Updated qresp version servers

qresp-code-development · Sep 20, 2019 · 65d776d · 65d776d
1 parent 183c1d3
commit 65d776d
Show file tree

Hide file tree

Showing 17 changed files with 179 additions and 295 deletions.
diff --git a/.gitignore b/.gitignore
@@ -9,5 +9,5 @@ web/project/__pycache__/
 web/build/
 web/qresp.egg-info/
 .cache/
-web/project/config.ini 
+web/project/config_test.ini 
 web/project/tests/__pycache__/
diff --git a/docker-compose.yml.services b/docker-compose.yml.services
@@ -5,28 +5,22 @@ services:
     restart: always
     build: ./web
     expose:
-      - 8080
-    ports:
-      - "8080:8080"
+      - "8080"
+    environment:
+      - PYTHONUNBUFFERED=TRUE
     volumes:
+      - /usr/src/app/web/project/static
       - ./web/:/usr/src/app/web
-    environment:
-      - KEY=<insert key>
-      - GOOGLE_CLIENT_ID=<insert google client id>
-      - GOOGLE_CLIENT_SECRET=<insert google client secret>
-      - REDIRECT_URI=<insert redirect uri>
-      - MAIL_ADDR=<administrators mail address>
-      - MAIL_PWD=<administrators password>
-    command: python run.py --host=0.0.0.0 --port 8080
+      - ./papercollection:/home/flask/app/web/papers
+    command: /usr/local/bin/gunicorn --enable-stdio-inheritance -w 4 -b :8080 project:app
 
   nginx:
     restart: always
     build: ./nginx
     ports:
-      - "8001:8001"
+      - "443:443"
     volumes:
       - /www/static
-      - ./papercollection:/usr/src/files
     volumes_from:
       - web
     depends_on:

