto_delete_vocab_file_on_delete(sender, instance, ...)
auto_delete_dataset_file_on_delete(sender, instance, ...)
_remove_file(instance, prop)
drop_collection(cdb_model)
import_all_concepts(cdb, cdb_model)
clear_cdb_cnf_addons(cdb, cdb_id)
reset_project(modeladmin, request, queryset)
download_without_text(modeladmin, request, queryset)
download_without_text_with_doc_names(modeladmin, ...)
download_projects_without_text(projects, with_doc_name)
download(modeladmin, request, queryset)
download_projects_with_text(projects)
retrieve_project_data(projects)	A function to convert a list of projects and:
clone_projects(modeladmin, request, queryset)
dataset_document_counts(dataset)
_reset_cdb_filters(id)
import_concepts_from_cdb(cdb_model_id)
reset_cdb_filters(modeladmin, request, queryset)
import_concepts(modeladmin, request, queryset)
delete_indexed_concepts(modeladmin, request, queryset)
remove_all_documents(modeladmin, request, queryset)
auto_delete_cdb_file_on_delete(sender, instance, **kwargs)
auto_delete_vocab_file_on_delete(sender, instance, ...)
auto_delete_dataset_file_on_delete(sender, instance, ...)
_remove_file(instance, prop)

Attributes

_PROJECT_ANNO_ENTS_SETTINGS_FIELD_ORDER
_PROJECT_FIELDS_ORDER
logger
_dt_fmt
STATUS_CHOICES
BOOL_CHOICES
cdb_name_validator
logger
_dt_fmt
STATUS_CHOICES
BOOL_CHOICES
cdb_name_validator
logger

api.admin._PROJECT_ANNO_ENTS_SETTINGS_FIELD_ORDER = ('concept_db', 'vocab', 'model_pack', 'cdb_search_filter', 'deid_model_annotation',...

api.admin._PROJECT_FIELDS_ORDER = ('cuis', 'cuis_file', 'annotation_classification', 'project_locked', 'project_status')

class api.admin.ReportErrorModelAdminMixin

Mixin to catch all errors in the Django Admin and map them to user-visible errors.

changeform_view(request, object_id=None, form_url='', extra_context=None)

class api.admin.DatasetAdmin

Bases: ReportErrorModelAdminMixin, django.contrib.admin.ModelAdmin

Mixin to catch all errors in the Django Admin and map them to user-visible errors.

model

form

list_display

class api.admin.ProjectAnnotateEntitiesAdmin

Bases: django.contrib.admin.ModelAdmin

model

actions

list_filter = ('members', 'project_status', 'project_locked', 'annotation_classification')

list_display = ['name']

fields

formfield_for_foreignkey(db_field, request, **kwargs)

formfield_for_manytomany(db_field, request, **kwargs)

class api.admin.ProjectGroupAdmin

Bases: django.contrib.admin.ModelAdmin

class Meta

model

model

list_display = ('name', 'description')

fields

get_form(request, obj=None, change=False, **kwargs)

_set_proj_from_group(proj, group, annotator, admins, cdb_search_filters, tasks, relations)

Parameters:

• proj (api.models.ProjectAnnotateEntities) –

• group (api.models.ProjectGroup) –

• annotator (api.models.settings.AUTH_USER_MODEL) –

• admins (List[django.contrib.auth.models.User]) –

• cdb_search_filters (List[api.models.ConceptDB]) –

• tasks (List[api.models.MetaTask]) –

• relations (List[api.models.Relation]) –

save_model(request, obj, form, change)

class api.admin.AnnotatedEntityAdmin

Bases: django.contrib.admin.ModelAdmin

list_display = ('user', 'project', 'entity', 'value', 'deleted', 'validated')

list_filter = ('user', 'project', 'deleted', 'validated')

model

class api.admin.ConceptDBAdmin

Bases: django.contrib.admin.ModelAdmin

model

actions

list_display = ('name', 'use_for_training', 'create_time', 'last_modified', 'last_modified_by')

