update docker files

Author: cbora

.dockerignore

@@ -1,5 +1,6 @@
 *.pyc
 *~
+recastfrontend/*.yaml
 recastfrontend/*.pyc
 recastfrontend/*~
 recastfrontend/templates/*~

README.md

@@ -46,3 +46,18 @@ deploying on Heroku
     git commit -m 'bla'
     git push heroku master
 
+
+##Docker instructions
+
+	 docker-compose build
+	 docker-compose up -d
+
+create database
+
+	docker-compose run recastfrontend recast-frontend-admin create_db
+
+fill database with dummy data		  
+     
+     docker-compose run recastfrontend recast-frontend fill_db
+     
+     

docker-compose.yml

@@ -2,34 +2,46 @@ recastfrontend:
   build: .
   ports:
    - "5000:5000"
+  environment:
+   - RECAST_DBPATH=postgresql://postgres:postgres@postgres:5432/postgres
   volumes:
    - ./recastfrontend:/recast-newfrontend/recastfrontend
    - ./config.yaml:/recast-newfrontend/recastfrontend/resources/defaultconfig.yaml
   links:
-   - db
-   - cache
-   - celery
-
-db:
-  image: postgres
-  
-celery:
-  image: celery
-
-cache:
-  image: redis
-  ports:
-   - "6379:6379"
+   - postgres
+   - redis
+   - api
 
 api:
   image: cbora/recastrestapi:0.1
   volumes:
    - ./config.yaml:/recast-rest-api/recastrestapi/resources/defaultconfig.yaml
   ports:
    - "6000:5000"
-  
-es:
-  image: elasticsearch
+  links:
+   - postgres
+
+data:
+  image: postgres:latest
+  volumes:
+    - /var/lib/postgresql
+  command: "true"
+
+postgres:
+  restart: always
+  image: postgres:latest
+  volumes_from:
+    - data
   ports:
-   - "9200:9200"
+    - "5432:5432"
+redis:
+  restart: always
+  image: redis:latest
+  ports:
+    - "6379:6379"
+  
+#es:
+#  image: elasticsearch
+#  ports:
+#   - "9200:9200"
 

recastfrontend/frontendconfig.py

@@ -5,9 +5,19 @@
 def default_config():
   return yaml.load(open(pkg_resources.resource_filename('recastfrontend','resources/defaultconfig.yaml')))
 
+def update_config(config):
+  #if we are runnning inside a container
+  if os.environ.has_key('REDIS_PORT'):
+    os.environ['RECAST_REDISURL'] = os.environ['REDIS_PORT'].replace('tcp', 'redis')
+  #update config with ENV variables that have RECAST_*
+  for k, v in os.environ.iteritems():
+    if k.startswith('RECAST_'):
+      config.update({k.replace('RECAST_',''): v})
+  return config
 
 def mk_config():
   the_config = default_config()
+  the_config = update_config(the_config)
   if os.environ.has_key('RECASTCONTROLCENTER_CONFIG'):
     custom_config = yaml.load(open(os.environ['RECASTCONTROLCENTER_CONFIG']))
     the_config.update(**custom_config)

recastfrontend/populate_db.py

@@ -6,7 +6,8 @@
 import asynctasks
 import synctasks
 
-from flask import Flask, redirect, jsonify, session, request, url_for, render_template, flash
+from flask import Flask, redirect, jsonify, session
+from flask import request, url_for, render_template, flash
 from flask.ext import login as login
 from frontendconfig import config as frontendconf
 from recastdb.database import db
@@ -690,6 +691,9 @@ def rows_to_dict(rows):
 def arxiv():
   if request.args.has_key('id'):
     arxiv_id = request.args.get('id')
+  else:
+	#No id found return an error
+	return
   print arxiv_id
   fields = "title,author,doi,abstract,corporate_name"
   url = "https://inspirehep.net/search?p={}&of=recjson&ot={}".format(arxiv_id,fields)
@@ -698,23 +702,33 @@ def arxiv():
 
   if not response.content or len(response.json()) > 1 or len(response.json()) == 0:
     """No record found"""
-    return "{}"
+    return
   if len(response.json()) > 1:
     """More than one record found"""
-    return "{N}"
+    return
 
