replace views with tables (#50)

cumulus_library/cli.py

@@ -296,7 +296,6 @@ def main(cli_args=None):
 
     if args.get("data_path"):
         args["data_path"] = get_abs_posix_path(args["data_path"])
-
     return run_cli(args)
 
 

cumulus_library/studies/core/condition.sql

@@ -47,7 +47,7 @@ FROM temp_condition AS tc,
     unnest(code.coding) AS t_coding (code_row) --noqa
 WHERE tc.recordeddate BETWEEN date('2016-01-01') AND current_date;
 
-CREATE OR REPLACE VIEW core__join_condition_icd AS
+CREATE TABLE core__join_condition_icd AS
 SELECT
     cc.subject_ref,
     cc.encounter_ref,
@@ -60,7 +60,7 @@ WHERE
     cc.encounter_ref = ce.encounter_ref
     AND cc.cond_code.coding[1].code = vil.code; --noqa
 
-CREATE OR REPLACE VIEW core__count_condition_icd10_month AS
+CREATE TABLE core__count_condition_icd10_month AS
 WITH powerset AS (
     SELECT
         count(DISTINCT cc.subject_ref) AS cnt_subject,

cumulus_library/studies/core/documentreference.sql

@@ -57,7 +57,7 @@ FROM temp_documentreference AS tdr,
 WHERE author_date BETWEEN date('2016-06-01') AND current_date;
 
 -- count *group by* DocumentReference.type
-CREATE OR REPLACE VIEW core__count_documentreference_month AS
+CREATE TABLE core__count_documentreference_month AS
 WITH powerset AS (
     SELECT
         count(DISTINCT d.subject_ref) AS cnt_subject,

cumulus_library/studies/core/encounter.sql

@@ -36,7 +36,7 @@ WHERE
     e.subject_ref = p.subject_ref
     AND start_date BETWEEN date('2016-06-01') AND current_date;
 
-CREATE OR REPLACE VIEW core__join_encounter_patient AS
+CREATE TABLE core__join_encounter_patient AS
 SELECT
     ce.enc_class,
     ce.enc_type,
@@ -58,7 +58,7 @@ FROM core__encounter AS ce, core__patient AS cp
 WHERE ce.subject_ref = cp.subject_ref;
 
 
-CREATE OR REPLACE VIEW core__count_encounter_month AS
+CREATE TABLE core__count_encounter_month AS
 WITH powerset AS (
     SELECT
         count(DISTINCT ce.subject_ref) AS cnt_subject,
@@ -68,8 +68,7 @@ WITH powerset AS (
         ce.age_at_visit,
         cp.gender,
         cp.race_display,
-        cp.ethnicity_display,
-        cp.postalcode3
+        cp.ethnicity_display
     FROM core__encounter AS ce, core__patient AS cp
     WHERE ce.subject_ref = cp.subject_ref
     GROUP BY
@@ -79,8 +78,7 @@ WITH powerset AS (
             ce.age_at_visit,
             cp.gender,
             cp.race_display,
-            cp.ethnicity_display,
-            cp.postalcode3
+            cp.ethnicity_display
         )
 )
 
@@ -91,14 +89,13 @@ SELECT DISTINCT
     powerset.age_at_visit,
     powerset.gender,
     powerset.race_display,
-    powerset.ethnicity_display,
-    powerset.postalcode3
+    powerset.ethnicity_display
 FROM powerset
 WHERE powerset.cnt_subject >= 10
 ORDER BY
     powerset.start_month ASC, powerset.enc_class_code ASC, powerset.age_at_visit ASC;
 
-CREATE OR REPLACE VIEW core__count_encounter_day AS
+CREATE TABLE core__count_encounter_day AS
 WITH powerset AS (
     SELECT
         count(DISTINCT ce.subject_ref) AS cnt_subject,

cumulus_library/studies/core/fhir_define.sql

@@ -1,7 +1,7 @@
 -- ############################################################
 -- FHIR Terminology
 
