import json
import logging
import re
from datetime import timedelta
from json import JSONDecodeError
from pathlib import Path
from celery import signature
from django import forms
from django.apps import apps
from django.conf import settings
from django.core.exceptions import ValidationError
from django.core.files import File
from django.core.files.base import ContentFile
from django.core.validators import (
MaxValueValidator,
MinValueValidator,
RegexValidator,
)
from django.db import models
from django.db.models import Avg, F, IntegerChoices, QuerySet, Sum
from django.db.transaction import on_commit
from django.forms import ModelChoiceField
from django.forms.models import model_to_dict
from django.utils.functional import cached_property
from django.utils.module_loading import import_string
from django.utils.text import get_valid_filename
from django.utils.timezone import now
from django.utils.translation import gettext_lazy as _
from django_deprecate_fields import deprecate_field
from django_extensions.db.fields import AutoSlugField
from panimg.models import MAXIMUM_SEGMENTS_LENGTH
from grandchallenge.cases.models import Image, ImageFile
from grandchallenge.cases.widgets import FlexibleImageField
from grandchallenge.charts.specs import components_line
from grandchallenge.components.schemas import INTERFACE_VALUE_SCHEMA
from grandchallenge.components.tasks import (
assign_docker_image_from_upload,
deprovision_job,
provision_job,
validate_docker_image,
)
from grandchallenge.components.validators import (
validate_no_slash_at_ends,
validate_safe_path,
)
from grandchallenge.core.storage import (
private_s3_storage,
protected_s3_storage,
)
from grandchallenge.core.validators import (
ExtensionValidator,
JSONSchemaValidator,
JSONValidator,
MimeTypeValidator,
)
from grandchallenge.uploads.models import UserUpload
from grandchallenge.workstation_configs.models import (
OVERLAY_SEGMENTS_SCHEMA,
LookUpTable,
)
logger = logging.getLogger(__name__)
DEFAULT_OUTPUT_INTERFACE_SLUG = "generic-overlay"
[docs]class InterfaceKindChoices(models.TextChoices):
"""Interface kind choices."""
STRING = "STR", _("String")
INTEGER = "INT", _("Integer")
FLOAT = "FLT", _("Float")
BOOL = "BOOL", _("Bool")
ANY = "JSON", _("Anything")
CHART = "CHART", _("Chart")
# Annotation Types
TWO_D_BOUNDING_BOX = "2DBB", _("2D bounding box")
MULTIPLE_TWO_D_BOUNDING_BOXES = "M2DB", _("Multiple 2D bounding boxes")
DISTANCE_MEASUREMENT = "DIST", _("Distance measurement")
MULTIPLE_DISTANCE_MEASUREMENTS = (
"MDIS",
_("Multiple distance measurements"),
)
POINT = "POIN", _("Point")
MULTIPLE_POINTS = "MPOI", _("Multiple points")
POLYGON = "POLY", _("Polygon")
MULTIPLE_POLYGONS = "MPOL", _("Multiple polygons")
LINE = "LINE", _("Line")
MULTIPLE_LINES = "MLIN", _("Multiple lines")
ANGLE = "ANGL", _("Angle")
MULTIPLE_ANGLES = "MANG", _("Multiple angles")
ELLIPSE = "ELLI", _("Ellipse")
MULTIPLE_ELLIPSES = "MELL", _("Multiple ellipses")
# Choice Types
CHOICE = "CHOI", _("Choice")
MULTIPLE_CHOICE = "MCHO", _("Multiple choice")
# Image types
IMAGE = "IMG", _("Image")
SEGMENTATION = "SEG", _("Segmentation")
HEAT_MAP = "HMAP", _("Heat Map")
# File types
PDF = "PDF", _("PDF file")
SQREG = "SQREG", _("SQREG file")
THUMBNAIL_JPG = "JPEG", _("Thumbnail jpg")
THUMBNAIL_PNG = "PNG", _("Thumbnail png")
OBJ = "OBJ", _("OBJ file")
MP4 = "MP4", _("MP4 file")
# Legacy support
CSV = "CSV", _("CSV file")
ZIP = "ZIP", _("ZIP file")
[docs]class InterfaceSuperKindChoices(models.TextChoices):
IMAGE = "I", "Image"
FILE = "F", "File"
VALUE = "V", "Value"
[docs]class InterfaceKind:
"""Interface kind."""
