aphp · npuchois-aphp · May 18, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,22 @@
 
 All notable changes to this project will be documented in this file.
 
+## [Unreleased]
+
+### 🚀 Features
+
+- *(health)* Return 503 error if spark context is stopped
+- Add local development documentation (#21)
+
+### 🚜 Refactor
+
+- Mep BC 3.1 - add _key field in list table omop pg
+- Resource pmsi changes (#16)
+
+### 📚 Documentation
+
+- Add missing mode documentation
+
 ## [2.10.0] - 2025-07-01
 
 ### 🚀 Features

diff --git a/src/main/scala/fr/aphp/id/eds/requester/cohort/pg/PGCohortCreation.scala b/src/main/scala/fr/aphp/id/eds/requester/cohort/pg/PGCohortCreation.scala
@@ -12,8 +12,8 @@ import org.apache.spark.sql.{DataFrame, SparkSession, functions => F}
 import org.hl7.fhir.r4.model.ListResource.ListMode
 
 /**
-  * @param pg           pgTool obj
-  */
+ * @param pg pgTool obj
+ */
 class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
   private final val cohort_item_table_rw = AppConfig.get.pg.get.cohortConfig.cohortItemsTableName
   private final val cohort_table_rw = AppConfig.get.pg.get.cohortConfig.cohortTableName
@@ -33,11 +33,12 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
     } else {
       ("", "")
     }
+    val key_col = baseCohortId.map(_.toString).getOrElse("-1")
     val stmt =
       s"""
-         |insert into ${cohort_table_rw}
-         |(hash, title, ${note_text_column_name},${indentifier_col} _sourcereferenceid, source__reference, _provider, source__type, mode, status, subject__type, date, _size)
-         |values (-1, ?, ?,${identifier_val} ?, ?, '$cohort_provider_name', 'Practitioner', '${mode.toCode}', '${CohortStatus.RUNNING}', ?, now(), ?)
+         |insert into $cohort_table_rw
+         |(hash, title, $note_text_column_name,$indentifier_col _sourcereferenceid, source__reference, _provider, source__type, mode, status, subject__type, date, _size, _key)
+         |values (-1, ?, ?,$identifier_val ?, ?, '$cohort_provider_name', 'Practitioner', '${mode.toCode}', '${CohortStatus.RUNNING}', ?, now(), ?, '$key_col')
          |returning id
          |""".stripMargin
     val result = pg
@@ -47,7 +48,7 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
           cohortDefinitionName,
           cohortDefinitionSyntax,
           ownerEntityId,
-          s"Practitioner/${ownerEntityId}",
+          s"Practitioner/$ownerEntityId",
           resourceType,
           size
         )
@@ -58,8 +59,8 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
   }
 
   /**
-    * This loads both a cohort and its definition into postgres and solr
-    */
+   * This loads both a cohort and its definition into postgres and solr
+   */
   override def updateCohort(cohortId: Long,
                             cohort: DataFrame,
                             sourcePopulation: SourcePopulation,
@@ -122,11 +123,11 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
   private def readCohortDiffEntries(cohortId: Long): DataFrame = {
     val stmt =
       s"""
-             |select date,_itemreferenceid,deleted
-             |from ${cohort_item_table_rw}
-             |join ${cohort_table_rw} on ${cohort_table_rw}.id = ${cohort_item_table_rw}._listid
-             |where ${cohort_table_rw}.identifier___official__value = '$cohortId'
-             |""".stripMargin
+         |select date,_itemreferenceid,deleted
+         |from ${cohort_item_table_rw}
+         |join ${cohort_table_rw} on ${cohort_table_rw}.id = ${cohort_item_table_rw}._listid
+         |where ${cohort_table_rw}.identifier___official__value = '$cohortId'
+         |""".stripMargin
     pg.sqlExecWithResult(stmt)
       .select(col("date"), col("_itemreferenceid"), col("deleted"))
       .orderBy(col("date").asc)
@@ -140,7 +141,7 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
       for (sc_id <- sourcePopulation.cohortList.get) {
         val (list_list_id, list_relationship_concept_id) =
           (List(List(cohortDefinitionId, sc_id), List(sc_id, cohortDefinitionId)),
-           List(44818821, 44818823))
+            List(44818821, 44818823))
         for ((list_id, relationship_concept_id) <- list_list_id zip list_relationship_concept_id) {
           val stmt =
             s"""
@@ -155,24 +156,24 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
   }
 
   /**
-    * This loads only a cohort definition into postgres.
-    *
-    * @param cohortDefinitionId   id of the cohort
-    * @param count                nb of patient of the cohort
-    */
+   * This loads only a cohort definition into postgres.
+   *
+   * @param cohortDefinitionId id of the cohort
+   * @param count              nb of patient of the cohort
+   */
   private def uploadCount(
-      cohortDefinitionId: Long,
-      count: Long
-  ): Unit = {
+                           cohortDefinitionId: Long,
+                           count: Long
+                         ): Unit = {
     setOmopCohortSize(cohortDefinitionId, count)
     setOmopCohortStatus(cohortDefinitionId, CohortStatus.FINISHED)
     setOmopCohortActive(cohortDefinitionId, status = true)
   }
 
   private def setOmopCohortSize(
-      cohortDefinitionId: Long,
-      count: Long
-  ): Unit = {
+                                 cohortDefinitionId: Long,
+                                 count: Long
+                               ): Unit = {
     val stmt =
       s"""
          |update ${cohort_table_rw}
@@ -183,9 +184,9 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
   }
 
