Added builder for SOE period

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 +1,58 @@
+""" 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 condition code table..."
+
+    def prepare_queries(self, cursor: object, schema: str):
+        """Constructs queries related to condition codeableConcept
+
+        :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",
+            )
+        )
+        self.write_queries()

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]

cumulus_library/studies/core/soe_sequence_of_events.sql

@@ -241,16 +241,17 @@ CREATE TABLE core__soe_document AS
 WITH soe_document_rawdata AS (
     SELECT DISTINCT
         cast(
-            from_iso8601_timestamp(context.period."start") AS timestamp
+            from_iso8601_timestamp(sdp."start") AS timestamp
         ) AS doc_start_datetime,
         cast(
-            from_iso8601_timestamp(context.period."end") AS timestamp
+            from_iso8601_timestamp(sdp."end") AS timestamp
         ) AS doc_end_datetime,
         doc.subject.reference AS subject_ref,
         doc.context,
         doc.id AS doc_id,
         concat('DocumentReference/', doc.id) AS doc_ref
     FROM documentreference AS doc
+    LEFT JOIN core__soe_doc_period AS sdp ON sdp.id = doc.id
 ),
 
 document AS (

cumulus_library/template_sql/object_denormalize.sql.jinja

@@ -0,0 +1,15 @@
+CREATE TABLE "{{schema}}"."{{ target_table }}" AS (
+    SELECT
+        {{ source_id }},
+        {%- for key in field_config.keys() %}
+        {%- if field_config[key]['present'] %}
+        {{ field }}."{{ key }}" as "{{ key }}"
+        {%- else %}
+        cast(NULL AS {{  field_config[key]['type'] }}) as "{{ key }}"
+        {%- endif %}
+        {%- if not loop.last -%}
+        , 
+        {%- endif -%}
+        {%- endfor %}
+    FROM {{ source_table }}
+);

cumulus_library/template_sql/templates.py

@@ -318,3 +318,23 @@ def get_show_views(schema_name: str, prefix: str) -> str:
         return Template(show_tables.read()).render(
             schema_name=schema_name, prefix=prefix
         )
+
+
+def get_object_denormalize_query(
+    schema: str,
+    source_table: str,
+    source_id: str,
+    field: str,
+    field_config: dict,
+    target_table: str,
+):
+    path = Path(__file__).parent
+    with open(f"{path}/object_denormalize.sql.jinja") as column_datatype:
+        return Template(column_datatype.read()).render(
+            schema=schema,
+            source_table=source_table,
+            source_id=source_id,
+            field=field,
+            field_config=field_config,
+            target_table=target_table,
+        )