Merge branch 'feature/generic-clustering' into develop

src/data-hub/community-detection-microservice/app/configs/clustering.yaml

+layers:
+    user:
+        properties:
+    
+    starting-point:
+        properties:
+            - Latitude_StartingPoint
+            - Longitude_StartingPoint
\ No newline at end of file

src/data-hub/community-detection-microservice/app/configs/swagger.yml

@@ -14,7 +14,7 @@ basePath: "/api"
 paths:
   /debug:
     post:
-      operationId: "rest.debug.echo"
+      operationId: "routes.debug.echo"
       tags:
         - "Echo"
       summary: "Echo function for debugging purposes"
@@ -29,9 +29,11 @@ paths:
         200:
           description: "Successful echo of request data"
           
+# Locations
+# TODO remove
   /locations:
     post:
-        operationId: "rest.location.post"
+        operationId: "routes.location.post"
         tags:
           - "Locations"
         summary: "Add new location data"
@@ -48,7 +50,7 @@ paths:
           400:
             description: "Invalid input"
     get:
-        operationId: "rest.location.get"
+        operationId: "routes.location.get"
         tags:
             - "Locations"
         summary: "Get location data"
@@ -61,7 +63,7 @@ paths:
   
   /location-collections:
     post:
-        operationId: "rest.location.post_many"
+        operationId: "routes.location.post_many"
         tags:
           - "Locations"
         summary: "Add new location data collection"
@@ -78,9 +80,77 @@ paths:
           400:
             description: "Invalid input"
 
+# Layers
+  /layers:
+    post:
+        operationId: "routes.layers.post"
+        tags:
+          - "Layers"
+        summary: "Add a new layer or overwrite an existing one"
+        parameters:
+          - in: body 
+            name: "Layer"
+            description: "The layer data to be added"
+            required: true
+            schema:
+                $ref: "#/definitions/Layer-UpperCase"
+        responses:
+            201:
+                description: "Successful operation"
+            400:
+                description: "Invalid input"
+    get:
+        operationId: "routes.layers.get"
+        tags:
+            - "Layers"
+        summary: "Get all layer data"
+        parameters: []
+        responses:
+            200:
+                description: "Successful operation"
+                schema:
+                    $ref: "#/definitions/LayerCollection"
+    
+  /layers/names:
+    get:
+        operationId: "routes.layers.get_names"
+        tags:
+            - "Layers"
+        summary: "Get all layer names"
+        parameters: []
+        responses:
+            200:
+                description: "Successful operation"
+                schema: 
+                    type: array
+                    items: 
+                        type: string
+                    
+  /layers/{name}:
+    get:
+        operationId: "routes.layers.get_by_name"
+        tags:
+            - "Layers"
+        summary: "Get layer data for layer-name"
+        parameters: 
+          - name: "name"
+            in: "path"
+            description: "Name of the layer to return"
+            required: true
+            type: "string"
+        responses:
+            200:
+                description: "Successful operation"
+                schema: 
+                    $ref: "#/definitions/Layer"
+            404:
+                description: "Layer not found"
+
+# Clusters
+# TODO remove partially
   /location-clusters:
     get:
-        operationId: "rest.cluster.get_locations"
+        operationId: "routes.cluster.get_locations"
         tags:
             - "Clusters"
         summary: "Get user communities clustered by location"
@@ -93,7 +163,7 @@ paths:
 
   # /clusters/cluster.png:
   #   get:
-  #       operationId: "rest.cluster.get_image"
+  #       operationId: "routes.cluster.get_image"
   #       tags:
   #           - "Clusters"
   #       summary: "Get user communities per date per hour as image"
@@ -106,7 +176,7 @@ paths:
   
   /time-clusters:
     get:
-        operationId: "rest.cluster.get_times"
+        operationId: "routes.cluster.get_times"
         tags:
             - "Clusters"
         summary: "Get user communities clustered by time per hour"
@@ -119,7 +189,7 @@ paths:
 
