From 42ea9c478542f3956ea5749e02b68fc9452847ee Mon Sep 17 00:00:00 2001 From: Samuel Wein Date: Wed, 4 Feb 2026 10:06:27 +0100 Subject: [PATCH 1/4] Update submodules: remove umetaflow-gui, rename FLASHViewer to FLASHApp with new URL --- .gitmodules | 10 +++------- FLASHViewer | 1 - umetaflow-gui | 1 - 3 files changed, 3 insertions(+), 9 deletions(-) delete mode 160000 FLASHViewer delete mode 160000 umetaflow-gui diff --git a/.gitmodules b/.gitmodules index 8d8939a..97ac6bb 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,16 +1,12 @@ [submodule "openms-streamlit-template"] path = openms-streamlit-template url = https://github.com/OpenMS/streamlit-template.git -[submodule "umetaflow-gui"] - path = umetaflow-gui - url = https://github.com/axelwalter/umetaflow-gui.git [submodule "nuxl-app"] path = nuxl-app url = https://github.com/Arslan-Siraj/nuxl-app -[submodule "FLASHViewer"] - path = FLASHViewer - url = https://github.com/t0mdavid-m/FLASHViewer - branch = TaggerViewerDeploy +[submodule "FLASHApp"] + path = FLASHApp + url = https://github.com/OpenMS/FLASHApp.git [submodule "naseweis"] path = naseweis url = https://github.com/poshul/nase-weis diff --git a/FLASHViewer b/FLASHViewer deleted file mode 160000 index 99dd5a2..0000000 --- a/FLASHViewer +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 99dd5a2f2d06e4df005d3a38673ccc7a45d5ea17 diff --git a/umetaflow-gui b/umetaflow-gui deleted file mode 160000 index a69a659..0000000 --- a/umetaflow-gui +++ /dev/null @@ -1 +0,0 @@ -Subproject commit a69a659bc2b0783ab40d2f2afb2831ffcedbf09b From e357e829d6f3ce044c92730d3ee45ad9edfefe24 Mon Sep 17 00:00:00 2001 From: Samuel Wein Date: Wed, 4 Feb 2026 10:55:29 +0100 Subject: [PATCH 2/4] update dockerfile with new names --- docker-compose.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index fca43e8..245aa61 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -17,7 +17,7 @@ services: command: streamlit run openms-streamlit-template/app.py umetaflow: build: - context: ./umetaflow-gui + context: ./umetaflow dockerfile: Dockerfile args: GITHUB_TOKEN: $GITHUB_TOKEN @@ -27,8 +27,8 @@ services: ports: - 28503:8501 # increment port numbers (here 28503) volumes: - - workspaces-umetaflow-gui:/workspaces-umetaflow-gui - command: streamlit run umetaflow-gui/Home.py + - workspaces-umetaflow:/workspaces-umetaflow + command: streamlit run umetaflow/Home.py nuxl-app: build: context: ./nuxl-app @@ -57,19 +57,19 @@ services: volumes: - workspaces-PTMScanner:/workspaces-PTMScanner command: streamlit run PTMScanner/run.py - FLASHViewer: + FLASHApp: build: - context: ./FLASHViewer + context: ./FLASHApp dockerfile: Dockerfile args: GITHUB_TOKEN: $GITHUB_TOKEN - image: flashviewer - container_name: flashviewer + image: flashapp + container_name: flashapp restart: always ports: - 28506:8501 # increment port numbers (here 28506) volumes: - - workspaces-flashviewer:/workspaces-flashviewer + - workspaces-flashapp:/workspaces-flashapp naseweis: build: context: ./naseweis @@ -156,9 +156,9 @@ services: volumes: workspaces-streamlit-template: - workspaces-umetaflow-gui: + workspaces-umetaflow: workspaces-nuxl-app: - workspaces-flashviewer: + workspaces-flashapp: workspaces-naseweis: workspaces-PTMScanner: workspaces-stream-sage: From 41845efbfcdc39ff01922ce17186049574f78a95 Mon Sep 17 00:00:00 2001 From: Samuel Wein Date: Wed, 4 Feb 2026 11:12:07 +0100 Subject: [PATCH 3/4] =?UTF-8?q?Update=20submodule=20names:=20FLASHViewer?= =?UTF-8?q?=E2=86=92FLASHApp,=20umetaflow-gui=E2=86=92umetaflow?