Merge pull request #78 from camicroscope/develop

for 3.5.2
camicroscope · Oct 9, 2019 · 20d34f8 · 20d34f8
2 parents 51b7e5e + 6164784
commit 20d34f8
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Showing 6 changed files with 21 additions and 25 deletions.
diff --git 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
@@ -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
@@ -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",
@@ -51,22 +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"]
         }
       }
@@ -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
@@ -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
@@ -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
@@ -27,6 +27,10 @@ describe('Minimal Distribution Test', function () {
         console.log(x)
         done(x)
       })
+    }).catch(x=>{
+      console.log("err")
+      console.log(x)
+      done(x)
     })
 
   });