From cfa1973f7e9e00da6f36a0b422af6be30332b9d7 Mon Sep 17 00:00:00 2001
From: CGDogan <126820728+CGDogan@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:25:13 +0100
Subject: [PATCH 1/5] Update routes.json

---
 config/routes.json | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/config/routes.json b/config/routes.json
index 8728200..4c0fcfa 100644
--- 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"]}
+    ]
   }
 ]

From b4f2eb441a4f343ad3bfba410da5a930a668fa5d Mon Sep 17 00:00:00 2001
From: CGDogan <126820728+CGDogan@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:28:45 +0100
Subject: [PATCH 2/5] yml files

---
 caMicroscope.yml | 20 ++++++++++++++++++++
 develop.yml      | 20 ++++++++++++++++++++
 2 files changed, 40 insertions(+)

diff --git a/caMicroscope.yml b/caMicroscope.yml
index bfee216..a7e197e 100644
--- a/caMicroscope.yml
+++ b/caMicroscope.yml
@@ -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"
+    container_name: ca-dicomsrv
+    restart: unless-stopped
+    stdin_open: true
+    tty: true
+    ports:
+      - "8042:8042"
+      - "11112:11112"
+    volumes:
+      - ./jwt_keys/:/root/keys/
+      - ./images/:/images/
+      - ./OrthancConfiguration.json:/root/src/Configuration.json
+    environment:
+      DICOM_PORT: "11112"
+      DICOM_UI_PORT: "8042"
+      CARACAL_BACK_HOST_PORT: "ca-back:4010"
diff --git a/develop.yml b/develop.yml
index e25fc62..ee20984 100644
--- a/develop.yml
+++ b/develop.yml
@@ -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/
+      - ./OrthancConfiguration.json:/root/src/Configuration.json
+    environment:
+      DICOM_PORT: "11112"
+      DICOM_UI_PORT: "8042"
+      CARACAL_BACK_HOST_PORT: "ca-back:4010"

From db35bce79b999b068fafcb9eac24d3d7654a17b8 Mon Sep 17 00:00:00 2001
From: CGDogan <126820728+CGDogan@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:45:28 +0100
Subject: [PATCH 3/5] Memory requirement for Orthanc

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 225986d..a2fdd34 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,8 @@ 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.
 

From c372e81e361580609d472928d6fd17468443271d Mon Sep 17 00:00:00 2001
From: CGDogan <126820728+CGDogan@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:46:47 +0100
Subject: [PATCH 4/5] Create OrthancConfiguration.json

---
 OrthancConfiguration.json | 64 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 OrthancConfiguration.json

diff --git a/OrthancConfiguration.json b/OrthancConfiguration.json
new file mode 100644
index 0000000..3a9d09b
--- /dev/null
+++ b/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
+}

From 9f4db2058abe55d37683bb30108a5f907ba160ec Mon Sep 17 00:00:00 2001
From: CGDogan <126820728+CGDogan@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:51:59 +0100
Subject: [PATCH 5/5] config json fits better in "config/"

---
 caMicroscope.yml                                              | 2 +-
 OrthancConfiguration.json => config/OrthancConfiguration.json | 0
 develop.yml                                                   | 2 +-
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename OrthancConfiguration.json => config/OrthancConfiguration.json (100%)

diff --git a/caMicroscope.yml b/caMicroscope.yml
index a7e197e..57868a9 100644
--- a/caMicroscope.yml
+++ b/caMicroscope.yml
@@ -73,7 +73,7 @@ services:
     volumes:
       - ./jwt_keys/:/root/keys/
       - ./images/:/images/
-      - ./OrthancConfiguration.json:/root/src/Configuration.json
+      - ./config/OrthancConfiguration.json:/root/src/Configuration.json
     environment:
       DICOM_PORT: "11112"
       DICOM_UI_PORT: "8042"
diff --git a/OrthancConfiguration.json b/config/OrthancConfiguration.json
similarity index 100%
rename from OrthancConfiguration.json
rename to config/OrthancConfiguration.json
diff --git a/develop.yml b/develop.yml
index ee20984..9ad7486 100644
--- a/develop.yml
+++ b/develop.yml
@@ -55,7 +55,7 @@ services:
     volumes:
       - ./jwt_keys/:/root/keys/
       - ./images/:/images/
-      - ./OrthancConfiguration.json:/root/src/Configuration.json
+      - ./config/OrthancConfiguration.json:/root/src/Configuration.json
     environment:
       DICOM_PORT: "11112"
       DICOM_UI_PORT: "8042"