Gha setup

db/README.md

@@ -8,4 +8,6 @@ Additional internal tables are created by model scripts.
 
 ## Usage
 
-	./setup.sh
+From repository root, with $DATABASE_URL connection defined as db superuser:
+
+	.jobs/setup

db/functions/break_streams.sql

@@ -1,4 +1,4 @@
-CREATE OR REPLACE FUNCTION bcfishpass.break_streams(point_table text, wsg text)
+CREATE FUNCTION bcfishpass.break_streams(point_table text, wsg text)
   RETURNS VOID
   LANGUAGE plpgsql AS
 $func$

db/functions/create_barrier_table.sql

@@ -1,6 +1,6 @@
 -- create table for holding barriers of given type
 
-CREATE OR REPLACE FUNCTION bcfishpass.create_barrier_table(barriertype text)
+CREATE FUNCTION bcfishpass.create_barrier_table(barriertype text)
   RETURNS VOID
   LANGUAGE plpgsql AS
 $func$

db/functions/load_dnstr.sql

@@ -1,6 +1,6 @@
 -- compare records in table a and table b,
 -- and record in output table (as an array) all ids from b that are downstream of given id for table a
-CREATE OR REPLACE FUNCTION bcfishpass.load_dnstr(
+CREATE FUNCTION bcfishpass.load_dnstr(
   table_a text, 
   table_a_id text, 
   table_b text, 

db/functions/load_upstr.sql

@@ -1,6 +1,6 @@
 -- compare records in table a and table b,
 -- and record in output table (as an array) all ids from b that are downstream of given id for table a
-CREATE OR REPLACE FUNCTION bcfishpass.load_upstr(
+CREATE FUNCTION bcfishpass.load_upstr(
   table_a text, 
   table_a_id text, 
   table_b text, 

db/functions/streamsasmvt.sql

@@ -1,4 +1,4 @@
-CREATE OR REPLACE FUNCTION bcfishpass.streamsasmvt(
+CREATE FUNCTION bcfishpass.streamsasmvt(
             z integer, x integer, y integer)
 RETURNS bytea
 AS $$

db/functions/utmzone.sql

@@ -3,7 +3,7 @@
 -- DROP FUNCTION utmzone(geometry);
 -- Usage: SELECT ST_Transform(the_geom, utmzone(ST_Centroid(the_geom)) )FROM sometable;
 
-CREATE OR REPLACE FUNCTION public.utmzone(geometry)
+CREATE FUNCTION public.utmzone(geometry)
    RETURNS integer AS
  $BODY$
  DECLARE

db/functions/wcrp_barrier_count.sql

@@ -1,5 +1,4 @@
 -- function to query the view (so it is visible in pgfs)
-DROP FUNCTION IF EXISTS postgisftw.wcrp_barrier_count;
 CREATE FUNCTION postgisftw.wcrp_barrier_count(
   watershed_group_code TEXT,
   model_status TEXT default 'ALL'

db/functions/wcrp_barrier_extent.sql

@@ -1,5 +1,3 @@
-DROP FUNCTION IF EXISTS postgisftw.wcrp_barrier_extent(TEXT);
-
 CREATE FUNCTION postgisftw.wcrp_barrier_extent(watershed_group_code TEXT)
 
 -- watershed_group_code: BULK, LNIC, HORS, BOWR, QUES, CARR, ELKR

db/functions/wcrp_barrier_severity.sql

@@ -1,5 +1,3 @@
-DROP FUNCTION IF EXISTS postgisftw.wcrp_barrier_severity(text);
-
 CREATE FUNCTION postgisftw.wcrp_barrier_severity(watershed_group_code TEXT)
 
 -- watershed_group_code: BULK, LNIC, HORS, BOWR, QUES, CARR, ELKR

db/functions/wcrp_habitat_connectivity_status.sql

@@ -1,7 +1,4 @@
 -- report on total modelled habitat vs accessible modelled habitat
-
-DROP FUNCTION IF EXISTS postgisftw.wcrp_habitat_connectivity_status(TEXT,TEXT);
-
 CREATE OR REPLACE FUNCTION postgisftw.wcrp_habitat_connectivity_status(
   watershed_group_code TEXT,
   habitat_type TEXT default 'ALL'

db/functions/wsg_crossing_summary.sql

@@ -2,8 +2,6 @@
 --   - total
 --   - accessible (per model)
 --   - with spawning rearing habitat upstream (per model)
-
-DROP FUNCTION IF EXISTS bcfishpass.wsg_crossing_summary();
 CREATE FUNCTION bcfishpass.wsg_crossing_summary()
 RETURNS table (
   watershed_group_code                  text,

db/functions/wsg_linear_summary.sql

@@ -10,7 +10,6 @@
 -- - spawning or rearing habitat not isolated by dam or a known pscis barrier (accessible_a)
 -- - spawning or rearing habitat not isolated by all anthropogenic barriers (observed and modelled) (accessible_b)
 
