Add handover

beacon_api/__init__.py

@@ -12,6 +12,10 @@
 __author__ = CONFIG_INFO.author
 __license__ = CONFIG_INFO.license
 __copyright__ = CONFIG_INFO.copyright
+__handover_drs__ = CONFIG_INFO.handover_drs
+__handover_datasets__ = CONFIG_INFO.handover_datasets
+__handover_beacon__ = CONFIG_INFO.handover_beacon
+__handover_base__ = CONFIG_INFO.handover_base
 
 __apiVersion__ = CONFIG_INFO.apiVersion
 __beaconId__ = CONFIG_INFO.beaconId

beacon_api/api/info.py

@@ -6,10 +6,11 @@
 .. note:: See ``beacon_api`` root folder ``__init__.py`` for changing values used here.
 """
 
-from .. import __apiVersion__, __title__, __version__, __description__, __url__, __alturl__
+from .. import __apiVersion__, __title__, __version__, __description__, __url__, __alturl__, __handover_beacon__
 from .. import __createtime__, __updatetime__, __org_id__, __org_name__, __org_description__
 from .. import __org_address__, __org_logoUrl__, __org_welcomeUrl__, __org_info__, __org_contactUrl__
-from ..utils.data_query import fetch_dataset_metadata
+from .. import __handover_drs__
+from ..utils.data_query import fetch_dataset_metadata, make_handover
 from aiocache import cached
 from aiocache.serializers import JsonSerializer
 
@@ -21,6 +22,7 @@ async def beacon_info(host, pool):
     :return beacon_info: A dict that contain information about the ``Beacon`` endpoint.
     """
     beacon_dataset = await fetch_dataset_metadata(pool)
+
     # If one sets up a beacon it is recommended to adjust these sample requests
     sample_allele_request = [{
         "alternateBases": "G",
@@ -73,7 +75,9 @@ async def beacon_info(host, pool):
         'updateDateTime': __updatetime__,
         'datasets': beacon_dataset,
         'sampleAlleleRequests': sample_allele_request,
-        'info': {"achievement": "World's first 1.0 Beacon"}
+        'info': {"achievement": "World's first 1.0 Beacon"},
     }
 
+    if __handover_drs__:
+        beacon_info['beaconHandover'] = make_handover(__handover_beacon__, [x['id'] for x in beacon_dataset])
     return beacon_info

beacon_api/api/query.py

@@ -6,8 +6,8 @@
 """
 
 from ..utils.logging import LOG
-from .. import __apiVersion__
-from ..utils.data_query import filter_exists, find_datasets, fetch_datasets_access
+from .. import __apiVersion__, __handover_beacon__, __handover_drs__
+from ..utils.data_query import filter_exists, find_datasets, fetch_datasets_access, make_handover
 from .exceptions import BeaconUnauthorised, BeaconForbidden, BeaconBadRequest
 
 
@@ -63,6 +63,7 @@ async def query_request_handler(params):
     """
     LOG.info(f'{params[1]} request to beacon endpoint "/query"')
     request = params[2]
+
     # Fills the Beacon variable with the found data.
     alleleRequest = {'referenceName': request.get("referenceName"),
                      'referenceBases': request.get("referenceBases"),
@@ -109,4 +110,6 @@ async def query_request_handler(params):
                        'alleleRequest': alleleRequest,
                        'datasetAlleleResponses': filter_exists(request.get("includeDatasetResponses", "NONE"), datasets)}
 
+    if __handover_drs__:
+        beacon_response['beaconHandover'] = make_handover(__handover_beacon__, [x['datasetId'] for x in datasets])
     return beacon_response

beacon_api/conf/__init__.py

@@ -5,6 +5,11 @@
 from collections import namedtuple
 
 
+def parse_drspaths(paths):
+    """Parse handover configuration."""
+    return [p.strip().split(',', 2) for p in paths.split('\n') if p.split()]
+
+
 def parse_config_file(path):
     """Parse configuration file."""
     config = ConfigParser()
@@ -15,6 +20,10 @@ def parse_config_file(path):
         'author': config.get('beacon_general_info', 'author'),
         'license': config.get('beacon_general_info', 'license'),
         'copyright': config.get('beacon_general_info', 'copyright'),
+        'handover_drs': config.get('handover_info', 'drs', fallback=''),
+        'handover_datasets': parse_drspaths(config.get('handover_info', 'dataset_paths', fallback='')),
+        'handover_beacon': parse_drspaths(config.get('handover_info', 'beacon_paths', fallback='')),
+        'handover_base': int(config.get('handover_info', 'handover_base', fallback=0)),
         'apiVersion': config.get('beacon_api_info', 'apiVersion'),
         'beaconId': config.get('beacon_api_info', 'beaconId'),
         'description': config.get('beacon_api_info', 'description'),

