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@birm
birm committed Oct 25, 2022
1 parent 5aaa94d commit 2fc5941
Showing 3 changed files with 506 additions and 9 deletions.
6 changes: 3 additions & 3 deletions caMicroscope.yml
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Original file line number Diff line number Diff line change
@@ -13,9 +13,9 @@ services:
- ./db:/data/db
back:
build:
context: "https://github.com/camicroscope/caracal.git#v3.9.11"
context: "https://github.com/camicroscope/caracal.git#v3.10.0"
args:
viewer: "v3.9.11"
viewer: "v3.10.0"
depends_on:
- "mongo"
ports:
@@ -48,7 +48,7 @@ services:
volumes:
- ./images/:/images/
loader:
build: "https://github.com/camicroscope/SlideLoader.git#v3.9.11"
build: "https://github.com/camicroscope/SlideLoader.git#v3.10.0"
container_name: ca-load
restart: always
logging:
497 changes: 497 additions & 0 deletions config/routes_pathdb.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,497 @@
[
{
"method":"static",
"use":"static"
},{
"method":"static",
"use":"camicroscope"
},

{
"method":"use",
"route": "/loader/",
"handlers":[
{"function": "loginHandler", "args":[]},
{"function":"permissionHandler", "args": [["Admin", "Editor"]]}
]
},{
"method":"use",
"route": "/loader/slide/delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin"]]}
]
},{
"method":"use",
"route": "/loader/",
"handlers":[
{"function":"proxyHandler", "args": ["http://ca-load:4000/"]}
]
},{
"method":"use",
"route": "/googleAuth/",
"handlers":[
{"function":"proxyHandler", "args": ["http://ca-load:4001/"]}
]
},

{
"method":"use",
"route": "/img/IIP/raw/",
"handlers":[
{"function": "loginHandler", "args":[]},
{"function":"preIip", "args": []},
{"function":"iipCheck", "args": []},
{"function":"iipHandler", "args": []}
]
},

{
"route":"/data",
"method":"use",
"handlers":[
{"function":"loginHandler", "args": []},
{"function":"sanitizeBody", "args": []}
]
},

{
"route":"/data/Slide/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "slide"]},
{"function":"filterHandler", "args": ["data", "userFilter", "filter"]}
]
},{
"route":"/data/Slide/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoAdd", "args": ["camic", "slide"]}
]
},{
"route":"/data/Slide/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoFind", "args": ["camic", "slide"]},
{"function":"editHandler", "args": ["data", "userFilter", "filter"]},
{"function":"mongoDelete", "args": ["camic", "slide"]}
]
},{
"route":"/data/Slide/update",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoFind", "args": ["camic", "slide"]},
{"function":"editHandler", "args": ["data", "userFilter", "filter"]},
{"function":"mongoUpdate", "args": ["camic", "slide"]}
]
},

{
"route":"/data/Request/find",
"method":"get",
"handlers":[
{"function":"permissionHandler", "args": [["Editor", "Admin"]]},
{"function":"mongoFind", "args": ["camic", "request"]}
]
},{
"route":"/data/Request/post",
"method":"post",
"handlers":[
{"function":"mongoAdd", "args": ["camic", "request"]}
]
},{
"route":"/data/Request/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Editor", "Admin"]]},
{"function":"mongoFind", "args": ["camic", "request"]},
{"function":"editHandler", "args": ["data", "userFilter", "filter"]},
{"function":"mongoDelete", "args": ["camic", "request"]}
]
},

