For 3.11.0

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2019, caMicroscope
+Copyright (c) 2019-2023, caMicroscope
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -2,8 +2,6 @@
   <a href="http://camicroscope.org/"><img src="https://avatars2.githubusercontent.com/u/12075069?s=400&v=4" style="background-color:rgba(0,0,0,0);" height=230 alt="camicroscope: a web-based image viewer optimized for large bio-medical image data viewing"></a>
 </h2>
 
-[![Build Status](https://travis-ci.org/camicroscope/Distro.svg?branch=master)](https://travis-ci.org/camicroscope/Distro)
-
 # caMicroscope distribution
 
 
@@ -14,14 +12,14 @@ Use `docker-compose -f caMicroscope.yml build` to rebuild the services.
 
 Once everything is up, go to http://localhost:4010/ to see the landing page.
 
+6GB memory is recommended (in total, 2GB RAM + 4GB swap should work well)
+
 ## SSL
 To enable ssl, mount the private key and certificate files to the ca-back service in /root/src/ssl/privatekey.pem and /root/src/ssl/certificate.pem respectively. HTTPS mode will only be enabled if both of these files are present.
 
 ## Component Services
 mongo - vanilla mongo container
 
-idxMongo - ephemeral container to index mongo (that is, this container is *expected* to exit once it's done its job)
-
 iip - slide tile server (see https://github.com/camicroscope/iipImage)
 
 loader - extracts metadata needed for image loading (see https://github.com/camicroscope/SlideLoader)
@@ -65,10 +63,6 @@ Alternatively, you can use kc_caMicroscope.yml for a keycloak configuration.
     * Set a password under credentials -> add password
 
 
-### Adding Users to caMicroscope
-
-Add users as in ./config/add\_users.js. This can be done either by editing this file before bringing up the stack, or by running similar code against the camic database in ca-mongo. Attributes can be added to deny access to routes (e.g. allow only some users to post and delete) and userFilters can be used to change visibility of particular documents.
-
 The email field is the email field (or failing that, sub field) in that priority from the identity provider.
 
 ## PathDB
@@ -85,8 +79,8 @@ Running QuIP with PathDB (https://github.com/SBU-BMI/PathDB):
 
 The default login for pathdb is `admin` with password `bluecheese2018`. Please change this password before exposing this service to the internet.
 
-## Support
-Feel free to add any support inquiry as a github issue to this repository. Other feedback can be given via [this form](https://docs.google.com/forms/d/e/1FAIpQLScL91LxrpAZjU88GBZP9gmcdgdf8__uNUwhws2lzU6Lr4qNwA/viewform).
+## Support and Questions
+For questions, comments, or any other discussion, please see the [caMicroscope discussion forum](https://github.com/orgs/camicroscope/discussions).
 
 ## System Recommendations
 As of 3.8.0, the non-pathdb caMicroscope deployment seems to peak about 500mb of memory per user from basic tests. The system is most likely to work optimally if the CPU can support two or three threads per concurrent user. The containers themselves take up a total of about 6gb of disk, but note that whole slide images typically use 0.5-2 gb of disk each.