beacon_api/conf/config.ini

@@ -39,6 +39,25 @@ alturl=
 createtime=2018-07-25T00:00:00Z
 
 
+[handover_info]
+# The base url for all handovers
+# if this url is empty or commented, handover feature is disabled
+#drs=https://examplebrowser.org
+
+# Make the handovers 1- or 0-based
+handover_base = 1
+
+# Handovers for datasets
+dataset_paths=
+  Variants,browse the variants matched by the query,dataset/{dataset}/browser/variant/{chr}-{start}-{ref}-{alt}
+  Region,browse data of the region matched by the query,dataset/{dataset}/browser/region/{chr}-{start}-{end}
+  Data,retrieve information of the datasets,dataset/{dataset}/browser
+
+# Handovers for general beacon
+beacon_paths=
+  Project,retrieve information about the datasets,dataset/{dataset}
+
+
 [organisation_info]
 # Globally unique identifier for organisation that hosts this Beacon service
 org_id=fi.csc

beacon_api/schemas/info.json

@@ -826,6 +826,35 @@
     },
     "info": {
       "type": "object"
+    },
+    "beaconHandover": {
+            "type": "array",
+            "required": [
+              "handoverType",
+              "url"
+            ],
+            "properties": {
+              "handoverType": {
+                "type": "object",
+                "required": [
+                  "id"
+                ],
+                "properties": {
+                  "id": {
+                    "type": "string"
+                  },
+                  "label": {
+                    "type": "string"
+                  }
+                }
+              },
+              "description": {
+                    "type": "string"
+              },
+              "url": {
+                    "type": "string"
+              }
+            }
     }
   }
 }

beacon_api/schemas/response.json

@@ -108,6 +108,35 @@
         }
       }
     },
+    "beaconHandover": {
+            "type": "array",
+            "required": [
+              "handoverType",
+              "url"
+            ],
+            "properties": {
+              "handoverType": {
+                "type": "object",
+                "required": [
+                  "id"
+                ],
+                "properties": {
+                  "id": {
+                    "type": "string"
+                  },
+                  "label": {
+                    "type": "string"
+                  }
+                }
+              },
+              "description": {
+                    "type": "string"
+              },
+              "url": {
+                    "type": "string"
+              }
+            }
+    },
     "datasetAlleleResponses": {
       "type": "array",
       "items": {
@@ -129,6 +158,35 @@
               }
             ]
           },
+          "datasetHandover": {
+            "type": "array",
+            "required": [
+              "handoverType",
+              "url"
+            ],
+            "properties": {
+              "handoverType": {
+                "type": "object",
+                "required": [
+                  "id"
+                ],
+                "properties": {
+                  "id": {
+                    "type": "string"
+                  },
+                  "label": {
+                    "type": "string"
+                  }
+                }
+              },
+              "description": {
+                    "type": "string"
+              },
+              "url": {
+                    "type": "string"
+              }
+            }
+          },
           "referenceBases": {
             "type": "string",
             "pattern": "^([ACGT]+)$"

beacon_api/utils/data_query.py

@@ -4,6 +4,7 @@
 from .logging import LOG
 from ..api.exceptions import BeaconServerError
 from ..conf.config import DB_SCHEMA
+from .. import __handover_drs__, __handover_datasets__, __handover_base__
 