-DROP FUNCTION IF EXISTS bcfishpass.wsg_linear_summary();
 CREATE FUNCTION bcfishpass.wsg_linear_summary() 
 RETURNS table (
  watershed_group_code                                     text,

db/schemas.sql

@@ -0,0 +1,11 @@
+create schema bcfishpass;
+create schema cabd;
+create schema whse_admin_boundaries;
+create schema whse_cadastre;
+create schema whse_environmental_monitoring;
+create schema whse_forest_tenure;
+create schema whse_forest_vegetation;
+create schema whse_imagery_and_base_maps;
+create schema whse_legal_admin_boundaries;
+create schema whse_mineral_tenure;
+create schema whse_tantalis;

db/tables/cabd.sql

@@ -1,6 +1,4 @@
 -- dams
-drop table if exists cabd.dams cascade;
-
 create table cabd.dams (
   cabd_id                      text                 ,
   use_pollution_code           integer              ,
@@ -108,8 +106,6 @@ create table cabd.dams (
 );
 
 -- waterfalls
-drop table if exists cabd.waterfalls cascade;
-
 create table cabd.waterfalls (
   cabd_id                  text                 ,
   fall_name_fr             text                 ,

db/tables/crossings.sql

@@ -7,9 +7,6 @@
 -- 3. Modelled crossings (culverts and bridges)
 -- 4. Other ?
 -- --------------
-
-drop table if exists bcfishpass.crossings cascade;
-
 create table bcfishpass.crossings
 (
   -- Note how the aggregated crossing id combines the various ids to create a unique integer, after assigning PSCIS crossings their source crossing id

db/tables/crossings_upstr_dnstr.sql

@@ -1,24 +1,20 @@
 -- note other crossings/barriers upstream / downstream of crossings in crossings table / barriers anth table
 
-drop table if exists bcfishpass.crossings_dnstr_crossings cascade;
 create table bcfishpass.crossings_dnstr_crossings (
 	aggregated_crossings_id text primary key, 
 	features_dnstr text[]
 );
 
-drop table if exists bcfishpass.crossings_dnstr_barriers_anthropogenic cascade;
 create table bcfishpass.crossings_dnstr_barriers_anthropogenic (
 	aggregated_crossings_id text primary key, 
 	features_dnstr text[]
 );
 
-drop table if exists bcfishpass.crossings_upstr_barriers_anthropogenic cascade;
 create table bcfishpass.crossings_upstr_barriers_anthropogenic (
 	aggregated_crossings_id text primary key, 
 	features_upstr text[]
 	);
 
-drop table if exists bcfishpass.barriers_anthropogenic_dnstr_barriers_anthropogenic cascade;
 create table bcfishpass.barriers_anthropogenic_dnstr_barriers_anthropogenic (
 	barriers_anthropogenic_id text primary key, 
 	features_dnstr text[]

db/tables/crossings_upstream_access.sql

@@ -1,6 +1,4 @@
 -- report on potentially accessible lengths and areas upstream, per species scenario / model
-drop table if exists bcfishpass.crossings_upstream_access cascade;
-
 create table bcfishpass.crossings_upstream_access (
   aggregated_crossings_id                                  text primary key,
   watershed_group_code                                     character varying (4),

db/tables/crossings_upstream_habitat.sql

@@ -1,6 +1,4 @@
 -- report on habitat upstream, per species
-drop table if exists bcfishpass.crossings_upstream_habitat cascade;
-
 create table bcfishpass.crossings_upstream_habitat (
   aggregated_crossings_id               text primary key,
   watershed_group_code                  character varying (4),
@@ -43,8 +41,6 @@ create table bcfishpass.crossings_upstream_habitat (
 --  - barriers only
 --  - currently ch/co/sk/st/wct where they exist in watersheds of interest
 --  - apply 1.5x multiplier to co rearing in wetlands and all sk rearing
-drop table if exists bcfishpass.crossings_upstream_habitat_wcrp cascade;
-
 create table bcfishpass.crossings_upstream_habitat_wcrp (
   aggregated_crossings_id               text primary key,
   watershed_group_code                  character varying (4),

