From 05c5bbe19a392f07bd2d9c4588d6ec07a17ebdab Mon Sep 17 00:00:00 2001 From: erich Date: Mon, 28 Oct 2019 11:04:03 -0400 Subject: [PATCH 1/8] bump imageloader to 2.0.1 --- quip-pathdb.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 0172ecef..f97730ab 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -66,7 +66,7 @@ services: command: - /config/pathdb_pre.sh imageloader: - build: "https://github.com/SBU-BMI/ImageLoader.git#2.0.0" + build: "https://github.com/SBU-BMI/ImageLoader.git#2.0.1" container_name: quip-imageloader volumes: - ./data:/data/ From 9c1d041e30f1f09d581a9b76f1d682c491d71daa Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Mon, 28 Oct 2019 14:14:14 -0400 Subject: [PATCH 2/8] basic collection query ac method --- caMicroscope.yml | 2 +- config/non-pathdb-routes.json | 95 +++++++++++++++++++++++++++++++++++ config/routes.json | 24 +++++---- develop.yml | 4 +- 4 files changed, 112 insertions(+), 13 deletions(-) create mode 100644 config/non-pathdb-routes.json diff --git a/caMicroscope.yml b/caMicroscope.yml index ba459659..1403311e 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -62,7 +62,7 @@ services: ports: - "4010:4010" volumes: - - ./config/routes.json:/root/src/routes.json + - ./config/non-pathdb-routes.json:/root/src/routes.json - ./jwt_keys/:/keys/ environment: - DISABLE_SEC=true diff --git a/config/non-pathdb-routes.json b/config/non-pathdb-routes.json new file mode 100644 index 00000000..49ddf99f --- /dev/null +++ b/config/non-pathdb-routes.json @@ -0,0 +1,95 @@ +{ + "root":"http://ca-front:80/", + "_root_public": "true", + "auth":{ + "permissions_field":"attrs", + "key_field": "accessCollection" + }, + "services":{ + "data":{ + "_base": "http://ca-data:9099/services/caMicroscope", + "Mark": { + "get":"/Mark/query/get", + "find":"/Mark/query/find", + "multi":"/Mark/query/multiFind", + "findBound":"/Mark/query/findBound", + "types":"/Mark/query/findTypes", + "typesExec":"/Mark/query/findTypesExec", + "post":{"path": "/Mark/submit/json", "attr": "write"}, + "delete":{"path": "/Mark/delete/deleteMark", "attr": "write"} + }, + "Heatmap": { + "get":"/Heatmap/query/get", + "find":"/Heatmap/query/find", + "types":"/Heatmap/query/findTypes", + "post":{"path": "/Heatmap/submit/json", "attr": "write"}, + "delete":{"path": "/Heatmap/delete/deleteHeatmap", "attr": "write"}, + "threshold":{"path": "/Heatmap/delete/updateThreshold", "attr": "write"} + }, + "Overlay": { + "get":"/Overlay/query/get", + "find":"/Overlay/query/find", + "post":{"path": "/Overlay/submit/json", "attr": "write"}, + "delete":{"path": "/Overlay/delete/deleteOverlay", "attr": "write"} + }, + "Slide": { + "get":"/Slide/query/get", + "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"}, + "test":{"path":"/Slide/query/find", "check_param": "collection"} + }, + "Template": { + "get":"/Template/query/get", + "find":"/Template/query/find", + "post":{"path": "/Template/submit/json", "attr": "write"}, + "delete":{"path": "/Template/delete/deleteTemplate", "attr": "write"} + }, + "HeatmapEdit": { + "get":"/HeatmapEdit/query/get", + "find":"/HeatmapEdit/query/find", + "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": { + "_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", + "before":["_files", ".dzi"] + } + } + }, + "load": { + "_base": "http://ca-load:4000", + "Upload": { + "start": {"path":"/upload/start", "attr": "write"}, + "continue":"/upload/continue", + "finish":"/upload/finish" + }, + "Slide":{ + "info":"/data/one", + "thumb":"/data/thumbnail" + } + }, + "auth": { + "_public": "true", + "_base": "http://ca-auth:8010", + "Token":{ + "check":"/check" + } + } + } +} diff --git a/config/routes.json b/config/routes.json index 2f7f27ee..b3b3567b 100644 --- a/config/routes.json +++ b/config/routes.json @@ -1,6 +1,9 @@ { "root":"http://ca-front:80/", "_root_public": "true", + "auth":{ + "key_field": "accessCollection" + }, "services":{ "data":{ "_base": "http://ca-data:9099/services/caMicroscope", @@ -33,7 +36,8 @@ "find":"/Slide/query/find", "post":{"path": "/Slide/submit/json", "attr": "write"}, "delete":{"path": "/Slide/delete/deleteSlide", "attr": "write"}, - "update":{"path": "/Slide/update/updateSlide", "attr": "write"} + "update":{"path": "/Slide/delete/updateSlide", "attr": "write"}, + "test":{"path":"/Slide/query/find", "check_param": "collection"} }, "Template": { "get":"/Template/query/get", @@ -47,10 +51,13 @@ "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":"" @@ -58,8 +65,8 @@ "Slide":{ "_resolver":{ "destination":"?DeepZoom={OUT}", - "url": "http://ca-pathdb/node/{IN}?