 
 # def transform_record(record, variantCount):
@@ -58,6 +59,31 @@ def transform_metadata(record):
     return response
 
 
+def add_handover(response):
+    """Add handover to a dataset response."""
+    response["datasetHandover"] = make_handover(__handover_datasets__, [response['datasetId']],
+                                                response['referenceName'], response['start'],
+                                                response['end'], response['referenceBases'],
+                                                response['alternateBases'], response['variantType'])
+    return response
+
+
+def make_handover(paths, datasetIds, chr='', start=0, end=0, ref='', alt='', variant=''):
+    """Create one handover for each path (specified in config)."""
+    alt = alt if alt else variant
+    handovers = []
+    start = start + __handover_base__
+    end = end + __handover_base__
+    for label, desc, path in paths:
+        for dataset in set(datasetIds):
+            handovers.append({"handoverType": {"id": "CUSTOM", "label": label},
+                              "description": desc,
+                              "url": __handover_drs__ + path.format(dataset=dataset, chr=chr, start=start,
+                                                                    end=end, ref=ref, alt=alt)})
+
+    return handovers
+
+
 async def fetch_datasets_access(db_pool, datasets):
     """Retrieve CONTROLLED datasets."""
     public = []
@@ -184,6 +210,9 @@ async def fetch_filtered_dataset(db_pool, assembly_id, position, chromosome, ref
                 LOG.info(f"Query for dataset(s): {datasets} that are {access_type} matching conditions.")
                 for record in list(db_response):
                     processed = transform_misses(record) if misses else transform_record(record)
+                    if __handover_drs__:
+                        # If handover feature is enabled, add handover object to response
+                        processed = add_handover(processed)
                     datasets.append(processed)
                 return datasets
             except Exception as e:

deploy/test/auth_test.ini

@@ -39,6 +39,24 @@ alturl=https://ega-archive.org/
 createtime=2018-07-25T00:00:00Z
 
 
+[handover_info]
+# The base url for all handovers
+drs=https://examplebrowser.org
+
+# Make the handovers 1- or 0-based
+handover_base = 1
+
+# Handovers for datasets
+dataset_paths=
+  Variants,browse the variants matched by the query,dataset/{dataset}/browser/variant/{chr}-{start}-{ref}-{alt}
+  Region,browse data of the region matched by the query,dataset/{dataset}/browser/region/{chr}-{start}-{end}
+  Data,retrieve information of the datasets,dataset/{dataset}/browser
+
+# Handovers for general beacon
+beacon_paths=
+  Project,retrieve information about the datasets,dataset/{dataset}
+
+
 [organisation_info]
 # Globally unique identifier for organisation that hosts this Beacon service
 org_id=CSC

tests/test_data_query.py

@@ -1,6 +1,7 @@
 import asynctest
+from unittest import mock
 from beacon_api.utils.data_query import filter_exists, transform_record
-from beacon_api.utils.data_query import transform_misses, transform_metadata, find_datasets
+from beacon_api.utils.data_query import transform_misses, transform_metadata, find_datasets, add_handover, make_handover
 from datetime import datetime
 # from beacon_api.utils.data_query import fetch_dataset_metadata
 from beacon_api.utils.data_query import handle_wildcard
@@ -110,6 +111,26 @@ def test_transform_metadata(self):
         result = transform_metadata(record)
         self.assertEqual(result, response)
 
+    def test_add_handover(self):
+        """Test that add handover."""
+        # Test that the handover actually is added
+        handovers = [{"handover1": "info"}, {"handover2": "url"}]
+        record = {"datasetId": "test", "referenceName": "22", "referenceBases": "A",
+                  "alternateBases": "C", "start": 10, "end": 11, "variantType": "SNP"}
+        with mock.patch('beacon_api.utils.data_query.make_handover', return_value=handovers):
+            result = add_handover(record)
+        record['datasetHandover'] = handovers
+        self.assertEqual(result, record)
+
+    def test_make_handover(self):
+        """Test make handover."""
+        paths = [('lab1', 'desc1', 'path1'), ('lab2', 'desc2', 'path2')]
+        result = make_handover(paths, ['id1', 'id2', 'id1'])
+        # The number of handovers = number of paths * number of unique datasets
+        self.assertEqual(len(result), 4)
+        self.assertIn("path1", result[0]["url"])
+        self.assertEqual(result[0]["description"], 'desc1')
+
     @asynctest.mock.patch('beacon_api.utils.data_query.fetch_filtered_dataset')
     async def test_find_datasets(self, mock_filtered):
         """Test find datasets."""