   # /agi/clusters/cluster.png:
   #   get:
-  #       operationId: "rest.agi_cluster.get_image"
+  #       operationId: "routes.agi_cluster.get_image"
   #       tags:
   #           - "Clusters"
   #       summary: "Get user communities per date per hour from agi data as image"
@@ -130,9 +200,58 @@ paths:
   #           200:
   #               description: "Successful operation"
           
+  /clustersets:
+    get:
+        operationId: "routes.clustersets.get"
+        tags:
+            - "Clusters"
+        summary: "Get clustersets for all layers"
+        parameters: []
+        responses:
+            200:
+                description: "Successful operation"
+                schema:
+                    $ref: "#/definitions/ClusterSetCollection"
+                    
+  /clustersets/names:
+    get:
+        operationId: "routes.clustersets.get_names"
+        tags:
+            - "Clusters"
+        summary: "Get clusterset names for all layers"
+        parameters: []
+        responses:
+            200:
+                description: "Successful operation"
+                schema:
+                    type: array
+                    items:
+                        type: string
+
+  /clustersets/{name}:
+    get:
+        operationId: "routes.clustersets.get_by_name"
+        tags:
+            - "Clusters"
+        summary: "Get clusterset for layer-name"
+        parameters: 
+          - name: "name"
+            in: "path"
+            description: "Name of the layer to return the clusterset for"
+            required: true
+            type: "string"
+        responses:
+            200:
+                description: "Successful operation"
+                schema:
+                    $ref: "#/definitions/ClusterSet"
+            404:
+                description: "Clusterset not found"
+
+# TODO remove                    
   /user-cluster-graphs:
     get:
-        operationId: "rest.user_cluster.get"
+        operationId: "routes.user_cluster.get"
         tags:
             - "User Graphs"
         summary: "Get user graphs per layer per cluster"
@@ -142,10 +261,11 @@ paths:
                 description: "Successful operation"
                 schema:
                   $ref: "#/definitions/UserClusterGraphCollection"
-  
+
+# Function Calls
   /rfc/run:
     post:
-        operationId: "rest.functions.run_agi_clustering_and_graph_creation"
+        operationId: "routes.functions.run_agi_clustering_and_graph_creation"
         tags:
             - "Remote function calls"
         summary: "Insert locations from AGI, create clusters for starting time and location layers, create graphs for the location clusters"
@@ -154,6 +274,7 @@ paths:
             204:
                 description: "Successful operation"
 
+
 definitions:
   Location:
     type: "object"
@@ -176,6 +297,24 @@ definitions:
     items:
       $ref: "#/definitions/Location"
 
+  Cluster:
+    type: object
+    properties:
+        cluster_label:
+            type: number
+        nodes:
+            type: array
+            items: 
+                type: object
+                example:
+                    "Finished_time": 1576631193265951
+                    "Latitude_Destination": -5.973257
+                    "Longitude_Destination": 37.416316
+                    "TravelID": "5e57ec9159bc0668543f156a"
+                    "TravelPrice": 15
+                    "UniqueID": "a95075f5042b1b27060080156d87fe34ec7e712c5e57ec9159bc0668543f156a"
+                    "UserID": "a95075f5042b1b27060080156d87fe34ec7e712c"
+
   LocationCluster:
     type: object
     properties:
@@ -235,4 +374,52 @@ definitions:
   UserClusterGraphCollection:
     type: array
     items:
-      $ref: "#/definitions/UserClusterGraph"
+      $ref: "#/definitions/UserClusterGraph"
\ No newline at end of file
+
+  Layer-UpperCase:
+    type: object
+    properties:
+        LayerName:
+            type: string
+        Nodes:
+            type: array
+            items: 
+                type: object
+        Properties:
+            type: array
+            items: 
+                type: string
+    
+  Layer:
+    type: object
+    properties:
+        layer_name:
+            type: string
+        nodes:
+            type: array
+            items: 
+                type: object
+        properties:
+            type: array
+            items: 
+                type: string
+
+  LayerCollection:
+    type: array
+    items:
+        $ref: "#/definitions/Layer"
+
+  ClusterSet:
+    type: object
+    properties:
+        layer_name: 
+            type: string
+        clusters:
+            type: array
+            items: 
+                $ref: "#/definitions/Cluster"
+
+  ClusterSetCollection:
+    type: array
+    items:
+      $ref: "#/definitions/ClusterSet"
\ No newline at end of file