InterfaceKindChoices = InterfaceKindChoices
[docs] @staticmethod
def interface_type_json():
"""Interface kinds that are json serializable:
* String
* Integer
* Float
* Bool
* Anything that is JSON serializable (any object)
* 2D bounding box
* Multiple 2D bounding boxes
* Distance measurement
* Multiple distance measurements
* Point
* Multiple points
* Polygon
* Multiple polygons
* Lines
* Multiple lines
* Angle
* Multiple angles
* Choice (string)
* Multiple choice (array of strings)
* Chart
* Ellipse
* Multiple ellipses
Example json for 2D bounding box annotation
required: "type", "corners", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Region of interest",
"type": "2D bounding box",
"corners": [
[ 130.80001831054688, 148.86666870117188, 0.5009999871253967],
[ 69.73332977294922, 148.86666870117188, 0.5009999871253967],
[ 69.73332977294922, 73.13333129882812, 0.5009999871253967],
[ 130.80001831054688, 73.13333129882812, 0.5009999871253967]
],
"probability": 0.95,
"version": { "major": 1, "minor": 0 }
}
Example json for Multiple 2D bounding boxes annotation
required: "type", "boxes", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Regions of interest",
"type": "Multiple 2D bounding boxes",
"boxes": [
{
"name": "ROI 1",
"corners": [
[ 92.66666412353516, 136.06668090820312, 0.5009999871253967],
[ 54.79999923706055, 136.06668090820312, 0.5009999871253967],
[ 54.79999923706055, 95.53333282470703, 0.5009999871253967],
[ 92.66666412353516, 95.53333282470703, 0.5009999871253967]
],
"probability": 0.95
},
{
"name": "ROI 2",
"corners": [
[ 92.66666412353516, 136.06668090820312, 0.5009999871253967],
[ 54.79999923706055, 136.06668090820312, 0.5009999871253967],
[ 54.79999923706055, 95.53333282470703, 0.5009999871253967],
[ 92.66666412353516, 95.53333282470703, 0.5009999871253967]
],
"probability": 0.92
}
],
"version": { "major": 1, "minor": 0 }
}
Example json for Distance measurement annotation
required: "type", "start", "end", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Distance between areas",
"type": "Distance measurement",
"start": [ 59.79176712036133, 78.76753997802734, 0.5009999871253967 ],
"end": [ 69.38014221191406, 143.75546264648438, 0.5009999871253967 ],
"probability": 0.92,
"version": { "major": 1, "minor": 0 }
}
Example json for Multiple distance measurement annotation
required: "type", "lines", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Distances between areas",
"type": "Multiple distance measurements",
"lines": [
{
"name": "Distance 1",
"start": [ 49.733333587646484, 103.26667022705078, 0.5009999871253967 ],
"end": [ 55.06666564941406, 139.26666259765625, 0.5009999871253967 ],
"probability": 0.92
},
{
"name": "Distance 2",
"start": [ 49.733333587646484, 103.26667022705078, 0.5009999871253967 ],
"end": [ 55.06666564941406, 139.26666259765625, 0.5009999871253967 ],
"probability": 0.92
}
],
"version": { "major": 1, "minor": 0 }
}
Example json for Point annotation
required: "type", "point", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Point of interest",
"type": "Point",
"point": [ 152.13333129882812, 111.0, 0.5009999871253967 ],
"probability": 0.92,
"version": { "major": 1, "minor": 0 }
}
Example json for Multiple points annotation
required: "type", "points", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Points of interest",
"type": "Multiple points",
"points": [
{
"name": "Point 1",
"point": [
96.0145263671875, 79.83292388916016, 0.5009999871253967
],
"probability": 0.92
},
{
"name": "Point 2",
"point": [
130.10653686523438, 115.52300262451172, 0.5009999871253967
],
"probability": 0.92
}
],
"version": { "major": 1, "minor": 0 }
}
Example json for Polygon annotation
required: "type", "seed_point", "path_points", "sub_type", "groups", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Area of interest",
"type": "Polygon",
"seed_point": [ 76.413756408691, 124.014717102050, 0.5009999871253967 ],
"path_points": [
[ 76.41375842260106, 124.01471710205078, 0.5009999871253967 ],
[ 76.41694876387268, 124.0511828696491, 0.5009999871253967 ],
[ 76.42642285078242, 124.0865406433515, 0.5009999871253967 ]
],
"sub_type": "brush",
"groups": [],
"probability": 0.92,
"version": { "major": 1, "minor": 0 }
}
Example json for Multiple polygon annotation
required: "type", "polygons", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Areas of interest",
"type": "Multiple polygons",
"polygons": [
{
"name": "Area 1",
"seed_point": [ 55.82666793823242, 90.46666717529297, 0.5009999871253967 ],
"path_points": [
[ 55.82667599387105, 90.46666717529297, 0.5009999871253967 ],
[ 55.93921357544119, 90.88666314747366, 0.5009999871253967 ],
[ 56.246671966051736, 91.1941215380842, 0.5009999871253967 ],
[ 56.66666793823242, 91.30665911965434, 0.5009999871253967 ]
],
"sub_type": "brush",
"groups": [ "manual"],
"probability": 0.67
},
{
"name": "Area 2",
"seed_point": [ 90.22666564941406, 96.06666564941406, 0.5009999871253967 ],
"path_points": [
[ 90.22667370505269, 96.06666564941406, 0.5009999871253967 ],
[ 90.33921128662283, 96.48666162159475, 0.5009999871253967 ],
[ 90.64666967723338, 96.7941200122053, 0.5009999871253967 ]
],
"sub_type": "brush",
"groups": [],
"probability": 0.92
}
],
"version": { "major": 1, "minor": 0 }
}
Example json for Line annotation
required: "type", "seed_points", "path_point_lists", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Some annotation",
"type": "Line",
"seed_points": [[1, 2, 3], [1, 2, 3]],
"path_point_lists": [
[[5, 6, 7], [8, 9, 10], [1, 0, 10], [2, 4, 2]],
[[5, 6, 7], [8, 9, 10], [1, 0, 10], [2, 4, 2]]
],
"probability": 0.92
"version": { "major": 1, "minor": 0 }
}
Example json for Multiple lines annotation
required: "type", "lines", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Some annotations",
