From a5f1848abe79c1d850de2f45710a26ccd6ae24b3 Mon Sep 17 00:00:00 2001 From: Birm Date: Thu, 11 Jan 2024 14:44:10 -0500 Subject: [PATCH 01/10] prepare for 3.11.1 viewer and back --- caMicroscope.yml | 4 ++-- kc_caMicroscope.yml | 28 ++++++++++++++++++++++++---- quip-pathdb.yml | 6 +++--- 3 files changed, 29 insertions(+), 9 deletions(-) diff --git a/caMicroscope.yml b/caMicroscope.yml index ac94225..4aaba59 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -13,9 +13,9 @@ services: - ./db:/data/db back: build: - context: "https://github.com/camicroscope/caracal.git#v3.11.0" + context: "https://github.com/camicroscope/caracal.git#v3.11.1" args: - viewer: "v3.11.0" + viewer: "v3.11.1" depends_on: - "mongo" ports: diff --git a/kc_caMicroscope.yml b/kc_caMicroscope.yml index 98715a1..1daa98b 100644 --- a/kc_caMicroscope.yml +++ b/kc_caMicroscope.yml @@ -51,9 +51,9 @@ services: - ./db:/data/db back: build: - context: "https://github.com/camicroscope/caracal.git#v3.10.0" + context: "https://github.com/camicroscope/caracal.git#v3.11.1" args: - viewer: "v3.10.1" + viewer: "v3.11.1" depends_on: - "mongo" ports: @@ -76,7 +76,7 @@ services: MONGO_URI: "mongodb://ca-mongo" 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: @@ -86,7 +86,7 @@ services: volumes: - ./images/:/images/ loader: - build: "https://github.com/camicroscope/SlideLoader.git#v3.10.0" + build: "https://github.com/camicroscope/SlideLoader.git#v3.11.0" container_name: ca-load restart: always logging: @@ -95,3 +95,23 @@ 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" \ No newline at end of file diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 46db5cf..6ca7673 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -15,9 +15,9 @@ services: - ./images/:/data/images/ back: build: - context: "https://github.com/camicroscope/caracal.git#v3.11.0" + context: "https://github.com/camicroscope/caracal.git#v3.11.1" args: - viewer: "v3.11.0" + viewer: "v3.11.1" depends_on: - "mongo" ports: @@ -37,7 +37,7 @@ services: build: context: "https://github.com/SBU-BMI/PathDB.git#2.0.0" args: - viewer: "v3.11.0" + viewer: "v3.11.1" container_name: quip-pathdb restart: unless-stopped ports: ["443:443","80:80"] From 68742b1e438f7edd87bb4bf5d228ce40dea03c88 Mon Sep 17 00:00:00 2001 From: Birm Date: Wed, 31 Jan 2024 11:33:21 -0500 Subject: [PATCH 02/10] update heatmaploader version --- quip-pathdb.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 6ca7673..61d5297 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -61,7 +61,7 @@ services: volumes: - ./data:/data heatmaploader: - build: "https://github.com/SBU-BMI/uploadHeatmaps.git#v1.5.4" + build: "https://github.com/SBU-BMI/uploadHeatmaps.git#v1.5.5" container_name: quip-hmloader volumes: - ./data:/mnt/data/ From 75e10550301b462df23b755a9d9652a1f6f0288d Mon Sep 17 00:00:00 2001 From: Birm Date: Wed, 31 Jan 2024 12:02:29 -0500 Subject: [PATCH 03/10] changes to let dicomsrv build --- caMicroscope.yml | 9 ++++++--- develop.yml | 3 ++- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/caMicroscope.yml b/caMicroscope.yml index 4aaba59..4e45e87 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -13,9 +13,9 @@ services: - ./db:/data/db back: build: - context: "https://github.com/camicroscope/caracal.git#v3.11.1" + context: "https://github.com/camicroscope/caracal.git#v3.11.0" args: - viewer: "v3.11.1" + viewer: "v3.11.0" depends_on: - "mongo" ports: @@ -62,7 +62,10 @@ services: DICOM_PORT: "11112" DICOM_UI_PORT: "8042" dicomsrv: - build: "https://github.com/camicroscope/dicomsrv.git#v3.11.0" + build: + context: "https://github.com/camicroscope/dicomsrv.git#v3.11.1" + args: + indexer: "v3.11.0" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true diff --git a/develop.yml b/develop.yml index 9ad7486..3df2694 100644 --- a/develop.yml +++ b/develop.yml @@ -44,7 +44,8 @@ services: DICOM_PORT: "11112" DICOM_UI_PORT: "8042" dicomsrv: - build: "https://github.com/camicroscope/dicomsrv.git" + build: + context: "https://github.com/camicroscope/dicomsrv.git" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true From 171a01994ef1b0bb13efda3dd2a137371e53073c Mon Sep 17 00:00:00 2001 From: Eslam Ashraf Date: Sat, 3 Feb 2024 03:12:55 +0200 Subject: [PATCH 04/10] Update in file develop.yml "https://github.com/camicroscope/dicomsrv.git" has main branch not master branch --- develop.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/develop.yml b/develop.yml index 3df2694..c33e26a 100644 --- a/develop.yml +++ b/develop.yml @@ -45,7 +45,7 @@ services: DICOM_UI_PORT: "8042" dicomsrv: build: - context: "https://github.com/camicroscope/dicomsrv.git" + context: "https://github.com/camicroscope/dicomsrv.git#main" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true From 06fcb01053846b1d6dc167799f292c677fe7e1c4 Mon Sep 17 00:00:00 2001 From: Birm Date: Sat, 9 Mar 2024 22:49:45 -0900 Subject: [PATCH 05/10] explicitly name main for dicomsrv --- develop.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/develop.yml b/develop.yml index 3df2694..9ad7486 100644 --- a/develop.yml +++ b/develop.yml @@ -44,8 +44,7 @@ services: DICOM_PORT: "11112" DICOM_UI_PORT: "8042" dicomsrv: - build: - context: "https://github.com/camicroscope/dicomsrv.git" + build: "https://github.com/camicroscope/dicomsrv.git" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true From 4e78ffed3c3bb20905daa677185643f404eb72e0 Mon Sep 17 00:00:00 2001 From: Birm Date: Wed, 24 Apr 2024 00:31:21 -0400 Subject: [PATCH 06/10] add csp for dicom, route fr count marks --- config/contentSecurityPolicy.json | 4 ++++ config/routes.json | 12 ++++++++++++ 2 files changed, 16 insertions(+) diff --git a/config/contentSecurityPolicy.json b/config/contentSecurityPolicy.json index 9849750..1ab8bb6 100644 --- a/config/contentSecurityPolicy.json +++ b/config/contentSecurityPolicy.json @@ -17,6 +17,10 @@ "cdn.datatables.net", "maxcdn.bootstrapcdn.com" ], +"connectSrc": [ + "'self'", + "*" +], "styleSrc": [ "'self'", "'unsafe-inline'", diff --git a/config/routes.json b/config/routes.json index 4c0fcfa..6d68514 100644 --- a/config/routes.json +++ b/config/routes.json @@ -116,6 +116,12 @@ "handlers":[ {"function":"mongoFind", "args": ["camic", "mark"]} ] + },{ + "route":"/data/Mark/count", + "method":"get", + "handlers":[ + {"function":"mongoCount", "args": ["camic", "mark"]} + ] },{ "route":"/data/Mark/post", "method":"post", @@ -147,6 +153,12 @@ "handlers":[ {"function":"mongoDistinct", "args": ["camic", "mark", "provenance.analysis"]} ] + },{ + "route":"/data/Mark/provenances", + "method":"get", + "handlers":[ + {"function":"mongoDistinct", "args": ["camic", "mark", "provenance"]} + ] },{ "route":"/data/Mark/multi", "method":"post", From 65c5241a58231e6ab3bdab539a79c41ed7fa538d Mon Sep 17 00:00:00 2001 From: Birm Date: Wed, 24 Apr 2024 00:31:29 -0400 Subject: [PATCH 07/10] allow attach chrome debugger --- develop.