_format=json", - "field":"field_iip_path[0].value", + "url":"http://ca-data:9099/services/caMicroscope/Slide/query/get?id={IN}", + "field":"location", "before":["_files", ".dzi"] } } @@ -76,12 +83,11 @@ "thumb":"/data/thumbnail" } }, - "pathdb":{ + "auth": { "_public": "true", - "_base": "http://quip-pathdb/", - "slide":{ - "info":"/node/", - "unmod":"" + "_base": "http://ca-auth:8010", + "Token":{ + "check":"/check" } } } diff --git a/develop.yml b/develop.yml index e91b88db..63935dac 100644 --- a/develop.yml +++ b/develop.yml @@ -49,10 +49,8 @@ services: ports: - "4010:4010" volumes: - - ./config/routes.json:/root/src/routes.json + - ./config/non-pathdb-routes.json:/root/src/routes.json - ./jwt_keys/:/keys/ - environment: - - DISABLE_SEC=true auth: build: "./Deps/auth_service/" volumes: From bef29e1767b1c8de42e65350912d10aadf982fc5 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Mon, 28 Oct 2019 15:14:03 -0400 Subject: [PATCH 3/8] some prep for camic pri dual --- .../caMicroscopePrivate.project | 1283 +++++++++++++++++ config/mongo_idx_pri.js | 1 + config/routes.json | 10 + config/run_idx.sh | 1 + 4 files changed, 1295 insertions(+) create mode 100644 config/bindaas_projects/caMicroscopePrivate.project create mode 100644 config/mongo_idx_pri.js diff --git a/config/bindaas_projects/caMicroscopePrivate.project b/config/bindaas_projects/caMicroscopePrivate.project new file mode 100644 index 00000000..356c8707 --- /dev/null +++ b/config/bindaas_projects/caMicroscopePrivate.project @@ -0,0 +1,1283 @@ +{ + "profiles": { + "Mark": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic-pri", + "collection": "mark", + "initialize": true + }, + "queryEndpoints": { + "get": { + "queryTemplate": "{\n\t\"_operation\" : \"find\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}} ,\n\t\t\t\t\t\t\t\"limit\" : 1\n\t\t\t\t\t\t}\n}\n ", + "metaData": {}, + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "get", + "timeCreated": "Wed Aug 29 18:40:50 UTC 2018", + "createdBy": "admin", + "description": " " + }, + "findTypesExec": { + "queryTemplate": "{ \"_operation\" : \"distinct\" , \"_operation_args\" : { \"field\" : \"provenance.analysis\", \"query\" : {\u0027provenance.image.slide\u0027: \"$slide$\",\u0027provenance.analysis.execution_id\u0027: $name$ } } } ", + "metaData": {}, + "tags": [], + "bindVariables": { + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "name": { + "name": "name", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "findTypesExec", + "timeCreated": "Thu May 09 15:09:53 GMT 2019", + "createdBy": "admin", + "description": " " + }, + "multiFind": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" :{$and: [\n{\"provenance.analysis.execution_id\": {$in: $name$},\n \"provenance.image.slide\" : \"$slide$\",\n \"footprint\": { $not: {$lt: $footprint$}},\n \"provenance.analysis.source\" : {$regex: \"$source$\", $options: \"i\"}},\n{\"x\": { $not: {$lt: $x0$}}},\n{\"x\": { $not: {$gt: $x1$}}},\n{\"y\": { $not: {$lt: $y0$}}},\n{\"y\": { $not: {$gt: $y1$}}}\n ]}\n}\n}\n ", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": true, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": false, + "defaultValue": "", + "description": "" + }, + "footprint": { + "name": "footprint", + "required": false, + "defaultValue": "0", + "description": "" + }, + "source": { + "name": "source", + "required": false, + "defaultValue": "", + "description": "" + }, + "x0": { + "name": "x0", + "required": false, + "defaultValue": "0", + "description": "" + }, + "x1": { + "name": "x1", + "required": false, + "defaultValue": "9", + "description": "" + }, + "y0": { + "name": "y0", + "required": false, + "defaultValue": "0", + "description": "" + }, + "y1": { + "name": "y1", + "required": false, + "defaultValue": "9", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "multiFind", + "timeCreated": "Tue