db/tables/gradient_barriers.sql

@@ -1,5 +1,3 @@
-DROP TABLE IF EXISTS bcfishpass.gradient_barriers;
-
 CREATE TABLE bcfishpass.gradient_barriers (
 	 gradient_barrier_id bigint GENERATED ALWAYS AS ((((blue_line_key::bigint + 1) - 354087611) * 10000000) + round(downstream_route_measure::bigint)) STORED PRIMARY KEY,
 	 blue_line_key             integer               ,
@@ -10,9 +8,9 @@ CREATE TABLE bcfishpass.gradient_barriers (
 	 gradient_class            integer
  );
 
-create index if not exists grdntbr_blk_idx on bcfishpass.gradient_barriers (blue_line_key);
-create index if not exists grdntbr_wsgcode_idx on bcfishpass.gradient_barriers (watershed_group_code);
-create index if not exists grdntbr_wscode_gidx on bcfishpass.gradient_barriers using gist (wscode_ltree);
-create index if not exists grdntbr_wscode_bidx on bcfishpass.gradient_barriers using btree (wscode_ltree);
-create index if not exists grdntbr_localcode_gidx on bcfishpass.gradient_barriers using gist (localcode_ltree);
-create index if not exists grdntbr_localcode_bidx on bcfishpass.gradient_barriers using btree (localcode_ltree);
+create index grdntbr_blk_idx on bcfishpass.gradient_barriers (blue_line_key);
+create index grdntbr_wsgcode_idx on bcfishpass.gradient_barriers (watershed_group_code);
+create index grdntbr_wscode_gidx on bcfishpass.gradient_barriers using gist (wscode_ltree);
+create index grdntbr_wscode_bidx on bcfishpass.gradient_barriers using btree (wscode_ltree);
+create index grdntbr_localcode_gidx on bcfishpass.gradient_barriers using gist (localcode_ltree);
+create index grdntbr_localcode_bidx on bcfishpass.gradient_barriers using btree (localcode_ltree);

db/tables/habitat_linear.sql

@@ -1,51 +1,43 @@
-drop table if exists bcfishpass.habitat_linear_bt cascade;
 create table bcfishpass.habitat_linear_bt (
   segmented_stream_id text primary key, 
   spawning boolean, 
   rearing boolean
 );
 
-drop table if exists bcfishpass.habitat_linear_ch cascade;
 create table bcfishpass.habitat_linear_ch (
   segmented_stream_id text primary key, 
   spawning boolean, 
   rearing boolean
 );
 
-drop table if exists bcfishpass.habitat_linear_cm cascade;
 create table bcfishpass.habitat_linear_cm (
   segmented_stream_id text primary key, 
   spawning boolean
 );
 
-drop table if exists bcfishpass.habitat_linear_co cascade;
 create table bcfishpass.habitat_linear_co (
   segmented_stream_id text primary key, 
   spawning boolean, 
   rearing boolean
 );
 
-drop table if exists bcfishpass.habitat_linear_pk cascade;
 create table bcfishpass.habitat_linear_pk (
   segmented_stream_id text primary key, 
   spawning boolean
 );
 
-drop table if exists bcfishpass.habitat_linear_sk cascade;
 create table bcfishpass.habitat_linear_sk (
   segmented_stream_id text primary key, 
   spawning boolean,
   rearing boolean
 );
 
-drop table if exists bcfishpass.habitat_linear_st cascade;
 create table bcfishpass.habitat_linear_st (
   segmented_stream_id text primary key,
   spawning boolean,
   rearing boolean
 );
 
-drop table if exists bcfishpass.habitat_linear_wct cascade;
 create table bcfishpass.habitat_linear_wct (
   segmented_stream_id text primary key, 
   spawning boolean,

db/tables/log.sql

@@ -6,7 +6,7 @@
 --drop table bcfishpass.parameters_habitat_thresholds_log;
 --drop table bcfishpass.wsg_linear_summary;
 --drop table bcfishpass.wsg_crossing_summary;
-create table if not exists bcfishpass.log (
+create table bcfishpass.log (
   model_run_id serial primary key,
   model_type text not null,
   date_completed timestamp not null default CURRENT_TIMESTAMP,
@@ -20,13 +20,13 @@ create table if not exists bcfishpass.log (
 
 
 -- log parameters used for the given model run
-create table if not exists bcfishpass.parameters_habitat_method_log (
+create table bcfishpass.parameters_habitat_method_log (
   model_run_id integer references bcfishpass.log(model_run_id),
   watershed_group_code character varying(4),
   model text
 );
 