-CREATE OR REPLACE VIEW core__fhir_vocab AS SELECT * FROM
+CREATE TABLE core__fhir_vocab AS SELECT * FROM
     (
         VALUES
         ('ICD10', 'http://hl7.org/fhir/sid/icd-10-cm'),
@@ -43,7 +43,7 @@ CREATE OR REPLACE VIEW core__fhir_vocab AS SELECT * FROM
 -- ############################################################
 -- FHIR StructureDefinition
 
-CREATE OR REPLACE VIEW core__fhir_define AS
+CREATE TABLE core__fhir_define AS
 SELECT * FROM
     (
         VALUES

cumulus_library/studies/core/medication_request.sql

@@ -18,7 +18,7 @@ FROM medicationrequest AS mr,
 WHERE med_coding.system = 'http://www.nlm.nih.gov/research/umls/rxnorm';
 
 
-CREATE OR REPLACE VIEW core__count_medicationrequest_month AS
+CREATE TABLE core__count_medicationrequest_month AS
 WITH powerset AS (
     SELECT
         count(DISTINCT cmr.subject_id) AS cnt_subject,

cumulus_library/studies/core/observation_lab.sql

@@ -54,7 +54,7 @@ WHERE tol.effectivedatetime BETWEEN date('2016-06-01') AND current_date;
 -- ###########################################################################
 -- COUNT Patients, Encounters, Lab Results
 -- ###########################################################################
-CREATE OR REPLACE VIEW core__count_observation_lab_month AS
+CREATE TABLE core__count_observation_lab_month AS
 WITH powerset AS (
     SELECT
         count(DISTINCT o.subject_ref) AS cnt_subject,

cumulus_library/studies/core/patient.sql

@@ -41,7 +41,7 @@ WHERE
     AND tp.gender IS NOT NULL;
 
 
-CREATE OR REPLACE VIEW core__count_patient AS
+CREATE TABLE core__count_patient AS
 WITH powerset AS (
     SELECT
         count(DISTINCT cp.subject_ref) AS cnt_subject,

cumulus_library/studies/core/setup.sql

@@ -1,6 +1,6 @@
 -- Emergency Department Notes
 --
-CREATE OR REPLACE VIEW core__ed_note AS
+CREATE TABLE core__ed_note AS
 SELECT
     t.from_system,
     t.from_code,

cumulus_library/studies/template/counts.sql

@@ -1,4 +1,4 @@
-CREATE OR REPLACE VIEW template__count_influenza_test_month AS
+CREATE TABLE template__count_influenza_test_month AS
 WITH powerset AS (
     SELECT
         count(DISTINCT tflo.subject_ref) AS cnt_subject,

cumulus_library/studies/template/setup.sql

@@ -1,4 +1,4 @@
-CREATE OR REPLACE VIEW template__influenza_codes AS
+CREATE TABLE template__influenza_codes AS
 SELECT
     t.from_system,
     t.analyte,

cumulus_library/studies/vocab/icd_legend.sql

@@ -1,4 +1,4 @@
-CREATE OR REPLACE VIEW vocab__icd_legend AS
+CREATE TABLE vocab__icd_legend AS
 SELECT
     code,
     display,

cumulus_library/studies/vocab/vocab_icd_builder.py

@@ -3,10 +3,8 @@
 
 from pathlib import Path
 
-from rich.progress import Progress
-
 from cumulus_library.base_runner import BaseRunner
-from cumulus_library.helper import query_console_output
+from cumulus_library.helper import query_console_output, get_progress_bar
 from cumulus_library.template_sql.templates import (
     get_ctas_query,
     get_insert_into_query,
@@ -49,7 +47,7 @@ def create_icd_legend(
                 sum(1 for i in open(f"{path}/{filename}.bsv", "rb")) / partition_size
             )
 
-        with Progress(disable=verbose) as progress:
+        with get_progress_bar(disable=verbose) as progress:
             task = progress.add_task(
                 f"Uploading {table_name} data...",
                 total=query_count,

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cumulus-library"
-version = "0.3.0"
+version = "0.3.1"
 # In order to support 3.12, we wil need to refactor out load_module, which is
 # targeted for deprecation in that version.
 requires-python = ">= 3.9, <3.12"