Jul 02 17:47:09 GMT 2019", + "createdBy": "admin", + "description": " " + }, + "find": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" :{$and: [\n{\"provenance.analysis.execution_id\" : {$regex: \"$name$\", $options: \"i\"},\n \"provenance.image.slide\" : \"$slide$\",\n \"footprint\": { $not: {$lt: $footprint$}},\n \"provenance.analysis.source\" : {$regex: \"$source$\", $options: \"i\"}},\n{\"x\": { $not: {$lt: $x0$}}},\n{\"x\": { $not: {$gt: $x1$}}},\n{\"y\": { $not: {$lt: $y0$}}},\n{\"y\": { $not: {$gt: $y1$}}}\n ]}\n}\n}\n ", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": false, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": false, + "defaultValue": "", + "description": "" + }, + "source": { + "name": "source", + "required": false, + "defaultValue": "", + "description": "" + }, + "footprint": { + "name": "footprint", + "required": false, + "defaultValue": "0", + "description": "" + }, + "x0": { + "name": "x0", + "required": false, + "defaultValue": "0", + "description": "" + }, + "x1": { + "name": "x1", + "required": false, + "defaultValue": "9", + "description": "" + }, + "y0": { + "name": "y0", + "required": false, + "defaultValue": "0", + "description": "" + }, + "y1": { + "name": "y1", + "required": false, + "defaultValue": "9", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "find", + "timeCreated": "Tue Jul 02 17:48:26 GMT 2019", + "createdBy": "admin", + "description": " " + }, + "findBound": { + "queryTemplate": "{ \"_operation\" : \"find\" , \"_operation_args\" : { \"query\" : {\"provenance.analysis.execution_id\" : {$regex: \"$name$\", $options: \"i\"},\n \"provenance.image.slide\" : \"$slide$\",\n \"provenance.analysis.source\" : {$regex: \"$key$\", $options: \"i\"}, \"geometries.features.bound\": { $geoIntersects: { $geometry: { \"type\": \"Polygon\", \"coordinates\": [[[ $x0$, $y0$ ],[ $x0$, $y1$ ],[ $x1$, $y1$ ],[ $x1$, $y0$ ],[ $x0$, $y0$ ]]] } } } }, \"limit\" : 1000} } ", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": false, + "defaultValue": "", + "description": "" + }, + "key": { + "name": "key", + "required": false, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": false, + "defaultValue": "", + "description": "" + }, + "x0": { + "name": "x0", + "required": true, + "defaultValue": "", + "description": "" + }, + "y0": { + "name": "y0", + "required": true, + "defaultValue": "", + "description": "" + }, + "x1": { + "name": "x1", + "required": true, + "defaultValue": "", + "description": "" + }, + "y1": { + "name": "y1", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "findBound", + "timeCreated": "Tue Jul 02 17:49:32 GMT 2019", + "createdBy": "admin", + "description": "find where bound intersects given rect " + }, + "findTypes": { + "queryTemplate": "{ \"_operation\" : \"distinct\" , \"_operation_args\" : { \"field\" : \"provenance.analysis\", \"query\" : {\u0027provenance.image.slide\u0027: \"$slide$\" } } } ", + "metaData": {}, + "tags": [], + "bindVariables": { + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "findTypes", + "timeCreated": "Tue Jul 02 18:37:03 GMT 2019", + "createdBy": "admin", + "description": " " + } + }, + "deleteEndpoints": { + "deleteMark": { + "queryTemplate": "{\n\t\"_operation\" : \"delete\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}, \u0027provenance.image.slide\u0027: \"$slide$\" }\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "deleteMark", + "timeCreated": "Tue Jul 02 18:20:50 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Wed Aug 01 17:23:41 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Wed Aug 01 17:23:41 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Wed Aug 01 17:23:41 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Wed Aug 01 17:23:41 UTC 2018", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Mark", + "timeCreated": "Wed Aug 01 17:23:41 UTC 2018", + "createdBy": "admin", + "description": "Geospatial Marking Objects" + }, + "Overlay": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic-pri", + "collection": "overlay", + "initialize": true + }, + "queryEndpoints": { + "get": { + "queryTemplate": "{\n\t\"_operation\" : \"find\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}} ,\n\t\t\t\t\t\t\t\"limit\" : 