postgres_init_01.sh - use functions so calls can be commented out easily

e.g. if you want to create everything except the indexes then do them later
SMI · Feb 19, 2024 · e163c08 · e163c08
1 parent e3095db
commit e163c08
Showing 1 changed file with 136 additions and 111 deletions.
diff --git a/src/tools/postgres_init_01.sh b/src/tools/postgres_init_01.sh
@@ -31,114 +31,139 @@ fi
 # Prevent errors from accessing current directory when sudo
 cd /tmp
 
-echo "$(date) Dropping old database/roles"
-$AUTH psql $CONNECTION postgres -c "DROP DATABASE ${DB};"
-$AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS ${UN};"
-$AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS ${UNAPI};"
-$AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS semehr_user;"
-$AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS semehr_admin;"
-
-# Create roles for read-only and read-write
-echo "$(date) Create new roles"
-$AUTH psql $CONNECTION postgres -c "CREATE ROLE semehr_user;"
-$AUTH psql $CONNECTION postgres -c "CREATE ROLE semehr_admin;"
-
-# Create user
-echo "$(date) Create new users ${UN} and ${UNAPI}"
-$AUTH psql $CONNECTION -c "CREATE ROLE ${UN} PASSWORD '${PW_SEMEHR}' LOGIN CREATEDB CREATEROLE;"
-$AUTH psql $CONNECTION -c "CREATE ROLE ${UNAPI} PASSWORD '${PW_SEMEHRAPI}' LOGIN;"
-
-# Assign the users to the roles
-echo "$(date) Assign users to roles"
-$AUTH psql $CONNECTION postgres -c "GRANT semehr_admin TO ${UN};"
-$AUTH psql $CONNECTION postgres -c "GRANT semehr_user  TO ${UNAPI};"
-
-# Create the database and allow connections to it from roles
-echo "$(date) Create database ${DB} and allow connections"
-$AUTH psql $CONNECTION postgres -c "CREATE DATABASE ${DB} OWNER semehr_admin;"
-$AUTH psql $CONNECTION postgres -c "GRANT CONNECT ON DATABASE ${DB} TO semehr_user;"
-$AUTH psql $CONNECTION postgres -c "GRANT CONNECT ON DATABASE ${DB} TO semehr_admin;"
-
-# Prevent the 'public' role (which everyone inherits) from everything!
-echo "$(date) Remove access to public schema"
-$AUTH psql $CONNECTION ${DB} -c "REVOKE CREATE ON SCHEMA public FROM PUBLIC;"
-$AUTH psql $CONNECTION ${DB} -c "REVOKE ALL ON DATABASE ${DB} FROM PUBLIC;"
-
-# Create the schema
-echo "$(date) Create schema ${SCH}"
-$AUTH psql $CONNECTION ${DB} -c "CREATE SCHEMA ${SCH} AUTHORIZATION semehr_admin;"
-$AUTH psql $CONNECTION ${DB} -c "CREATE SCHEMA ${UMLS_SCH} AUTHORIZATION semehr_admin;"
-
-# Allow access to schema
-echo "$(date) Allow access to schema"
-$AUTH psql $CONNECTION ${DB} -c "GRANT USAGE ON SCHEMA ${SCH} TO semehr_user;"
-$AUTH psql $CONNECTION ${DB} -c "GRANT USAGE ON SCHEMA ${UMLS_SCH} TO semehr_user;"
-$AUTH psql $CONNECTION ${DB} -c "GRANT USAGE,CREATE ON SCHEMA ${SCH} TO semehr_admin;"
-
-# Allow access to tables
-echo "$(date) Allow access to tables"
-$AUTH psql $CONNECTION ${DB} -c "GRANT SELECT ON ALL TABLES IN SCHEMA ${SCH} TO semehr_user;"
-$AUTH psql $CONNECTION ${DB} -c "GRANT SELECT ON ALL TABLES IN SCHEMA ${UMLS_SCH} TO semehr_user;"
-$AUTH psql $CONNECTION ${DB} -c "GRANT SELECT, INSERT, UPDATE, DELETE ON ALL TABLES IN SCHEMA ${SCH} TO semehr_admin;"
-
-# Allow access to future tables
-echo "$(date) Allow access to future tables"
-$AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${SCH} GRANT SELECT ON TABLES TO semehr_user;"
-$AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${UMLS_SCH} GRANT SELECT ON TABLES TO semehr_user;"
-$AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${SCH} GRANT SELECT, INSERT, UPDATE, DELETE ON TABLES TO semehr_admin;"
-
-# Same for sequences
-echo "$(date) Allow access to sequences"
-$AUTH psql $CONNECTION ${DB} -c "GRANT USAGE ON ALL SEQUENCES IN SCHEMA ${SCH} TO semehr_admin;"
-$AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${SCH} GRANT USAGE ON SEQUENCES TO semehr_admin;"
-
-# Remove access to the 'postgres' database
-echo "$(date) Remove access to system database"
-$AUTH psql $CONNECTION postgres -c "REVOKE ALL PRIVILEGES ON DATABASE postgres FROM ${UN};"
-
-# Create the main table
-echo "$(date) Create ${SCH}.semehr_results"
