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Merge pull request #79 from camicroscope/release
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For 3.5.2
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birm authored Oct 9, 2019
2 parents d31cd89 + 20d34f8 commit 4883339
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Showing 6 changed files with 21 additions and 25 deletions.
4 changes: 2 additions & 2 deletions caMicroscope.yml
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ services:
volumes:
- ./images/:/images/
viewer:
build: "https://github.com/camicroscope/caMicroscope.git#v3.5.1"
build: "https://github.com/camicroscope/caMicroscope.git#v3.5.2"
container_name: ca-front
restart: unless-stopped
volumes:
Expand All @@ -56,7 +56,7 @@ services:
volumes:
- ./images/:/images/
security:
build: "https://github.com/camicroscope/Security.git#v3.4.6"
build: "https://github.com/camicroscope/Security.git#v3.5.2"
container_name: ca-security
restart: unless-stopped
ports:
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2 changes: 1 addition & 1 deletion config/mongo_uuid_conv.js
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ db.slide.find({}).forEach(function(slide){
db.heatmap.find({'provenance.image.slide':slide.name, 'provenance.image.study':slide.study, 'provenance.image.specimen':slide.specimen}).forEach(function(hm){
delete hm.provenance.image.study
delete hm.provenance.image.specimen
mark.provenance.image.slide = slide._id.valueOf()
hm.provenance.image.slide = slide._id.valueOf()
db.heatmap.save(hm)
})
db.heatmap.find({'provenance.image.case_id':slide.name}).forEach(function(hm){
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26 changes: 10 additions & 16 deletions config/routes.json
Original file line number Diff line number Diff line change
@@ -1,10 +1,6 @@
{
"root":"http://ca-front:80/",
"_root_public": "true",
"auth":{
"permissions_field":"attrs",
"key_field": "accessCollection"
},
"services":{
"data":{
"_base": "http://ca-data:9099/services/caMicroscope",
Expand Down Expand Up @@ -34,10 +30,10 @@
},
"Slide": {
"get":"/Slide/query/get",
"find":{"path":"/Slide/query/find", "key_method": "filter"},
"find":"/Slide/query/find",
"post":{"path": "/Slide/submit/json", "attr": "write"},
"delete":{"path": "/Slide/delete/deleteSlide", "attr": "write"},
"update":{"path": "/Slide/delete/updateSlide", "attr": "write"}
"update":{"path": "/Slide/update/updateSlide", "attr": "write"}
},
"Template": {
"get":"/Template/query/get",
Expand All @@ -51,22 +47,19 @@
"post":{"path": "/HeatmapEdit/submit/json", "attr": "write"},
"delete":{"path": "/HeatmapEdit/delete/delete", "attr": "write"},
"update":{"path": "/HeatmapEdit/delete/update", "attr": "write"}
},
"Auth": {
"get":{"path": "/Authorization/query/getAuth", "attr": "admin"},
"post":{"path": "/Authorization/submit/json", "attr": "admin"}
}
},
"img": {
"_public": "true",
"_base":"http://ca-iip/fcgi-bin/iipsrv.fcgi",
"IIP": {
"raw":""
},
"Slide":{
"_resolver":{
"destination":"?DeepZoom={OUT}",
"url":"http://ca-data:9099/services/caMicroscope/Slide/query/get?id={IN}",
"field":"location",
"url": "http://ca-pathdb/node/{IN}?_format=json",
"field":"field_iip_path[0].value",
"before":["_files", ".dzi"]
}
}
Expand All @@ -83,11 +76,12 @@
"thumb":"/data/thumbnail"
}
},
"auth": {
"pathdb":{
"_public": "true",
"_base": "http://ca-auth:8010",
"Token":{
"check":"/check"
"_base": "http://quip-pathdb/",
"slide":{
"info":"/node/",
"unmod":""
}
}
}
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3 changes: 1 addition & 2 deletions dev-pathdb.yml
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ services:
restart: unless-stopped
ports: ["4010:4010"]
volumes:
- ./config/routes.json:/root/src/routes.json
- ./config/pathdb_routes.json:/root/src/routes.json
environment:
- DISABLE_SEC=true
auth:
Expand Down Expand Up @@ -85,4 +85,3 @@ services:
ports: ["27017:27017"]
volumes:
- ./data:/mnt/data/

7 changes: 3 additions & 4 deletions quip-pathdb.yml
Original file line number Diff line number Diff line change
Expand Up @@ -39,12 +39,12 @@ services:
volumes:
- ./images/:/data/images/
security:
build: "https://github.com/camicroscope/Security.git#v3.4.6"
build: "https://github.com/camicroscope/Security.git#v3.5.2"
container_name: ca-security
restart: unless-stopped
ports: ["4010:4010"]
volumes:
- ./config/routes.json:/root/src/routes.json
- ./config/pathdb_routes.json:/root/src/routes.json
environment:
- DISABLE_SEC=true
auth:
Expand All @@ -53,7 +53,7 @@ services:
logging:
driver: none
pathdb:
build: "https://github.com/SBU-BMI/PathDB.git#1.1.2"
build: "https://github.com/SBU-BMI/PathDB.git#1.1.5"
container_name: quip-pathdb
restart: unless-stopped
ports: ["443:443","80:80"]
Expand Down Expand Up @@ -85,4 +85,3 @@ services:
ports: ["27017:27017"]
volumes:
- ./data:/mnt/data/

4 changes: 4 additions & 0 deletions test/test_viewer_basic.js
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,10 @@ describe('Minimal Distribution Test', function () {
console.log(x)
done(x)
})
}).catch(x=>{
console.log("err")
console.log(x)
done(x)
})

});
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