"type": "Multiple lines",
"lines": [
{
"name": "Annotation 1",
"seed_points": [[1, 2, 3], [1, 2, 3]],
"path_point_lists": [
[[5, 6, 7], [8, 9, 10], [1, 0, 10], [2, 4, 2]],
[[5, 6, 7], [8, 9, 10], [1, 0, 10], [2, 4, 2]],
],
"probability": 0.78
},
{
"name": "Annotation 2",
"seed_points": [[1, 2, 3], [1, 2, 3]],
"path_point_lists": [
[[5, 6, 7], [8, 9, 10], [1, 0, 10], [2, 4, 2]],
[[5, 6, 7], [8, 9, 10], [1, 0, 10], [2, 4, 2]],
],
"probability": 0.92
}
],
"version": { "major": 1, "minor": 0 }
}
Example json for Angle annotation
required: "type", "lines", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Some angle",
"type": "Angle",
"lines": [[[180, 10, 0.5], [190, 10, 0.5]],[[180, 25, 0.5], [190, 15, 0.5]]],
"probability": 0.92,
"version": {"major": 1, "minor": 0}
}
Example json for Multiple angles annotation
required: "type", "angles", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Some angles",
"type": "Multiple angles",
"angles": [
{
"name": "First angle",
"lines": [[[110, 135, 0.5], [60, 165, 0.5]],[[70, 25, 0.5], [85, 65, 0.5]]],
"probability": 0.82
},
{
"name": "Second angle",
"lines": [[[130, 210, 0.5], [160, 130, 0.5]], [[140, 40, 0.5], [180, 75, 0.5]]],
"probability": 0.52
},
{
"name": "Third angle",
"lines": [[[20, 30, 0.5], [20, 100, 0.5]], [[180, 200, 0.5], [210, 200, 0.5]]],
"probability": 0.98
}
],
"version": {"major": 1, "minor": 0}
}
Example json for Chart (for more examples, see `here<https://vega.github.io/vega-lite/examples/>` and `here<https://grand-challenge.org/blogs/visualisations-for-challenges/>`)
.. code-block:: json
{
"$schema":"https://vega.github.io/schema/vega-lite/v5.json",
"width":300,
"height":300,
"data":{
"values":[
{
"target":"Negative",
"prediction":"Negative",
"value":198
},
{
"target":"Negative",
"prediction":"Positive",
"value":9
},
{
"target":"Positive",
"prediction":"Negative",
"value":159
},
{
"target":"Positive",
"prediction":"Positive",
"value":376
}
],
"format":{
"type":"json"
}
},
"layer":[
{
"mark":"rect",
"encoding":{
"y":{
"field":"target",
"type":"ordinal"
},
"x":{
"field":"prediction",
"type":"ordinal"
},
"color":{
"field":"value",
"type":"quantitative",
"title":"Count of Records",
"legend":{
"direction":"vertical",
"gradientLength":300
}
}
}
},
{
"mark":"text",
"encoding":{
"y":{
"field":"target",
"type":"ordinal"
},
"x":{
"field":"prediction",
"type":"ordinal"
},
"text":{
"field":"value",
"type":"quantitative"
},
"color":{
"condition":{
"test":"datum['value'] < 40",
"value":"black"
},
"value":"white"
}
}
}
],
"config":{
"axis":{
"grid":True,
"tickBand":"extent"
}
}
}
Example json for Ellipse annotation
required: "type", "major_axis, "minor_axis" "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "an Ellipse",
"type": "Ellipse",
"major_axis": [[ 130, 148.86, 0.50], [10, 10, 0]],
"minor_axis": [[ 69.73, 148.86, 0.50], [10, 0, 0]],
"probability": 0.95,
"version": { "major": 1, "minor": 0 }
}
Example json for Multiple ellipses annotation
required: "type", "ellipses", "version"
optional: "name", "probability"
.. code-block:: json
{
"name": "Some Ellipses",
"type": "Multiple ellipses",
"ellipses": [
{
"name": "First Ellipse",
"major axis": [[10, 10, 0.5], [10, 20, 0]],
"minor_axis": [[10, 20, 0.5], [10.6, 0, 0]],
"probability": 0.82
},
{
"name": "Second Ellipse",
"major axis": [[10, 10, 0.5], [10, 20, 0]],
"minor_axis": [[10, 20, 0.5], [10.6, 0, 0]],
"probability": 0.52
},
{
"name": "Third Ellipse",
"major axis": [[10, 10, 0.5], [10, 20, 0]],
"minor_axis": [[10, 20, 0.5], [10.6, 0, 0]],
"probability": 0.98
}
],
"version": {"major": 1, "minor": 0}
}
"""
return {
InterfaceKind.InterfaceKindChoices.STRING,
InterfaceKind.InterfaceKindChoices.INTEGER,
InterfaceKind.InterfaceKindChoices.FLOAT,
InterfaceKind.InterfaceKindChoices.BOOL,
InterfaceKind.InterfaceKindChoices.TWO_D_BOUNDING_BOX,
InterfaceKind.InterfaceKindChoices.MULTIPLE_TWO_D_BOUNDING_BOXES,
InterfaceKind.InterfaceKindChoices.DISTANCE_MEASUREMENT,
InterfaceKind.InterfaceKindChoices.MULTIPLE_DISTANCE_MEASUREMENTS,
InterfaceKind.InterfaceKindChoices.POINT,
InterfaceKind.InterfaceKindChoices.MULTIPLE_POINTS,
InterfaceKind.InterfaceKindChoices.POLYGON,
InterfaceKind.InterfaceKindChoices.MULTIPLE_POLYGONS,
InterfaceKind.InterfaceKindChoices.CHOICE,
InterfaceKind.InterfaceKindChoices.MULTIPLE_CHOICE,
InterfaceKind.InterfaceKindChoices.ANY,
InterfaceKind.InterfaceKindChoices.CHART,
InterfaceKind.InterfaceKindChoices.LINE,
InterfaceKind.InterfaceKindChoices.MULTIPLE_LINES,
InterfaceKind.InterfaceKindChoices.ANGLE,
InterfaceKind.InterfaceKindChoices.MULTIPLE_ANGLES,
InterfaceKind.InterfaceKindChoices.ELLIPSE,
InterfaceKind.InterfaceKindChoices.MULTIPLE_ELLIPSES,
}
[docs] @staticmethod
def interface_type_image():
"""Interface kinds that are images:
* Image
* Heat Map
* Segmentation
"""
return {
InterfaceKind.InterfaceKindChoices.IMAGE,
InterfaceKind.InterfaceKindChoices.HEAT_MAP,
InterfaceKind.InterfaceKindChoices.SEGMENTATION,
}
[docs] @staticmethod
def interface_type_file():
"""Interface kinds that are files:
* CSV file
* ZIP file
* PDF file
* SQREG file
* Thumbnail JPG
* Thumbnail PNG
* OBJ file
* MP4 file
"""
return {
InterfaceKind.InterfaceKindChoices.CSV,
InterfaceKind.InterfaceKindChoices.ZIP,
InterfaceKind.InterfaceKindChoices.PDF,
InterfaceKind.InterfaceKindChoices.SQREG,
InterfaceKind.InterfaceKindChoices.THUMBNAIL_JPG,
InterfaceKind.InterfaceKindChoices.THUMBNAIL_PNG,
InterfaceKind.InterfaceKindChoices.OBJ,
InterfaceKind.InterfaceKindChoices.MP4,
}
class OverlaySegmentsMixin(models.Model):
overlay_segments = models.JSONField(
blank=True,
default=list,
help_text=(
"The schema that defines how categories of values in the overlay "
"images are differentiated."
