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idx_mongo.js
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// Create indexes and essential defaults for mongo
// replace this file before startup (e.g. container mount) to change how this runs
const mongodb = require("./service/database");
function indexes() {
db = "camic";
mongodb.createIndex(db, "authorization", {"name": 1}, {unique: true});
mongodb.createIndex(db, "user", {"email": 1}, {unique: true});
mongodb.createIndex(db, "mark", {"provenance.image.slide": 1,
"provenance.analysis.execution_id": 1, "footprint": 1, "x": 1, "y": 1});
mongodb.createIndex(db, "mark", {"provenance.image.slide": 1,
"provenance.analysis.execution_id": 1, "provenance.analysis": 1});
mongodb.createIndex(db, "mark", {"provenance.image.slide": 1, "provenance.analysis": 1});
mongodb.createIndex(db, "mark", {"provenance.image.slide": 1, "provenance.analysis.execution_id": 1});
mongodb.createIndex(db, "mark", {"provenance.image.slide": 1, "provenance.analysis.source": 1});
mongodb.createIndex(db, "mark", {"provenance.image.slide": 1});
mongodb.createIndex(db, "mark", {"provenance.analysis.labelId": 1});
mongodb.createIndex(db, "slide", {'study': 1, 'specimen': 1, 'name': 1});
mongodb.createIndex(db, "template", {'id': 1});
mongodb.createIndex(db, "template", {'name': 1});
mongodb.createIndex(db, "heatmap", {"provenance.image.slide": 1, "provenance.analysis.execution_id": 1});
mongodb.createIndex(db, "heatmap", {"provenance.image.slide": 1});
mongodb.createIndex(db, "heatmapEdit", {"provenance.image.slide": 1,
"provenance.analysis.execution_id": 1, "user_id": 1});
mongodb.createIndex(db, "configuration", {'config_name': 1}, {unique: true});
}
function collections() {
db = "camic";
mongodb.createCollection(db, "slide", {
validator: {
$jsonSchema: {
bsonType: 'object',
required: ['name', 'location'],
properties: {
name: {
bsonType: 'string',
description: 'Slide display name',
},
location: {
bsonType: 'string',
description: 'Slide location, used for opening',
},
},
},
},
}, true);
mongodb.createCollection(db, "mark", {
validator: {
$jsonSchema: {
bsonType: 'object',
required: ['provenance'],
properties: {
provenance: {
bsonType: 'object',
required: ['image', 'analysis'],
properties: {
image: {
bsonType: 'object',
required: ['slide'],
},
analysis: {
bsonType: 'object',
required: ['execution_id'],
},
},
},
},
},
},
}, true);
mongodb.createCollection(db, "heatmap", {
validator: {
$jsonSchema: {
bsonType: 'object',
required: ['provenance'],
properties: {
provenance: {
bsonType: 'object',
required: ['image', 'analysis'],
properties: {
image: {
bsonType: 'object',
required: ['slide'],
},
analysis: {
bsonType: 'object',
required: ['execution_id'],
},
},
},
},
},
},
}, true);
mongodb.createCollection(db, "heatmapedit", {
validator: {
$jsonSchema: {
bsonType: 'object',
required: ['user_id', 'provenance'],
properties: {
provenance: {
bsonType: 'object',
required: ['image', 'analysis'],
properties: {
image: {
bsonType: 'object',
required: ['slide'],
},
analysis: {
bsonType: 'object',
required: ['fields', 'execution_id'],
},
},
},
},
},
},
}, true);
mongodb.createCollection(db, "template", {
validator: {
$jsonSchema: {
bsonType: 'object',
required: ['id', 'name', 'properties'],
properties: {
id: {
bsonType: 'string',
description: 'template identifier',
},
name: {
bsonType: 'string',
description: 'template display name',
},
properties: {
bsonType: 'object',
description: 'pure-form questions object',
additionalProperties: {
bsonType: 'object',
required: ['title', 'type'],
},
},
},
},
},
}, true);
}
function defaults() {
db = "camic";
let defaultTemplate = {
"_id": "0",
"type": "object",
"id": "annotation-form",
"name": "AnnotSchema",
"description": "",
"links": [],
"additionalProperties": false,
"properties": {
"name": {
"id": "a0",
"title": "Identity Name",
"type": "string",
"required": true,
"description": "note name",
}, "notes": {
"id": "a1",
"title": "Notes: ",
"type": "string",
"format": "textarea",
"maxLength": 128,
},
},
};
mongodb.add(db, 'template', defaultTemplate, true);
var defaultConfigs = [{
"configuration": [
{
"id": "001",
"color": "#ff6296",
"mode": "grid",
"type": "Lymph-Positive",
"size": 100,
},
{
"id": "002",
"color": "#ff6296",
"mode": "point",
"type": "Lymph-Positive",
},
{
"id": "003",
"color": "#62ffcb",
"mode": "grid",
"type": "Lymph-Negative",
"size": 100,