-  ret = response.json()[0]
-  ret = json.dumps(ret)
-  return ret
+  result = response.json()[0]
+  
+  data = {}
+  data['title'] = result['title']['title'] or None
+  data['collaboration'] = result['corporate_name'][0]['collaboration'] or None
+  data['doi'] = result['doi'][0] or None
+  data['description'] = result['abstract'][1]['summary']
+  return jsonify(data)
 
 @app.route("/add-parameter/<int:request_id>", methods=['GET', 'POST'])
+@login.login_required
 def add_parameter_point(request_id):
-  coordinate = request.form['value']
-  coordinate_name = request.form['name']
-  zip_file = request.files['file']
 
-  request_query = db.session.query(dbmodels.ScanRequest).filter(
-    dbmodels.ScanRequest.id == request_id).one()
+  request_query = db.session.query(dbmodels.ScanRequest).filter(dbmodels.ScanRequest.id == request_id).one()
+  
+  zenodo_deposition_id = request_query.zenodo_deposition_id
+
+  point_request_id = synctasks.createPointRequest(app,
+                                                  request_id,
+                                                  login.current_user
+                                                  )  
+  zip_file = request.files['file']
 
   file_uuid = str(uuid.uuid1())
   zip_file.save(zip_file.filename)
@@ -726,54 +740,61 @@ def add_parameter_point(request_id):
                         file_uuid)
 
   deposition_file_id = synctasks.uploadToZenodo(ZENODO_ACCESS_TOKEN,
-                                                request_query.zenodo_deposition_id,
+                                                zenodo_deposition_id,
                                                 file_uuid,
                                                 zip_file)
 
-  point_request_id = synctasks.createPointRequest(app,
-                                                  request_id,
-                                                  login.current_user
-                                                  )
-
-  synctasks.createPointCoordinate(app,
-                                  login.current_user,
-                                  coordinate_name,
-                                  coordinate,
-                                  point_request_id
-                                  )
-
   synctasks.createRequestArchive(app,
                                  login.current_user,
                                  point_request_id,
                                  file_uuid,
                                  deposition_file_id,
                                  zip_file.filename)
-  return ""
-
 
+  for k in request.form:
+	coordinate = json.loads(request.form[k])
+	if k == 'file':
+	  continue
+	  
+	if coordinate.has_key('value'):
+	  value = coordinate['value']
+	  name = None
+	  if coordinate.has_key('name'):
+		name = coordinate['name']
+                
+	  synctasks.createPointCoordinate(app,
+                                          login.current_user,
+                                          name,
+                                          float(value),
+                                          point_request_id
+          )	  								    
+  response = {}
+  response['success'] = True
+  return jsonify(response)
 
 @app.route("/add-coordinate", methods=['GET', 'POST'])
 @app.route("/add-coordinate/<int:point_request_id>", methods=['GET', 'POST'])
 def add_coordinate(point_request_id):
+  
   if request.method == 'POST':
 
     point_request_query = db.session.query(dbmodels.PointRequest).filter(
       dbmodels.PointRequest.id == point_request_id).one()
 
-
     data = json.loads(request.data.decode())
     coordinate = data['value']
     coordinate_name = data['name']
     point_coordinate_id = synctasks.createPointCoordinate(app,
                                                           login.current_user,
                                                           coordinate_name,
                                                           coordinate,
-                                                          point_request_query.id)
+                                                          point_request_query.id
+    )
     #return point_coordinate_id
-    return ""
 
   return ""
-           
+  
+
 @app.route("/analysis-number")
 def analysis_number():
   analyses = db.session.query(dbmodels.Analysis).all()

recastfrontend/server.py

@@ -3,6 +3,7 @@
 //angular App
 angular.module('recastApp', [])
     .controller('HomeCtrl', ['$http', '$interval', function($http, $interval) {
+	/* home page controller */
 	var self = this;
 	self.analyses = 0;
 	self.requests = 0;
@@ -40,28 +41,48 @@ angular.module('recastApp', [])
     }])
 