fields = ('name', 'cdb_file', 'use_for_training')

save_model(request, obj, form, change)

class api.admin.VocabularyAdmin

Bases: django.contrib.admin.ModelAdmin

model

list_display = ('name', 'create_time', 'last_modified', 'last_modified_by')

fields = ('name', 'vocab_file', 'create_time', 'last_modified', 'last_modified_by')

save_model(request, obj, form, change)

class api.admin.ModelPackAdmin

Bases: django.contrib.admin.ModelAdmin

model

list_display = ('name', 'model_pack', 'concept_db', 'vocab', 'metacats')

fields = ['name', 'model_pack']

metacats(obj)

save_model(request, obj, form, change)

class api.admin.MetaCATModelAdmin

Bases: django.contrib.admin.ModelAdmin

model

list_display = ('name', 'meta_cat_dir')

class api.admin.MetaAnnotationAdmin

Bases: django.contrib.admin.ModelAdmin

model

list_display = ('annotated_entity', 'meta_task', 'meta_task_value', 'acc', 'predicted_meta_task_value',...

list_filter = ('meta_task', 'meta_task_value', 'predicted_meta_task_value', 'validated')

class api.admin.DocumentAdmin

Bases: django.contrib.admin.ModelAdmin

model

actions

list_filter = ('dataset',)

list_display = ['name', 'create_time', 'dataset', 'last_modified']

class api.admin.ExportedProjectAdmin

Bases: django.contrib.admin.ModelAdmin

model

class api.admin.ProjectMetricsAdmin

Bases: django.contrib.admin.ModelAdmin

model

list_display = ('report_name', 'report_name_generated')

list_filter = ['projects']

class api.admin.AnnotatedEntity

Bases: django.db.models.Model

class Meta

ordering = ['id']

user

project

document

entity

value

start_ind

end_ind

acc

comment

validated

correct

alternative

manually_created

deleted

killed

irrelevant

create_time

last_modified

save(*args, **kwargs)

__str__()

class api.admin.MetaAnnotation

Bases: django.db.models.Model

annotated_entity

meta_task

meta_task_value

acc

predicted_meta_task_value

validated

last_modified

save(*args, **kwargs)

__str__()

class api.admin.EntityRelation

Bases: django.db.models.Model

class Meta

ordering = ['id']

user

project

document

relation

start_entity

end_entity

validated

create_time

last_modified

save(*args, **kwargs)

__str__()

class api.admin.Document

Bases: django.db.models.Model

class Meta

ordering = ['id']

name

create_time

last_modified

text

dataset

__str__()

class api.admin.ConceptDB(*args, **kwargs)

Bases: django.db.models.Model

name

cdb_file

use_for_training

create_time

last_modified

last_modified_by

__init__(*args, **kwargs)

classmethod from_db(db, field_names, values)

save(*args, skip_load=False, **kwargs)

__str__()

api.admin.drop_collection(cdb_model)

Parameters:

cdb_model (api.models.ConceptDB) –

api.admin.import_all_concepts(cdb, cdb_model)

Parameters:

• cdb (medcat.cdb.CDB) –

• cdb_model (api.models.ConceptDB) –

api.admin.clear_cdb_cnf_addons(cdb, cdb_id)

Parameters:

• cdb (medcat.cdb.CDB) –

• cdb_id (str | int) –

api.admin.logger

api.admin._dt_fmt = '%Y-%m-%d %H:%M:%S.%f'

api.admin.reset_project(modeladmin, request, queryset)

api.admin.download_without_text(modeladmin, request, queryset)

api.admin.download_without_text_with_doc_names(modeladmin, request, queryset)

api.admin.download_projects_without_text(projects, with_doc_name)

api.admin.download(modeladmin, request, queryset)

api.admin.download_projects_with_text(projects)

Parameters:

projects (django.db.models.QuerySet) –

api.admin.retrieve_project_data(projects)

A function to convert a list of projects and:

• their associated documents,

• their associated annotations,

• their associated Meta annotations and Relation Annotations

for serialization. Output schema is as follows: ((optional) indicates this field isn’t required for training a MedCAT model) { “projects”: [

{

“name”: “<project_name” # name of the project “id”: “<id>” # the auto-generated id of the project (optional) “project_group_id”: “<id>” # the auto-generated id of the project - nullable “project_group_name”: “<group_name>” # the name of the project group if set. “project_status”: “<project_status>” # status - either annotating, discontinued, complete “project_locked”: “<project_locked>” # locked - for no further annotations “cuis”: [“cui_1”, “cui_2” … ] # the CUI filter for the project, includes those from file / and text-box “meta_anno_defs”: [

# list of meta annotation tasks configured for this project. {

“name”: “Name of meta annotation task”, “values”: [

“<first value>”, “<second value>” …

],

}, … more meta_annotation tasks configured for this project

], “relation_anno_defs”: [

“<name1>”, “<name2>” … more relation annotation task names configured for this project

] “documents”: [

{ “id”: “<id>” # the auto-generated id of the document (optional) “name”: “<name>” # the name of the document (optional), but used in stat printing during training “text”: “<text>” # the text of the document “last_modified”: “<date time>” # the last modified-time (optional) “annotations”: [{

“id”: “<id>” # the auto-generated id of the document (optional) “name”: “<username string>” # the user who made the annotation (optional) “cui”: “<cui string>” # the cui label for this annotation “value”: “<string>” # the text span for this annotation “start”: <integer> # the start index of this annotation with respect to the document text “end”: <integer> # the end index of this annotation with respect to the document text “validated”: <boolean> # if the annotation has been marked by a human annotator “correct”: <boolean> # if the text span is correctly linked to the CUI of this annotation “deleted”: <boolean> # if the text span was incorrectly linked or ‘not’ linked by MedCAT due to low scores “alternative”: <boolean> # if the text span was incorrectly linked by MedCAT, then correctly linked by a human annotator “killed”: <boolean> # if a human annotator ‘terminated’ this annotation “irrelevant”: <boolean> # if a human annotator has marked an annotation as irrelevant (optional) “acc”: <float> # accuracy provided by MedCAT (optional) “comment”: “<comment string>” # the text entered by an annotator during annotation (optional) “meta_anns”: [

# list of meta annotations if applicable to project {

“name”: <string> # Meta anno task name, i.e. temporality “value”: <string> # the selected meta anno task value for, ie. “past” or “present” “acc”: <float> # default 1, (optional) “validated”: <boolean> # Meta annotation has been made by a human annotator, default (true)

}, … <more meta annotations of the same as above structure>

]}, … <more annotations of the same above structure>

] “relations”: [

{

“start_entity”: <integer> # id of above annotation that is the start of this relation “start_entity_cui”: “<string>” # the cui label of the start of this relation “start_entity_value”: <string> # value of the start annotation for this relation “start_entity_start_idx”: <integer> # start index of text span of start of relation “start_entity_end_idx”: <integer> # end index of text span of start of relation “end_entity”: <integer> # id of the above annotation that is the end of this relation “end_entity_cui”: “<string>” # the cui label of the end of this relation “end_entity_value”: <string> # value of the end annotation for this relation “end_entity_start_idx”: <integer> # end index of text span of end of relation “end_entity_end_idx”: <integer> # end index of text span of end of relation “user”: <string> # username of annotator for relation (optional) “relation”: <string> # label for this relation “validated”: <boolean> # if the annotation has been validated by a human annotator, default true.

} … < more relations of the samve above structure>

]

… <more documents of the same above structure>

]

]

Args:

projects (QuerySet): the projects to export data for.

Parameters:

projects (django.db.models.QuerySet) –

Return type:

Dict[str, List]

api.admin.clone_projects(modeladmin, request, queryset)

api.admin.dataset_document_counts(dataset)

api.admin._reset_cdb_filters(id)

api.admin.import_concepts_from_cdb(cdb_model_id)

Parameters:

cdb_model_id (int) –

api.admin.reset_cdb_filters(modeladmin, request, queryset)

api.admin.import_concepts(modeladmin, request, queryset)

api.admin.delete_indexed_concepts(modeladmin, request, queryset)

api.admin.remove_all_documents(modeladmin, request, queryset)

api.admin.STATUS_CHOICES = [(0, 'Not Validated'), (1, 'Validated')]

api.admin.BOOL_CHOICES = [(0, 'False'), (1, 'True')]

api.admin.cdb_name_validator

class api.admin.ModelPack

Bases: django.db.models.Model

name

model_pack

concept_db

vocab

meta_cats

create_time

last_modified

last_modified_by

save(*args, skip_load=False, **kwargs)

__str__()

class api.admin.Vocabulary

Bases: django.db.models.Model

name

vocab_file

create_time

last_modified

last_modified_by

save(*args, skip_load=False, **kwargs)

__str__()

class api.admin.MetaCATModel

Bases: django.db.models.Model

name

meta_cat_dir

get_or_create_meta_tasks_and_values(meta_cat)

Parameters:

meta_cat (medcat.components.addons.meta_cat.meta_cat.MetaCAT) –

save(*args, unpack_load_meta_cat_dir=False, **kwargs)

__str__()

class api.admin.Dataset

Bases: django.db.models.Model

name

original_file

create_time

description

__str__()

class api.admin.DatasetForm

Bases: django.forms.ModelForm

clean()

class api.admin.ProjectFields

Bases: django.db.models.Model

class Meta

abstract = True

PROJECT_STATUSES = [('A', 'Annotating'), ('D', 'Discontinued (Fail)'), ('C', 'Complete')]

name

description

dataset

annotation_guideline_link

create_time

last_modified

cuis

cuis_file

annotation_classification

meta_cat_predictions

project_locked

project_status

class api.admin.Project

Bases: polymorphic.models.PolymorphicModel, ProjectFields

members

group

validated_documents

prepared_documents

__str__()

class api.admin.Entity

Bases: django.db.models.Model

label

__str__()

class api.admin.Relation

Bases: django.db.models.Model

class Meta

ordering = ['id']

label

__str__()

class api.admin.MetaTaskValue

Bases: django.db.models.Model

class Meta

ordering = ['ordering', 'name']

name

ordering

__str__()

class api.admin.MetaTask

Bases: django.db.models.Model

class Meta

ordering = ['ordering', 'name']

name

values

default

description

ordering

prediction_model

__str__()

class api.admin.ProjectAnnotateEntitiesFields

Bases: django.db.models.Model

Abstract class for all model fields for ProjectAnnotateEntities models.

class Meta

abstract = True

concept_db

vocab

model_pack

cdb_search_filter

require_entity_validation

train_model_on_submit

add_new_entities

restrict_concept_lookup

terminate_available

irrelevant_available

deid_model_annotation

enable_entity_annotation_comments

tasks

relations

use_model_service

model_service_url

save(*args, **kwargs)

class api.admin.ProjectAnnotateEntities

Bases: Project, ProjectAnnotateEntitiesFields

Class for any single ProjectAnnotateEntities model fields that should not be inherited by ProjectGroup In practise its unlikely further fields are needed.

class api.admin.ProjectGroup

Bases: ProjectFields, ProjectAnnotateEntitiesFields

Abstract class for all model fields for ProjectAnnotateEntities models.

administrators

annotators

cdb_search_filter

create_associated_projects

__str__()

class api.admin.ExportedProject

Bases: django.db.models.Model

trainer_export_file

import_project_name_suffix

members

cdb_id

vocab_id

modelpack_id

cdb_search_filter_id

set_validated_docs

__str__()

class api.admin.ProjectMetrics

Bases: django.db.models.Model

report_name_generated

report_name

report

projects

__str__()

api.admin.auto_delete_cdb_file_on_delete(sender, instance, **kwargs)

api.admin.auto_delete_vocab_file_on_delete(sender, instance, **kwargs)

api.admin.auto_delete_dataset_file_on_delete(sender, instance, **kwargs)

api.admin._remove_file(instance, prop)

exception api.admin.MedCATLoadException(message)

Bases: Exception

Common base class for all non-exit exceptions.

__init__(message)

Initialize self. See help(type(self)) for accurate signature.

class api.admin.AnnotatedEntity

Bases: django.db.models.Model

class Meta

ordering = ['id']

user

project

document

entity

value

start_ind

end_ind

acc

comment

validated

correct

alternative

manually_created

deleted

killed

irrelevant

create_time

last_modified

save(*args, **kwargs)

__str__()

class api.admin.MetaAnnotation

Bases: django.db.models.Model

annotated_entity

meta_task

meta_task_value

acc

predicted_meta_task_value

validated

last_modified

save(*args, **kwargs)

__str__()

class api.admin.EntityRelation

Bases: django.db.models.Model

class Meta

ordering = ['id']

user

project

document

relation

start_entity

end_entity

validated

create_time

last_modified

save(*args, **kwargs)

__str__()

class api.admin.Document

Bases: django.db.models.Model

class Meta

ordering = ['id']

name

create_time

last_modified

text

dataset

__str__()

class api.admin.ConceptDB(*args, **kwargs)

Bases: django.db.models.Model

name

cdb_file

use_for_training

create_time

last_modified

last_modified_by

__init__(*args, **kwargs)

classmethod from_db(db, field_names, values)

save(*args, skip_load=False, **kwargs)

__str__()

api.admin.drop_collection(cdb_model)

Parameters:

cdb_model (api.models.ConceptDB) –

api.admin.import_all_concepts(cdb, cdb_model)

Parameters:

• cdb (medcat.cdb.CDB) –

• cdb_model (api.models.ConceptDB) –

api.admin.clear_cdb_cnf_addons(cdb, cdb_id)

Parameters:

• cdb (medcat.cdb.CDB) –

• cdb_id (str | int) –

api.admin.logger

api.admin._dt_fmt = '%Y-%m-%d %H:%M:%S.%f'

api.admin.reset_project(modeladmin, request, queryset)

api.admin.download_without_text(modeladmin, request, queryset)

api.admin.download_without_text_with_doc_names(modeladmin, request, queryset)

api.admin.download_projects_without_text(projects, with_doc_name)

api.admin.download(modeladmin, request, queryset)

api.admin.download_projects_with_text(projects)

Parameters:

projects (django.db.models.QuerySet) –

api.admin.retrieve_project_data(projects)

A function to convert a list of projects and:

• their associated documents,

• their associated annotations,

• their associated Meta annotations and Relation Annotations

for serialization. Output schema is as follows: ((optional) indicates this field isn’t required for training a MedCAT model) { “projects”: [

{

“name”: “<project_name” # name of the project “id”: “<id>” # the auto-generated id of the project (optional) “project_group_id”: “<id>” # the auto-generated id of the project - nullable “project_group_name”: “<group_name>” # the name of the project group if set. “project_status”: “<project_status>” # status - either annotating, discontinued, complete “project_locked”: “<project_locked>” # locked - for no further annotations “cuis”: [“cui_1”, “cui_2” … ] # the CUI filter for the project, includes those from file / and text-box “meta_anno_defs”: [

# list of meta annotation tasks configured for this project. {

“name”: “Name of meta annotation task”, “values”: [

“<first value>”, “<second value>” …

],

}, … more meta_annotation tasks configured for this project

], “relation_anno_defs”: [

“<name1>”, “<name2>” … more relation annotation task names configured for this project

] “documents”: [

{ “id”: “<id>” # the auto-generated id of the document (optional) “name”: “<name>” # the name of the document (optional), but used in stat printing during training “text”: “<text>” # the text of the document “last_modified”: “<date time>” # the last modified-time (optional) “annotations”: [{