},
{
"id": "004",
"color": "#62ffcb",
"mode": "point",
"type": "Lymph-Negative",
},
{
"id": "005",
"color": "#ffcb62",
"mode": "grid",
"type": "Neutrophil-Positive",
"size": 50,
},
{
"color": "#6296ff",
"mode": "grid",
"type": "Neutrophil-Negative",
"size": 50,
"id": "006",
},
{
"color": "#ff00d9",
"mode": "grid",
"type": "Necrosis-Positive",
"size": 100,
"id": "007",
},
{
"color": "#ff00d9",
"mode": "grid",
"type": "Necrosis-Positive",
"size": 500,
"id": "008",
},
{
"color": "#00ff26",
"mode": "grid",
"type": "Necrosis-Negative",
"size": 100,
"id": "009",
},
{
"color": "#00ff26",
"mode": "grid",
"type": "Necrosis-Negative",
"size": 500,
"id": "010",
},
{
"color": "#790cff",
"mode": "grid",
"type": "Tumor-Positive",
"size": 100,
"id": "011",
},
{
"color": "#790cff",
"mode": "grid",
"type": "Tumor-Positive",
"size": 300,
"id": "012",
},
{
"color": "#790cff",
"mode": "grid",
"type": "Tumor-Positive",
"size": 1000,
"id": "013",
},
{
"color": "#790cff",
"mode": "grid",
"type": "Tumor-Positive",
"size": 2000,
"id": "014",
},
{
"color": "#92ff0c",
"mode": "grid",
"type": "Tumor-Negative",
"size": 100,
"id": "015",
},
{
"color": "#92ff0c",
"mode": "grid",
"type": "Tumor-Negative",
"size": 300,
"id": "016",
},
{
"color": "#92ff0c",
"mode": "grid",
"type": "Tumor-Negative",
"size": 1000,
"id": "017",
},
{
"color": "#92ff0c",
"mode": "grid",
"type": "Tumor-Negative",
"size": 2000,
"id": "018",
}, {
"color": "#8dd3c7",
"mode": "free",
"type": "Prostate-Benign",
"id": "019",
}, {
"color": "#ffffb3",
"mode": "free",
"type": "Prostate-Gleason3",
"id": "020",
}, {
"color": "#bebada",
"mode": "free",
"type": "Prostate-Gleason4",
"id": "021",
}, {
"color": "#fb8072",
"mode": "free",
"type": "Prostate-Gleason5",
"id": "022",
}, {
"color": "#80b1d3",
"mode": "free",
"type": "Prostate-CancerNOS",
"id": "023",
}, {
"color": "#fdb462",
"mode": "free",
"type": "NSCLC-Benign",
"id": "024",
}, {
"color": "#b3de69",
"mode": "free",
"type": "NSCLC-SquamousCA",
"id": "025",
}, {
"color": "#fccde5",
"mode": "free",
"type": "NSCLC-AdenoCA(all)",
"id": "026",
}, {
"color": "#d9d9d9",
"mode": "free",
"type": "NSCLC-Acinar",
"id": "027",
}, {
"color": "#bc80bd",
"mode": "free",
"type": "NSCLC-Lapidic",
"id": "028",
}, {
"color": "#ccebc5",
"mode": "free",
"type": "NSCLC-Solid",
"id": "029",
}, {
"color": "#ffed6f",
"mode": "free",
"type": "NSCLC-Papillary",
"id": "030",
}, {
"color": "#6a3d9a",
"mode": "free",
"type": "NSCLC-Micropapillary",
"id": "031",
},
],
"config_name": "preset_label",
"version": "1.0.0",
}];
mongodb.add(db, 'configuration', defaultConfigs, true);
var defaultLinks = {
"configuration": [
{
"displayName": "Bug Report",
"url": "https://goo.gl/forms/mgyhx4ADH0UuEQJ53",
"icon": "bug_report",
"openInNewTab": true,
},
],
"config_name": "additional_links",
"version": "1.0.0",
};
mongodb.add(db, 'configuration', defaultLinks, true);
var evaluationForm = {
"config_name": "evaluation_form",
"enable": true,
"configuration": {
"schema": {
"type": "object",
"properties": {
"slide_quality": {
"type": "string",
"title": "Slide Quality",
"enum": ["satisfactory", "unsatisfactory"],
"default": "satisfactory",
"required": true,
},
"tumor_presence": {
"type": "string",
"title": "Tumor Presence",
"enum": ["presence", "absent"],
"default": "presence",
"required": true,
},
"informativeness": {
"type": "string",
"title": "Informativeness",
"enum": ["informative", "uninformative"],
"default": "informative",
"required": true,
},
"score": {
"minimum": 0,
"maximum": 100,
"default": 50,
},
"wrong_tumor_type": {
"type": "boolean",
"default": false,
},
"tumor_note": {
"type": "string",
"required": true,
},
},
"dependencies": {
"tumor_note": ["wrong_tumor_type"],
"score": ["informativeness"],
},
},
"options": {
"fields": {
"score": {
"type": "integer",
"label": "Score",
"slider": true,
"dependencies": {
"informativeness": "informative",
},
},
"wrong_tumor_type": {
"rightLabel": "Wrong Tumor Type",
"helper": "Check If Tumor Type Is Wrong",
"helpersPosition": "above",
},
"tumor_note": {
"type": "textarea",
"label": "Tumor Note",
"helper": "Please Enter the Correct Tumor Type",
"helpersPosition": "above",
"rows": 2,
"dependencies": {
"wrong_tumor_type": true,
},
},
},
},
},
"version": "1.0.0",
};
mongodb.add(db, 'configuration', evaluationForm, true);
}
module.exports = {
indexes: indexes,
collections: collections,
defaults: defaults,
};