),
validators=[JSONValidator(schema=OVERLAY_SEGMENTS_SCHEMA)],
)
look_up_table = models.ForeignKey(
to=LookUpTable,
blank=True,
null=True,
on_delete=models.SET_NULL,
help_text="The look-up table that is applied when an overlay image is first shown",
)
@property
def voxel_values(self):
allowed_values = {x["voxel_value"] for x in self.overlay_segments}
# An implicit background value of 0 is always allowed, this saves the
# user having to declare it and the annotator mark it
allowed_values.add(0)
return allowed_values
def _validate_voxel_values(self, image):
if not self.overlay_segments:
return
if image.segments is None:
raise ValidationError(
"Image segments could not be determined, ensure the file is "
"not a tiff file, its voxel values are integers and that it "
f"contains no more than {MAXIMUM_SEGMENTS_LENGTH} segments."
)
invalid_values = set(image.segments) - self.voxel_values
if invalid_values:
raise ValidationError(
f"The valid voxel values for this segmentation are: "
f"{self.voxel_values}. This segmentation is invalid as "
f"it contains the voxel values: {invalid_values}."
)
class Meta:
abstract = True
[docs]class ComponentInterface(OverlaySegmentsMixin):
Kind = InterfaceKind.InterfaceKindChoices
title = models.CharField(
max_length=255,
help_text="Human readable name of this input/output field.",
unique=True,
)
slug = AutoSlugField(populate_from="title")
description = models.TextField(
blank=True, help_text="Description of this input/output field."
)
default_value = models.JSONField(
blank=True,
null=True,
default=None,
help_text="Default value for this field, only valid for inputs.",
)
schema = models.JSONField(
default=dict,
blank=True,
help_text=(
"Additional JSON schema that the values for this interface must "
"satisfy. See https://json-schema.org/. "
"Only Draft 7, 6, 4 or 3 are supported."
),
validators=[JSONSchemaValidator()],
)
kind = models.CharField(
blank=False,
max_length=5,
choices=Kind.choices,
help_text=(
"What is the type of this interface? Used to validate interface "
"values and connections between components."
),
)
relative_path = models.CharField(
max_length=255,
help_text=(
"The path to the entity that implements this interface relative "
"to the input or output directory."
),
unique=True,
validators=[
validate_safe_path,
validate_no_slash_at_ends,
# No uuids in path
RegexValidator(
regex=r".*[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}.*",
inverse_match=True,
flags=re.IGNORECASE,
),
],
)
store_in_database = models.BooleanField(
default=True,
editable=True,
help_text=(
"Should the value be saved in a database field, "
"only valid for outputs."
),
)
[docs] def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._overlay_segments_orig = self.overlay_segments
def __str__(self):
return f"{self.title} ({self.get_kind_display()})"
@property
def is_image_kind(self):
return self.kind in InterfaceKind.interface_type_image()
@property
def is_json_kind(self):
return self.kind in InterfaceKind.interface_type_json()
@property
def is_file_kind(self):
return self.kind in InterfaceKind.interface_type_file()
@property
def super_kind(self):
if self.saved_in_object_store:
if self.is_image_kind:
return InterfaceSuperKindChoices.IMAGE
else:
return InterfaceSuperKindChoices.FILE
else:
return InterfaceSuperKindChoices.VALUE
@property
def saved_in_object_store(self):
# files and images should always be saved to S3, others are optional
return (
self.is_image_kind
or self.is_file_kind
or not self.store_in_database
)
@property
def requires_file(self):
return (
self.is_file_kind
or self.is_json_kind
and not self.store_in_database
)
@property
def default_field(self):
if self.requires_file:
return ModelChoiceField
elif self.is_image_kind:
return FlexibleImageField
elif self.kind in {
InterfaceKind.InterfaceKindChoices.STRING,
InterfaceKind.InterfaceKindChoices.CHOICE,
}:
return forms.CharField
elif self.kind == InterfaceKind.InterfaceKindChoices.INTEGER:
return forms.IntegerField
elif self.kind == InterfaceKind.InterfaceKindChoices.FLOAT:
return forms.FloatField
elif self.kind == InterfaceKind.InterfaceKindChoices.BOOL:
return forms.BooleanField
else:
return forms.JSONField
@property
def file_mimetypes(self):
if self.kind == InterfaceKind.InterfaceKindChoices.CSV:
return (
"application/csv",
"application/vnd.ms-excel",
"text/csv",
"text/plain",
)
elif self.kind == InterfaceKind.InterfaceKindChoices.ZIP:
return ("application/zip", "application/x-zip-compressed")
