Merge pull request #96 from RationAI/development

Improving annotation visuals setting, consistent swapping & bugfixing.

.dockerignore

@@ -0,0 +1,17 @@
+*
+!*.html
+!*.js
+!*.json
+!*.md
+!docs/assets
+!docs/*.js
+!src
+!server
+!plugins
+!modules
+!env
+!/tmp/openseadragon/build
+!docker/php/apache-dev.conf
+!docker/php/apache.conf
+!.htaccess
+!*php

CHANGELOG.md

@@ -4,12 +4,15 @@ The changelog file describes changes made since v2.0.0, which made significant c
 to the versions 1.x.x.
 
 ### Unreleased 2.1.0
-**Features:** new system for module/plugin building
+**Features:** new system for module/plugin building, improvements of annotation listing features,
+support for generic annotation visual style changes.
 
-**Maintenance:** removed outdated plugins
+**Maintenance:** removed outdated plugins.
+
+**Bugfixes:** plugins use also Cache API, annotation visuals updated also with history.
 
 ### 2.0.4
-**Features:** vertical magnification slider, allow 2x artificial zoom, annotation areas
+**Features:** vertical magnification slider, allow 2x artificial zoom, annotation areas.
 
 **Bugfixes:** OIDC module, magic wand annotation tool, stacktrace capture.
 

docker/node/Dockerfile

@@ -0,0 +1,52 @@
+##################
+# VIEWER: BUILD###
+##################
+FROM node:20 AS viewer-build
+WORKDIR /tmp
+RUN git clone https://github.com/RationAI/openseadragon.git \
+    && cd openseadragon \
+    && git reset --hard ea54427f42a076e1a7a33f8590e0de22e7a335f4 \
+    && npm i \
+    && cd ..
+
+#############################
+# VIEWER: PROD GIT       ####
+#############################
+# Viewer that creates php runtime but does not include code - it must be fetched by the container on startup.
+FROM node:20 AS viewer-git
+
+ENV LANG=en_US.UTF-8
+ENV LANGUAGE=en_US:en
+ENV LC_ALL=en_US.UTF-8
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update -y && apt-get install --no-install-recommends --fix-missing -y \
+        curl \
+        locales \
+        tzdata \
+        git \
+        ca-certificates \
+        vim \
+        nano \
+    && ln -fs /usr/share/zoneinfo/Europe/Prague /etc/localtime \
+    && dpkg-reconfigure --frontend noninteractive tzdata \
+    && apt clean \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /usr/app
+
+RUN rm -f /bin/sh && ln -s /bin/bash /bin/sh \
+    # User Id 1000 for kubernetes
+    && usermod --non-unique --uid 1000 node
+
+EXPOSE 9000
+USER node
+WORKDIR /app
+
+###############################
+# VIEWER: PROD STANDALONE  ####
+###############################
+# Viewer with all the necessities
+FROM viewer-git AS viewer-standalone
+COPY --chown=node:1000 . /app
+RUN cd /app && npm install

docker/node/docker-compose.yml

@@ -0,0 +1,49 @@
+services:
+  xopat-node:
+    build:
+      context: ../../
+      dockerfile: docker/node/Dockerfile
+      target: viewer-standalone
+    entrypoint: ["node", "index.js"]
+    ports:
+      - "9001:9000"
+    environment:
+      XOPAT_ENV: >-
+        {
+          "core": {
+            "gateway": "https://xopat.readthedocs.io",
+            "active_client": "localhost",
+            "client": {
+              "localhost": {
+                "domain": "http://localhost:9001",
+                "path": "/",
+                "image_group_server": "http://localhost:9002",
+                "image_group_protocol": "`$${path}/v3/batch/info?slides=$${data}`",
+                "image_group_preview": "`$${path}/v3/batch/thumbnail/max_size/250/250?slides=$${data}`",
+                "data_group_server": "http://localhost:9002",
+                "data_group_protocol": "`$${path}/v3/batch/info?slides=$${data.join(\",\")}`",
+                "headers": {},
+                "js_cookie_expire": 365,
+                "js_cookie_path": "/",
+                "js_cookie_same_site": "",
+                "js_cookie_secure": "",
+                "secureMode": false,
+              }
+            },
+            "setup": {
+              "locale": "en",
+              "customBlending": false,
+              "debugMode": false,
+              "webglDebugMode": false,
+            },
+            "openSeadragonPrefix": "https://cdn.jsdelivr.net/npm/openseadragon@4.1.1/build/openseadragon/",
+            "openSeadragon": "openseadragon.min.js"
+          },
+          "plugins": {
+          },
+          "modules": {
+            "empaia-wsi-tile-source": {
+              "permaLoad": true
+            }
+          }
+        }