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .gitmodules | 3 +++ docker-compose.yml | 29 ----------------------------- 2 files changed, 3 insertions(+), 29 deletions(-) diff --git a/.gitmodules b/.gitmodules index 97ac6bb..161979b 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,6 +1,9 @@ [submodule "openms-streamlit-template"] path = openms-streamlit-template url = https://github.com/OpenMS/streamlit-template.git +[submodule "umetaflow"] + path = umetaflow + url = https://github.com/OpenMS/umetaflow.git [submodule "nuxl-app"] path = nuxl-app url = https://github.com/Arslan-Siraj/nuxl-app diff --git a/docker-compose.yml b/docker-compose.yml index 245aa61..a32f15e 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -15,20 +15,6 @@ services: volumes: - workspaces-streamlit-template:/workspaces-streamlit-template command: streamlit run openms-streamlit-template/app.py - umetaflow: - build: - context: ./umetaflow - dockerfile: Dockerfile - args: - GITHUB_TOKEN: $GITHUB_TOKEN - image: umetaflow_app - container_name: umetaflow-app - restart: always - ports: - - 28503:8501 # increment port numbers (here 28503) - volumes: - - workspaces-umetaflow:/workspaces-umetaflow - command: streamlit run umetaflow/Home.py nuxl-app: build: context: ./nuxl-app @@ -57,19 +43,6 @@ services: volumes: - workspaces-PTMScanner:/workspaces-PTMScanner command: streamlit run PTMScanner/run.py - FLASHApp: - build: - context: ./FLASHApp - dockerfile: Dockerfile - args: - GITHUB_TOKEN: $GITHUB_TOKEN - image: flashapp - container_name: flashapp - restart: always - ports: - - 28506:8501 # increment port numbers (here 28506) - volumes: - - workspaces-flashapp:/workspaces-flashapp naseweis: build: context: ./naseweis @@ -156,9 +129,7 @@ services: volumes: workspaces-streamlit-template: - workspaces-umetaflow: workspaces-nuxl-app: - workspaces-flashapp: workspaces-naseweis: workspaces-PTMScanner: workspaces-stream-sage: From 319d4120e884dacc767072e4d3344e2d54260e23 Mon Sep 17 00:00:00 2001 From: Samuel Wein Date: Wed, 4 Feb 2026 11:14:38 +0100 Subject: [PATCH 4/4] readd flashapp and umetaflow to docker-compose --- FLASHApp | 1 + docker-compose.yml | 29 +++++++++++++++++++++++++++++ umetaflow | 1 + 3 files changed, 31 insertions(+) create mode 160000 FLASHApp create mode 160000 umetaflow diff --git a/FLASHApp b/FLASHApp new file mode 160000 index 0000000..286207c --- /dev/null +++ b/FLASHApp @@ -0,0 +1 @@ +Subproject commit 286207cd2768d5d06998cb5b73750bcfefe94d93 diff --git a/docker-compose.yml b/docker-compose.yml index a32f15e..245aa61 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -15,6 +15,20 @@ services: volumes: - workspaces-streamlit-template:/workspaces-streamlit-template command: streamlit run openms-streamlit-template/app.py + umetaflow: + build: + context: ./umetaflow + dockerfile: Dockerfile + args: + GITHUB_TOKEN: $GITHUB_TOKEN + image: umetaflow_app + container_name: umetaflow-app + restart: always + ports: + - 28503:8501 # increment port numbers (here 28503) + volumes: + - workspaces-umetaflow:/workspaces-umetaflow + command: streamlit run umetaflow/Home.py nuxl-app: build: context: ./nuxl-app @@ -43,6 +57,19 @@ services: volumes: - workspaces-PTMScanner:/workspaces-PTMScanner command: streamlit run PTMScanner/run.py + FLASHApp: + build: + context: ./FLASHApp + dockerfile: Dockerfile + args: + GITHUB_TOKEN: $GITHUB_TOKEN + image: flashapp + container_name: flashapp + restart: always + ports: + - 28506:8501 # increment port numbers (here 28506) + volumes: + - workspaces-flashapp:/workspaces-flashapp naseweis: build: context: ./naseweis @@ -129,7 +156,9 @@ services: volumes: workspaces-streamlit-template: + workspaces-umetaflow: workspaces-nuxl-app: + workspaces-flashapp: workspaces-naseweis: workspaces-PTMScanner: workspaces-stream-sage: diff --git a/umetaflow b/umetaflow new file mode 160000 index 0000000..957843c --- /dev/null +++ b/umetaflow @@ -0,0 +1 @@ +Subproject commit 957843c4f0a41f15adaa46be498e75e307821c25