“id”: “<id>” # the auto-generated id of the document (optional) “name”: “<username string>” # the user who made the annotation (optional) “cui”: “<cui string>” # the cui label for this annotation “value”: “<string>” # the text span for this annotation “start”: <integer> # the start index of this annotation with respect to the document text “end”: <integer> # the end index of this annotation with respect to the document text “validated”: <boolean> # if the annotation has been marked by a human annotator “correct”: <boolean> # if the text span is correctly linked to the CUI of this annotation “deleted”: <boolean> # if the text span was incorrectly linked or ‘not’ linked by MedCAT due to low scores “alternative”: <boolean> # if the text span was incorrectly linked by MedCAT, then correctly linked by a human annotator “killed”: <boolean> # if a human annotator ‘terminated’ this annotation “irrelevant”: <boolean> # if a human annotator has marked an annotation as irrelevant (optional) “acc”: <float> # accuracy provided by MedCAT (optional) “comment”: “<comment string>” # the text entered by an annotator during annotation (optional) “meta_anns”: [

# list of meta annotations if applicable to project {

“name”: <string> # Meta anno task name, i.e. temporality “value”: <string> # the selected meta anno task value for, ie. “past” or “present” “acc”: <float> # default 1, (optional) “validated”: <boolean> # Meta annotation has been made by a human annotator, default (true)

}, … <more meta annotations of the same as above structure>

]}, … <more annotations of the same above structure>

] “relations”: [

{

“start_entity”: <integer> # id of above annotation that is the start of this relation “start_entity_cui”: “<string>” # the cui label of the start of this relation “start_entity_value”: <string> # value of the start annotation for this relation “start_entity_start_idx”: <integer> # start index of text span of start of relation “start_entity_end_idx”: <integer> # end index of text span of start of relation “end_entity”: <integer> # id of the above annotation that is the end of this relation “end_entity_cui”: “<string>” # the cui label of the end of this relation “end_entity_value”: <string> # value of the end annotation for this relation “end_entity_start_idx”: <integer> # end index of text span of end of relation “end_entity_end_idx”: <integer> # end index of text span of end of relation “user”: <string> # username of annotator for relation (optional) “relation”: <string> # label for this relation “validated”: <boolean> # if the annotation has been validated by a human annotator, default true.

} … < more relations of the samve above structure>

]

… <more documents of the same above structure>

]

]

Args:

projects (QuerySet): the projects to export data for.

Parameters:

projects (django.db.models.QuerySet) –

Return type:

Dict[str, List]

api.admin.clone_projects(modeladmin, request, queryset)

api.admin.dataset_document_counts(dataset)

api.admin._reset_cdb_filters(id)

api.admin.import_concepts_from_cdb(cdb_model_id)

Parameters:

cdb_model_id (int) –

api.admin.reset_cdb_filters(modeladmin, request, queryset)

api.admin.import_concepts(modeladmin, request, queryset)

api.admin.delete_indexed_concepts(modeladmin, request, queryset)

api.admin.remove_all_documents(modeladmin, request, queryset)

api.admin.STATUS_CHOICES = [(0, 'Not Validated'), (1, 'Validated')]

api.admin.BOOL_CHOICES = [(0, 'False'), (1, 'True')]

api.admin.cdb_name_validator

api.admin.logger

class api.admin.ModelPack

Bases: django.db.models.Model

name

model_pack

concept_db

vocab

meta_cats

create_time

last_modified

last_modified_by

save(*args, skip_load=False, **kwargs)

__str__()

class api.admin.ConceptDB(*args, **kwargs)

Bases: django.db.models.Model

name

cdb_file

use_for_training

create_time

last_modified

last_modified_by

__init__(*args, **kwargs)

classmethod from_db(db, field_names, values)

save(*args, skip_load=False, **kwargs)

__str__()

class api.admin.Vocabulary

Bases: django.db.models.Model

name

vocab_file

create_time

last_modified

last_modified_by

save(*args, skip_load=False, **kwargs)

__str__()

class api.admin.MetaCATModel

Bases: django.db.models.Model

name

meta_cat_dir

get_or_create_meta_tasks_and_values(meta_cat)

Parameters:

meta_cat (medcat.components.addons.meta_cat.meta_cat.MetaCAT) –

save(*args, unpack_load_meta_cat_dir=False, **kwargs)