{
"route":"/data/Mark/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "mark"]}
]
},{
"route":"/data/Mark/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoAdd", "args": ["camic", "mark"]}
]
},{
"route":"/data/Mark/delete",
"method":"delete",
"handlers":[
{"function":"mongoFind", "args": ["camic", "mark"]},
{"function":"editHandler", "args": ["data"]},
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "mark"]}
]
},{
"route":"/data/Mark/update",
"method":"post",
"handlers":[
{"function":"mongoFind", "args": ["camic", "mark"]},
{"function":"editHandler", "args": ["data"]},
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoUpdate", "args": ["camic", "mark"]}
]
},{
"route":"/data/Mark/types",
"method":"get",
"handlers":[
{"function":"mongoDistinct", "args": ["camic", "mark", "provenance.analysis"]}
]
},{
"route":"/data/Mark/multi",
"method":"post",
"handlers":[
{"function":"markMulti", "args": []}
]
},{
"route":"/data/Mark/spatial",
"method":"get",
"handlers":[
{"function":"markSpatial", "args": []}
]
},{
"route":"/data/Mark/findMarkTypes",
"method":"get",
"handlers":[
{"function":"findMarkTypes", "args": []}
]
},{
"route":"/data/Mark/updateMarksLabel",
"method":"post",
"handlers":[
{"function":"updateMarksLabel", "args": []}
]
},{
"route":"/data/Presetlabels/add",
"method":"post",
"handlers":[
{"function":"addPresetlabels", "args": []}
]
},{
"route":"/data/Presetlabels/update",
"method":"post",
"handlers":[
{"function":"updatePresetlabels", "args": []}
]
},{
"route":"/data/Presetlabels/remove",
"method":"post",
"handlers":[
{"function":"removePresetlabels", "args": []}
]
},
{
"route":"/data/Template/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "template"]}
]
},{
"route":"/data/Template/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoAdd", "args": ["camic", "template"]}
]
},{
"route":"/data/Template/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "template"]}
]
},{
"route":"/data/Template/update",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin"]]},
{"function":"mongoUpdate", "args": ["camic", "template"]}
]
},

{
"route":"/data/Heatmap/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "heatmap"]}
]
},{
"route":"/data/Heatmap/types",
"method":"get",
"handlers":[
{"function":"heatmapTypes", "args": []}
]
},{
"route":"/data/Heatmap/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoAdd", "args": ["camic", "heatmap"]}
]
},{
"route":"/data/Heatmap/delete",
"method":"delete",
"handlers":[
{"function":"mongoFind", "args": ["camic", "heatmap"]},
{"function":"editHandler", "args": ["data"]},
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "heatmap"]}
]
},{
"route":"/data/Heatmap/update",
"method":"post",
"handlers":[
{"function":"mongoFind", "args": ["camic", "heatmap"]},
{"function":"editHandler", "args": ["data"]},
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoUpdate", "args": ["camic", "heatmap"]}
]
},

{
"route":"/data/HeatmapEdit/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "heatmapEdit"]}
]
},{
"route":"/data/HeatmapEdit/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoAdd", "args": ["camic", "heatmapEdit"]}
]
},{
"route":"/data/HeatmapEdit/delete",
"method":"delete",
"handlers":[
{"function":"mongoFind", "args": ["camic", "heatmapEdit"]},
{"function":"editHandler", "args": ["data"]},
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "heatmapEdit"]}
]
},{
"route":"/data/HeatmapEdit/update",
"method":"post",
"handlers":[
{"function":"mongoFind", "args": ["camic", "heatmapEdit"]},
{"function":"editHandler", "args": ["data"]},
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoUpdate", "args": ["camic", "heatmapEdit"]}
]
},

{
"route":"/data/Log/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "log"]}
]
},{
"route":"/data/Log/post",
"method":"post",
"handlers":[
{"function":"mongoAdd", "args": ["camic", "log"]}
]
},{
"route":"/data/Log/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "log"]}
]
},{
"route":"/data/Log/update",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoUpdate", "args": ["camic", "log"]}
]
},

{
"route":"/data/Evaluation/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "evaluation"]}
]
},{
"route":"/data/Evaluation/post",
"method":"post",
"handlers":[
{"function":"mongoAdd", "args": ["camic", "evaluation"]}
]
},{
"route":"/data/Evaluation/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "evaluation"]}
]
},{
"route":"/data/Evaluation/update",
"method":"post",
"handlers":[
{"function":"mongoUpdate", "args": ["camic", "evaluation"]}
]
},