src/data-hub/community-detection-microservice/app/db/agi/agi_repository.py

@@ -29,6 +29,24 @@ class AgiRepository:
 
         return locations
 
+    def getLocationsBasedOnNewDataSchema(self):
+        '''Creates the new data generic schema to be used beginning on 24.03.2020'''
+        data = {
+            'layer_name': 'Destination',
+            'nodes': self.getLocations(),
+            'properties': ['latitude', 'longitude']
+        }
+        return data
+        
+    def getTimesBasedOnNewDataSchema(self):
+        '''Creates the new data generic schema to be used beginning on 24.03.2020'''
+        data = {
+            'layer_name': 'Starting_Time',
+            'nodes': self.getLocations(),
+            'properties': ['timestamp']
+        }
+        return data
+
     def readDataFromFile(self) -> List[Dict]:
         with open('./db/agi/travels.json', 'r') as f_travels:
             travels = json.loads(f_travels.read())

src/data-hub/community-detection-microservice/app/db/entities/__init__.py

 from db.entities.location import Location
 from db.entities.popular_location import PopularLocation
 from db.entities.cluster import Cluster, LocationCluster, TimeCluster
-from db.entities.user_cluster_graph import UserClusterGraph
+from db.entities.clusterset import ClusterSet
\ No newline at end of file
+from db.entities.user_cluster_graph import UserClusterGraph
+from db.entities.layer import Layer

src/data-hub/community-detection-microservice/app/db/entities/cluster.py

@@ -4,10 +4,38 @@ from datetime import date, datetime
 
 
 class Cluster:
-    def __init__(self, cluster_label: int = None, nodes: List = None):
+    '''
+    A cluster for an arbitrary layer containing some nodes.
+
+    :param cluster_label: The label of the cluster unique for the layer
+    :param nodes: The individual nodes of the cluster
+    '''
+
+    def __init__(self, cluster_label: int = None, nodes: List = None,
+                 cluster_dict: Dict = None, from_db=False):
         self.cluster_label = cluster_label
         self.nodes = nodes
 
+        if cluster_dict is not None:
+            self.from_serializable_dict(cluster_dict, from_db)
+
+    def to_serializable_dict(self, for_db=False) -> Dict:
+        return {
+            "cluster_label": self.cluster_label,
+            "nodes": json.dumps(self.nodes) if for_db else self.nodes
+        }
+
+    def from_serializable_dict(self, cluster_dict: Dict, from_db=False):
+        self.cluster_label = cluster_dict["cluster_label"]
+        self.nodes = json.loads(cluster_dict["nodes"]) \
+            if from_db else cluster_dict["nodes"]
+
+    def __repr__(self):
+        return json.dumps(self.to_serializable_dict())
+
+    def __str__(self):
+        return f"Cluster({self.__repr__()})"
+
 
 class LocationCluster(Cluster):
     def __init__(self, cluster_label: int = None, nodes: List = None,
@@ -67,7 +95,7 @@ class TimeCluster(Cluster):
             if from_db else time_dict["nodes"]
 
     def __repr__(self):
-        return json.dumps(self.to_serializable_dict())
+        return json.dumps(self.to_serializable_dict(True))
 
     def __str__(self):
         return f"TimeCluster({self.__repr__()})"