elif self.kind == InterfaceKind.InterfaceKindChoices.PDF:
return ("application/pdf",)
elif self.kind == InterfaceKind.InterfaceKindChoices.THUMBNAIL_JPG:
return ("image/jpeg",)
elif self.kind == InterfaceKind.InterfaceKindChoices.THUMBNAIL_PNG:
return ("image/png",)
elif self.kind == InterfaceKind.InterfaceKindChoices.SQREG:
return (
"application/octet-stream",
"application/x-sqlite3",
"application/vnd.sqlite3",
)
elif self.kind == InterfaceKind.InterfaceKindChoices.OBJ:
return ("text/plain", "application/octet-stream")
elif self.kind in InterfaceKind.interface_type_json():
return (
"text/plain",
"application/json",
)
elif self.kind == InterfaceKind.InterfaceKindChoices.MP4:
return ("video/mp4",)
else:
raise RuntimeError(f"Unknown kind {self.kind}")
def create_instance(self, *, image=None, value=None, fileobj=None):
civ = ComponentInterfaceValue.objects.create(interface=self)
if image:
civ.image = image
elif fileobj:
container = File(fileobj)
civ.file.save(Path(self.relative_path).name, container)
elif self.saved_in_object_store:
civ.file = ContentFile(
json.dumps(value).encode("utf-8"),
name=Path(self.relative_path).name,
)
else:
civ.value = value
civ.full_clean()
civ.save()
return civ
[docs] def clean(self):
super().clean()
self._clean_overlay_segments()
self._clean_store_in_database()
self._clean_relative_path()
def _clean_overlay_segments(self):
if (
self.kind == InterfaceKindChoices.SEGMENTATION
and not self.overlay_segments
):
raise ValidationError(
"Overlay segments must be set for this interface"
)
if (
self.kind != InterfaceKindChoices.SEGMENTATION
and self.overlay_segments
):
raise ValidationError(
"Overlay segments should only be set for segmentations"
)
Question = apps.get_model("reader_studies", "question") # noqa: N806
if (
self.pk is not None
and self._overlay_segments_orig != self.overlay_segments
and (
ComponentInterfaceValue.objects.filter(interface=self).exists()
or Question.objects.filter(interface=self).exists()
)
):
raise ValidationError(
"Overlay segments cannot be changed, as values or questions "
"for this ComponentInterface exist."
)
def _clean_relative_path(self):
if self.is_json_kind:
if not self.relative_path.endswith(".json"):
raise ValidationError("Relative path should end with .json")
elif self.is_file_kind and not self.relative_path.endswith(
f".{self.kind.lower()}"
):
raise ValidationError(
f"Relative path should end with .{self.kind.lower()}"
)
if self.is_image_kind:
if not self.relative_path.startswith("images/"):
raise ValidationError(
"Relative path should start with images/"
)
if Path(self.relative_path).name != Path(self.relative_path).stem:
# Maybe not in the future
raise ValidationError("Images should be a directory")
else:
if self.relative_path.startswith("images/"):
raise ValidationError(
"Relative path should not start with images/"
)
def _clean_store_in_database(self):
object_store_required = self.kind in {
*InterfaceKind.interface_type_image(),
*InterfaceKind.interface_type_file(),
# These values can be large, so for any new interfaces of this
# type always add them to the object store
InterfaceKind.InterfaceKindChoices.MULTIPLE_TWO_D_BOUNDING_BOXES,
InterfaceKind.InterfaceKindChoices.MULTIPLE_DISTANCE_MEASUREMENTS,
InterfaceKind.InterfaceKindChoices.MULTIPLE_POINTS,
InterfaceKind.InterfaceKindChoices.MULTIPLE_POLYGONS,
InterfaceKind.InterfaceKindChoices.MULTIPLE_LINES,
InterfaceKind.InterfaceKindChoices.MULTIPLE_ANGLES,
InterfaceKind.InterfaceKindChoices.MULTIPLE_ELLIPSES,
}
if object_store_required and self.store_in_database:
raise ValidationError(
f"Interface {self.kind} objects cannot be stored in the database"
)
[docs] def validate_against_schema(self, *, value):
"""Validates values against both default and custom schemas"""
JSONValidator(
schema={
**INTERFACE_VALUE_SCHEMA,
"anyOf": [{"$ref": f"#/definitions/{self.kind}"}],
}
)(value=value)
if self.schema:
JSONValidator(schema=self.schema)(value=value)
class Meta:
ordering = ("pk",)
def component_interface_value_path(instance, filename):
# Convert the pk to a hex, padded to 4 chars with zeros
pk_as_padded_hex = f"{instance.pk:04x}"
return (
f"{instance._meta.app_label.lower()}/"
f"{instance._meta.model_name.lower()}/"
f"{pk_as_padded_hex[-4:-2]}/{pk_as_padded_hex[-2:]}/{instance.pk}/"
f"{get_valid_filename(filename)}"
)
[docs]class ComponentInterfaceValue(models.Model):
"""Encapsulates the value of an interface at a certain point in the graph."""
