Merge pull request #78 from feup-infolab/lazaroDevelop

Lazaro develop

conf/run.sh

@@ -40,7 +40,19 @@ nvm use v10
 echo "Starting archgraph server at $ROOT_DIR"
 cd "$ROOT_DIR"
 
-python "$ROOT_DIR/src/Routes/routes.py" --neo4j="$NEO4J_CONNECTION_STRING" --mongodb="$MONGODB_CONNECTION_STRING" &
+if [[ "$NEO4J_CONNECTION_STRING" != "" ]]; then
+    echo "Neo4j Server at $NEO4J_CONNECTION_STRING";
+fi
+
+if [[ "$MONGODB_CONNECTION_STRING" != "" ]]; then
+    echo "MongoDB Server at $MONGODB_CONNECTION_STRING";
+fi
+
+if [[ "$CUSTOM_HOST_FOR_SERVER_BIND" != "" ]]; then
+    echo "Flask Server binding to host with address $CUSTOM_HOST_FOR_SERVER_BIND";
+fi
+
+python "$ROOT_DIR/src/Routes/routes.py" --neo4j="$NEO4J_CONNECTION_STRING" --mongodb="$MONGODB_CONNECTION_STRING"  --host="$CUSTOM_HOST_FOR_SERVER_BIND" &
 SERVER_PID=$!
 cd "$ROOT_DIR/frontend" || ( echo "folder missing " && exit 1 )
 if [[ "$RUN_IN_PRODUCTION" != "" ]] ; then

docker-compose.yml

@@ -4,6 +4,7 @@ services:
   mongodb:
     container_name: archgraph-mongodb
     image: mongo:latest
+    command: ["--bind_ip_all"]
     environment:
       MONGO_INITDB_ROOT_USERNAME: root
       MONGO_INITDB_ROOT_PASSWORD: rootpassword
@@ -32,11 +33,12 @@ services:
         dockerfile: Dockerfile
         args:
           SOURCE_BRANCH: master
-          PRELOAD_GRAPH: "true"
+          PRELOAD_GRAPH: "1"
         context: .
       environment:
-        - "NEO4J_CONNECTION_STRING=bolt://neo4j:password@neo4j:7687"
-        - "MONGODB_CONNECTION_STRING=mongodb://root:rootpassword@mongodb:27017"
+        - "NEO4J_CONNECTION_STRING=bolt://neo4j:password@archgraph-neo4j:7687"
+        - "MONGODB_CONNECTION_STRING=mongodb://root:rootpassword@archgraph-mongodb:27017"
+        - "CUSTOM_HOST_FOR_SERVER_BIND=0.0.0.0"
         - "RUN_IN_PRODUCTION=1"
       ports:
         - published: 4200

src/Models/CRM/v5_0_2/NodeEntities/E1_CRM_Entity.py

@@ -1,11 +1,10 @@
 from marshmallow import Schema, fields
 from neomodel import (
-    One,
     RelationshipTo,
     StringProperty,
     StructuredNode,
     UniqueIdProperty,
-    db, ZeroOrOne,
+    ZeroOrOne,
 )
 from src.GCF.decorators.OntologyClass import ontology_class, decorator_schema
 from src.Models.CRM.v5_0_2.NodeProperties.has_value import has_value
@@ -32,7 +31,7 @@ class E1_CRM_EntitySchema(Schema):
     P137_exemplifies = fields.List(fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E55_Type.E55_TypeSchema"))
     P48_has_preferred_identifier = fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E42_Identifier.E42_IdentifierSchema")
     P139_has_alternative_form = fields.List(fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E41_Appellation.E41_AppellationSchema"))
-    P1_is_identified_by = fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E55_Type.E55_TypeSchema")
+    P1_is_identified_by = fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E41_Appellation.E41_AppellationSchema")
     has_value = fields.List(
         fields.Nested("src.Models.DataObject.v0_0_2.DataObject.DataObjectSchema")
     )

src/Models/DataObject/v0_0_2/RegexString.py

@@ -26,7 +26,7 @@ def __init__(self, schema=None, *args, **kwargs):
 
         expression = ""
         if kwargs.get("expression") is None:
-            # TODO falta arranjar isto
+            # todo falta arranjar isto
             expression = "regex/[a-zA-Z]([a-zA-Z 0-9])*$"
         else:
             expression = json.dumps(kwargs.get("expression"))

src/Models/DataObject/v0_0_2/SuperClass.py

@@ -7,11 +7,12 @@ class SuperClass:
     def __init__(self, schema):
         self.schema = schema
 