src/data-hub/community-detection-microservice/app/db/entities/clusterset.py

+import json
+from db.entities.cluster import Cluster
+from typing import List, Dict
+from datetime import date, datetime
+
+
+class ClusterSet:
+    '''
+    A clusterset for an arbitrary layer containing all clusters.
+
+    :param layer_name: The name of the layer
+    :param clusters: The individual clusters
+    '''
+
+    def __init__(self, layer_name: str = None, clusters: List[Cluster] = None,
+                 cluster_set_dict: Dict = None, from_db=False):
+        self.layer_name = layer_name
+        self.clusters = clusters
+
+        if cluster_set_dict is not None:
+            self.from_serializable_dict(cluster_set_dict, from_db)
+
+    def to_serializable_dict(self, for_db=False) -> Dict:
+        serialized_dict_clusters = [cluster.to_serializable_dict(for_db)
+                                    for cluster in self.clusters]
+        return {
+            "layer_name": self.layer_name,
+            "clusters": json.dumps(serialized_dict_clusters) if for_db else serialized_dict_clusters
+        }
+
+    def from_serializable_dict(self, cluster_set_dict: Dict, from_db=False):
+        self.layer_name = cluster_set_dict["layer_name"]
+
+        serialized_dict_clusters = json.loads(cluster_set_dict["clusters"]) \
+            if from_db else cluster_set_dict["clusters"]
+        self.clusters = [Cluster(cluster_dict=cluster_dict, from_db=from_db)
+                         for cluster_dict in serialized_dict_clusters]
+
+    def __repr__(self):
+        return json.dumps(self.to_serializable_dict())
+
+    def __str__(self):
+        return f"ClusterSet({self.__repr__()})"

src/data-hub/community-detection-microservice/app/db/entities/layer.py

+import json
+from datetime import datetime
+from typing import Dict
+
+
+class Layer:
+    '''
+    This class represents a single layer of the Multilayer Graph.
+
+    :param layer_info: Information as dictionary to restore the layer object.
+    '''
+
+    def __init__(self, layer_info: Dict = None, from_db=False):
+        if layer_info is not None:
+            self.from_serializable_dict(layer_info, from_db)
+
+    def to_serializable_dict(self, for_db=False) -> Dict:
+        return {
+            "layer_name": self.layer_name,
+            "properties": self.properties,
+            "nodes": json.dumps(self.nodes) if for_db else self.nodes
+        }
+
+    def from_serializable_dict(self, layer_info: Dict, from_db=False):
+        self.layer_name = layer_info['layer_name']
+        self.properties = layer_info['properties']
+        self.nodes = json.loads(layer_info["nodes"]) \
+            if from_db else layer_info["nodes"]
+
+    def __repr__(self):
+        return json.dumps(self.to_serializable_dict())
+
+    def __str__(self):
+        return f"Layer({self.__repr__()})"

src/data-hub/community-detection-microservice/app/db/repository.py

@@ -5,12 +5,12 @@ import json
 
 from db.agi.agi_repository import AgiRepository
 
-from db.entities import Location, TimeCluster, PopularLocation, LocationCluster, UserClusterGraph
+from db.entities import *
 from typing import List
 
 
 class Repository(MongoRepositoryBase):
-    '''This repository stores and loads locations and clusters with MongoDb.'''
+    '''This is a repository for MongoDb.'''
 
     def __init__(self):
         super().__init__(netconst.COMMUNITY_DETECTION_DB_HOSTNAME,
@@ -21,9 +21,12 @@ class Repository(MongoRepositoryBase):
         self._location_cluster_collection = 'location_cluster'
         self._time_cluster_collection = 'time_cluster'
         self._user_cluster_graph_collection = 'user_cluster_graph'
+        self._layer_collection = 'layer'
+        self._clusterset_collection = 'cluster_set'
 
         self.agi_repo = AgiRepository()
 
+#region Location
     def add_location(self, location: Location):
         super().insert_entry(self._location_collection, location.to_serializable_dict())
 
@@ -34,7 +37,9 @@ class Repository(MongoRepositoryBase):
     def get_agi_locations(self) -> List[Location]:
         agi_locations = self.agi_repo.getLocations()
         return [Location(agi_loc) for agi_loc in agi_locations]
+#endregion
 
+#region Specific Clusters
     def add_location_cluster(self, cluster: LocationCluster):
         super().insert_entry(self._location_cluster_collection,
                              cluster.to_serializable_dict(for_db=True))
@@ -50,7 +55,9 @@ class Repository(MongoRepositoryBase):
     def get_time_clusters(self) -> List[TimeCluster]:
         clusters = super().get_entries(self._time_cluster_collection)
         return [TimeCluster(time_dict=c, from_db=True) for c in clusters]
+#endregion
 
