diff --git a/caMicroscope.yml b/caMicroscope.yml index 4c403df3..97fd4c34 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -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: @@ -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: diff --git a/config/mongo_uuid_conv.js b/config/mongo_uuid_conv.js index 024583c0..53258c61 100644 --- a/config/mongo_uuid_conv.js +++ b/config/mongo_uuid_conv.js @@ -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){ diff --git a/config/routes.json b/config/routes.json index 6c3cd4d8..2f7f27ee 100644 --- a/config/routes.json +++ b/config/routes.json @@ -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", @@ -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", @@ -51,13 +47,10 @@ "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":"" @@ -65,8 +58,8 @@ "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"] } } @@ -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":"" } } } diff --git a/dev-pathdb.yml b/dev-pathdb.yml index b6e8a16a..9c3cb803 100644 --- a/dev-pathdb.yml +++ b/dev-pathdb.yml @@ -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: @@ -85,4 +85,3 @@ services: ports: ["27017:27017"] volumes: - ./data:/mnt/data/ - diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 659c8088..14a6a8af 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -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: @@ -53,7 +53,7 @@ services: logging: driver: none pathdb: - build: "https://github.com/SBU-BMI/PathDB.git#1.1.1" + build: "https://github.com/SBU-BMI/PathDB.git#1.1.5" container_name: quip-pathdb restart: unless-stopped ports: ["443:443","80:80"] @@ -85,4 +85,3 @@ services: ports: ["27017:27017"] volumes: - ./data:/mnt/data/ - diff --git a/test/test_viewer_basic.js b/test/test_viewer_basic.js index a458df50..93f878ab 100644 --- a/test/test_viewer_basic.js +++ b/test/test_viewer_basic.js @@ -27,6 +27,10 @@ describe('Minimal Distribution Test', function () { console.log(x) done(x) }) + }).catch(x=>{ + console.log("err") + console.log(x) + done(x) }) });