   private def setOmopCohortStatus(
-      cohortDefinitionId: Long,
-      status: CohortStatus.Value
-  ): Unit = {
+                                   cohortDefinitionId: Long,
+                                   status: CohortStatus.Value
+                                 ): Unit = {
     val stmt =
       s"""
          |update ${cohort_table_rw}
@@ -196,9 +197,9 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
   }
 
   private def setOmopCohortActive(
-      cohortDefinitionId: Long,
-      status: Boolean
-  ): Unit = {
+                                   cohortDefinitionId: Long,
+                                   status: Boolean
+                                 ): Unit = {
     val mode = if (status) "working" else "snapshot"
     val stmt =
       s"""
@@ -220,22 +221,22 @@ class PGCohortCreation(pg: PGTool) extends CohortCreation with LazyLogging {
       "cohort dataframe shall have _listid, _provider, _provider and item__reference"
     )
     pg.outputBulk(cohort_item_table_rw,
-                  dfAddHash(df),
-                  Some(4),
-                  primaryKeys = Seq("_listid", "_itemreferenceid", "_provider"))
+      dfAddHash(df),
+      Some(4),
+      primaryKeys = Seq("_listid", "_itemreferenceid", "_provider"))
   }
 
   /**
-    * Adds a hash column based on several other columns
-    *
-    * @param df               DataFrame
-    * @param columnsToExclude List[String] the columns not to be hashed
-    * @return DataFrame
-    */
+   * Adds a hash column based on several other columns
+   *
+   * @param df               DataFrame
+   * @param columnsToExclude List[String] the columns not to be hashed
+   * @return DataFrame
+   */
   private def dfAddHash(
-      df: DataFrame,
-      columnsToExclude: List[String] = Nil
-  ): DataFrame = {
+                         df: DataFrame,
+                         columnsToExclude: List[String] = Nil
+                       ): DataFrame = {
     df.withColumn(
       "hash",
       hash(

diff --git a/src/test/resources/testCases/occurences/resource_2.csv b/src/test/resources/testCases/occurences/resource_2.csv
@@ -1,4 +1,4 @@
-patient;_ref.encounter.period.start;_ref.encounter.period.end;recordedDate
+patient;_ref.encounter.period.start;_ref.encounter.period.end;onsetDateTime
 22;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z
 22;2016-03-07T12:04:00Z;2016-03-07T12:04:00Z;2016-03-07T12:04:00Z
 23;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z

diff --git a/src/test/resources/testCases/temporalConstraintDirectChronologicalOrder/resource_1.csv b/src/test/resources/testCases/temporalConstraintDirectChronologicalOrder/resource_1.csv
@@ -1,4 +1,4 @@
-patient;_ref.encounter.period.start;_ref.encounter.period.end;recordedDate
+patient;_ref.encounter.period.start;_ref.encounter.period.end;onsetDateTime
 22;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z
 23;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z
 24;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z;2016-03-06T12:04:00Z

diff --git a/src/test/scala/fr/aphp/id/eds/requester/cohort/pg/PGCohortCreationTest.scala b/src/test/scala/fr/aphp/id/eds/requester/cohort/pg/PGCohortCreationTest.scala
@@ -41,8 +41,8 @@ class PGCohortCreationTest
       pgTools.sqlExecWithResult(
         """
         |insert into list_cohort360
-        |(hash, title, note__text, _sourcereferenceid, source__reference, _provider, source__type, mode, status, subject__type, date, _size)
-        |values (-1, ?, ?, ?, ?, 'Cohort360', 'Practitioner', 'snapshot', 'retired', ?, now(), ?)
+        |(hash, title, note__text, _sourcereferenceid, source__reference, _provider, source__type, mode, status, subject__type, date, _size, _key)
+        |values (-1, ?, ?, ?, ?, 'Cohort360', 'Practitioner', 'snapshot', 'retired', ?, now(), ?, '-1')
         |returning id
         |""".stripMargin,
         List("test", "test", "test", "Practitioner/test", "test", 1)
@@ -57,6 +57,31 @@ class PGCohortCreationTest
                                   1)
   }
 
+  test("testCreateCohortWithBaseCohort") {
+    val pgTools = mock[PGTool]
+    val pgCohortCreation = new PGCohortCreation(pgTools)
+    val expectedResult: Dataset[Row] = mock[Dataset[Row]]
+    when(expectedResult.collect()).thenReturn(Array(Row(1L)))
+    when(
+      pgTools.sqlExecWithResult(
+        """
+        |insert into list_cohort360
+        |(hash, title, note__text, identifier, _sourcereferenceid, source__reference, _provider, source__type, mode, status, subject__type, date, _size, _key)
+        |values (-1, ?, ?, 42, ?, ?, 'Cohort360', 'Practitioner', 'snapshot', 'retired', ?, now(), ?, '42')
+        |returning id
+        |""".stripMargin,
+        List("test", "test", "test", "Practitioner/test", "test", 1)
+      )).thenReturn(expectedResult)
+    pgCohortCreation.createCohort("test",
+                                  Some("test"),
+                                  "test",
+                                  "test",
+                                  "test",
+                                  Some(42L),
+                                  ListMode.SNAPSHOT,
+                                  1)
+  }
+
   test("testUpdateCohort") {
     val pgTools = mock[PGTool]