docker/php/docker-compose-example.yml

@@ -0,0 +1,46 @@
+services:
+  xopat-php:
+    image: ghcr.io/rationai/xopat:dev2.0.4 
+    ports:
+      - "9001:8000"
+    environment:
+      XOPAT_ENV: >-
+        {
+          "core": {
+            "gateway": "https://xopat.readthedocs.io",
+            "active_client": "localhost",
+            "client": {
+              "localhost": {
+                "domain": "http://localhost:9001",
+                "path": "/",
+                "image_group_server": "http://localhost:9002",
+                "image_group_protocol": "`$${path}/v3/batch/info?slides=$${data}`",
+                "image_group_preview": "`$${path}/v3/batch/thumbnail/max_size/250/250?slides=$${data}`",
+                "data_group_server": "http://localhost:9002",
+                "data_group_protocol": "`$${path}/v3/batch/info?slides=$${data.join(\",\")}`",
+                "headers": {},
+                "js_cookie_expire": 365,
+                "js_cookie_path": "/",
+                "js_cookie_same_site": "",
+                "js_cookie_secure": "",
+                "secureMode": false,
+              }
+            },
+            "setup": {
+              "locale": "en",
+              "customBlending": false,
+              "debugMode": false,
+              "webglDebugMode": false,
+            },
+            "openSeadragonPrefix": "https://cdn.jsdelivr.net/npm/openseadragon@4.1.1/build/openseadragon/",
+            "openSeadragon": "openseadragon.min.js"
+          },
+          "plugins": {
+          },
+          "modules": {
+            "empaia-wsi-tile-source": {
+              "permaLoad": true
+            }
+          }
+        }
+    

docker/wsi-service/docker-compose.yml

@@ -0,0 +1,18 @@
+services:
+  wsi_service:
+      image: ghcr.io/rationai/wsi-service:test0.15
+      environment:
+      - WS_CORS_ALLOW_CREDENTIALS=False
+      - WS_CORS_ALLOW_ORIGINS=["*"]
+      - WS_DEBUG=False
+      - WS_DISABLE_OPENAPI=True
+      - WS_MAPPER_ADDRESS=http://localhost:8080/slides/storage?slide={slide_id}
+      - WS_LOCAL_MODE=wsi_service.simple_mapper:SimpleMapper
+      - WS_ENABLE_VIEWER_ROUTES=False
+      - WS_INACTIVE_HISTO_IMAGE_TIMEOUT_SECONDS=600
+      - WS_MAX_RETURNED_REGION_SIZE=25000000
+      volumes:
+      - /home/novby/Documents/RationAI/test_wsis:/data
+      ports:
+      - 9002:8080
+

docs/include.js

@@ -1,11 +1,13 @@
 /**
+ * TODO - Move to utils
+ * 
  * Generates list of source files for documentation out of the ENV configuration.
  * For now, static only.
  */
 
 
 'use strict';
-var fs =require("fs");
+var fs = require("fs");
 const { parse } = require('comment-json');
 const parseJsonFile = (file, ...args) => {
     try {

modules/annotations/EVENTS.md

@@ -2,7 +2,8 @@
 
 ##### factory-registered | e: `{factory: OSDAnnotations.AnnotationObjectFactory}`
 
-##### opacity-changed | ``{opacity: float}``
+##### visual-property-changed | ``{[name]: any}``
+Common visual property changed.
 
 ##### osd-interactivity-toggle
 
@@ -24,7 +25,7 @@ This event is fired when annotation is replaced, e.g. free-form-tool edit. Such
 in fact replace annotation with a new one. This event is called only once per update, 
 at the end.
 
-##### annotation-replace-helper | ``{previous: fabric.Object, next: fabric.Object}``
+##### annotation-replace-doppelganger | ``{previous: fabric.Object, next: fabric.Object}``
 This event is fired when annotations are replaced, but only temporarily (e.g. via free form tool).
 It can be called several times during one edit action.
 
@@ -43,6 +44,10 @@ This event is fired when user performs direct annotation editing.
 
 ##### preset-meta-add | ``{preset: OSDAnnotations.Preset, key: string}``
 
+##### annotation-preset-change | ``{object: fabric.Object, presetID: string}``
+
+##### history-select | ``{incrementId: number, originalEvent: MouseEvent}``
+
 ##### import | ``{options: object, clear: boolean, data: object}``
 
 ##### export-partial | ``{options: object, data: object}``