Merge pull request #10 from smart-on-fhir/mg/umls_descriptions

Added static description tables

.gitignore

@@ -1,10 +1,11 @@
 downloads/
 generated_parquet/
-
+*.parquet
 # project specific
 downloads/
 generated_parquet/
 output.sql
+.DS_Store
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.sqlfluffignore

@@ -0,0 +1 @@
+cumulus_library_umls/reference_sql

cumulus_library_umls/umls/manifest.toml → cumulus_library_umls/manifest.toml

@@ -2,7 +2,8 @@ study_prefix = "umls"
 
 [table_builder_config]
 file_names = [
-    "umls_builder.py"
+    "umls_builder.py",
+    "static_builder.py"
 ]
 
 [advanced_options]

cumulus_library_umls/reference_sql/static_builder.sql

@@ -0,0 +1,69 @@
+-- noqa: disable=all
+-- This sql was autogenerated as a reference example using the library
+-- CLI. Its format is tied to the specific database it was run against,
+-- and it may not be correct for all databases. Use the CLI's build 
+-- option to derive the best SQL for your dataset.
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__semantic_types` (
+    abbrev STRING,
+    TUI STRING,
+    full_type_name STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucket/db_path/umls/SemanticTypes_2018AB'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__semantic_groups` (
+    abbrev STRING,
+    group_name STRING,
+    TUI STRING,
+    full_type_name STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucket/db_path/umls/SemGroups_2018'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__rel_description` (
+    REL STRING,
+    REL_STR STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucket/db_path/umls_rel'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__rela_description` (
+    RELA STRING,
+    RELA_STR STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucket/db_path/umls_rela'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__tty_description` (
+    TTY STRING,
+    TTY_STR STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucket/db_path/umls_tty'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__tui_description` (
+    STY STRING,
+    TUI STRING,
+    TUI_STR STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucket/db_path/umls_tui'
+tblproperties ("parquet.compression"="SNAPPY");