id = models.BigAutoField(primary_key=True)
interface = models.ForeignKey(
to=ComponentInterface, on_delete=models.PROTECT
)
value = models.JSONField(null=True, blank=True, default=None)
file = models.FileField(
null=True,
blank=True,
upload_to=component_interface_value_path,
storage=protected_s3_storage,
validators=[
ExtensionValidator(
allowed_extensions=(
".json",
".zip",
".csv",
".png",
".jpg",
".jpeg",
".pdf",
".sqreg",
".obj",
".mp4",
)
),
MimeTypeValidator(
allowed_types=(
"application/json",
"application/zip",
"text/plain",
"application/csv",
"application/pdf",
"image/png",
"image/jpeg",
"application/octet-stream",
"application/x-sqlite3",
"application/vnd.sqlite3",
"video/mp4",
)
),
],
)
image = models.ForeignKey(
to=Image, null=True, blank=True, on_delete=models.PROTECT
)
_user_upload_validated = False
@property
def title(self):
if self.value is not None:
return str(self.value)
if self.file:
return Path(self.file.name).name
if self.image:
return self.image.name
return ""
@property
def has_value(self):
return self.value is not None or self.image or self.file
@property
def decompress(self):
"""
Should the CIV be decompressed?
This is only for legacy support of zip file submission for
prediction evaluation. We should not support this anywhere
else as it clobbers the input directory.
"""
return self.interface.kind == InterfaceKindChoices.ZIP
@cached_property
def image_file(self):
"""The single image file for this interface"""
return (
self.image.files.filter(
image_type__in=[
ImageFile.IMAGE_TYPE_MHD,
ImageFile.IMAGE_TYPE_TIFF,
]
)
.get()
.file
)
@property
def relative_path(self):
"""
Where should the file be located?
Images need special handling as their names are fixed.
"""
path = Path(self.interface.relative_path)
if self.image:
path /= Path(self.image_file.name).name
return path
def __str__(self):
if self.value is None:
return self.title
else:
return f"Component Interface Value {self.pk} for {self.interface}"
[docs] def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._value_orig = self.value
self._image_orig = self._dict["image"]
self._file_orig = self.file
@property
def _dict(self):
return model_to_dict(
self, fields=[field.name for field in self._meta.fields]
)
[docs] def save(self, *args, **kwargs):
if (
(
self._value_orig not in (None, self.interface.default_value)
and self.value is not None
and self._value_orig != self.value
)
or (self._image_orig and self._image_orig != self.image.pk)
or (
self._file_orig.name not in (None, "")
and self._file_orig != self.file
)
):
raise ValidationError(
"You cannot change the value, file or image of an existing CIV. "
"Please create a new CIV instead."
)
super().save(*args, **kwargs)
[docs] def clean(self):
super().clean()
attributes = [
attribute
for attribute in [self.value, self.image, self.file.name]
if attribute is not None
if attribute != ""
]
if len(attributes) > 1:
raise ValidationError(
"Only one of image, value and file can be defined."
)
if self.interface.is_image_kind:
self._validate_image_only()
if self.interface.kind == InterfaceKindChoices.SEGMENTATION:
self.interface._validate_voxel_values(self.image)
elif self.interface.is_file_kind:
self._validate_file_only()
else:
self._validate_value()
def _validate_image_only(self):
if not self.image:
raise ValidationError("Image must be set")
if self.file or self.value is not None:
raise ValidationError(
f"File ({self.file}) or value should not be set for images"
)
def _validate_file_only(self):
if not self._user_upload_validated and not self.file:
raise ValidationError("File must be set")
if self.image or self.value is not None:
raise ValidationError(
f"Image ({self.image}) or value must not be set for files"
)
def _validate_value_only(self):
# Do not check self.value here, it can be anything including None.
# This is checked later with interface.validate_against_schema.
if self.image or self.file:
raise ValidationError(
f"Image ({self.image}) or file ({self.file}) must not be set for values"
)
def _validate_value(self):
if self._user_upload_validated:
return
if self.interface.saved_in_object_store:
self._validate_file_only()
with self.file.open("r") as f:
try:
value = json.loads(f.read().decode("utf-8"))
except JSONDecodeError as e:
raise ValidationError(e)
else:
self._validate_value_only()
value = self.value
self.interface.validate_against_schema(value=value)
def validate_user_upload(self, user_upload):
if not user_upload.is_completed:
raise ValidationError("User upload is not completed.")
if self.interface.is_json_kind:
try:
value = json.loads(user_upload.read_object())
except JSONDecodeError as e:
raise ValidationError(e)
self.interface.validate_against_schema(value=value)
self._user_upload_validated = True
class Meta:
ordering = ("pk",)
[docs]class ComponentJobManager(models.QuerySet):
[docs] def with_duration(self):
"""Annotate the queryset with the duration of completed jobs"""
return self.annotate(duration=F("completed_at") - F("started_at"))
[docs] def average_duration(self):
"""Calculate the average duration that completed jobs ran for"""
return (
self.with_duration()
.exclude(duration=None)
.aggregate(Avg("duration"))["duration__avg"]
)
def total_duration(self):
return (
self.with_duration()
.exclude(duration=None)
.aggregate(Sum("duration"))["duration__sum"]
)
def active(self):
return self.exclude(
status__in=[
ComponentJob.SUCCESS,
ComponentJob.CANCELLED,
ComponentJob.FAILURE,
]
)
class ComponentJob(models.Model):
# The job statuses come directly from celery.result.AsyncResult.status:
# http://docs.celeryproject.org/en/latest/reference/celery.result.html
PENDING = 0
STARTED = 1
RETRY = 2
FAILURE = 3
SUCCESS = 4
CANCELLED = 5
PROVISIONING = 6
PROVISIONED = 7
EXECUTING = 8
EXECUTED = 9
PARSING = 10
EXECUTING_PREREQUISITES = 11
STATUS_CHOICES = (
(PENDING, "Queued"),
(STARTED, "Started"),
(RETRY, "Re-Queued"),
(FAILURE, "Failed"),
(SUCCESS, "Succeeded"),
(CANCELLED, "Cancelled"),
(PROVISIONING, "Provisioning"),
(PROVISIONED, "Provisioned"),
(EXECUTING, "Executing"),
(EXECUTED, "Executed"),
(PARSING, "Parsing Outputs"),
(EXECUTING_PREREQUISITES, "Executing Algorithm"),
)
status = models.PositiveSmallIntegerField(
choices=STATUS_CHOICES, default=PENDING, db_index=True
)
attempt = models.PositiveSmallIntegerField(editable=False, default=0)
stdout = models.TextField()
stderr = models.TextField(default="")
runtime_metrics = models.JSONField(default=dict, editable=False)
error_message = models.CharField(max_length=1024, default="")
started_at = models.DateTimeField(null=True)
completed_at = models.DateTimeField(null=True)
input_prefixes = models.JSONField(
default=dict,
editable=False,
help_text=(
"Map of the ComponentInterfaceValue id to the path prefix to use "
"for this input, e.g. {'1': 'foo/bar/'} will place CIV 1 at "
"/input/foo/bar/<relative_path>"
),
)
task_on_success = models.JSONField(
default=None,
null=True,
editable=False,
help_text="Serialized task that is run on job success",
)
task_on_failure = models.JSONField(
default=None,
null=True,
editable=False,
help_text="Serialized task that is run on job failure",
)
time_limit = models.PositiveSmallIntegerField(
default=60 * 60,
help_text="Time limit for the job in seconds",
validators=[
MinValueValidator(limit_value=60),
MaxValueValidator(limit_value=60 * 60),
],
)
inputs = models.ManyToManyField(
to=ComponentInterfaceValue,
related_name="%(app_label)s_%(class)ss_as_input",
)
outputs = models.ManyToManyField(
to=ComponentInterfaceValue,
related_name="%(app_label)s_%(class)ss_as_output",
)
objects = ComponentJobManager.as_manager()
def update_status(
self,
*,
status: STATUS_CHOICES,
stdout: str = "",
stderr: str = "",
error_message="",
duration: timedelta | None = None,
runtime_metrics=None,
):
self.status = status
if stdout:
self.stdout = stdout
if stderr:
self.stderr = stderr
if error_message:
self.error_message = error_message[:1024]
if (
status in [self.STARTED, self.EXECUTING]
and self.started_at is None
):
self.started_at = now()
elif (
status
in [self.EXECUTED, self.SUCCESS, self.FAILURE, self.CANCELLED]
and self.completed_at is None
):
self.completed_at = now()
if duration and self.started_at:
# TODO: maybe add separate timings for provisioning, executing, parsing and total
self.started_at = self.completed_at - duration
if runtime_metrics is not None:
self.runtime_metrics = runtime_metrics
self.save()
if self.status == self.SUCCESS:
on_commit(self.execute_task_on_success)
elif self.status in [self.FAILURE, self.CANCELLED]:
on_commit(self.execute_task_on_failure)
@property
def executor_kwargs(self):
return {
"job_id": f"{self._meta.app_label}-{self._meta.model_name}-{self.pk}-{self.attempt:02}",
"exec_image_repo_tag": self.container.shimmed_repo_tag,
"memory_limit": self.container.requires_memory_gb,
"time_limit": self.time_limit,
"requires_gpu": self.container.requires_gpu,
}
def get_executor(self, *, backend):
Executor = import_string(backend) # noqa: N806
return Executor(**self.executor_kwargs)
@property
def container(self) -> "ComponentImage":
"""
Returns the container object associated with this instance, which
should be a foreign key to an object that is a subclass of
ComponentImage
"""
raise NotImplementedError
@property
def output_interfaces(self) -> QuerySet:
"""Returns an unevaluated QuerySet for the output interfaces"""
raise NotImplementedError
@property
def signature_kwargs(self):
return {
"kwargs": {
"job_pk": str(self.pk),
"job_app_label": self._meta.app_label,
"job_model_name": self._meta.model_name,
"backend": settings.COMPONENTS_DEFAULT_BACKEND,
},
"immutable": True,
}
def execute(self):
return provision_job.signature(**self.signature_kwargs).apply_async()
def execute_task_on_success(self):
deprovision_job.signature(**self.signature_kwargs).apply_async()
if self.task_on_success:
signature(self.task_on_success).apply_async()
def execute_task_on_failure(self):
deprovision_job.signature(**self.signature_kwargs).apply_async()
if self.task_on_failure:
signature(self.task_on_failure).apply_async()
@property
def animate(self):
return self.status in {
self.STARTED,
self.PROVISIONING,
self.PROVISIONED,
self.EXECUTING,
self.EXECUTED,
self.PARSING,
self.EXECUTING_PREREQUISITES,
}
@property
def status_context(self):