{
"route":"/data/Freeform/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "freeform"]}
]
},{
"route":"/data/Freeform/post",
"method":"post",
"handlers":[
{"function":"mongoAdd", "args": ["camic", "freeform"]}
]
},{
"route":"/data/Freeform/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "freeform"]}
]
},{
"route":"/data/Freeform/update",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoUpdate", "args": ["camic", "freeform"]}
]
},

{
"route":"/data/Configuration/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "configuration"]}
]
},{
"route":"/data/Configuration/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoAdd", "args": ["camic", "configuration"]}
]
},{
"route":"/data/Configuration/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "configuration"]}
]
},{
"route":"/data/Configuration/update",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoUpdate", "args": ["camic", "configuration"]}
]
},{
"route":"/data/Collection/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "collection"]}
]
},{
"route":"/data/Collection/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoAdd", "args": ["camic", "collection"]}
]
},{
"route":"/data/Collection/update",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoUpdate", "args": ["camic", "collection"]}
]
},{
"route":"/data/Collection/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"mongoDelete", "args": ["camic", "collection"]}
]
},

{
"route":"/data/User/find",
"method":"get",
"handlers":[
{"function":"mongoFind", "args": ["camic", "user"]}
]
},{
"route":"/data/User/post",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin"]]},
{"function":"mongoAdd", "args": ["camic", "user"]}
]
},{
"route":"/data/User/delete",
"method":"delete",
"handlers":[
{"function":"permissionHandler", "args": [["Admin"]]},
{"function":"mongoDelete", "args": ["camic", "user"]}
]
},{
"route":"/data/User/update",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin"]]},
{"function":"mongoUpdate", "args": ["camic", "user"]}
]
},{
"route":"/data/User/wcido",
"method":"get",
"handlers":[
{"function":"wcido", "args": []}
]
},{
"route":"/workbench/uploadDataset",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"getDataset", "args": []}
]
},{
"route":"/workbench/trainModel",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"trainModel", "args": []}
]
},{
"route":"/workbench/deleteUserData",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"deleteDataset", "args": []}
]
},{
"route":"/workbench/modelDownload",
"method":"post",
"handlers":[
{"function":"permissionHandler", "args": [["Admin", "Editor"]]},
{"function":"sendTrainedModel", "args": []}
]
}
]
12 changes: 6 additions & 6 deletions quip-pathdb.yml
View file
Original file line number Diff line number Diff line change
@@ -15,17 +15,17 @@ services:
- ./images/:/data/images/
back:
build:
context: "https://github.com/camicroscope/caracal.git#v3.9.11"
context: "https://github.com/camicroscope/caracal.git#v3.10.0"
args:
viewer: "v3.9.11"
viewer: "v3.10.0"
depends_on:
- "mongo"
ports:
- "4010:4010"
container_name: ca-security
volumes:
- ./keys/:/src/keys/
- ./config/routes.json:/src/routes.json
- ./config/routes_pathdb.json:/src/routes.json
environment:
JWK_URL: "https://www.googleapis.com/oauth2/v3/certs"
IIP_PATH: "http://ca-iip:8080/fcgi-bin/iipsrv.fcgi"
@@ -35,9 +35,9 @@ services:
DISABLE_CSP: "true"
pathdb:
build:
context: "https://github.com/SBU-BMI/PathDB.git#1.7.1"
context: "https://github.com/SBU-BMI/PathDB.git#2.0.0"
args:
viewer: "v3.9.10"
viewer: "v3.10.0"
container_name: quip-pathdb
restart: unless-stopped
ports: ["443:443","80:80"]
@@ -50,7 +50,7 @@ services:
command:
- /config/pathdb_pre.sh
imageloader:
build: "https://github.com/SBU-BMI/ImageLoader.git#2.1.1"
build: "https://github.com/SBU-BMI/ImageLoader.git#3.0.0"
container_name: quip-imageloader
volumes:
- ./data:/data/

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