+#region Cluster Graph
     def add_user_cluster_graph(self, user_graph: UserClusterGraph):
         super().insert_entry(self._user_cluster_graph_collection,
                              user_graph.to_serializable_dict(for_db=True))
@@ -58,3 +65,48 @@ class Repository(MongoRepositoryBase):
     def get_user_cluster_graphs(self) -> List[UserClusterGraph]:
         user_graphs = super().get_entries(self._user_cluster_graph_collection)
         return [UserClusterGraph(dict_=u, from_db=True) for u in user_graphs]
+#endregion
+
+#region Layers
+    def add_layer(self, layer: Layer):
+        super().insert_entry(self._layer_collection, layer.to_serializable_dict())
+
+    def get_layers(self) -> List[Layer]:
+        entries = super().get_entries(self._layer_collection)
+        return [Layer(e) for e in entries]
+
+    def get_layer_names(self) -> List[str]:
+        entries = super().get_entries(self._layer_collection, projection={'layer_name': 1})
+        return [e['layer_name'] for e in entries]
+
+    def get_layer(self, layer_name) -> Layer:
+        entries = super().get_entries(self._layer_collection, selection={'layer_name': layer_name})
+        entries = [Layer(e) for e in entries]
+
+        if entries is not None and len(entries) > 0:
+            return entries[0]
+        else:
+            return None
+#endregion
+
+#region ClusterSet
+    def add_clusterset(self, cluster_set: ClusterSet):
+        super().insert_entry(self._clusterset_collection, cluster_set.to_serializable_dict())
+
+    def get_clustersets(self) -> List[ClusterSet]:
+        entries = super().get_entries(self._clusterset_collection)
+        return [ClusterSet(cluster_set_dict=e) for e in entries]
+
+    def get_clusterset_names(self) -> List[str]:
+        entries = super().get_entries(self._clusterset_collection, projection={'layer_name': 1})
+        return [e['layer_name'] for e in entries]
+
+    def get_clusterset(self, layer_name) -> ClusterSet:
+        entries = super().get_entries(self._clusterset_collection, selection={'layer_name': layer_name})
+        entries = [ClusterSet(cluster_set_dict=e) for e in entries]
+
+        if entries is not None and len(entries) > 0:
+            return entries[0]
+        else:
+            return None
+#endregion

src/data-hub/community-detection-microservice/app/processing/clusterer.py → src/data-hub/community-detection-microservice/app/processing/clustering/clusterer.py

@@ -2,9 +2,20 @@ import json
 import numpy as np
 import matplotlib.pyplot as plt
 from sklearn.cluster import DBSCAN
-from typing import List, Dict
+from typing import List, Dict, Any, TypeVar
+from deprecated import deprecated
+
+T = TypeVar('T')
+ClusterGroup = Dict[Any, List[Dict]]
 
 class Clusterer:
+    '''
+    Clusterer for applying density-based clustering on datasets.
+    The clustering is done with DBSCAN.
+
+    :param epsilon: Epsilon used in DBSCAN 
+    :param min_points: Min_points used in DBSCAN
+    '''
     def __init__(self, epsilon=11, min_points=2):
         self.epsilon = epsilon
         self.min_points = min_points
@@ -43,7 +54,8 @@ class Clusterer:
             
         return fig
     
-    def create_labels(self, features:np.ndarray) -> List:
+    def create_labels(self, features:np.ndarray) -> List[int]:
+        '''Creates labels for the items based on DBSCAN.'''
         if features is None or len(features) == 0:
             return features # trash in trash out
     
@@ -53,13 +65,25 @@ class Clusterer:
 
         return labels.tolist()
 
+    @deprecated(reason="Use generic version instead")
     def extract_location_features(self, locations: List[dict]) -> np.ndarray:
         return np.asarray([(float(l['latitude']), float(l['longitude'])) for l in locations])
 
+    @deprecated(reason="Use generic version instead")
     def extract_time_features(self, times: List[Dict]) -> np.ndarray:
-        return np.asarray([((t['timestamp']), 0) for t in times])
+        return np.asarray([[float(t['timestamp'])] for t in times])
+
+    def _extract_features(self, dataset: List[Dict], features:List[str]) -> np.ndarray:
+        '''Extracts the feature values from the dataset into a np array with same order as original dataset.'''
+        extracted_features = []
+        for data in dataset:
+            entry = [float(data[feature]) for feature in features]
+            extracted_features.append(entry)
 