1\n\t\t\t\t\t\t}\n}\n ", + "metaData": {}, + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "get", + "timeCreated": "Wed Aug 29 18:41:00 UTC 2018", + "createdBy": "admin", + "description": " " + }, + "find": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" : { \"name\" : {$regex: \"$name$\", $options: \"i\"},\n\"slide\" : \"$slide$\",\n\"location\" : {$regex: \"$location$\", $options: \"i\"}}\n}\n} ", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": false, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "location": { + "name": "location", + "required": false, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "find", + "timeCreated": "Mon Jul 08 16:18:19 GMT 2019", + "createdBy": "admin", + "description": " " + } + }, + "deleteEndpoints": { + "updateOverlay": { + "queryTemplate": "{\n\t\"_operation\" : \"update\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027slide\u0027 : \"$slide$\", \u0027_id\u0027 : {\"$oid\":\"$id$\"}} ,\n\t\t\t\t\t\t\t\"update\": {$set: { \u0027$field$\u0027 : \u0027$value$\u0027 }},\n\t\t\t\t\t\t\t\"upsert\": \u0027true\u0027,\n\t\t\t\t\t\t\t\"multi\" : \u0027false\u0027\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + }, + "field": { + "name": "field", + "required": true, + "defaultValue": "", + "description": "" + }, + "value": { + "name": "value", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "updateOverlay", + "timeCreated": "Tue Jul 02 18:21:53 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "deleteOverlay": { + "queryTemplate": "{\n\t\"_operation\" : \"delete\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}, \u0027slide\u0027: \"$slide$\" }\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "deleteOverlay", + "timeCreated": "Tue Jul 02 18:22:07 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Wed Aug 01 17:24:16 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Wed Aug 01 17:24:16 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Wed Aug 01 17:24:16 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Wed Aug 01 17:24:16 UTC 2018", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Overlay", + "timeCreated": "Wed Aug 01 17:24:16 UTC 2018", + "createdBy": "admin", + "description": "Overlay Representation" + }, + "Slide": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic-pri", + "collection": "slide", + "initialize": true + }, + "queryEndpoints": { + "get": { + "queryTemplate": "{\n\t\"_operation\" : \"find\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}} ,\n\t\t\t\t\t\t\t\"limit\" : 1\n\t\t\t\t\t\t}\n}\n ", + "metaData": {}, + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "get", + "timeCreated": "Wed Aug 29 18:41:29 UTC 2018", + "createdBy": "admin", + "description": " " + }, + "find": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" : {\u0027name\u0027: {$regex: \"$slide$\", $options: \"i\"},\n \u0027specimen\u0027: {$regex: \"$specimen$\", $options: \"i\"},\n \u0027study\u0027: {$regex: \"$study$\", $options: \"i\"},\n \u0027location\u0027: {$regex: \"$location$\", $options: \"i\"},\n \u0027collection: $collection$\"\n}\n}\n} ", + "metaData": {}, + "tags": [], + "bindVariables": { + "slide": { + "name": "slide", + "required": false, + "defaultValue": "", + "description": "" + }, + "location": { + "name": "location", + "required": false, + "defaultValue": "", + "description": "" + }, + "specimen": { + "name": "specimen", + "required": false, + "defaultValue": "", + "description": "" + }, + "study": { + "name": "study", + "required": false, + "defaultValue": "", + "description": "" + }, + "collection": { + "name": "collection", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "find", + "timeCreated": "Mon Oct 28 19:07:35 GMT 2019", + "createdBy": "admin", + "description": " " + } + }, + "deleteEndpoints": { + "updateSlide": { + "queryTemplate": "{\n\t\"_operation\" : \"update\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027name\u0027 : $slide$} ,\n\t\t\t\t\t\t\t\"update\": {$set: { \u0027$field$\u0027 : \u0027$value$\u0027 }},\n\t\t\t\t\t\t\t\"upsert\": \u0027true\u0027,\n\t\t\t\t\t\t\t\"multi\" : \u0027false\u0027\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "field": { + "name": "field", + "required": true, + "defaultValue": "", + "description": "" + }, + "value": { + "name": "value", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "updateSlide", + "timeCreated": "Tue Jul 02 18:21:13 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "deleteSlide": { + "queryTemplate": "{\n\t\"_operation\" : \"delete\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027slide.name\u0027 : \"\"$slide$\"\" }\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "deleteSlide", + "timeCreated": "Tue Jul 02 18:21:26 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Wed Aug 01 17:24:37 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Wed Aug 01 17:24:37 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Wed Aug 01 17:24:37 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Wed Aug 01 17:24:37 UTC 2018", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Slide", + "timeCreated": "Wed Aug 01 17:24:37 UTC 2018", + "createdBy": "admin", + "description": "Represents Slide Objects" + }, + "Template": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic-pri", + "collection": "template", + "initialize": true + }, + "queryEndpoints": { + "find": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" : {\"name\": {$regex: \"$name$\", $options: \"i\"},\n \"type\": {$regex: \"$type$\", $options: \"i\"}}\n}\n} ", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": false, + "defaultValue": "", + "description": "" + }, + "type": { + "name": "type", + "required": false, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "find", + "timeCreated": "Mon Aug 27 15:46:51 UTC 2018", + "createdBy": "admin", + "description": " " + }, + "get": { + "queryTemplate": "{\n\t\"_operation\" : \"find\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}} ,\n\t\t\t\t\t\t\t\"limit\" : 1\n\t\t\t\t\t\t}\n}\n ", + "metaData": {}, + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "get", + "timeCreated": "Wed Aug 29 18:41:36 UTC 2018", + "createdBy": "admin", + "description": " " + } + }, + "deleteEndpoints": { + "deleteTemplate": { + "queryTemplate": "{\n\t\"_operation\" : \"delete\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}}\n\t\t\t\t\t\t}\n} ", + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "deleteTemplate", + "timeCreated": "Wed Aug 29 18:44:30 UTC 2018", + "createdBy": "admin", + "description": "" + } + }, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Wed Aug 01 17:25:14 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Wed Aug 01 17:25:14 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Wed Aug 01 17:25:14 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Wed Aug 01 17:25:14 UTC 2018", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Template", + "timeCreated": "Wed Aug 01 17:25:14 UTC 2018", + "createdBy": "admin", + "description": "Templates for Forms, JSONFORM type" + }, + "Authorization": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic-pri", + "collection": "authorization", + "initialize": true + }, + "queryEndpoints": { + "getAuth": { + "queryTemplate": "{\n\t\"_operation\" : \"find\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027name\u0027 : \u0027$name$\u0027 }\n\t\t\t\t\t\t}\n}\n", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "getAuth", + "timeCreated": "Fri Aug 10 19:27:36 UTC 2018", + "createdBy": "admin", + "description": "get auth for user" + } + }, + "deleteEndpoints": {}, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Fri Aug 10 19:26:51 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Fri Aug 10 19:26:51 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Fri Aug 10 19:26:51 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Fri Aug 10 19:26:51 UTC 2018", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Authorization", + "timeCreated": "Fri Aug 10 19:26:51 UTC 2018", + "createdBy": "admin", + "description": "authorization for slides and collections" + }, + "Heatmap": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic-pri", + "collection": "heatmap", + "initialize": true + }, + "queryEndpoints": { + "findTypes": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" : { \"provenance.analysis.execution_id\" : {$regex: \"$name$\", $options: \"i\"},\n\"provenance.image.slide\" : \"$slide$\"},\n\"fields\" :{ \u0027data\u0027 : 0 }\n}\n\n} ", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": false, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": false, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "findTypes", + "timeCreated": "Thu Jun 27 19:39:21 GMT 2019", + "createdBy": "admin", + "description": " " + }, + "find": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" : { \"provenance.analysis.execution_id\" : {$regex: \"$name$\", $options: \"i\"},\n\"provenance.image.slide\" : \"$slide$\"\n}\n} ", + "metaData": {}, + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": false, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": false, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "find", + "timeCreated": "Thu Jun 27 19:40:22 GMT 2019", + "createdBy": "admin", + "description": " " + }, + "get": { + "queryTemplate": "{\n\t\u0027_operation\u0027: \u0027find\u0027,\n\t\u0027_operation_args\u0027: \n\t{\n\t\u0027query\u0027: {\n\t\t\"provenance.image.slide\": \"$slide$\",\n\t\t\"provenance.analysis.execution_id\":\"$name$\"\n\t},\n\t\t\u0027fields\u0027: {\n\t\t\t\u0027provenance\u0027:1,\n\u0027data\u0027:1,\n\t\t\t\u0027_id\u0027: 1\n\t\t}\n\t}\n} ", + "metaData": {}, + "tags": [], + "bindVariables": { + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "name": { + "name": "name", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "get", + "timeCreated": "Mon Jul 01 20:07:42 GMT 2019", + "createdBy": "admin", + "description": " " + } + }, + "deleteEndpoints": { + "deleteHeatmap": { + "queryTemplate": "{\n\t\"_operation\" : \"delete\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}, \u0027provenance.image.slide\u0027: \"$slide$\" }\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "deleteHeatmap", + "timeCreated": "Wed Nov 14 16:24:04 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "updateThreshold": { + "queryTemplate": "{\n\t\"_operation\" : \"update\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : {\u0027provenance.analysis.execution_id\u0027 : \u0027$name$\u0027,\u0027provenance.image.slide\u0027 : \"$slide$\"} ,\n\t\t\t\t\t\t\t\"update\": {$set: { \u0027provenance.analysis.fields\u0027 : $fields$,\u0027provenance.analysis.setting\u0027 : $setting$ }},\n\t\t\t\t\t\t\t\"upsert\": true,\n\t\t\t\t\t\t\t\"multi\" : true\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "name": { + "name": "name", + "required": true, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "fields": { + "name": "fields", + "required": true, + "defaultValue": "", + "description": "" + }, + "setting": { + "name": "setting", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "updateThreshold", + "timeCreated": "Tue Jul 02 17:06:06 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Wed Nov 14 15:49:26 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Wed Nov 14 15:49:26 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Wed Nov 14 15:49:26 UTC 2018", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Wed Nov 14 15:49:26 UTC 2018", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Heatmap", + "timeCreated": "Wed Nov 14 15:49:26 UTC 2018", + "createdBy": "admin", + "description": "Point Marking Objects" + }, + "HeatmapEdit": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic-pri", + "collection": "heatmapEdit", + "initialize": true + }, + "queryEndpoints": { + "get": { + "queryTemplate": "{\n\t\"_operation\" : \"find\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027_id\u0027 : {\"$oid\":\"$id$\"}} ,\n\t\t\t\t\t\t\t\"limit\" : 1\n\t\t\t\t\t\t}\n}", + "metaData": {}, + "tags": [], + "bindVariables": { + "id": { + "name": "id", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "get", + "timeCreated": "Wed Apr 24 18:10:50 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "find": { + "queryTemplate": "{\n \"_operation\" : \"find\" ,\n \"_operation_args\" : {\n\"query\" : {\u0027user_id\u0027: {$regex: \"$user$\", $options: \"i\"},\n \u0027provenance.image.slide\u0027: \"$slide$\",\n \u0027provenance.analysis.execution_id\u0027: {$regex: \"$name$\", $options: \"i\"}}\n}\n}", + "metaData": {}, + "tags": [], + "bindVariables": { + "user": { + "name": "user", + "required": false, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": false, + "defaultValue": "", + "description": "" + }, + "name": { + "name": "name", + "required": false, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "outputFormat": { + "outputFormat": "JSON" + }, + "name": "find", + "timeCreated": "Thu Jun 27 19:40:01 GMT 2019", + "createdBy": "admin", + "description": " " + } + }, + "deleteEndpoints": { + "update": { + "queryTemplate": "{\n\t\"_operation\" : \"update\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027user_id\u0027 : \u0027$user$\u0027, \u0027provenance.image.specimen\u0027:\u0027$specimen$\u0027, \n\u0027provenance.image.slide\u0027:\"$slide$\",\u0027provenance.analysis.execution_id\u0027:\u0027$name$\u0027 } ,\n\t\t\t\t\t\t\t\"update\": {$set: { \u0027data\u0027 : $data$}},\n\t\t\t\t\t\t\t\"upsert\": true,\n\t\t\t\t\t\t\t\"multi\" : true\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "user": { + "name": "user", + "required": true, + "defaultValue": "", + "description": "" + }, + "specimen": { + "name": "specimen", + "required": true, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "name": { + "name": "name", + "required": true, + "defaultValue": "", + "description": "" + }, + "data": { + "name": "data", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "update", + "timeCreated": "Tue Jul 02 17:50:23 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "delete": { + "queryTemplate": "{\n\t\"_operation\" : \"delete\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027user_id\u0027 : \u0027$user$\u0027,\u0027provenance.image.slide\u0027: \"$slide$\", \u0027provenance.analysis.execution_id\u0027: \"$name$\" }\n\t\t\t\t\t\t}\n}\n ", + "tags": [], + "bindVariables": { + "user": { + "name": "user", + "required": true, + "defaultValue": "", + "description": "" + }, + "slide": { + "name": "slide", + "required": true, + "defaultValue": "", + "description": "" + }, + "name": { + "name": "name", + "required": true, + "defaultValue": "", + "description": "" + } + }, + "stage": "UNVERIFIED", + "name": "delete", + "timeCreated": "Tue Jul 02 18:24:29 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Wed Apr 24 18:02:23 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Wed Apr 24 18:02:23 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Wed Apr 24 18:02:23 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Wed Apr 24 18:02:23 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "HeatmapEdit", + "timeCreated": "Wed Apr 24 18:02:21 GMT 2019", + "createdBy": "admin", + "description": "Edit Data for Heatmaps" + } + }, + "params": {}, + "name": "caMicroscopePrivate", + "timeCreated": "Wed Aug 01 17:17:55 UTC 2018", + "createdBy": "admin", + "description": "caMicroscope using another db and some additional fields" +} \ No newline at end of file diff --git a/config/mongo_idx_pri.js b/config/mongo_idx_pri.js new file mode 100644 index 00000000..2617db89 --- /dev/null +++ b/config/mongo_idx_pri.js @@ -0,0 +1 @@ +db.slide.createIndex({'study':1, 'specimen': 1, 'name': 1, 'collection': 1}) diff --git a/config/routes.json b/config/routes.json index b3b3567b..d7d94f7f 100644 --- a/config/routes.json +++ b/config/routes.json @@ -57,6 +57,16 @@ "post":{"path": "/Authorization/submit/json", "attr": "admin"} } }, + "private":{ + "_base": "http://ca-data:9099/services/caMicroscopePrivate", + "Slide": { + "get":"/Slide/query/get", + "find":{"path": "/Slide/query/find","check_param": "collection"}, + "post":{"path": "/Slide/submit/json", "attr": "write"}, + "delete":{"path": "/Slide/delete/deleteSlide", "attr": "write"}, + "update":{"path": "/Slide/delete/updateSlide", "attr": "write"} + } + }, "img": { "_base":"http://ca-iip/fcgi-bin/iipsrv.fcgi", "IIP": { diff --git a/config/run_idx.sh b/config/run_idx.sh index 314f02a1..25b43aab 100755 --- a/config/run_idx.sh +++ b/config/run_idx.sh @@ -4,6 +4,7 @@ do done mongo --host ca-mongo camic /config/mongo_idx.js +mongo --host ca-mongo camic-pri /config/mongo_idx_pri.js echo "indexes created" mongo --host ca-mongo camic /config/add_mongo_users.js echo "users created" From