Make some changes to cohorts to keep compatibility between Analysis and Experience

Rebase, update citation and contributors

Author: MaryanMorel

CONTRIBUTORS.md

@@ -6,4 +6,5 @@ The _SCALPEL-Analysis_ package was initially implemented by researchers, develop
 
 - Youcef Sebiat
 - Maryan Morel
-- Dinh Phong Nguyen
+- Dinh Phong Nguyen
+- Dian Sun

README.md

@@ -237,6 +237,7 @@ If you use a library part of _SCALPEL3_ in a scientific publication, we would ap
       year={2020},
       publisher={Elsevier}
     }
+
 
 ## Contributing
 The development cycle is opinionated. Each time you commit, git will

scalpel/core/cohort.py

@@ -284,6 +284,12 @@ def load(input: Dict) -> "Cohort":
     def from_description(description: str) -> "Cohort":
         raise NotImplementedError
 
+    def cache(self) -> "Cohort":
+        self.subjects = self.subjects.cache()
+        if self.events is not None:
+            self.events = self.events.cache()
+        return self
+
 
 def _union(a: Cohort, b: Cohort) -> Cohort:
     if a.events is None or b.events is None:

tests/core/cohort_test.py

@@ -297,3 +297,19 @@ def test_save_cohort(self, mock_method):
             },
             cohort_2.save_cohort("../../output"),
         )
+
+    def test_cache(self):
+        patients_pd = pd.DataFrame({"patientID": [1, 2, 3]})
+        events_pd = pd.DataFrame({"patientID": [1, 2, 3], "value": ["DP", "DAS", "DR"]})
+
+        patients = self.spark.createDataFrame(patients_pd)
+
+        events = self.spark.createDataFrame(events_pd)
+        cohort = Cohort("liberal_fractures", "liberal_fractures", patients, events)
+        cohort.cache()
+        assert cohort.subjects.storageLevel.useMemory
+        assert cohort.events.storageLevel.useMemory
+
+    def test_from_description(self):
+        self.assertRaises(NotImplementedError, Cohort.from_description,
+                          description='some string')