Make concept based table IDs 64 bit · catmaid/CATMAID@c23ea2d

Commit

Make concept based table IDs 64 bit

While we still have some headroom for the datasets we work with at the
moment, keeping the IDs of concept table based tables (inheritance) at
32 bit would have been a limit at some point. Already we see large
segmentation datasets that make this headroom rather small. Therefore
this migration will rewrite all concept based tables as well as tables
that reference them through foreign keys so that 64 bit IDs are used.

This migration also updates the review table to use 64 bit IDs. It also
fixes the history views of the catmaid_sampler table, which haven't been
kept up to date with column changes.

In addition a lot of missing foreign key constraints have been added.
They shouldn't have a big import on performance and in fact no real
difference could be measured.

The column order of concept changed slightly to improve the column
alignment and reduce padding. So far we wasted 4 Bytes per row, because
project_id occupied 4 Bytes and required 4 Bytes of padding, because it
was followed by a bigint. This is changed now and no more padding is
needed. This also lowers the impact on storage of the change to 64 bit
IDs.

Also, the indices backing the primary keys of many semantic tables
include now additional data like the class_id for class instances and
the relation_id for some relation instance types. This Postgres 11
feature allows to use more index-only scans.

In addition many index names follow now a more consistent pattern.

I tested this migration by multiple reviews and analyzing the schema
diff generated by pgquarrel for both migration 98 vs 99 as well as 99 vs
(99 -> 98) (i.e. a rollback). These migrations look reasonable and the
effective migration (diff) from 98 to 99 is attached at the end of this
commit message. The actual migration is more complicated, because it
cares also about column ordering, which below schema changes don't.

Fixes catmaid/CATMAID#1848

---

Effective migration 99:

ALTER SEQUENCE public.catmaid_sampler_id_seq AS integer MAXVALUE 2147483647;

CREATE SEQUENCE public.skeleton_origin_id_seq AS integer NO MINVALUE NO MAXVALUE;

ALTER TABLE ONLY public.cardinality_restriction ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.cardinality_restriction ALTER COLUMN restricted_link_id SET DATA TYPE integer;

ALTER TABLE ONLY public.cardinality_restriction ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.cardinality_restriction
	DROP CONSTRAINT cardinality_restriction_project_id_fkey;

ALTER TABLE ONLY public.cardinality_restriction__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.cardinality_restriction__history ALTER COLUMN restricted_link_id SET DATA TYPE integer;

ALTER TABLE ONLY public.catmaid_sampler ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.catmaid_sampler ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.catmaid_sampler
	ADD CONSTRAINT catmaid_sampler_sampler_state_id_80e7961f_fk_catmaid_s FOREIGN KEY (sampler_state_id) REFERENCES catmaid_samplerstate(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_sampler
	DROP CONSTRAINT catmaid_sampler_sampler_state_id_fkey;

ALTER TABLE ONLY public.catmaid_sampler
	ADD CONSTRAINT catmaid_sampler_skeleton_id_dfc98008_fk_class_instance_id FOREIGN KEY (skeleton_id) REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_sampler
	DROP CONSTRAINT catmaid_sampler_skeleton_id_fkey;

ALTER TABLE ONLY public.catmaid_sampler
	ADD CONSTRAINT catmaid_sampler_user_id_8d1c228f_fk_auth_user_id FOREIGN KEY (user_id) REFERENCES auth_user(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_sampler
	DROP CONSTRAINT catmaid_sampler_user_id_fkey;

ALTER TABLE ONLY public.catmaid_sampler__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.catmaid_sampler__history ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.catmaid_samplerdomain
	ADD CONSTRAINT catmaid_samplerdomain_sampler_id_ed4aa3f0_fk_catmaid_sampler_id FOREIGN KEY (sampler_id) REFERENCES catmaid_sampler(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_samplerdomain
	DROP CONSTRAINT catmaid_samplerdomain_sampler_id_fkey;

ALTER TABLE ONLY public.catmaid_samplerdomain
	ADD CONSTRAINT catmaid_samplerdomain_start_node_id_4ae2c16c_fk_treenode_id FOREIGN KEY (start_node_id) REFERENCES treenode(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_samplerdomain
	DROP CONSTRAINT catmaid_samplerdomain_start_node_id_fkey;

ALTER TABLE ONLY public.catmaid_samplerdomainend
	ADD CONSTRAINT catmaid_samplerdomainend_end_node_id_31859f80_fk_treenode_id FOREIGN KEY (end_node_id) REFERENCES treenode(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_samplerdomainend
	DROP CONSTRAINT catmaid_samplerdomainend_end_node_id_fkey;