f7a1a817787618eae405b80908bf3a5b802e6a20 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Tue, 29 Oct 2019 16:56:26 -0400 Subject: [PATCH 4/8] log item post support --- config/bindaas_projects/caMicroscope.project | 55 ++++++++++++++++++++ config/routes.json | 3 ++ 2 files changed, 58 insertions(+) diff --git a/config/bindaas_projects/caMicroscope.project b/config/bindaas_projects/caMicroscope.project index da2fc9c3..5d2ecd6e 100644 --- a/config/bindaas_projects/caMicroscope.project +++ b/config/bindaas_projects/caMicroscope.project @@ -1267,6 +1267,61 @@ "timeCreated": "Wed Apr 24 18:02:21 GMT 2019", "createdBy": "admin", "description": "Edit Data for Heatmaps" + }, + "Log": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic", + "collection": "log", + "initialize": true + }, + "queryEndpoints": {}, + "deleteEndpoints": {}, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Log", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin", + "description": "log" } }, "params": {}, diff --git a/config/routes.json b/config/routes.json index d7d94f7f..120b8419 100644 --- a/config/routes.json +++ b/config/routes.json @@ -55,6 +55,9 @@ "Auth": { "get":{"path": "/Authorization/query/getAuth", "attr": "admin"}, "post":{"path": "/Authorization/submit/json", "attr": "admin"} + }, + "Log": { + "post": "/Log/submit/json" } }, "private":{ From 5db1c9060128e2e8141a804291eefac7561e2460 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Tue, 29 Oct 2019 17:54:12 -0400 Subject: [PATCH 5/8] add log to routes --- config/non-pathdb-routes.json | 3 +++ config/pathdb_routes.json | 3 +++ 2 files changed, 6 insertions(+) diff --git a/config/non-pathdb-routes.json b/config/non-pathdb-routes.json index 49ddf99f..6de515c2 100644 --- a/config/non-pathdb-routes.json +++ b/config/non-pathdb-routes.json @@ -56,6 +56,9 @@ "Auth": { "get":{"path": "/Authorization/query/getAuth", "attr": "admin"}, "post":{"path": "/Authorization/submit/json", "attr": "admin"} + }, + "Log": { + "post": "/Log/submit/json" } }, "img": { diff --git a/config/pathdb_routes.json b/config/pathdb_routes.json index 6ca916e0..95cf3fec 100644 --- a/config/pathdb_routes.json +++ b/config/pathdb_routes.json @@ -47,6 +47,9 @@ "post":{"path": "/HeatmapEdit/submit/json", "attr": "write"}, "delete":{"path": "/HeatmapEdit/delete/delete", "attr": "write"}, "update":{"path": "/HeatmapEdit/delete/update", "attr": "write"} + }, + "Log": { + "post": "/Log/submit/json" } }, "img": { From 5c38157200df184ef5257b849de8a131b320cbd9 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Wed, 30 Oct 2019 12:55:13 -0400 Subject: [PATCH 6/8] bump camic to 3.5.7 --- caMicroscope.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/caMicroscope.yml b/caMicroscope.yml index 1403311e..e2ab945d 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -40,7 +40,7 @@ services: volumes: - ./images/:/images/ viewer: - build: "https://github.com/camicroscope/caMicroscope.git#v3.5.6" + build: "https://github.com/camicroscope/caMicroscope.git#v3.5.7" container_name: ca-front restart: unless-stopped volumes: From adffd624bc92e0e004206fdb04901945d0c6c82e Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Wed, 30 Oct 2019 15:42:04 -0400 Subject: [PATCH 7/8] Update quip-pathdb.yml --- quip-pathdb.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/quip-pathdb.yml b/quip-pathdb.yml index f97730ab..bdc1a4c7 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -53,7 +53,7 @@ services: logging: driver: none pathdb: - build: "https://github.com/SBU-BMI/PathDB.git#1.2.1" + build: "https://github.com/SBU-BMI/PathDB.git#1.2.2" container_name: quip-pathdb restart: unless-stopped ports: ["443:443","80:80"] From 1ec5690e786f2940227864a1eb79cbc47c719b63 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Wed, 30 Oct 2019 16:28:42 -0400 Subject: [PATCH 8/8] re disable dev sec --- develop.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/develop.yml b/develop.yml index 63935dac..787ee55a 100644 --- a/develop.yml +++ b/develop.yml @@ -48,6 +48,8 @@ services: container_name: ca-security ports: - "4010:4010" + environment: + - DISABLE_SEC=true volumes: - ./config/non-pathdb-routes.json:/root/src/routes.json - ./jwt_keys/:/keys/