diff --git a/web/papers/files_paper/data.json b/web/papers/files_paper/data.json
@@ -1,53 +1,90 @@
 {
    "PIs":[
       {
-         "firstName":"Giulia",
-         "lastName":"Galli",
+         "firstName":"John",
+         "lastName":"Doe",
          "middleName":""
       },
       {
-         "firstName":"Marco",
-         "lastName":"Govoni",
-         "middleName":"L"
+         "firstName":"Jane",
+         "lastName":"Gill",
+         "middleName":""
+      }
+   ],
+   "charts":[
+      {
+         "caption":"c0",
+         "extraFields":[
+            {
+               "extrakey":"",
+               "extravalue":""
+            }
+         ],
+         "files":[
+            "/charts/figure1/figure1.csv",
+            "/charts/figure1/figure1.ipynb",
+            "/charts/figure1/figure1.jpg"
+         ],
+         "id":"c0",
+         "imageFile":"/charts/figure1/figure1.jpg",
+         "notebookFile":"/charts/figure1/figure1.ipynb",
+         "number":"0",
+         "properties":[
+            "band gap"
+         ]
       }
    ],
-   "charts":[],
    "collections":[
       "MICCOM"
    ],
-   "datasets":[],
+   "datasets":[
+      {
+         "URLs":[
+            ""
+         ],
+         "extraFields":[
+            {
+               "extrakey":"",
+               "extravalue":""
+            }
+         ],
+         "files":[
+            "/datasets/datasetA.dat",
+            "/datasets/datasetB.dat"
+         ],
+         "id":"d0",
+         "readme":"These are datasets"
+      }
+   ],
    "documentation":{
-      "readme":""
+      "readme":"This is additional content"
    },
    "heads":[
       {
-         "URLs":null,
-         "id":"t0",
-         "readme":null
-      },
-      {
-         "URLs":null,
-         "id":"d0",
-         "readme":null
+         "URLs":[
+            ""
+         ],
+         "id":"h0",
+         "readme":"External setup info"
       }
    ],
    "info":{
       "ProjectName":"paper",
       "doi":null,
-      "downloadPath":"",
+      "downloadPath":"https://app.globus.org/file-manager?origin_id=72277ed4-1ad3-11e7-bbe1-22000b9a448b&origin_path=",
       "fileServerPath":"https://notebook.rcc.uchicago.edu/files/paper",
-      "gitPath":"",
+      "gitPath":"Y",
       "insertedBy":{
-         "affiliation":"Department of Chem",
+         "affiliation":"Dept of Chem, UC",
          "emailId":"[email protected]",
          "firstName":"John",
          "lastName":"Doe",
-         "middleName":""
+         "middleName":"H."
       },
       "isPublic":true,
-      "notebookFile":"toc.ipynb",
-      "notebookPath":"",
-      "timeStamp":"2019-09-19 21:00:59"
+      "notebookFile":"/toc.ipynb",
+      "notebookPath":"https://notebook.rcc.uchicago.edu/files",
+      "timeStamp":"2019-09-20 12:32:56"
    },
    "reference":{
       "DOI":"10.1021/jacs.6b00225",
@@ -62,26 +99,6 @@
             "firstName":"Marco",
             "lastName":"Govoni",
             "middleName":""
-         },
-         {
-            "firstName":"Robert",
-            "lastName":"Seidel",
-            "middleName":""
-         },
-         {
-            "firstName":"Jonathan",
-            "lastName":"Skone",
-            "middleName":"H."
-         },
-         {
-            "firstName":"Bernd",
-            "lastName":"Winter",
-            "middleName":""
-         },
-         {
-            "firstName":"Giulia",
-            "lastName":"Galli",
-            "middleName":""
          }
       ],
       "journal":{
@@ -90,7 +107,7 @@
       },
       "kind":"journal",
       "page":"6912-6915",
-      "publishedAbstract":"We present a combined computational and experimental study of the photoelectron spectrum of a simple aqueous solution of NaCl. Measurements were conducted on microjets, and first-principles calculations were performed using hybrid functionals and many-body perturbation theory at the G0W0 level, starting with wave functions computed in ab initio molecular dynamics simulations. We show excellent agreement between theory and experiments for the positions of both the solute and solvent excitation energies on an absolute energy scale and for peak intensities. The best comparison was obtained using wave functions obtained with dielectric-dependent self-consistent and range-separated hybrid functionals. Our computational protocol opens the way to accurate, predictive calculations of the electronic properties of electrolytes, of interest to a variety of energy problems.",
+      "publishedAbstract":"This is abstract",
       "school":"",
       "title":"Photoelectron Spectra of Aqueous Solutions from First Principles",
       "volume":"138",
@@ -109,28 +126,11 @@
             }
          ],
          "files":[
-            "scripts/fileA.py",
-            "scripts/fileB.py"
+            "/scripts/fileA.py",
+            "/scripts/fileB.py"
          ],
          "id":"s0",
-         "readme":"Python scripts"
-      },
-      {
-         "URLs":[
-            ""
-         ],
-         "extraFields":[
-            {
-               "extrakey":"",
-               "extravalue":""
-            }
-         ],
-         "files":[
-            "datasets/datasetA.dat",
-            "datasets/datasetB.dat"
-         ],
-         "id":"s1",
-         "readme":"DAT files"
+         "readme":"These are scripts"
       }
    ],
    "tags":[
@@ -142,7 +142,7 @@
          "URLs":[
             ""
          ],
-         "description":"Modified west code",
+         "description":"This is a software",
          "extraFields":[
             {
                "extrakey":"",
@@ -155,10 +155,32 @@
          "measurement":"",
          "packageName":"West",
          "patches":[
-            "tools/modded_qbox.diff"
+            "/tools/modded_qbox.diff"
          ],
          "programName":"wstat.x",
          "version":"3.0.0"
+      },
+      {
+         "URLs":[
+            ""
+         ],
+         "description":"",
+         "extraFields":[
+            {
+               "extrakey":"",
+               "extravalue":""
+            }
+         ],
+         "facilityName":"APS",
+         "id":"t1",
+         "kind":"experiment",
+         "measurement":"X-ray emission",
+         "packageName":"",
+         "patches":[
+            ""
+         ],
+         "programName":"",
+         "version":""
       }
    ],
    "version":2,
@@ -177,24 +199,26 @@
             "t0",
             "s0"
          ],
+         [
+            "t1",
+            "s0"
+         ],
          [
             "s0",
             "d0"
          ],
          [
             "d0",
             "c0"
-         ],
-         [
-            "t1",
-            "s0"
          ]
       ],
       "nodes":[
+         "t0",
+         "c0",
+         "d0",
+         "t1",
          "h0",
-         "s0",
-         "s1",
-         "t0"
+         "s0"
       ]
    }
 }
diff --git a/web/project/__init__.py b/web/project/__init__.py
@@ -26,13 +26,13 @@
 CORS(app)
 
 #initialize db
-if Config.get_setting('DEV','MONGODB_HOST'):
+if Config.get_setting('PROD','MONGODB_HOST'):
     db = MongoEngine()
-    app.config['MONGODB_HOST'] = Config.get_setting('DEV','MONGODB_HOST')
-    app.config['MONGODB_PORT'] = int(Config.get_setting('DEV','MONGODB_PORT'))
-    app.config['MONGODB_USERNAME'] = Config.get_setting('DEV','MONGODB_USERNAME')
-    app.config['MONGODB_PASSWORD'] = Config.get_setting('DEV','MONGODB_PASSWORD')
-    app.config['MONGODB_DB'] = Config.get_setting('DEV','MONGODB_DB_NAME')
+    app.config['MONGODB_HOST'] = Config.get_setting('PROD','MONGODB_HOST')
+    app.config['MONGODB_PORT'] = int(Config.get_setting('PROD','MONGODB_PORT'))
+    app.config['MONGODB_USERNAME'] = Config.get_setting('PROD','MONGODB_USERNAME')
+    app.config['MONGODB_PASSWORD'] = Config.get_setting('PROD','MONGODB_PASSWORD')
+    app.config['MONGODB_DB'] = Config.get_setting('PROD','MONGODB_DB_NAME')
     db.init_app(app)
 
 from project import routes
diff --git a/web/project/config.ini b/web/project/config.ini
@@ -0,0 +1,46 @@
+[GLOBAL] # please set these if you'd like to run your own version of Qresp service
+FLASK_APP = run.py
+FLASK_DEBUG = 1
+HOST_ADDR = 172.17.0.1
+FROM_ADDR = [email protected]
+;MAIL_ADDR = # mail address from which emails are sent to administrators about insertion of metadata
+QRESP_SERVER_URL = https://paperstack.uchicago.edu/static/qresp_servers.json
+SCHEMA_URL = https://paperstack.uchicago.edu/static/v1_1.json
+HTTP_SERVER_URL = https://paperstack.uchicago.edu/static/http_servers.json
+
+[DEV] #development environment variables
+;REDIRECT_URI = #https://domain.edu/oauth2callback
+;# optional section to add google api use google api to add qresp app and generate client id
+;GOOGLE_CLIENT_ID = # google client id
+;GOOGLE_CLIENT_SECRET = # The google api secret key
+;# optional section to host own version of mongo database
+;MONGODB_HOST = # x.univ.edu
+;MONGODB_PORT = 27017
+;MONGODB_USERNAME = # mongodb username
+;MONGODB_PASSWORD = # mongodb password
+;MONGODB_DB_NAME = # mongodb name
+;QRESP_DB_SECRET_KEY = # /admin database access secret key
+
+[PROD] #production environment variables
+;REDIRECT_URI = #https://domain.edu/oauth2callback
+;# optional section to add google api use google api to add qresp app and generate client id
+;GOOGLE_CLIENT_ID = # google client id
+;GOOGLE_CLIENT_SECRET = # The google api secret key
+;# optional section to host own version of mongo database
+;MONGODB_HOST = # mongodb hostname, e.g. x.univ.edu
+;MONGODB_PORT = 27017
+;MONGODB_USERNAME = # mongodb username
+;MONGODB_PASSWORD = # mongodb password
+;MONGODB_DB_NAME = # mongodb name
+;QRESP_DB_SECRET_KEY = # /admin database access secret key
+
+[SECRETS]
+# Random flask key, change it to a random value
+FLASK_SECRET_KEY = //bndsn/sdalkjdlkadjasd/123kdlasjkljlk/
+;MAIL_PWD = # a mail account password to mail administrator about insertion/deletion of metadata
+
+[GOOGLE_API] # Google api section
+AUTH_URI = https://accounts.google.com/o/oauth2/auth
+TOKEN_URI = https://accounts.google.com/o/oauth2/token
+USER_INFO = https://www.googleapis.com/userinfo/v2/me
+SCOPE = https://www.googleapis.com/auth/userinfo.profile,https://www.googleapis.com/auth/userinfo.email
diff --git a/web/project/config.py b/web/project/config.py
@@ -21,5 +21,5 @@ def get_setting(cls, section, key):
             ret = cls.configParser.get(section, key)
         except:
             ret = None
-        return  ret
+        return ret