caMicroscope.yml

@@ -13,9 +13,9 @@ services:
       - ./db:/data/db
   back:
     build:
-      context: "https://github.com/camicroscope/caracal.git#v3.10.2"
+      context: "https://github.com/camicroscope/caracal.git#v3.11.0"
       args:
-        viewer: "v3.10.2"
+        viewer: "v3.11.0"
     depends_on:
       - "mongo"
     ports:
@@ -39,7 +39,7 @@ services:
       DISABLE_SEC: "true"
       GENERATE_KEY_IF_MISSING: "true"
   iip:
-    image: camicroscope/iipimage:version-3.10.2
+    image: camicroscope/iipimage:version-3.11.0
     container_name: ca-iip
     logging:
       options:
@@ -49,7 +49,7 @@ services:
     volumes:
       - ./images/:/images/
   loader:
-    build: "https://github.com/camicroscope/SlideLoader.git#v3.10.2"
+    build: "https://github.com/camicroscope/SlideLoader.git#v3.11.0"
     container_name: ca-load
     restart: always
     logging:
@@ -58,3 +58,23 @@ services:
           max-size: "10m"
     volumes:
       - ./images/:/images/
+    environment:
+      DICOM_PORT: "11112"
+      DICOM_UI_PORT: "8042"
+  dicomsrv:
+    build: "https://github.com/camicroscope/dicomsrv.git#v3.11.0"
+    container_name: ca-dicomsrv
+    restart: unless-stopped
+    stdin_open: true
+    tty: true
+    ports:
+      - "8042:8042"
+      - "11112:11112"
+    volumes:
+      - ./jwt_keys/:/root/keys/
+      - ./images/:/images/
+      - ./config/OrthancConfiguration.json:/root/src/Configuration.json
+    environment:
+      DICOM_PORT: "11112"
+      DICOM_UI_PORT: "8042"
+      CARACAL_BACK_HOST_PORT: "ca-back:4010"

config/OrthancConfiguration.json

@@ -0,0 +1,64 @@
+{
+  // https://hg.orthanc-server.com/orthanc/file/Orthanc-1.12.1/OrthancServer/Resources/Configuration.json
+  // Configuration.json supports importing ENV vars with ${YourEnvVarName}
+  // NOTE about file paths: /images/ and all paths in this file starting with /root
+  // are set correctly to match what caMicroscope Dockerfiles set up.
+  // Changing these might cause issues. Besides, Dockerfiles will copy
+  // OrthancConfiguration.json from caMicroscope/Distro as well so please don't rename this file.
+  "Plugins" : [
+    "/root/src/libOrthancIndexer.so"
+  ],
+  "Indexer" : {
+    "Enable" : true,
+    "Folders" : ["/images/"],
+    "Interval" : 10 // Delay between two synchronizations (seconds)
+  },
+  "StorageCompression" : false, // "true" is incompatible with caMicroscope
+  "Name" : "camic-orthanc",
+  "DicomAet" : "CAMIC-ORTHANC",
+  "StorageDirectory" : "/images/",
+  "IndexDirectory" : "/root/orthanc-index",
+  "HttpServerEnabled" : true, // Rest API and GUI
+  "OrthancExplorerEnabled" : true, // GUI
+  "HttpPort" : ${DICOM_UI_PORT}, // Rest API and GUI
+  "RestApiWriteToFileSystemEnabled" : true, // Rest API and GUI
+  "RemoteAccessAllowed" : true,
+  "AuthenticationEnabled" : false, // Basic HTTP auth for GUI as in http://httpbin.org/basic-auth/foo/bar
+  //"RegisteredUsers" : {
+    // "alice" : "alicePassword"
+  //},
+  "SslEnabled" : false, // HTTP server
+  "SslCertificate" : "/root/keys/keyandpub.pem", // both cert and private key
+  "HttpsVerifyPeers" : true, // Verify SSL of other orthanc servers
+
+  "MallocArenaMax" : 5, // Suggested by docs to regulate memory use
+  "DicomThreadsCount" : 3,
+
+  "DicomPort" : ${DICOM_PORT},
+
+  // NOTE: Due to a bug in Orthanc 1.12.1 and lower, to disable DICOM TLS,
+  // "DicomTlsEnabled" : false is not enough; please also comment out the line with
+  // DicomTlsPrivateKey
+  "DicomTlsEnabled" : false, // DICOM server
+  // For DICOM, unlike HTTP, cert (cer or cert or pub or pem) and pkey need to be provided as separate files.
+  // For example, the latter means that when the file is opened with a text editor,
+  // there's "BEGIN PRIVATE KEY" and "BEGIN CERTIFICATE" in the same file.
+  //"DicomTlsPrivateKey" : "/root/keys/key",
+  "DicomTlsCertificate" : "/root/keys/key.pub",
+  "DicomTlsRemoteCertificateRequired" : true, // Verify certificate of dicom peers
+
+  // AlwaysAllow: If false, only those listed under "DicomModalities" will be capable of these
+  "DicomAlwaysAllowStore" : true,
+  // The following ones allow retrieving data, which you might not want everyone to do
+  "DicomAlwaysAllowFind" : true,
+  "DicomAlwaysAllowFindWorklist" : true,
+  "DicomAlwaysAllowGet" : true,
+  "DicomAlwaysAllowMove" : true,
+
+  //"DicomModalities" : {
+    // AET, IP, port
+    // "sample" : ["MYSRV", "192.168.1.40", 1300]
+    // See the link at the beginning of the file for selectively giving permissions
+  //},
+  "DicomCheckModalityHost" : false // Check the IP as well or only check the modality
+}