-$AUTH psql $CONNECTION ${DB} -c "SET ROLE semehr_admin; CREATE TABLE ${SCH}.semehr_results(SOPInstanceUID varchar(64), semehr_results JSONB, PRIMARY KEY (SOPInstanceUID));"
-
-# Create the table holding a count of each CUI
-echo "$(date) Create CUI count table"
-$AUTH psql $CONNECTION ${DB} -c "SET ROLE semehr_admin; CREATE TABLE ${SCH}.cui_count (cui varchar(20) primary key, count bigint);"
-
-# Create the table holding CUI for doc
-echo "$(date) Create CUI mapping table"
-$AUTH psql $CONNECTION ${DB} -c "SET ROLE semehr_admin; CREATE TABLE ${SCH}.cui_sop (cui varchar(20), SOPInstanceUID varchar(64));"
-
-# Add the trigram extension
-echo "$(date) Add PostgreSQL extensions"
-$AUTH psql $CONNECTION ${DB} -c "CREATE EXTENSION pg_trgm WITH SCHEMA pg_catalog;"
-$AUTH psql $CONNECTION ${DB} -c "CREATE EXTENSION pg_trgm WITH SCHEMA semehr;"
-
-# Define functions used for indexing
-echo "$(date) Define functions"
-$AUTH psql $CONNECTION ${DB} -c 'create or replace function semehr.annotation_array_as_text(doc jsonb, fieldname text) returns text as $$ '\
-" select array_agg(x)::text from (select jsonb_array_elements(doc->'annotations')->>fieldname) as f(x); "\
-' $$ language sql strict immutable;'
-$AUTH psql $CONNECTION ${DB} -c 'create or replace function semehr.annotation_array_as_text_array(doc jsonb, fieldname text) returns text[] as $$ '\
-"   select array_agg(x) from (select jsonb_array_elements(doc->'annotations')->>fieldname) as f(x); "\
-' $$ language sql strict immutable;'
-$AUTH psql $CONNECTION ${DB} -c 'create or replace function semehr.cast_to_date(str text) returns date as $$ '\
-"   select to_date(str, 'YYYYMMDD'); "\
-' $$ language sql strict immutable;'
-
-# Create indexes
-echo "$(date) Create indexes"
-#$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX cui_count_idx ON semehr.cui_count (cui);" # cui is already primary key
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX cui_sop_idx ON semehr.cui_sop (cui);"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX sopinstanceuid_idx ON semehr.semehr_results (SOPInstanceUID);"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX sopclassuid_idx ON semehr.semehr_results ((semehr_results->>'SOPClassUID'));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX seriesinstanceuid_idx ON semehr.semehr_results ((semehr_results->>'SeriesInstanceUID'));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX studyinstanceuid_idx ON semehr.semehr_results ((semehr_results->>'StudyInstanceUID'));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX patientid_idx ON semehr.semehr_results ((semehr_results->>'PatientID'));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX cui_as_array_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text_array(semehr_results, 'cui'));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX sty_as_array_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text_array(semehr_results, 'sty'));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX pref_as_text_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text(semehr_results, 'pref') gin_trgm_ops);"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX str_as_text_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text(semehr_results, 'str') gin_trgm_ops);"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX str_as_english_idx ON semehr.semehr_results USING GIN (to_tsvector('english', semehr.annotation_array_as_text(semehr_results, 'str')));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX pref_as_english_idx ON semehr.semehr_results USING GIN (to_tsvector('english', semehr.annotation_array_as_text(semehr_results, 'pref')));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX content_date_idx ON semehr.semehr_results (semehr.cast_to_date(semehr_results->>'ContentDate'));"
-$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX modalities_idx ON semehr.semehr_results (regexp_split_to_array(semehr_results->>'ModalitiesInStudy', '\\\\'));"
+drop()
+{
+    echo "$(date) Dropping old database/roles"