if self.status == self.SUCCESS:
if self.stderr:
return "warning"
else:
return "success"
elif self.status in {self.FAILURE, self.CANCELLED}:
return "danger"
elif self.status in {
self.PENDING,
self.STARTED,
self.RETRY,
self.PROVISIONING,
self.PROVISIONED,
self.EXECUTING,
self.EXECUTED,
self.PARSING,
self.EXECUTING_PREREQUISITES,
}:
return "info"
else:
return "secondary"
@property
def runtime_metrics_chart(self):
instance_metrics = self.runtime_metrics["instance"]
cpu_limit = 100 * instance_metrics["cpu"]
if instance_metrics["gpus"]:
gpu_str = (
f"{instance_metrics['gpus']}x {instance_metrics['gpu_type']}"
)
else:
gpu_str = "No"
title = f"{instance_metrics['name']} / {instance_metrics['cpu']} CPU / {instance_metrics['memory']} GB Memory / {gpu_str} GPU"
return components_line(
values=[
{
"Metric": metric["label"],
"Timestamp": timestamp,
"Percent": value / 100.0,
}
for metric in self.runtime_metrics["metrics"]
for timestamp, value in zip(
metric["timestamps"], metric["values"], strict=True
)
],
title=title,
cpu_limit=cpu_limit,
tooltip=[
{
"field": metric["label"],
"type": "quantitative",
"format": ".2%",
}
for metric in self.runtime_metrics["metrics"]
],
)
class Meta:
abstract = True
def docker_image_path(instance, filename):
return (
f"docker/"
f"images/"
f"{instance._meta.app_label.lower()}/"
f"{instance._meta.model_name.lower()}/"
f"{instance.pk}/"
f"{get_valid_filename(filename)}"
)
[docs]class ImportStatusChoices(IntegerChoices):
INITIALIZED = 0, "Initialized"
QUEUED = 1, "Queued"
RETRY = 2, "Re-Queued"
STARTED = 3, "Started"
CANCELLED = 4, "Cancelled"
FAILED = 5, "Failed"
COMPLETED = 6, "Completed"
class ComponentImageManager(models.Manager):
def executable_images(self):
queryset = self.filter(is_manifest_valid=True, is_in_registry=True)
if (
self.model.SHIM_IMAGE
and settings.COMPONENTS_CREATE_SAGEMAKER_MODEL
):
# SageMaker models are only created for shimmed images
# See validate_docker_image
return queryset.filter(is_on_sagemaker=True)
else:
return queryset
class ComponentImage(models.Model):
SHIM_IMAGE = True
ImportStatusChoices = ImportStatusChoices
objects = ComponentImageManager()
creator = models.ForeignKey(
settings.AUTH_USER_MODEL, null=True, on_delete=models.SET_NULL
)
user_upload = models.ForeignKey(
UserUpload, blank=True, null=True, on_delete=models.SET_NULL
)
image = models.FileField(
blank=True,
upload_to=docker_image_path,
validators=[
ExtensionValidator(
allowed_extensions=(".tar", ".tar.gz", ".tar.xz")
)
],
help_text=(
".tar.xz archive of the container image produced from the command "
"'docker save IMAGE | xz -T0 -c > IMAGE.tar.xz'. See "
"https://docs.docker.com/engine/reference/commandline/save/"
),
storage=private_s3_storage,
)
image_sha256 = models.CharField(editable=False, max_length=71)
latest_shimmed_version = models.CharField(
editable=False, max_length=8, default=""
)
ready = deprecate_field(
models.BooleanField(
default=False,
editable=False,
help_text="Is this image ready to be used?",
)
)
import_status = models.PositiveSmallIntegerField(
choices=ImportStatusChoices.choices,
default=ImportStatusChoices.INITIALIZED,
db_index=True,
)
is_manifest_valid = models.BooleanField(
default=None,
null=True,
editable=False,
help_text="Is this image's manifest valid?",
)
is_in_registry = models.BooleanField(
default=False,
editable=False,
help_text="Is this image in the container registry?",
)
is_on_sagemaker = models.BooleanField(
default=False,
editable=False,
help_text="Does a SageMaker model for this image exist?",
)
status = models.TextField(editable=False)
requires_gpu = models.BooleanField(default=False)
requires_memory_gb = models.PositiveIntegerField(default=4)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._image_orig = self.image
@cached_property
def can_execute(self):
return (
self.__class__.objects.executable_images()
.filter(pk=self.pk)
.exists()
)
def save(self, *args, **kwargs):
image_needs_validation = (
self.import_status == ImportStatusChoices.INITIALIZED
and self.is_manifest_valid is None
)
validate_image_now = False
if self._image_orig:
if self.image != self._image_orig:
raise RuntimeError("The image cannot be changed")
if image_needs_validation:
self.import_status = ImportStatusChoices.QUEUED
validate_image_now = True
elif self.image and image_needs_validation:
self.import_status = ImportStatusChoices.QUEUED
validate_image_now = True
super().save(*args, **kwargs)
if validate_image_now:
on_commit(
validate_docker_image.signature(
kwargs={
"app_label": self._meta.app_label,
"model_name": self._meta.model_name,
"pk": self.pk,
}
).apply_async
)
def assign_docker_image_from_upload(self):
on_commit(
assign_docker_image_from_upload.signature(
kwargs={
"app_label": self._meta.app_label,
"model_name": self._meta.model_name,
"pk": self.pk,
}
).apply_async
)
@property
def original_repo_tag(self):
"""The tag of this image in the container repository"""
return (
f"{settings.COMPONENTS_REGISTRY_URL}/"
f"{settings.COMPONENTS_REGISTRY_PREFIX}/"
f"{self._meta.app_label}/{self._meta.model_name}:{self.pk}"
)
@property
def shimmed_repo_tag(self):
return f"{self.original_repo_tag}-{self.latest_shimmed_version}"
class Meta:
abstract = True
@property
def animate(self):
return self.import_status == self.ImportStatusChoices.STARTED
@property
def import_status_context(self):
if self.import_status == self.ImportStatusChoices.COMPLETED:
return "success"
elif self.import_status in {
self.ImportStatusChoices.FAILED,
self.ImportStatusChoices.CANCELLED,
}:
return "danger"
elif self.import_status in {
self.ImportStatusChoices.INITIALIZED,
self.ImportStatusChoices.QUEUED,
self.ImportStatusChoices.RETRY,
self.ImportStatusChoices.STARTED,
}:
return "info"
else:
return "secondary"