config/routes.json

@@ -498,5 +498,17 @@
       {"function":"permissionHandler", "args": [["Admin", "Editor"]]},
       {"function":"sendTrainedModel", "args": []}
     ]
+  },{
+    "route":"/fs/addedFile",
+    "method":"get",
+    "handlers":[
+      {"function":"addedFileToFS", "args": ["camic", "slide", "http://ca-load:4000"]}
+    ]
+  },{
+    "route":"/fs/deletedFile",
+    "method":"get",
+    "handlers":[
+      {"function":"removedFileFromFS", "args": ["camic", "slide", "http://ca-load:4000"]}
+    ]
   }
 ]

develop.yml

@@ -29,7 +29,7 @@ services:
       DISABLE_SEC: "true"
       ALLOW_PUBLIC: "true"
   iip:
-    build: "https://github.com/camicroscope/iipimage.git#develop"
+    build: "https://github.com/camicroscope/iipImage.git#develop"
     container_name: ca-iip
     restart: unless-stopped
     volumes:
@@ -40,3 +40,23 @@ services:
     volumes:
       - ./images/:/images/
       - ./cloud-upload-apis/:/cloud-upload-apis/
+    environment:
+      DICOM_PORT: "11112"
+      DICOM_UI_PORT: "8042"
+  dicomsrv:
+    build: "https://github.com/camicroscope/dicomsrv.git"
+    container_name: ca-dicomsrv
+    restart: unless-stopped
+    stdin_open: true
+    tty: true
+    ports:
+      - "8042:8042"
+      - "11112:11112"
+    volumes:
+      - ./jwt_keys/:/root/keys/
+      - ./images/:/images/
+      - ./config/OrthancConfiguration.json:/root/src/Configuration.json
+    environment:
+      DICOM_PORT: "11112"
+      DICOM_UI_PORT: "8042"
+      CARACAL_BACK_HOST_PORT: "ca-back:4010"

quip-pathdb.yml

@@ -8,16 +8,16 @@ services:
     volumes:
       - ./db:/data/db
   iip:
-    image: camicroscope/iipimage:version-3.10.2
+    image: camicroscope/iipimage:version-3.11.0
     container_name: ca-iip
     restart: unless-stopped
     volumes:
       - ./images/:/data/images/
   back:
     build:
-      context: "https://github.com/camicroscope/caracal.git#v3.10.2"
+      context: "https://github.com/camicroscope/caracal.git#v3.11.0"
       args:
-        viewer: "v3.10.1"
+        viewer: "v3.11.0"
     depends_on:
       - "mongo"
     ports:
@@ -37,7 +37,7 @@ services:
     build:
       context: "https://github.com/SBU-BMI/PathDB.git#2.0.0"
       args:
-        viewer: "v3.10.2"
+        viewer: "v3.11.0"
     container_name: quip-pathdb
     restart: unless-stopped
     ports: ["443:443","80:80"]