+    $AUTH psql $CONNECTION postgres -c "DROP DATABASE ${DB};"
+    $AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS ${UN};"
+    $AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS ${UNAPI};"
+    $AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS semehr_user;"
+    $AUTH psql $CONNECTION postgres -c "DROP ROLE IF EXISTS semehr_admin;"
+}
+
+create_roles()
+{
+    # Create roles for read-only and read-write
+    echo "$(date) Create new roles"
+    $AUTH psql $CONNECTION postgres -c "CREATE ROLE semehr_user;"
+    $AUTH psql $CONNECTION postgres -c "CREATE ROLE semehr_admin;"
+
+    # Create user
+    echo "$(date) Create new users ${UN} and ${UNAPI}"
+    $AUTH psql $CONNECTION -c "CREATE ROLE ${UN} PASSWORD '${PW_SEMEHR}' LOGIN CREATEDB CREATEROLE;"
+    $AUTH psql $CONNECTION -c "CREATE ROLE ${UNAPI} PASSWORD '${PW_SEMEHRAPI}' LOGIN;"
+
+    # Assign the users to the roles
+    echo "$(date) Assign users to roles"
+    $AUTH psql $CONNECTION postgres -c "GRANT semehr_admin TO ${UN};"
+    $AUTH psql $CONNECTION postgres -c "GRANT semehr_user  TO ${UNAPI};"
+}
+
+create_database()
+{
+    # Create the database and allow connections to it from roles
+    echo "$(date) Create database ${DB} and allow connections"
+    $AUTH psql $CONNECTION postgres -c "CREATE DATABASE ${DB} OWNER semehr_admin;"
+    $AUTH psql $CONNECTION postgres -c "GRANT CONNECT ON DATABASE ${DB} TO semehr_user;"
+    $AUTH psql $CONNECTION postgres -c "GRANT CONNECT ON DATABASE ${DB} TO semehr_admin;"
+
+    # Prevent the 'public' role (which everyone inherits) from everything!
+    echo "$(date) Remove access to public schema"
+    $AUTH psql $CONNECTION ${DB} -c "REVOKE CREATE ON SCHEMA public FROM PUBLIC;"
+    $AUTH psql $CONNECTION ${DB} -c "REVOKE ALL ON DATABASE ${DB} FROM PUBLIC;"
+
+    # Create the schema
+    echo "$(date) Create schema ${SCH}"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE SCHEMA ${SCH} AUTHORIZATION semehr_admin;"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE SCHEMA ${UMLS_SCH} AUTHORIZATION semehr_admin;"
+
+    # Allow access to schema
+    echo "$(date) Allow access to schema"
+    $AUTH psql $CONNECTION ${DB} -c "GRANT USAGE ON SCHEMA ${SCH} TO semehr_user;"
+    $AUTH psql $CONNECTION ${DB} -c "GRANT USAGE ON SCHEMA ${UMLS_SCH} TO semehr_user;"
+    $AUTH psql $CONNECTION ${DB} -c "GRANT USAGE,CREATE ON SCHEMA ${SCH} TO semehr_admin;"
+
+    # Allow access to tables
+    echo "$(date) Allow access to tables"
+    $AUTH psql $CONNECTION ${DB} -c "GRANT SELECT ON ALL TABLES IN SCHEMA ${SCH} TO semehr_user;"
+    $AUTH psql $CONNECTION ${DB} -c "GRANT SELECT ON ALL TABLES IN SCHEMA ${UMLS_SCH} TO semehr_user;"
+    $AUTH psql $CONNECTION ${DB} -c "GRANT SELECT, INSERT, UPDATE, DELETE ON ALL TABLES IN SCHEMA ${SCH} TO semehr_admin;"
+
+    # Allow access to future tables
+    echo "$(date) Allow access to future tables"
+    $AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${SCH} GRANT SELECT ON TABLES TO semehr_user;"
+    $AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${UMLS_SCH} GRANT SELECT ON TABLES TO semehr_user;"
+    $AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${SCH} GRANT SELECT, INSERT, UPDATE, DELETE ON TABLES TO semehr_admin;"
+
+    # Same for sequences
+    echo "$(date) Allow access to sequences"
+    $AUTH psql $CONNECTION ${DB} -c "GRANT USAGE ON ALL SEQUENCES IN SCHEMA ${SCH} TO semehr_admin;"
+    $AUTH psql $CONNECTION ${DB} -c "ALTER DEFAULT PRIVILEGES FOR ROLE semehr_admin IN SCHEMA ${SCH} GRANT USAGE ON SEQUENCES TO semehr_admin;"
+
+    # Remove access to the 'postgres' database
+    echo "$(date) Remove access to system database"
+    $AUTH psql $CONNECTION postgres -c "REVOKE ALL PRIVILEGES ON DATABASE postgres FROM ${UN};"
+}
+
+create_tables()
+{
+    # Create the main table
+    echo "$(date) Create ${SCH}.semehr_results"
+    $AUTH psql $CONNECTION ${DB} -c "SET ROLE semehr_admin; CREATE TABLE ${SCH}.semehr_results(SOPInstanceUID varchar(64), semehr_results JSONB, PRIMARY KEY (SOPInstanceUID));"
+