-    def label_dataset(self, dataset:List[Dict], labels:List) -> List:
+        return np.asarray(extracted_features)
+
+    def label_dataset(self, dataset:List[Dict], labels:List[Any]) -> List:
+        '''Adds the labels to the elements of the dataset at the same position. The new key is called cluster_label.'''
         if dataset is None or labels is None:
             return
 
@@ -67,16 +91,21 @@ class Clusterer:
             raise ValueError("dataset and labels has to have same length")
 
         for i in range(len(dataset)):
+            if 'cluster_label' in dataset[i]:
+                continue
             dataset[i]['cluster_label'] = labels[i]
 
-    def group_by_clusters(self, dataset:List[Dict], labels:List) -> Dict[int, List[Dict]]:
+    def group_by_clusters(self, dataset:List[Dict], labels:List[Any]) -> ClusterGroup:
+        self.label_dataset(dataset, labels)
+
         clusters = {}
         for label in labels:
             clusters[label] = [ds for ds in dataset if ds['cluster_label'] == label]
         
         return clusters
 
-    def cluster_locations(self, locations:List[Dict]) -> Dict[int, List[Dict]]:
+    @deprecated(reason="Use generic version instead")
+    def cluster_locations(self, locations:List[Dict]) -> ClusterGroup:
         '''Returns a dictionary with identified clusters and their locations copied from the input'''
         if locations is None or len(locations) == 0:
             # raise Exception("locations has to contain something")
@@ -88,12 +117,29 @@ class Clusterer:
         self.label_dataset(locations, labels)
 
         return self.group_by_clusters(locations, labels)
-        
-    def cluster_times(self, times:List[Dict]) -> Dict[int, List[Dict]]:
+       
+    @deprecated(reason="Use generic version instead") 
+    def cluster_times(self, times:List[Dict]) -> ClusterGroup:
         '''Returns a dictionary with identified clusters and their times copied from the input'''
         features = self.extract_time_features(times)
     
         labels = self.create_labels(features)
         self.label_dataset(times, labels)
 
-        return self.group_by_clusters(times, labels)
+        return self.group_by_clusters(times, labels)
\ No newline at end of file
+
+    def cluster_dataset(self, dataset:List[Dict], features:List[str]) -> ClusterGroup:
+        '''
+        Returns the identified clusters containing a subset of nodes from the dataset.
+        
+        :param dataset: The nodes to assign to clusters
+        :param features: The feature names of the nodes to use for clustering
+
+        :returns: A dictionary of clusters, where each value is a non-empty subset of dataset if dataset was not empty
+        '''
+        arr = self._extract_features(dataset, features)
+
+        labels = self.create_labels(arr)
+
+        return self.group_by_clusters(dataset, labels)
+

src/data-hub/community-detection-microservice/app/processing/clustering/clustering_config.py

+import yaml
+from typing import Generator
+
+### init logging ###
+import logging
+LOG_FORMAT = (
+    '%(levelname) -5s %(asctime)s %(name)s:%(funcName) -35s %(lineno) -5d:  %(message)s')
+logging.basicConfig(level=logging.INFO, format=LOG_FORMAT)
+LOGGER = logging.getLogger(__name__)
+
+
+class ClusteringConfig:
+    '''Contains the configuration for the clustering algorithm defined in configs/clustering.yaml.'''
+
+    config_path = 'configs/clustering.yaml'
+    config: dict = None
+
+    def __init__(self):
+        self.config = self._load_config()
+
+    def _load_config(self) -> dict:
+        '''Loads the whole configuration from file.'''
+        config = None
+
+        with open(self.config_path, 'r') as stream:
+            try:
+                config = yaml.safe_load(stream)
+            except yaml.YAMLError as exc:
+                LOGGER.error(exc)
+                config = {}
+
+        return config
+
+    def get_config(self):
+        return self.config
+
+    def get_layer_configs(self) -> Generator[dict, None, None]:
+        """
+        Returns a generator for the individual layer configs.
+        
+        Layer configs are dicts including a layer-name.
+        """
+        for key, layer in self.config['layers'].items():
+            layer['layer-name'] = key
+            yield layer

