Soe sequence of events

.sqlfluffignore

@@ -7,3 +7,5 @@ show_views.sql.jinja
 # This is a temporary ignore due to time pressure - not sure of root cause,
 # but the table in question builds
 codeable_concept_denormalize.sql.jinja
+
+output.sql

cumulus_library/.sqlfluff

@@ -26,6 +26,7 @@ conditions = ["1 > 0", "1 < 2"]
 dataset = [["foo","foo"],["bar","bar"]]
 ext_systems = ["omb", "text"]
 field = 'column_name'
+field_config = {'col1':{'present':True, 'type': 'varchar'},'col2':{'present':False, 'type': 'varchar'}}
 fhir_extension = fhir_extension
 id = 'id'
 medication_datasources = {"by_contained_ref" : True, "by_external_ref" : True}

cumulus_library/base_table_builder.py

@@ -59,6 +59,7 @@ def execute_queries(
                         table_name = table_name.split(".")[1].replace('"', "")
                     table_names.append(table_name)
             for table_name in table_names:
+                table_name = table_name.replace('"', "")
                 cursor.execute(f"DROP TABLE IF EXISTS {table_name}")
         with get_progress_bar(disable=verbose) as progress:
             task = progress.add_task(

cumulus_library/studies/core/builder_soe.py

@@ -0,0 +1,57 @@
+""" Module for generating condition codeableConcept table"""
+import re
+from cumulus_library.base_table_builder import BaseTableBuilder
+from cumulus_library.helper import get_progress_bar, query_console_output
+from cumulus_library.template_sql.templates import (
+    get_column_datatype_query,
+    get_object_denormalize_query,
+)
+
+
+class SOEBuilder(BaseTableBuilder):
+    display_text = "Creating SoE support tables..."
+
+    def prepare_queries(self, cursor: object, schema: str):
+        """Constructs tables for SOE QA verification
+
+        :param cursor: A database cursor object
+        :param schema: the schema/db name, matching the cursor
+
+        """
+        table = "documentreference"
+        column = "context"
+        with get_progress_bar(transient=True) as progress:
+            task = progress.add_task(
+                "Detecting SOE...",
+                total=1,
+            )
+
+        query = get_column_datatype_query(schema, table, column)
+        cursor.execute(query)
+        progress.advance(task)
+        result = str(cursor.fetchone()[0])
+        field_config = {
+            "start": {
+                "present": False,
+                "type": "varchar",
+            },
+            "end": {"present": False, "type": "varchar"},
+        }
+        if "period row" in result:
+            # The following will get all text between parenthesis following
+            # period row - i.e. the schema of the period object
+            field_schema_str = re.search(r"period row\(\s*([^\n\r]*)\),", result)[1]
+            for key in field_config.keys():
+                if f"{key} {field_config[key]['type']}" in field_schema_str:
+                    field_config[key]["present"] = True
+
+        self.queries.append(
+            get_object_denormalize_query(
+                schema,
+                table,
+                "id",
+                f"{column}.period",
+                field_config,
+                "core__soe_doc_period",
+            )
+        )

cumulus_library/studies/core/manifest.toml

@@ -6,6 +6,7 @@ file_names = [
     "builder_encounter_coding.py",
     "builder_core_medication.py",
     "builder_patient_extension.py",
+    "builder_soe.py"
 ]
 
 [sql_config]
@@ -23,6 +24,7 @@ file_names = [
     "observation_vital_signs.sql",
     "medication_request.sql",
     "study_period.sql",
+    "soe_sequence_of_events.sql",
 ]
 
 [counts_builder_config]
@@ -42,4 +44,7 @@ export_list = [
     "core__count_medicationrequest_month",
     "core__meta_date",
     "core__meta_version",
+    "core__count_soe_cond_week",
+    "core__count_soe_document_week",
+    "core__count_soe_medreq_week"
 ]