+    # Create the table holding a count of each CUI
+    echo "$(date) Create CUI count table"
+    $AUTH psql $CONNECTION ${DB} -c "SET ROLE semehr_admin; CREATE TABLE ${SCH}.cui_count (cui varchar(20) primary key, count bigint);"
+
+    # Create the table holding CUI for doc
+    echo "$(date) Create CUI mapping table"
+    $AUTH psql $CONNECTION ${DB} -c "SET ROLE semehr_admin; CREATE TABLE ${SCH}.cui_sop (cui varchar(20), SOPInstanceUID varchar(64));"
+}
+
+create_functions()
+{
+    # Add the trigram extension
+    echo "$(date) Add PostgreSQL extensions"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE EXTENSION pg_trgm WITH SCHEMA pg_catalog;"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE EXTENSION pg_trgm WITH SCHEMA semehr;"
+
+    # Define functions used for indexing
+    echo "$(date) Define functions"
+    $AUTH psql $CONNECTION ${DB} -c 'create or replace function semehr.annotation_array_as_text(doc jsonb, fieldname text) returns text as $$ '\
+    " select array_agg(x)::text from (select jsonb_array_elements(doc->'annotations')->>fieldname) as f(x); "\
+    ' $$ language sql strict immutable;'
+    $AUTH psql $CONNECTION ${DB} -c 'create or replace function semehr.annotation_array_as_text_array(doc jsonb, fieldname text) returns text[] as $$ '\
+    "   select array_agg(x) from (select jsonb_array_elements(doc->'annotations')->>fieldname) as f(x); "\
+    ' $$ language sql strict immutable;'
+    $AUTH psql $CONNECTION ${DB} -c 'create or replace function semehr.cast_to_date(str text) returns date as $$ '\
+    "   select to_date(str, 'YYYYMMDD'); "\
+    ' $$ language sql strict immutable;'
+}
+
+create_indexes()
+{
+    # Create indexes
+    echo "$(date) Create indexes"
+    #$AUTH psql $CONNECTION ${DB} -c "CREATE INDEX cui_count_idx ON semehr.cui_count (cui);" # cui is already primary key
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX cui_sop_idx ON semehr.cui_sop (cui);"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX sopinstanceuid_idx ON semehr.semehr_results (SOPInstanceUID);"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX sopclassuid_idx ON semehr.semehr_results ((semehr_results->>'SOPClassUID'));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX seriesinstanceuid_idx ON semehr.semehr_results ((semehr_results->>'SeriesInstanceUID'));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX studyinstanceuid_idx ON semehr.semehr_results ((semehr_results->>'StudyInstanceUID'));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX patientid_idx ON semehr.semehr_results ((semehr_results->>'PatientID'));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX cui_as_array_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text_array(semehr_results, 'cui'));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX sty_as_array_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text_array(semehr_results, 'sty'));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX pref_as_text_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text(semehr_results, 'pref') gin_trgm_ops);"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX str_as_text_idx ON semehr.semehr_results USING GIN (semehr.annotation_array_as_text(semehr_results, 'str') gin_trgm_ops);"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX str_as_english_idx ON semehr.semehr_results USING GIN (to_tsvector('english', semehr.annotation_array_as_text(semehr_results, 'str')));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX pref_as_english_idx ON semehr.semehr_results USING GIN (to_tsvector('english', semehr.annotation_array_as_text(semehr_results, 'pref')));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX content_date_idx ON semehr.semehr_results (semehr.cast_to_date(semehr_results->>'ContentDate'));"
+    $AUTH psql $CONNECTION ${DB} -c "CREATE INDEX modalities_idx ON semehr.semehr_results (regexp_split_to_array(semehr_results->>'ModalitiesInStudy', '\\\\'));"
+}
+
+drop
+create_roles
+create_database
+create_tables
+create_functions
+create_indexes