src/data-hub/community-detection-microservice/app/requirements.txt

@@ -5,9 +5,11 @@ certifi==2019.11.28
 chardet==3.0.4
 Click==7.0
 clickclick==1.2.2
+colorama==0.4.3
 connexion==2.6.0
 cycler==0.10.0
 decorator==4.4.1
+Deprecated==1.2.7
 Flask==1.1.1
 idna==2.8
 importlib-metadata==1.5.0

src/data-hub/community-detection-microservice/app/rest/cluster.py → src/data-hub/community-detection-microservice/app/routes/cluster.py

 import io
 from flask import request, Response
 from db.repository import Repository
-from processing.clusterer import Clusterer
+from processing.clustering.clusterer import Clusterer
 from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
 
 repo = Repository()

src/data-hub/community-detection-microservice/app/routes/clustersets.py

+from flask import request, Response
+from db.repository import Repository
+from db.entities import ClusterSet
+
+repo = Repository()
+
+def get():
+    return [c.to_serializable_dict() for c in repo.get_clustersets()]
+
+def get_names():
+    return repo.get_clusterset_names()
+
+def get_by_name(name):
+    res = repo.get_clusterset(name)
+    if res is not None:
+        return res.to_serializable_dict() 
+    else:
+        return Response(status=404)
\ No newline at end of file

src/data-hub/community-detection-microservice/app/routes/layers.py

+from flask import request, Response
+from db.repository import Repository
+from db.entities import Layer
+
+repo = Repository()
+
+def post():
+    body = request.json
+    _insert_layer(body)
+    return Response(status=201)
+
+def _insert_layer(layer_data: dict):
+    # convert object keys from ext source
+    layer_data['layer_name'] = layer_data.pop('LayerName')
+    layer_data['nodes'] = layer_data.pop('Nodes')
+    layer_data['properties'] = layer_data.pop('Properties')
+
+    repo.add_layer(Layer(layer_data))
+
+def get():
+    return [l.to_serializable_dict() for l in repo.get_layers()]
+
+def get_names():
+    return repo.get_layer_names()
+
+def get_by_name(name):
+    res = repo.get_layer(name)
+    if res is not None:
+        return res.to_serializable_dict() 
+    else:
+        return Response(status=404)
\ No newline at end of file

src/data-hub/community-detection-microservice/app/run_clustering.py

@@ -4,15 +4,40 @@ modules_path = '../../../modules/'
 if os.path.exists(modules_path):
     sys.path.insert(1, modules_path)
 
-from db.entities import Location, PopularLocation, LocationCluster, TimeCluster
+from db.entities import *
 from typing import List, Dict, Tuple
-from db.repository import Repository
-from processing.clusterer import Clusterer
+from db.repository import Repository, AgiRepository
+from processing.clustering.clusterer import Clusterer
 
 
 DEBUG = False
 
 repo = Repository()
+test_repo = AgiRepository()
+
+
+def run_generic_clustering():
+    '''Runs the clustering for all layers found in the repository.'''
+    all_layers:List[Layer] = repo.get_layers()
+
+    for layer in all_layers:
+        print(f"Clustering {layer.layer_name}")
+        clusters = run_clustering_for_layer(layer)
+        
+        cluster_set = ClusterSet(layer.layer_name, clusters)
+        repo.add_clusterset(cluster_set)
+
+
+def run_clustering_for_layer(layer: Layer) -> List[Cluster]:
+    clusterer = Clusterer()
+
+    res = clusterer.cluster_dataset(
+        layer.nodes,
+        layer.properties
+    )
+
+    return [Cluster(key, value) for key, value in res.items()]
+
 
 def run_location_clustering():
     user_clusterer = Clusterer()
@@ -74,5 +99,7 @@ def store_clusters(type: str, clusters: List):
 
 
 if __name__ == "__main__":
-    run_location_clustering()
-    run_time_clustering()
+    run_generic_clustering()
+
+    # run_location_clustering()
+    # run_time_clustering()

src/data-hub/community-detection-microservice/app/tests/test_clusterer.py

 import unittest
 import sys
-sys.path.insert(1, '../')
+for path in ['../', './']:
+    sys.path.insert(1, path)
 
