Merge pull request #15 from umccr/implement-tsa-schema-spreadsheet-li…

…brary-tracking-metadata

Implemented OrcaVault tsa schema

dev/Makefile

@@ -27,6 +27,12 @@ ods:
 	@docker compose cp ./src/ods.sql postgres:/tmp/ods.sql
 	@docker compose exec -e PGPASSWORD=dev -it postgres psql -h 0.0.0.0 -d orcavault -U dev -f /tmp/ods.sql
 
+tsa:
+	@docker compose cp ./src/tsa.sql postgres:/tmp/tsa.sql
+	@docker compose exec -e PGPASSWORD=dev -it postgres psql -h 0.0.0.0 -d orcavault -U dev -f /tmp/tsa.sql
+
+all: ods tsa
+
 load:
 	@docker compose cp ./src/load.sh postgres:/tmp/load.sh
 	@docker compose exec -it postgres bash /tmp/load.sh

dev/src/load.sh

@@ -16,4 +16,5 @@ PGPASSWORD=dev psql -h 0.0.0.0 -d orcavault -U dev <<EOF
 \copy ods.metadata_manager_libraryprojectlink from '/data/orcavault_ods_metadata_manager_libraryprojectlink.csv' with (format csv, header true, delimiter ',');
 \copy ods.metadata_manager_contact from '/data/orcavault_ods_metadata_manager_contact.csv' with (format csv, header true, delimiter ',');
 \copy ods.metadata_manager_projectcontactlink from '/data/orcavault_ods_metadata_manager_projectcontactlink.csv' with (format csv, header true, delimiter ',');
+\copy tsa.spreadsheet_library_tracking_metadata from '/data/orcavault_tsa_spreadsheet_library_tracking_metadata.csv' with (format csv, header true, delimiter ',');
 EOF

dev/src/tsa.sql

@@ -0,0 +1,36 @@
+SELECT current_database();
+
+-- create tsa schema
+CREATE SCHEMA IF NOT EXISTS tsa AUTHORIZATION dev;
+SET search_path TO tsa;
+
+SELECT current_schema();
+
+CREATE TABLE IF NOT EXISTS orcavault.tsa.spreadsheet_library_tracking_metadata
+(
+    assay                 varchar,
+    comments              varchar,
+    coverage              varchar,
+    experiment_id         varchar,
+    external_sample_id    varchar,
+    external_subject_id   varchar,
+    library_id            varchar,
+    override_cycles       varchar,
+    phenotype             varchar,
+    project_name          varchar,
+    project_owner         varchar,
+    qpcr_id               varchar,
+    quality               varchar,
+    run                   varchar,
+    sample_id             varchar,
+    sample_name           varchar,
+    samplesheet_sample_id varchar,
+    source                varchar,
+    subject_id            varchar,
+    truseq_index          varchar,
+    type                  varchar,
+    workflow              varchar,
+    r_rna                 varchar,
+    study                 varchar,
+    sheet_name            varchar
+);

orcavault/Makefile

@@ -23,10 +23,16 @@ psql:
 ods:
 	@(cd ../dev/ && $(MAKE) ods)
 
+tsa:
+	@(cd ../dev/ && $(MAKE) tsa)
+
+all:
+	@(cd ../dev/ && $(MAKE) all)
+
 load:
 	@(cd ../dev/ && $(MAKE) load)
 
-reload: down up ods load
+reload: down up ods tsa load
 
 sync:
 	@(cd ../dev/ && $(MAKE) sync)

orcavault/README.md

@@ -7,7 +7,7 @@ OrcaVault is a dbt project. It contains data warehouse models.
 ```
 make up
 make ps
-make ods
+make all
 make psql
 orcavault=> \l
 orcavault=> \dn
@@ -16,6 +16,10 @@ orcavault=> set search_path to ods;
 orcavault=> \dt
 orcavault=> \d data_portal_labmetadata
 orcavault=> select count(1) from data_portal_labmetadata;
+orcavault=> set search_path to tsa;
+orcavault=> \dt
+orcavault=> \d spreadsheet_library_tracking_metadata
+orcavault=> select count(1) from spreadsheet_library_tracking_metadata;
 orcavault=> \q
 ```
 

orcavault/models/tsa/sources.yml

@@ -0,0 +1,8 @@
+version: 2
+
+sources:
+  - name: tsa
+    database: orcavault
+    schema: tsa
+    tables:
+      - name: spreadsheet_library_tracking_metadata