diff --git a/caMicroscope.yml b/caMicroscope.yml index c904c8ca..bbde4aaf 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -40,7 +40,7 @@ services: volumes: - ./images/:/images/ viewer: - build: "https://github.com/camicroscope/caMicroscope.git#v3.5.9" + build: "https://github.com/camicroscope/caMicroscope.git#v3.5.10" container_name: ca-front restart: unless-stopped volumes: diff --git a/config/default_data.js b/config/default_data.js index abc320f4..0105eb09 100644 --- a/config/default_data.js +++ b/config/default_data.js @@ -24,3 +24,411 @@ let defaultTemplate = { } db.template.insert(defaultTemplate) + +var defaultConfigs=[{ + config_name:"preset_label", + configuration:[ + { + title:"Lymph", + value:"Lymph", + children:[ + { + title:"Positive", + value:"Positive", + children:[ + { + title:100, + value:100, + color:"#ff6296", + checked:true, + data:{ + color:"#ff6296", + mode:"grid", + type:"Lymph-Positive", + size:100 + } + }, + { + title:"Point", + value:"Point", + color:"#ff6296", + data:{ + color:"#ff6296", + mode:"point", + type:"Lymph-Positive" + } + } + ] + }, + { + title:"Negative", + value:"Negative", + children:[ + { + title:100, + value:100, + color:"#62ffcb", + data:{ + color:"#62ffcb", + mode:"grid", + type:"Lymph-Negative", + size:100 + } + }, + { + title:"Point", + value:"Point", + color:"#62ffcb", + data:{ + color:"#62ffcb", + mode:"point", + type:"Lymph-Negative" + } + } + ] + } + ] + }, + { + title:"Neutrophil", + value:"Neutrophil", + children:[ + { + title:"Positive", + value:"Positive", + color:"#ffcb62", + data:{ + color:"#ffcb62", + mode:"grid", + type:"Neutrophil-Positive", + size:50 + } + }, + { + title:"Negative", + value:"Negative", + color:"#6296ff", + data:{ + color:"#6296ff", + mode:"grid", + type:"Neutrophil-Negative", + size:50 + } + } + ] + }, + { + title:"Necrosis", + value:"Necrosis", + children:[ + { + title:"Positive", + value:"Positive", + children:[ + { + title:100, + value:100, + color:"#ff00d9", + data:{ + color:"#ff00d9", + mode:"grid", + type:"Necrosis-Positive", + size:100 + } + }, + { + title:500, + value:500, + color:"#ff00d9", + data:{ + color:"#ff00d9", + mode:"grid", + type:"Necrosis-Positive", + size:500 + } + } + ] + }, + { + title:"Negative", + value:"Negative", + children:[ + { + title:100, + value:100, + color:"#00ff26", + data:{ + color:"#00ff26", + mode:"grid", + type:"Necrosis-Negative", + size:100 + } + }, + { + title:500, + value:500, + color:"#00ff26", + data:{ + color:"#00ff26", + mode:"grid", + type:"Necrosis-Negative", + size:500 + } + } + ] + } + ] + }, + { + title:"Tumor", + value:"Tumor", + children:[ + { + title:"Positive", + value:"Positive", + children:[ + { + title:100, + value:100, + color:"#790cff", + data:{ + color:"#790cff", + mode:"grid", + type:"Tumor-Positive", + size:100 + } + }, + { + title:300, + value:300, + color:"#790cff", + data:{ + color:"#790cff", + mode:"grid", + type:"Tumor-Positive", + size:300 + } + }, + { + title:1000, + value:1000, + color:"#790cff", + data:{ + color:"#790cff", + mode:"grid", + type:"Tumor-Positive", + size:1000 + } + }, + { + title:2000, + value:2000, + color:"#790cff", + data:{ + color:"#790cff", + mode:"grid", + type:"Tumor-Positive", + size:2000 + } + } + ] + }, + { + title:"Negative", + value:"Negative", + children:[ + { + title:100, + value:100, + color:"#92ff0c", + data:{ + color:"#92ff0c", + mode:"grid", + type:"Tumor-Negative", + size:100 + } + }, + { + title:300, + value:300, + color:"#92ff0c", + data:{ + color:"#92ff0c", + mode:"grid", + type:"Tumor-Negative", + size:300 + } + }, + { + title:1000, + value:1000, + color:"#92ff0c", + data:{ + color:"#92ff0c", + mode:"grid", + type:"Tumor-Negative", + size:1000 + } + }, + { + title:2000, + value:2000, + color:"#92ff0c", + data:{ + color:"#92ff0c", + mode:"grid", + type:"Tumor-Negative", + size:2000 + } + } + ] + } + ] + }, + { + title:"Prostate", + value:"Prostate", + children:[ + { + title:"Benign", + value:"Benign", + color:"#8dd3c7", + checked:true, + data:{ + color:"#8dd3c7", + mode:"free", + type:"Prostate-Benign" + } + }, + { + title:"Gleason 3", + value:"Gleason 3", + color:"#ffffb3", + data:{ + color:"#ffffb3", + mode:"free", + type:"Prostate-Gleason 3" + } + }, + { + title:"Gleason 4", + value:"Gleason 4", + color:"#bebada", + data:{ + color:"#bebada", + mode:"free", + type:"Prostate-Gleason 4" + } + }, + { + title:"Gleason 5", + value:"Gleason 5", + color:"#fb8072", + data:{ + color:"#fb8072", + mode:"free", + type:"Prostate-Gleason 5" + } + }, + { + title:"Cancer NOS", + value:"Cancer NOS", + color:"#80b1d3", + data:{ + color:"#80b1d3", + mode:"free", + type:"Prostate-Cancer NOS" + } + } + ] + }, + { + title:"NSCLC", + value:"NSCLC", + children:[ + { + title:"Benign", + value:"Benign", + color:"#fdb462", + data:{ + color:"#fdb462", + mode:"free", + type:"NSCLC-Benign" + } + }, + { + title:"Squamous CA", + value:"Squamous CA", + color:"#b3de69", + data:{ + color:"#b3de69", + mode:"free", + type:"NSCLC-Squamous CA" + } + }, + { + title:"Adeno CA (all)", + value:"Adeno CA (all)", + color:"#fccde5", + data:{ + color:"#fccde5", + mode:"free", + type:"NSCLC-Adeno CA (all)" + } + }, + { + title:"Acinar", + value:"Acinar", + color:"#d9d9d9", + data:{ + color:"#d9d9d9", + mode:"free", + type:"NSCLC-Acinar" + } + }, + { + title:"Lapidic", + value:"Lapidic", + color:"#bc80bd", + data:{ + color:"#bc80bd", + mode:"free", + type:"NSCLC-Lapidic" + } + }, + { + title:"Solid", + value:"Solid", + color:"#ccebc5", + data:{ + color:"#ccebc5", + mode:"free", + type:"NSCLC-Solid" + } + }, + { + title:"Papillary", + value:"Papillary", + color:"#ffed6f", + data:{ + color:"#ffed6f", + mode:"free", + type:"NSCLC-Papillary" + } + }, + { + title:"Micropapillary", + value:"Micropapillary", + color:"#6a3d9a", + data:{ + color:"#6a3d9a", + mode:"free", + type:"NSCLC-Micropapillary" + } + } + ] + } + ] +}]; + +db.configuration.insertMany(defaultConfigs) diff --git a/config/mongo_idx.js b/config/mongo_idx.js index 5a74fe66..a728c3b5 100644 --- a/config/mongo_idx.js +++ b/config/mongo_idx.js @@ -10,3 +10,4 @@ db.template.createIndex({'name': 1}) db.heatmap.createIndex({"provenance.image.slide": 1, "provenance.analysis.execution_id": 1}) db.heatmap.createIndex({"provenance.image.slide": 1}) db.heatmapEdit.createIndex({"provenance.image.slide":1, "provenance.analysis.execution_id":1, "user_id":1}) +db.configuration.createIndex({'config_name': 1}, { unique: true }) diff --git a/config/pathdb_routes.json b/config/pathdb_routes.json index 95cf3fec..c7be7704 100644 --- a/config/pathdb_routes.json +++ b/config/pathdb_routes.json @@ -50,7 +50,11 @@ }, "Log": { "post": "/Log/submit/json" + }, + "Configuration": { + "getConfigByName": "/Configuration/query/getConfigByName" } + }, "img": { "_public": "true", diff --git a/config/test_seed.js b/config/test_seed.js index 649ef476..eaacbd27 100644 --- a/config/test_seed.js +++ b/config/test_seed.js @@ -278,8 +278,6 @@ const algorithm_2_schema = { }; - - var templates = [algorithm_2_schema, algorithm_1_schema, annotation_schema] db.slide.insertMany(slides) db.mark.insertMany(marks) diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 5f19115e..645d8f53 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -53,7 +53,10 @@ services: logging: driver: none pathdb: - build: "https://github.com/SBU-BMI/PathDB.git#1.3.1" + build: + context: "https://github.com/SBU-BMI/PathDB.git#1.3.2" + args: + viewer: "v3.5.10" container_name: quip-pathdb restart: unless-stopped ports: ["443:443","80:80"]