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/develop.yml b/develop.yml index 9ad7486..fa95b43 100644 --- a/develop.yml +++ b/develop.yml @@ -16,7 +16,9 @@ services: - "mongo" ports: - "4010:4010" + - "9229:9229" container_name: ca-back + command: node --inspect=0.0.0.0:9229 --prof caracal.js volumes: - ./config/login.html:/src/static/login.html - ./jwt_keys/:/src/keys/ @@ -28,6 +30,7 @@ services: MONGO_URI: "mongodb://ca-mongo" DISABLE_SEC: "true" ALLOW_PUBLIC: "true" + NUM_THREADS: 1 iip: build: "https://github.com/camicroscope/iipImage.git#develop" container_name: ca-iip From ef4a8d0aa05225401c6dae0959ee97574c1b90ca Mon Sep 17 00:00:00 2001 From: Birm Date: Wed, 24 Apr 2024 15:29:06 -0400 Subject: [PATCH 08/10] Explicit different paginated find --- config/routes.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/routes.json b/config/routes.json index 6d68514..908acaf 100644 --- a/config/routes.json +++ b/config/routes.json @@ -114,7 +114,7 @@ "route":"/data/Mark/find", "method":"get", "handlers":[ - {"function":"mongoFind", "args": ["camic", "mark"]} + {"function":"mongoPaginatedFind", "args": ["camic", "mark"]} ] },{ "route":"/data/Mark/count", From 8e5df0fecb36a122ff7203d59403aca34a815765 Mon Sep 17 00:00:00 2001 From: Birm Date: Mon, 29 Apr 2024 15:45:01 -0400 Subject: [PATCH 09/10] bump tags to 3.12 --- caMicroscope.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/caMicroscope.yml b/caMicroscope.yml index 4e45e87..aafb001 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -13,9 +13,9 @@ services: - ./db:/data/db back: build: - context: "https://github.com/camicroscope/caracal.git#v3.11.0" + context: "https://github.com/camicroscope/caracal.git#v3.12.0" args: - viewer: "v3.11.0" + viewer: "v3.12.0" depends_on: - "mongo" ports: @@ -49,7 +49,7 @@ services: volumes: - ./images/:/images/ loader: - build: "https://github.com/camicroscope/SlideLoader.git#v3.11.0" + build: "https://github.com/camicroscope/SlideLoader.git#v3.12.0" container_name: ca-load restart: always logging: @@ -65,7 +65,7 @@ services: build: context: "https://github.com/camicroscope/dicomsrv.git#v3.11.1" args: - indexer: "v3.11.0" + indexer: "v3.12.0" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true From cf2a5ff1a3302716214aecc41be6672b8fca729d Mon Sep 17 00:00:00 2001 From: Birm Date: Thu, 2 May 2024 12:59:03 -0400 Subject: [PATCH 10/10] update more tags --- kc_caMicroscope.yml | 8 ++++---- quip-pathdb.yml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/kc_caMicroscope.yml b/kc_caMicroscope.yml index 1daa98b..0be9fdd 100644 --- a/kc_caMicroscope.yml +++ b/kc_caMicroscope.yml @@ -51,9 +51,9 @@ services: - ./db:/data/db back: build: - context: "https://github.com/camicroscope/caracal.git#v3.11.1" + context: "https://github.com/camicroscope/caracal.git#v3.12.0" args: - viewer: "v3.11.1" + viewer: "v3.12.0" depends_on: - "mongo" ports: @@ -86,7 +86,7 @@ services: volumes: - ./images/:/images/ loader: - build: "https://github.com/camicroscope/SlideLoader.git#v3.11.0" + build: "https://github.com/camicroscope/SlideLoader.git#v3.12.0" container_name: ca-load restart: always logging: @@ -99,7 +99,7 @@ services: DICOM_PORT: "11112" DICOM_UI_PORT: "8042" dicomsrv: - build: "https://github.com/camicroscope/dicomsrv.git#v3.11.0" + build: "https://github.com/camicroscope/dicomsrv.git#v3.11.1" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 61d5297..d440106 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -15,9 +15,9 @@ services: - ./images/:/data/images/ back: build: - context: "https://github.com/camicroscope/caracal.git#v3.11.1" + context: "https://github.com/camicroscope/caracal.git#v3.12.0" args: - viewer: "v3.11.1" + viewer: "v3.12.0" depends_on: - "mongo" ports: