Passing initialization script to the ./conf/run.sh file

Reformatted code

Dockerfile

@@ -1,6 +1,4 @@
 FROM ubuntu:18.04 as dependencies_ready
-ARG PRELOAD_GRAPH
-ENV PRELOAD_GRAPH "$PRELOAD_GRAPH"
 
 RUN apt-get update -qq
 RUN apt-get install -y -qq git curl wget build-essential

conf/install.sh

@@ -79,10 +79,3 @@ npm install -g npm@latest
 npm config set python "$PYTHON27_PATH"
 npm install
 
-# preload graph
-if [ -z "$PRELOAD_GRAPH" ] ; then
-    echo "Preload graph flag is not active, skipping tests"
-else
-    echo "Preload graph flag is active, loading graph through tests"
-    coverage run -m unittest discover test || true
-fi

conf/run.sh

@@ -37,6 +37,20 @@ export NVM_DIR="$([[ -z "${XDG_CONFIG_HOME-}" ]] && printf %s "${HOME}/.nvm" ||
 [[ -s "$NVM_DIR/nvm.sh" ]] && \. "$NVM_DIR/nvm.sh" # This loads nvm
 nvm use v10
 
+# preload graph
+if [[ -z "$INIT_GRAPH" ]] ; then
+    echo "Preload graph flag is not active, skipping tests"
+elif [[ ! -f "$ROOT_DIR/.preloaded.txt" ]] || [[ "$FORCE_RELOAD_GRAPH" == "1" ]] ; then
+    rm -f "$ROOT_DIR/.preloaded.txt"
+    echo "Preload graph flag is active, loading graph through tests"
+    coverage run -m unittest discover test
+    echo "true" > "$ROOT_DIR/.preloaded.txt"
+else
+    echo "Preload graph flag is active but the database has already been initialized once. \
+    To re-initialize, delete the $ROOT_DIR/.preloaded.txt file and run this script again, or \
+    set the FORCE_RELOAD_GRAPH environment variable before re-running this script."
+fi
+
 echo "Starting archgraph server at $ROOT_DIR"
 cd "$ROOT_DIR"
 
@@ -52,7 +66,7 @@ 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" &
+python "$ROOT_DIR/src/Routes/routes.py" &
 SERVER_PID=$!
 cd "$ROOT_DIR/frontend" || ( echo "folder missing " && exit 1 )
 if [[ "$RUN_IN_PRODUCTION" != "" ]] ; then

docker-compose.yml

@@ -32,14 +32,15 @@ services:
       build:
         dockerfile: Dockerfile
         args:
-          SOURCE_BRANCH: master
-          PRELOAD_GRAPH: "1"
+          SOURCE_BRANCH: "master"
         context: .
       environment:
         - "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"
+        - "INIT_GRAPH=1"
+        - "FORCE_RELOAD_GRAPH=0"
       ports:
         - published: 4200
           target: 4200

src/GCF/decorators/OntologyClass.py

@@ -3,15 +3,15 @@
 from marshmallow import Schema
 from marshmallow_jsonschema import JSONSchema
 
-#from src.Utils.Utils import find_name_of_classes_in_project
+# from src.Utils.Utils import find_name_of_classes_in_project
 
 
 def decorator_schema(cls):
     def getSchema(self):
         json_schema = JSONSchema()
         return json_schema.dump(self)
 
-    setattr(cls, 'getSchema', getSchema)
+    setattr(cls, "getSchema", getSchema)
 
     def get_labels(self, base_class):
         supper_classes_and_self_class = cls.mro()
@@ -23,7 +23,7 @@ def get_labels(self, base_class):
                 labels.append(class_name.split("Schema")[0])
         return labels
 
-    setattr(cls, 'get_labels', get_labels)
+    setattr(cls, "get_labels", get_labels)
 
     def generate_default_template(self, class__):
         schema = self.getSchema()
@@ -38,7 +38,7 @@ def generate_default_template(self, class__):
         template = {
             "classes_name": classes_name,
             "template": template_aux,
-            "schema": json.dumps(schema)
+            "schema": json.dumps(schema),
         }
         for property_name in properties_of_entity:
             property = properties_of_entity[property_name]
@@ -58,14 +58,13 @@ def generate_default_template(self, class__):
             range_class_name = range_schema_class_name.split("Schema")[0]
             template_aux[class_name][title] = range_class_name
 
-
         schema = class__().get_schema_with_template(template_aux)
         template["schema"] = json.dumps(schema)
         print(schema)
 
         return template
 
-    setattr(cls, 'generate_default_template', generate_default_template)
+    setattr(cls, "generate_default_template", generate_default_template)
 
     return cls
 

src/GCF/utils/db.py

@@ -2,9 +2,15 @@
 
 # Create graph
 
+import src.Utils.EnvVarManager as EnvVarManager
+
 
 def get_connection():
-    return Graph(host="localhost", port=7687)
+    return Graph(
+        uri=EnvVarManager.get_from_env_or_return_default(
+            "NEO4J_CONNECTION_STRING", "bolt://neo4j:password@localhost:7687"
+        )
+    )
 
 
 def get_node_count(graph):

src/Models/ArchOnto/v0_1/NodeEntities/ARE1_Level_of_Description.py

@@ -8,11 +8,13 @@
 class ARE1_Level_of_DescriptionSchema(E55_TypeSchema):
     upper_level = fields.List(
         fields.Nested(
-            "src.Models.ArchOnto.v0_1.NodeEntities.ARE1_Level_of_Description.ARE1_Level_of_DescriptionSchema",)
+            "src.Models.ArchOnto.v0_1.NodeEntities.ARE1_Level_of_Description.ARE1_Level_of_DescriptionSchema",
+        )
     )
     lower_level = fields.List(
         fields.Nested(
-            "src.Models.ArchOnto.v0_1.NodeEntities.ARE1_Level_of_Description.ARE1_Level_of_DescriptionSchema",)
+            "src.Models.ArchOnto.v0_1.NodeEntities.ARE1_Level_of_Description.ARE1_Level_of_DescriptionSchema",
+        )
     )
 
 
@@ -33,4 +35,3 @@ def __init__(self, schema=None, *args, **kwargs):
             schema = ARE1_Level_of_DescriptionSchema()
 
         super().__init__(schema, *args, **kwargs)
-

src/Models/ArchOnto/v0_1/NodeEntities/ARE2_Formal_Title.py

@@ -6,7 +6,6 @@ class ARE2_Formal_TitleSchema(E35_TitleSchema):
 
 
 class ARE2_Formal_Title(E35_Title):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE2_Formal_TitleSchema()

src/Models/ArchOnto/v0_1/NodeEntities/ARE3_Supplied_Title.py

@@ -6,7 +6,6 @@ class ARE3_Supplied_TitleSchema(E35_TitleSchema):
 
 
 class ARE3_Supplied_Title(E35_Title):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE3_Supplied_TitleSchema()

src/Models/ArchOnto/v0_1/NodeEntities/ARE4_Extension.py

@@ -1,12 +1,14 @@
-from src.Models.CRM.v5_0_2.NodeEntities.E54_Dimension import E54_Dimension, E54_DimensionSchema
+from src.Models.CRM.v5_0_2.NodeEntities.E54_Dimension import (
+    E54_Dimension,
+    E54_DimensionSchema,
+)
 
 
 class ARE4_ExtensionSchema(E54_DimensionSchema):
     pass
 
 
 class ARE4_Extension(E54_Dimension):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE4_ExtensionSchema()

src/Models/ArchOnto/v0_1/NodeEntities/ARE5_Identifier_Type.py

@@ -6,7 +6,6 @@ class ARE5_Identifier_TypeSchema(E55_TypeSchema):
 
 
 class ARE5_Identifier_Type(E55_Type):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE5_Identifier_TypeSchema()

src/Models/ArchOnto/v0_1/NodeEntities/ARE6_Date_Type.py

@@ -6,9 +6,8 @@ class ARE5_Date_TypeSchema(E55_TypeSchema):
 
 
 class ARE5_Date_Type(E55_Type):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE5_Date_TypeSchema()
 
-        super().__init__(schema, *args, **kwargs)
+        super().__init__(schema, *args, **kwargs)

src/Models/ArchOnto/v0_1/NodeEntities/ARE7_Name.py

@@ -6,7 +6,6 @@ class ARE7_NameSchema(E55_TypeSchema):
 
 
 class ARE7_Name(E55_Type):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE7_NameSchema()

src/Models/ArchOnto/v0_1/NodeEntities/ARE8_Role.py

@@ -6,9 +6,8 @@ class ARE8_RoleSchema(E55_TypeSchema):
 
 
 class ARE8_Role(E55_Type):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE8_RoleSchema()
 
-        super().__init__(schema, *args, **kwargs)
+        super().__init__(schema, *args, **kwargs)

src/Models/ArchOnto/v0_1/NodeEntities/ARE9_Date_Certainty.py

@@ -6,7 +6,6 @@ class ARE9_Date_CertaintySchema(E55_TypeSchema):
 
 
 class ARE9_Date_Certainty(E55_Type):
-
     def __init__(self, schema=None, *args, **kwargs):
         if schema is None:
             schema = ARE9_Date_CertaintySchema()

src/Models/CRM/v5_0_2/NodeEntities/E10_Transfer_of_Custody.py

@@ -1,7 +1,10 @@
 from marshmallow import fields
 from neomodel import RelationshipTo
 from src.GCF.decorators.OntologyClass import decorator_schema
-from src.Models.CRM.v5_0_2.NodeEntities.E7_Activity import E7_Activity, E7_ActivitySchema
+from src.Models.CRM.v5_0_2.NodeEntities.E7_Activity import (
+    E7_Activity,
+    E7_ActivitySchema,
+)
 from src.Models.CRM.v5_0_2.NodeProperties.P28_custody_surrenedered_by import (
     P28_custody_surrendered_by,
 )
@@ -15,14 +18,16 @@
 
 @decorator_schema
 class E10_Transfer_of_CustodySchema(E7_ActivitySchema):
-    custody_surrendered_by = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E53_Place.E53_PlaceSchema")
+    custody_surrendered_by = fields.List(
+        fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E53_Place.E53_PlaceSchema")
     )
-    transferred_custody_of = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E18_Physical_Thing.E18_Physical_ThingSchema")
+    transferred_custody_of = fields.List(
+        fields.Nested(
+            "src.Models.CRM.v5_0_2.NodeEntities.E18_Physical_Thing.E18_Physical_ThingSchema"
+        )
     )
-    custody_received_by = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E39_Actor.E39_ActorSchema")
+    custody_received_by = fields.List(
+        fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E39_Actor.E39_ActorSchema")
     )
 
 

src/Models/CRM/v5_0_2/NodeEntities/E11_Modification.py

@@ -1,18 +1,25 @@
 from marshmallow import fields
 from neomodel import RelationshipTo
 from src.GCF.decorators.OntologyClass import decorator_schema
-from src.Models.CRM.v5_0_2.NodeEntities.E7_Activity import E7_Activity, E7_ActivitySchema
+from src.Models.CRM.v5_0_2.NodeEntities.E7_Activity import (
+    E7_Activity,
+    E7_ActivitySchema,
+)
 from src.Models.CRM.v5_0_2.NodeProperties.P31_has_modified import P31_has_modified
 from src.Models.CRM.v5_0_2.NodeProperties.P126_employed import P126_employed
 
 
 @decorator_schema
 class E11_ModificationSchema(E7_ActivitySchema):
-    employed = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E57_Material.E57_MaterialSchema")
+    employed = fields.List(
+        fields.Nested(
+            "src.Models.CRM.v5_0_2.NodeEntities.E57_Material.E57_MaterialSchema"
+        )
     )
-    has_modified = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E18_Physical_Thing.E18_Physical_ThingSchema")
+    has_modified = fields.List(
+        fields.Nested(
+            "src.Models.CRM.v5_0_2.NodeEntities.E18_Physical_Thing.E18_Physical_ThingSchema"
+        )
     )
 
 
@@ -31,4 +38,3 @@ def __init__(self, schema=None, *args, **kwargs):
             schema = E11_ModificationSchema()
 
         super().__init__(schema, *args, **kwargs)
-

src/Models/CRM/v5_0_2/NodeEntities/E12_Production.py

@@ -1,17 +1,19 @@
 from marshmallow import fields
 from neomodel import RelationshipTo
 from src.GCF.decorators.OntologyClass import decorator_schema
-from src.Models.CRM.v5_0_2.NodeEntities.E11_Modification import E11_Modification, E11_ModificationSchema
+from src.Models.CRM.v5_0_2.NodeEntities.E11_Modification import (
+    E11_Modification,
+    E11_ModificationSchema,
+)
 from src.Models.CRM.v5_0_2.NodeEntities.E99_Product_Type import E99_Product_TypeSchema
 from src.Models.CRM.v5_0_2.NodeProperties.P186_produced_thing_of_product_type import (
     P186_produced_thing_of_product_type,
 )
 
+
 @decorator_schema
 class E12_ProductionSchema(E11_ModificationSchema):
-    produced_thing_of_product_type = fields.List(fields.Nested(
-        E99_Product_TypeSchema)
-    )
+    produced_thing_of_product_type = fields.List(fields.Nested(E99_Product_TypeSchema))
 
 
 class E12_Production(E11_Modification):

src/Models/CRM/v5_0_2/NodeEntities/E13_Attribute_Assignment.py

@@ -1,7 +1,10 @@
 from marshmallow import fields
 from neomodel import RelationshipTo
 from src.GCF.decorators.OntologyClass import decorator_schema
-from src.Models.CRM.v5_0_2.NodeEntities.E7_Activity import E7_Activity, E7_ActivitySchema
+from src.Models.CRM.v5_0_2.NodeEntities.E7_Activity import (
+    E7_Activity,
+    E7_ActivitySchema,
+)
 from src.Models.CRM.v5_0_2.NodeProperties.P140_assigned_attribute_to import (
     P140_assigned_attribute_to,
 )
@@ -13,14 +16,18 @@
 
 @decorator_schema
 class E13_Attribute_AssignmentSchema(E7_ActivitySchema):
-    assigned_attribute_to = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E1_CRM_Entity.E1_CRM_EntitySchema")
+    assigned_attribute_to = fields.List(
+        fields.Nested(
+            "src.Models.CRM.v5_0_2.NodeEntities.E1_CRM_Entity.E1_CRM_EntitySchema"
+        )
     )
-    assigned = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E1_CRM_Entity.E1_CRM_EntitySchema")
+    assigned = fields.List(
+        fields.Nested(
+            "src.Models.CRM.v5_0_2.NodeEntities.E1_CRM_Entity.E1_CRM_EntitySchema"
+        )
     )
-    assigned_property_type = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E55_Type.E55_TypeSchema")
+    assigned_property_type = fields.List(
+        fields.Nested("src.Models.CRM.v5_0_2.NodeEntities.E55_Type.E55_TypeSchema")
     )
 
 

src/Models/CRM/v5_0_2/NodeEntities/E14_Condition_Assessment.py

@@ -3,18 +3,23 @@
 from src.GCF.decorators.OntologyClass import decorator_schema
 from src.Models.CRM.v5_0_2.NodeEntities.E13_Attribute_Assignment import (
     E13_Attribute_Assignment,
-    E13_Attribute_AssignmentSchema)
+    E13_Attribute_AssignmentSchema,
+)
 from src.Models.CRM.v5_0_2.NodeProperties.P34_concerned import P34_concerned
 from src.Models.CRM.v5_0_2.NodeProperties.P35_has_identified import P35_has_identified
 
 
 @decorator_schema
 class E14_Condition_AssessmentSchema(E13_Attribute_AssignmentSchema):
-    has_identified = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E3_Condition_State.E3_Condition_StateSchema")
+    has_identified = fields.List(
+        fields.Nested(
+            "src.Models.CRM.v5_0_2.NodeEntities.E3_Condition_State.E3_Condition_StateSchema"
+        )
     )
-    concerned = fields.List(fields.Nested(
-        "src.Models.CRM.v5_0_2.NodeEntities.E18_Physical_Thing.E18_Physical_ThingSchema")
+    concerned = fields.List(
+        fields.Nested(
+            "src.Models.CRM.v5_0_2.NodeEntities.E18_Physical_Thing.E18_Physical_ThingSchema"
+        )
     )