Change request dataset from omop (it was kind of hardcoded, to regula…

…r mongo)

beacon/connections/omopcdm/datasets.py

@@ -1,44 +1,117 @@
-from beacon.logs.logs import log_with_args
+from beacon.connections.mongo.__init__ import client
+from beacon.exceptions.exceptions import raise_exception
+from beacon.logs.logs import log_with_args, log_with_args_mongo
+from beacon.logs.logs import LOG
+
+from beacon.connections.mongo.utils import get_count, get_documents
+from beacon.connections.mongo.request_parameters import apply_request_parameters
+from beacon.connections.mongo.utils import get_docs_by_response_type, query_id
+
 from beacon.conf.conf import level
 from typing import Optional
 from beacon.response.schemas import DefaultSchemas
 from beacon.request.parameters import RequestParams
 from beacon.connections.omopcdm.biosamples import get_biosamples
 from beacon.connections.omopcdm.individuals import get_individuals
 
+@log_with_args_mongo(level)
+def get_datasets(self):
+    try:
+        collection = client.beacon.datasets
+        query = {}
+        query = collection.find(query)
+        return query
+    except Exception as e:# pragma: no cover
+        err = str(e)
+        errcode=500
+        raise_exception(err, errcode)
 
-# There are no different datasets in OMOPCDM
-@log_with_args(level)
+@log_with_args_mongo(level)
 def get_full_datasets(self, entry_id: Optional[str], qparams: RequestParams):
-    schema = DefaultSchemas.DATASETS
-    response = [{'id':'cdm', 'name':'OMOP CDM dataset'}]
-    count = 1
-    return response, count, schema
+    try:
+        collection = client.beacon.datasets
+        if entry_id == None:
+            query = {}
+        else:# pragma: no cover
+            query = {'id': entry_id}
+        count = get_count(self, client.beacon.datasets, query)
+        query = collection.find(query)
+        entity_schema = DefaultSchemas.DATASETS
+        response_converted = (
+            [r for r in query] if query else []
+        )
+        return response_converted, count, entity_schema
+    except Exception as e:# pragma: no cover
+        err = str(e)
+        errcode=500
+        raise_exception(err, errcode)
 
-@log_with_args(level)
+@log_with_args_mongo(level)
 def get_list_of_datasets(self):
-    datasets, count, schema = get_full_datasets(self, None, None)
-    return datasets
+    try:
+        datasets = get_datasets(self)
+        beacon_datasets = [ r for r in datasets ]
+        LOG.debug(beacon_datasets)
+        return beacon_datasets
+    except Exception as e:# pragma: no cover
+        err = str(e)
+        errcode=500
+        raise_exception(err, errcode)
 
-@log_with_args(level)
+@log_with_args_mongo(level)
 def get_dataset_with_id(self, entry_id: Optional[str], qparams: RequestParams):
+    limit = qparams.query.pagination.limit
+    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams, entry_id)
+    if parameters_as_filters == True:
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, entry_id)# pragma: no cover
+    else:
+        query={}
+    query = query_id(self, query, entry_id)
     schema = DefaultSchemas.DATASETS
-    if entry_id=='cdm':
-        response = [{'id':'cdm', 'name':'OMOP CDM dataset'}]
-        count = 1
-        return response, count, schema
-    return {}, 0, schema
-
-@log_with_args(level)
-def get_biosamples_of_dataset(self, entry_id: Optional[str], qparams: RequestParams, dataset: str):
-    schema = DefaultSchemas.BIOSAMPLES
-    if entry_id=='cdm':
-        return get_biosamples(self, None, qparams, dataset)
-    return schema, 0, 0, {}, dataset
-
-@log_with_args(level)
-def get_individuals_of_dataset(self, entry_id: Optional[str], qparams: RequestParams, dataset: str):
-    schema = DefaultSchemas.INDIVIDUALS
-    if entry_id=='cdm':
-        return get_individuals(self, None, qparams, dataset)
-    return schema, 0, 0, {}, dataset
+    count = get_count(self, client.beacon.datasets, query)
+    docs = get_documents(self,
+        client.beacon.datasets,
+        query,
+        qparams.query.pagination.skip,
+        qparams.query.pagination.skip*limit
+    )
+    response_converted = (
+                [r for r in docs] if docs else []
+            )
+    return response_converted, count, schema
+
+# # There are no different datasets in OMOPCDM
+# @log_with_args(level)
+# def get_full_datasets(self, entry_id: Optional[str], qparams: RequestParams):
+#     schema = DefaultSchemas.DATASETS
+#     response = [{'id':'cdm', 'name':'OMOP CDM dataset'}]
+#     count = 1
+#     return response, count, schema
+
+# @log_with_args(level)
+# def get_list_of_datasets(self):
+#     datasets, count, schema = get_full_datasets(self, None, None)
+#     return datasets
+
+# @log_with_args(level)
+# def get_dataset_with_id(self, entry_id: Optional[str], qparams: RequestParams):
+#     schema = DefaultSchemas.DATASETS
+#     if entry_id=='cdm':
+#         response = [{'id':'cdm', 'name':'OMOP CDM dataset'}]
+#         count = 1
+#         return response, count, schema
+#     return {}, 0, schema
+
+# @log_with_args(level)
+# def get_biosamples_of_dataset(self, entry_id: Optional[str], qparams: RequestParams, dataset: str):
+#     schema = DefaultSchemas.BIOSAMPLES
+#     if entry_id=='cdm':
+#         return get_biosamples(self, None, qparams, dataset)
+#     return schema, 0, 0, {}, dataset
+
+# @log_with_args(level)
+# def get_individuals_of_dataset(self, entry_id: Optional[str], qparams: RequestParams, dataset: str):
+#     schema = DefaultSchemas.INDIVIDUALS
+#     if entry_id=='cdm':
+#         return get_individuals(self, None, qparams, dataset)
+#     return schema, 0, 0, {}, dataset