for 3.11.0

SBU-BMI · Nov 17, 2023 · 13acb5c · 13acb5c
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diff --git a/LICENSE b/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

diff --git a/README.md b/README.md
@@ -69,8 +69,8 @@ Please see README at https://github.com/SBU-BMI/SegmentationLoader for user inst
 results to QuIP.
 
 
-## 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).
 
 ## PathDB
 

diff --git a/caMicroscope.yml b/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"
diff --git a/config/OrthancConfiguration.json b/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
+}
diff --git a/config/routes.json b/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"]}
+    ]
   }
 ]
diff --git a/develop.yml b/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"
diff --git a/quip-pathdb.yml b/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"]