+    """The function returns the node schema"""
     def getSchema(self):
         json_schema = JSONSchema()
         return json_schema.dump(self.schema)
 
-    # Json to string
+    """The function returns the node information in string"""
     def encodeJSON(self):
         data = {}
         for key, val in self.__properties__.items():
@@ -24,18 +25,21 @@ def my_converter(o):
 
         return json.dumps(data, default=my_converter)
 
-    # string to json
+    """The function returns the node information at format json"""
     def decodeJSON(self):
         return json.loads(self.encodeJSON())
 
+    """The function returns the property of entity with name property_name"""
     def get_property_from_entity(self, property_name):
         schema_node = self.getSchema()
         class_name = self.__class__.__name__ + "Schema"
         return schema_node['definitions'][class_name]['properties'][property_name]
 
+    """The function returns its superclasses names"""
     def get_superclasses_name(self):
         return list(set(self.labels()))
 
+    """The function returns the schema according to the template provided"""
     def get_schema_with_template(self, template):
         jsonSchema = self.getSchema()
         newJsonSchema = {
@@ -46,6 +50,7 @@ def get_schema_with_template(self, template):
         self.__get_schema_with_template_aux(jsonSchema["definitions"], template, newJsonSchema)
         return newJsonSchema
 
+    """Auxiliary function - The function returns the schema according to the template provided"""
     def __get_schema_with_template_aux(self, definitions, json_template, new_json_schema):
         if isinstance(json_template, str):
             entity_name = json_template
@@ -69,7 +74,7 @@ def __get_schema_with_template_aux(self, definitions, json_template, new_json_sc
 
         properties = definitions[current_entity]['properties']
 
-        self.__get_entity_properties_without_ref(definitions[current_entity], entity)
+        self.__set_entity_properties_without_ref(definitions[current_entity], entity)
 
         if isinstance(json_template, str):
             return
@@ -81,7 +86,7 @@ def __get_schema_with_template_aux(self, definitions, json_template, new_json_sc
 
             self.__get_schema_with_template_aux(definitions, next_entity, new_json_schema)
 
-    def __get_entity_properties_without_ref(self, current_entity, entity):
+    def __set_entity_properties_without_ref(self, current_entity, entity):
         for property_name in current_entity['properties']:
             property_entity = current_entity['properties'][property_name]
 
@@ -97,6 +102,7 @@ def __get_entity_properties_without_ref(self, current_entity, entity):
             #         'type': 'string'}
             #     changed_property['title'] = property_entity['title']
 
+    """The function merges between node and customer data, then saves the node"""
     def merge_node(self, updated_node):
         merged_node = dict(self.decodeJSON(), **updated_node)
         field_type_date = self.__get_field_of_type_date()
@@ -111,30 +117,26 @@ def merge_node(self, updated_node):
             self.save()
         except BaseException:
             return None
-
-        # array_uid = read_relationships(node_name, relationship_name)
-        #
-        # for uid in array_uid:
-        #     node = get_node_by_uid(uid)
-
         return True
 
-    def node_self_build(self, updated_node):
-        object = {'self_node': {},
+    """The function returns the node with updated fields and relationships"""
+    def build_node(self, data):
+        node = {'self_node': {},
                   'relationships': {}}
-        for property in updated_node.keys():
-            if isinstance(updated_node[property], str):
-                object['self_node'][property] = updated_node[property]
-            elif isinstance(updated_node[property], dict):
-                object['relationships'][property] = []
-                object['relationships'][property].append(updated_node[property])
-            elif isinstance(updated_node[property], list):
+        for property in data.keys():
+            if isinstance(data[property], str):
+                node['self_node'][property] = data[property]
+            elif isinstance(data[property], dict):
+                node['relationships'][property] = []
+                node['relationships'][property].append(data[property])
+            elif isinstance(data[property], list):
                 relationships = []
-                for element in updated_node[property]:
+                for element in data[property]:
                     relationships.append(element)
-                object['relationships'][property] = relationships
-        return object
+                node['relationships'][property] = relationships
+        return node
 
+    """The function returns entity's fields of type date"""
     def __get_field_of_type_date(self):
         result = []
         get_schema = self.getSchema()
@@ -146,10 +148,3 @@ def __get_field_of_type_date(self):
                 result.append(field["title"])
         return result
 
-    # def get_labels(target, base_class):
-    #     return (
-    #         c.__name__
-    #         for c in target.__mro__
-    #         if issubclass(c, base_class)
-    #     )
-

src/Routes/mongo.py

@@ -1,18 +1,22 @@
 import json
 from datetime import datetime
-from pymongo import MongoClient
-import argparse
+from pymongo import MongoClient, uri_parser
 
-parser = argparse.ArgumentParser(description="Starts the archgraph server.")
-parser.add_argument("--mongodb", nargs="?", help="Address of the mongodb server")
-parser.add_argument("--neo4j", nargs="?", help="Address of the neo4j server")
 
-args = parser.parse_args()
+import src.Utils.ArgParser as ArgParser
+args = ArgParser.parse()
 
-if args.mongodb is not None:
+MONGODB_URL = "mongodb://root:rootpassword@localhost:27017"
+
+if args.mongodb is not None and args.mongodb != "":
+    # mongodb_arguments = uri_parser.parse_uri(args.mongodb)
+    # client = MongoClient(host=mongodb_arguments.nodelist.first(),
+    #                      port= mongodb_arguments.port,
+    #                      username=mongodb_arguments.username,
+    #                      password=mongodb_arguments.password,
+    #                      server_selection_timeout=1
+    #                      )
     MONGODB_URL = args.mongodb
-else:
-    MONGODB_URL = "mongodb://root:rootpassword@localhost:27017"
 
 client = MongoClient(MONGODB_URL)
 db = client.mydatabase

src/Routes/routes.py

@@ -1,7 +1,6 @@
 import json
 from pathlib import Path
 import os, sys
-import argparse
 
 
 # returns the project root path (assumes that the script is started from src/Routes/routes.py)
@@ -15,10 +14,6 @@ def get_project_root():
 print("Archgraph running at " + get_project_root().as_posix())
 sys.path.append(get_project_root().as_posix())
 
-parser = argparse.ArgumentParser(description="Starts the archgraph server.")
-parser.add_argument("--neo4j", nargs="?", help="Address of the neo4j server")
-parser.add_argument("--mongodb", nargs="?", help="Address of the mongodb server")
-args = parser.parse_args()
 
 from flask import Flask, Response, jsonify, make_response, request, send_from_directory
 
@@ -28,20 +23,35 @@ def get_project_root():
 from src.Utils.JsonEncoder import search_cidoc, search_specific_cidoc
 from src.Utils.Utils import get_node_by_uid, build_next_json, updated_node, make_result
 
-if args.neo4j:
+import src.Utils.ArgParser as ArgParser
+args = ArgParser.parse()
+
+if args.neo4j and args.neo4j != "":
     config.DATABASE_URL = args.neo4j
 else:
     config.DATABASE_URL = "bolt://neo4j:password@localhost:7687"
 
-from src.Routes.mongo import insert_template_in_mongo, get_all_records_from_collection, get_schema_from_mongo, \
-    get_templates_from_mongo_by_classes_name
+from src.Routes.mongo import insert_template_in_mongo, get_all_records_from_collection, get_schema_from_mongo, get_templates_from_mongo_by_classes_name
 
 app = Flask(__name__)
 
 CORS(app)
 cors = CORS(app, resources={r"/*": {"origins": "*"}})
 app = Flask(__name__, static_url_path="")
+app.debug = True
+
+@app.before_request
+def log_request_info():
+    app.logger.debug('Headers: %s', request.headers)
+    app.logger.debug('Body: %s', request.get_data())
 
+@app.after_request
+def after(response):
+    # todo with response
+    print(response.status)
+    print(response.headers)
+    print(response.get_data())
+    return response
 
 @app.route("/favicon.ico")
 def favicon():
@@ -234,6 +244,9 @@ def search_specific(class_name, query):
 # json = read_file("../Utils/defaultTemplates.json")
 # populate_template_collection(json)
 # get_all_records_from_collection("createdTemplate")
-
 if __name__ == "__main__":
-    app.run(host='127.0.0.1')
+    if args.host is not None and args.host != "":
+        app.logger.debug('Archgraph running with a custom host setting: %s', args.host)
+        app.run(host=args.host)
+    else:
+        app.run(host='127.0.0.1')

src/Utils/ArgParser.py

@@ -0,0 +1,16 @@
+import argparse
+
+
+def parse():
+    parser = argparse.ArgumentParser(description="Starts the archgraph server.")
+    parser.add_argument("--mongodb", nargs="?", help="Address of the mongodb server")
+    parser.add_argument("--neo4j", nargs="?", help="Address of the neo4j server")
+    parser.add_argument("--host", nargs="?", help="Address of the neo4j server")
+
+    args = parser.parse_args()
+
+    return args
+
+
+class ArgParser:
+    pass