From 0e8db3439355a10e267d0951906a66f95a3e6aac Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Thu, 7 Nov 2019 12:26:01 -0500 Subject: [PATCH 1/3] ignore pathdb relics --- config/.gitignore | 2 ++ data/.gitignore | 1 + 2 files changed, 3 insertions(+) create mode 100644 config/.gitignore create mode 100644 data/.gitignore diff --git a/config/.gitignore b/config/.gitignore new file mode 100644 index 00000000..fc9ec9dd --- /dev/null +++ b/config/.gitignore @@ -0,0 +1,2 @@ +pathdbmysql.cnf +pathdb/*.css diff --git a/data/.gitignore b/data/.gitignore new file mode 100644 index 00000000..db19e7e7 --- /dev/null +++ b/data/.gitignore @@ -0,0 +1 @@ +pathdb/mysql From 7c0be9535bc00186163602bc3bc46be0abe76c4b Mon Sep 17 00:00:00 2001 From: Nan Li Date: Fri, 8 Nov 2019 04:25:36 -0500 Subject: [PATCH 2/3] add 'configuration' collection for configuring preset labels. add 'getConfigByName' function/router for API (get different configurations by using `name`). --- config/bindaas_projects/caMicroscope.project | 93 +++++++++++++++++++- config/routes.json | 3 + 2 files changed, 92 insertions(+), 4 deletions(-) diff --git a/config/bindaas_projects/caMicroscope.project b/config/bindaas_projects/caMicroscope.project index 5d2ecd6e..fdad1bb4 100644 --- a/config/bindaas_projects/caMicroscope.project +++ b/config/bindaas_projects/caMicroscope.project @@ -1286,7 +1286,8 @@ }, "name": "csvFile", "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", - "createdBy": "admin" + "createdBy": "admin", + "description": "" }, "jsonFile": { "type": "MULTIPART", @@ -1295,7 +1296,8 @@ }, "name": "jsonFile", "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", - "createdBy": "admin" + "createdBy": "admin", + "description": "" }, "csv": { "type": "FORM_DATA", @@ -1304,7 +1306,8 @@ }, "name": "csv", "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", - "createdBy": "admin" + "createdBy": "admin", + "description": "" }, "json": { "type": "FORM_DATA", @@ -1313,7 +1316,8 @@ }, "name": "json", "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", - "createdBy": "admin" + "createdBy": "admin", + "description": "" } }, "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", @@ -1322,6 +1326,87 @@ "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", "createdBy": "admin", "description": "log" + }, + "Configuration": { + "dataSource": { + "host": "ca-mongo", + "port": "27017", + "db": "camic", + "collection": "configuration", + "initialize": true + }, + "queryEndpoints": { + "getConfigByName": { + "queryTemplate": "{\n\t\"_operation\" : \"find\" ,\n\t\"_operation_args\" : {\n\t\t\t\t\t\t\t\"query\" : { \u0027config_name\u0027 : \"$name$\"} ,\n\t\t\t\t\t\t\t\"limit\" : 1\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": "getConfigByName", + "timeCreated": "Thu Nov 07 17:09:07 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "deleteEndpoints": {}, + "submitEndpoints": { + "csvFile": { + "type": "MULTIPART", + "properties": { + "inputType": "CSV_FILE" + }, + "name": "csvFile", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "jsonFile": { + "type": "MULTIPART", + "properties": { + "inputType": "JSON_FILE" + }, + "name": "jsonFile", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "csv": { + "type": "FORM_DATA", + "properties": { + "inputType": "CSV" + }, + "name": "csv", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin", + "description": "" + }, + "json": { + "type": "FORM_DATA", + "properties": { + "inputType": "JSON" + }, + "name": "json", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin", + "description": "" + } + }, + "providerId": "edu.emory.cci.bindaas.datasource.provider.mongodb.MongoDBProvider", + "providerVersion": 1, + "name": "Configuration", + "timeCreated": "Tue Oct 29 20:54:11 GMT 2019", + "createdBy": "admin", + "description": "configuration" } }, "params": {}, diff --git a/config/routes.json b/config/routes.json index 120b8419..208643e5 100644 --- a/config/routes.json +++ b/config/routes.json @@ -58,6 +58,9 @@ }, "Log": { "post": "/Log/submit/json" + }, + "Configuration": { + "getConfigByName": "/Configuration/query/getConfigByName" } }, "private":{ From d8680b1cea5fa97c3c91b5405a1295bb2a954c45 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Mon, 11 Nov 2019 11:16:02 -0500 Subject: [PATCH 3/3] 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 20306d3a..34321216 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#1.2.3" + build: "https://github.com/SBU-BMI/PathDB.git#1.3.0" container_name: quip-pathdb restart: unless-stopped ports: ["443:443","80:80"]