 
-    .controller('parameterCtrl', ['$http', 'IDService', function($http, ris) {
+    .controller('parameterCtrl', ['$http', 'IDService', 'ItemService', function($http, ris, coordinates) {
+	/* Controller to add parameter */
 	var self = this;
+
+	self.items = function() {
+	    return coordinates.items();
+	};
+
+	self.addCoordinate = function() {
+	    coordinates.push();
+	};
+
 	self.addParameter = function(rid) {
+	    console.log("add parameter");
 	    ris.setID(rid);
+	    coordinates.clear();
+	    coordinates.push();
 	    $('#zip-file-request-page').val('');
 	    $('#modal-add-parameter').modal('show');	    
 	};
+
 	self.submit = function() {
 	    self.hideModal();
 	    NProgress.start();
 	    NProgress.inc(0.4);
 	    var form_data = new FormData();
 	    form_data.append('file', self.zipFile);
-	    for (var k in self.parameter){
-		form_data.append(k, self.parameter[k]);
+
+	    for (var k in self.items()){
+		parameter = {};
+		parameter.name = self.items()[k].name;
+		parameter.value = self.items()[k].value;
+		par = angular.toJson(parameter);
+		form_data.append(k, par);
 	    }
+
 	    $http({
 		method: 'POST',
 		url:'/add-parameter/'+ris.getID(),
 		data: form_data,		
 		headers: {'Content-Type': undefined},
-		trnasformRequest: angular.identity
+		transformRequest: angular.identity
 	    })
 		.success(function(response){
 		    NProgress.inc(0.5);
@@ -79,6 +100,7 @@ angular.module('recastApp', [])
     }])
 
     .controller('coordinateCtrl', ['$http', 'IDService', function($http, prs) {
+	/* Controller to add coordinate on request page */
 	var self = this;
 	self.addCoordinate = function(pid) {
 	    prs.setID(pid);
@@ -97,11 +119,61 @@ angular.module('recastApp', [])
 		});
 	};
 	self.hideModal = function() {
-	    console.log('hide modal');
 	    $('#modal-add-coordinate').modal('hide');
 	};
     }])
 
+    .controller('arxivImportCtrl', ['$http', 'IDService', function($http, id_service) {
+	
+	var self = this;
+	self.arxiv_id;
+	self.example = "this";
+	self.here = "hello";
+	self.title = "";
+	self.collaboration = "";
+	self.doi = "";
+	self.abstract = "";
+	
+	self.import = function() {
+	    console.log("clicked");
+	    console.log(self.arxiv_id);
+	    $('#modal-arxiv-data').modal('show');
+	    $http.post('/arxiv?id='+self.arxiv_id)
+		.then(function(response) {
+		    console.log(response);
+		    self.title = response.data['title'];
+		    self.collaboration = response.data['collaboration'];
+		    self.doi = response.data['doi'];
+		    self.abstract = response.data['description'];	
+		    console.log(self.title);
+		    console.log(self.collaboration);
+		    console.log(self.doi);
+		    console.log(self.abstract);
+		});
+	};
+    }])
+
+    .factory('ItemService', [function() {
+	items = [];
+
+	return {
+	    push: function() {
+		items.push({
+		    name: "",
+		    value: "",
+		    namePlaceholder: "Name",
+		    valuePlaceholder: "Value",
+		});
+	    },
+	    clear: function() {
+		items = [];
+	    },
+	    items: function() {
+		return items;
+	    }
+	}
+    }])
+
     .factory('IDService', [function() {
 	/* Service to store ID's */
 	variable_id = 0;