__str__()

class api.admin.Dataset

Bases: django.db.models.Model

name

original_file

create_time

description

__str__()

class api.admin.DatasetForm

Bases: django.forms.ModelForm

clean()

class api.admin.Document

Bases: django.db.models.Model

class Meta

ordering = ['id']

name

create_time

last_modified

text

dataset

__str__()

class api.admin.ProjectFields

Bases: django.db.models.Model

class Meta

abstract = True

PROJECT_STATUSES = [('A', 'Annotating'), ('D', 'Discontinued (Fail)'), ('C', 'Complete')]

name

description

dataset

annotation_guideline_link

create_time

last_modified

cuis

cuis_file

annotation_classification

meta_cat_predictions

project_locked

project_status

class api.admin.Project

Bases: polymorphic.models.PolymorphicModel, ProjectFields

members

group

validated_documents

prepared_documents

__str__()

class api.admin.Entity

Bases: django.db.models.Model

label

__str__()

class api.admin.Relation

Bases: django.db.models.Model

class Meta

ordering = ['id']

label

__str__()

class api.admin.EntityRelation

Bases: django.db.models.Model

class Meta

ordering = ['id']

user

project

document

relation

start_entity

end_entity

validated

create_time

last_modified

save(*args, **kwargs)

__str__()

class api.admin.AnnotatedEntity

Bases: django.db.models.Model

class Meta

ordering = ['id']

user

project

document

entity

value

start_ind

end_ind

acc

comment

validated

correct

alternative

manually_created

deleted

killed

irrelevant

create_time

last_modified

save(*args, **kwargs)

__str__()

class api.admin.MetaTaskValue

Bases: django.db.models.Model

class Meta

ordering = ['ordering', 'name']

name

ordering

__str__()

class api.admin.MetaTask

Bases: django.db.models.Model

class Meta

ordering = ['ordering', 'name']

name

values

default

description

ordering

prediction_model

__str__()

class api.admin.ProjectAnnotateEntitiesFields

Bases: django.db.models.Model

Abstract class for all model fields for ProjectAnnotateEntities models.

class Meta

abstract = True

concept_db

vocab

model_pack

cdb_search_filter

require_entity_validation

train_model_on_submit

add_new_entities

restrict_concept_lookup

terminate_available

irrelevant_available

deid_model_annotation

enable_entity_annotation_comments

tasks

relations

use_model_service

model_service_url

save(*args, **kwargs)

class api.admin.ProjectAnnotateEntities

Bases: Project, ProjectAnnotateEntitiesFields

Class for any single ProjectAnnotateEntities model fields that should not be inherited by ProjectGroup In practise its unlikely further fields are needed.

class api.admin.ProjectGroup

Bases: ProjectFields, ProjectAnnotateEntitiesFields

Abstract class for all model fields for ProjectAnnotateEntities models.

administrators

annotators

cdb_search_filter

create_associated_projects

__str__()

class api.admin.MetaAnnotation

Bases: django.db.models.Model

annotated_entity

meta_task

meta_task_value

acc

predicted_meta_task_value

validated

last_modified

save(*args, **kwargs)

__str__()

class api.admin.ExportedProject

Bases: django.db.models.Model

trainer_export_file

import_project_name_suffix

members

cdb_id

vocab_id

modelpack_id

cdb_search_filter_id

set_validated_docs

__str__()

class api.admin.ProjectMetrics

Bases: django.db.models.Model

report_name_generated

report_name

report

projects

__str__()

api.admin.auto_delete_cdb_file_on_delete(sender, instance, **kwargs)

api.admin.auto_delete_vocab_file_on_delete(sender, instance, **kwargs)

api.admin.auto_delete_dataset_file_on_delete(sender, instance, **kwargs)

api.admin._remove_file(instance, prop)

exception api.admin.MedCATLoadException(message)

Bases: Exception

Common base class for all non-exit exceptions.

__init__(message)

Initialize self. See help(type(self)) for accurate signature.