 # python -m unittest discover
-from processing.clusterer import Clusterer
+from processing.clustering.clusterer import Clusterer
 
 class TestClusterer(unittest.TestCase):
     clusterer:Clusterer = None
@@ -71,11 +72,50 @@ class TestClusterer(unittest.TestCase):
         self.assertEqual(3, len(locations))
         self.assertHaveLabelsAsNewKey(locations, labels)
 
+    def test_cluster_locations_multInput_correctlyLabeled(self):
+        locations = [self.location(1,2), self.location(2,2), self.location(20,20)]
+        labels = [0,0,-1]
+
+        res = self.clusterer.cluster_locations(locations)
+        
+        self.assertHaveLabelsAsNewKey(locations, labels)
+        self.assertDictEqual(res, {0: [{'latitude': 1, 'longitude': 2, 'cluster_label': 0}, {'latitude': 2, 'longitude': 2, 'cluster_label': 0}], -1: [{'latitude': 20, 'longitude': 20, 'cluster_label': -1}]})
+
+    def test_cluster_times_multInput_correctlyLabeled(self):
+        times = [self.time(123), self.time(128), self.time(223)]
+        labels = [0,0,-1]
+
+        res = self.clusterer.cluster_times(times)
+        
+        self.assertHaveLabelsAsNewKey(times, labels)
+        self.assertDictEqual(res, {0: [{'timestamp': 123, 'cluster_label': 0}, {'timestamp': 128, 'cluster_label': 0}], -1: [{'timestamp': 223, 'cluster_label': -1}]})
+
+    def test_cluster_dataset_locationsMultInput_correctlyLabeled(self):
+        locations = [self.location(1,2), self.location(2,2), self.location(20,20)]
+        labels = [0,0,-1]
+
+        res = self.clusterer.cluster_dataset(locations, ['latitude', 'longitude'])
+        
+        self.assertHaveLabelsAsNewKey(locations, labels)
+        self.assertDictEqual(res, {0: [{'latitude': 1, 'longitude': 2, 'cluster_label': 0}, {'latitude': 2, 'longitude': 2, 'cluster_label': 0}], -1: [{'latitude': 20, 'longitude': 20, 'cluster_label': -1}]})
+
+    def test_cluster_dataset_timesMultInput_correctlyLabeled(self):
+        times = [self.time(123), self.time(128), self.time(223)]
+        labels = [0,0,-1]
+
+        res = self.clusterer.cluster_dataset(times, ['timestamp'])
+        
+        self.assertHaveLabelsAsNewKey(times, labels)
+        self.assertDictEqual(res, {0: [{'timestamp': 123, 'cluster_label': 0}, {'timestamp': 128, 'cluster_label': 0}], -1: [{'timestamp': 223, 'cluster_label': -1}]})
+
 
     # helper methods:
     def location(self, lat, long_) -> dict:
         return {'latitude': lat, 'longitude':long_}
 
+    def time(self, ts) -> dict:
+        return {'timestamp': ts}
+
     def assertHaveLabelsAsNewKey(self, locations, labels):
         for i in range(len(locations)):
             self.assertEqual(labels[i], locations[i]['cluster_label'])

src/data-hub/community-detection-microservice/app/tests/test_clustering_config.py

+import unittest
+import sys
+for path in ['../', './']:
+    sys.path.insert(1, path)
+
+# python -m unittest discover
+from processing.clustering.clustering_config import ClusteringConfig
+
+class TestClusteringConfig(unittest.TestCase):
+    
+    def setUp(self):
+        self.clustering_config = ClusteringConfig()
+
+    def test_get_layer_configs_noneInput_noneOutput(self):
+        for layer_config in self.clustering_config.get_layer_configs():
+            self.assertIn('layer-name', layer_config)
+
+if __name__ == '__main__':
+    unittest.main()