-create table if not exists bcfishpass.parameters_habitat_thresholds_log (
+create table bcfishpass.parameters_habitat_thresholds_log (
  model_run_id integer references bcfishpass.log(model_run_id),
  species_code             text   ,
  spawn_gradient_max       numeric,
@@ -42,7 +42,7 @@ create table if not exists bcfishpass.parameters_habitat_thresholds_log (
  rear_lake_ha_min         integer
 );
 
-create table if not exists bcfishpass.wsg_linear_summary (
+create table bcfishpass.wsg_linear_summary (
  model_run_id                                             integer references bcfishpass.log(model_run_id),
  watershed_group_code                                     text,
  length_total                                             numeric,
@@ -112,7 +112,7 @@ create table if not exists bcfishpass.wsg_linear_summary (
  length_spawning_rearing_wct_accessible_b                 numeric
 );
 
-create table if not exists bcfishpass.wsg_crossing_summary (
+create table bcfishpass.wsg_crossing_summary (
   model_run_id                          integer references bcfishpass.log(model_run_id),
   watershed_group_code                  text,
   crossing_feature_type                 text,

db/tables/observations.sql

@@ -1,5 +1,3 @@
-DROP TABLE IF EXISTS bcfishpass.observations cascade;
-
 CREATE TABLE bcfishpass.observations
 (
   fish_obsrvtn_event_id bigint primary key,
@@ -16,11 +14,11 @@ CREATE TABLE bcfishpass.observations
 );
 
 -- index
-create index if not exists obsrvtn_linear_feature_id_idx on bcfishpass.observations (linear_feature_id);
-create index if not exists obsrvtn_blue_line_key_idx on bcfishpass.observations (blue_line_key);
-create index if not exists obsrvtn_watershed_group_code_idx on bcfishpass.observations (watershed_group_code);
-create index if not exists obsrvtn_wsc_gidx on bcfishpass.observations using gist (wscode_ltree);
-create index if not exists obsrvtn_wsc_bidx on bcfishpass.observations using btree (wscode_ltree);
-create index if not exists obsrvtn_lc_gidx on bcfishpass.observations using gist (localcode_ltree);
-create index if not exists obsrvtn_lc_bidx on bcfishpass.observations using btree (localcode_ltree);
-create index if not exists obsrvtn_geom_idx on bcfishpass.observations using gist (geom);
+create index obsrvtn_linear_feature_id_idx on bcfishpass.observations (linear_feature_id);
+create index obsrvtn_blue_line_key_idx on bcfishpass.observations (blue_line_key);
+create index obsrvtn_watershed_group_code_idx on bcfishpass.observations (watershed_group_code);
+create index obsrvtn_wsc_gidx on bcfishpass.observations using gist (wscode_ltree);
+create index obsrvtn_wsc_bidx on bcfishpass.observations using btree (wscode_ltree);
+create index obsrvtn_lc_gidx on bcfishpass.observations using gist (localcode_ltree);
+create index obsrvtn_lc_bidx on bcfishpass.observations using btree (localcode_ltree);
+create index obsrvtn_geom_idx on bcfishpass.observations using gist (geom);

db/tables/parameters.sql

@@ -4,7 +4,6 @@
 -- method
 -- specify which watersheds to include, which habitat model to use
 -- --------------
-drop table if exists bcfishpass.parameters_habitat_method cascade;
 create table bcfishpass.parameters_habitat_method
 (
   watershed_group_code character varying(4),
@@ -15,7 +14,6 @@ create table bcfishpass.parameters_habitat_method
 -- thresholds
 -- define various spawning/rearing thresholds for species to be modelled
 -- --------------
-drop table if exists bcfishpass.parameters_habitat_thresholds cascade;
 create table bcfishpass.parameters_habitat_thresholds (
   species_code text,
   spawn_gradient_max numeric,
@@ -31,10 +29,9 @@ create table bcfishpass.parameters_habitat_thresholds (
   rear_lake_ha_min integer
 );
 
-
 -- --------------
 -- list of watershed groups to process in access model/crossings
--- defaults to all
 -- --------------
-drop table if exists bcfishpass.watershed_groups_access;
-create table bcfishpass.watershed_groups_access as select watershed_group_code from whse_basemapping.fwa_watershed_groups_poly;
+create table bcfishpass.watershed_groups_access (
+  watershed_group_code character varying(4)
+);