ALTER TABLE ONLY public.catmaid_samplerinterval
	ADD CONSTRAINT catmaid_samplerinterval_end_node_id_c82f43df_fk_treenode_id FOREIGN KEY (end_node_id) REFERENCES treenode(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_samplerinterval
	DROP CONSTRAINT catmaid_samplerinterval_end_node_id_fkey;

ALTER TABLE ONLY public.catmaid_samplerinterval
	ADD CONSTRAINT catmaid_samplerinterval_start_node_id_ead5c637_fk_treenode_id FOREIGN KEY (start_node_id) REFERENCES treenode(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_samplerinterval
	DROP CONSTRAINT catmaid_samplerinterval_start_node_id_fkey;

ALTER TABLE ONLY public.catmaid_skeleton_summary ADD COLUMN num_imported_nodes bigint DEFAULT 0 NOT NULL;

ALTER TABLE ONLY public.catmaid_skeleton_summary ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.catmaid_skeleton_summary
	ADD CONSTRAINT catmaid_skeleton_sum_skeleton_id_034079eb_fk_class_ins FOREIGN KEY (skeleton_id) REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.catmaid_skeleton_summary
	DROP CONSTRAINT catmaid_skeleton_summary_last_editor_id_fkey;

ALTER TABLE ONLY public.catmaid_skeleton_summary
	ADD CONSTRAINT catmaid_skeleton_summary_skeleton_id_fk FOREIGN KEY (skeleton_id) REFERENCES class_instance(id) ON DELETE CASCADE;

ALTER TABLE ONLY public.catmaid_skeleton_summary
	DROP CONSTRAINT catmaid_skeleton_summary_skeleton_id_fkey;

ALTER TABLE ONLY public.catmaid_skeleton_summary
	ADD CONSTRAINT last_editor_id_fkey FOREIGN KEY (last_editor_id) REFERENCES auth_user(id);

ALTER TABLE ONLY public.catmaid_skeleton_summary
	DROP CONSTRAINT catmaid_skeleton_id_pkey;

ALTER TABLE ONLY public.catmaid_skeleton_summary
	ADD CONSTRAINT catmaid_skeleton_summary_pkey PRIMARY KEY (skeleton_id);

ALTER TABLE ONLY public.change_request ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.change_request ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.change_request
	DROP CONSTRAINT change_request_connector_id_fkey;

ALTER TABLE ONLY public.change_request
	ADD CONSTRAINT change_request_connector_id_fkey FOREIGN KEY (connector_id) REFERENCES connector(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.change_request
	DROP CONSTRAINT change_request_recipient_id_fkey;

ALTER TABLE ONLY public.change_request
	DROP CONSTRAINT change_request_treenode_id_fkey;

ALTER TABLE ONLY public.change_request
	ADD CONSTRAINT change_request_treenode_id_fkey FOREIGN KEY (treenode_id) REFERENCES treenode(id) ON DELETE CASCADE;

ALTER TABLE ONLY public.change_request
	DROP CONSTRAINT change_request_user_id_fkey;

ALTER TABLE ONLY public.change_request
	ADD CONSTRAINT change_request_user_id_fkey FOREIGN KEY (user_id) REFERENCES auth_user(id);

ALTER TABLE ONLY public.change_request
	ADD CONSTRAINT recipient_id_refs_id FOREIGN KEY (recipient_id) REFERENCES auth_user(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.change_request__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class ALTER COLUMN class_name SET DATA TYPE character varying(255);

ALTER TABLE ONLY public.class ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.class
	DROP CONSTRAINT class_user_id_fkey;

ALTER TABLE ONLY public.class
	DROP CONSTRAINT class_id_pkey;

ALTER TABLE ONLY public.class
	ADD CONSTRAINT class_pkey PRIMARY KEY (id);

ALTER TABLE ONLY public.class__history ALTER COLUMN class_name SET DATA TYPE character varying(255);

ALTER TABLE ONLY public.class__history ALTER COLUMN class_name SET DEFAULT NULL::character varying;

ALTER TABLE ONLY public.class__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class ALTER COLUMN class_a SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class ALTER COLUMN class_a DROP NOT NULL;

ALTER TABLE ONLY public.class_class ALTER COLUMN class_b SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class ALTER COLUMN class_b DROP NOT NULL;

ALTER TABLE ONLY public.class_class ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.class_class
	DROP CONSTRAINT class_class_class_a_fkey;

ALTER TABLE ONLY public.class_class
	DROP CONSTRAINT class_class_class_b_fkey;

ALTER TABLE ONLY public.class_class
	DROP CONSTRAINT class_class_project_id_fkey;

ALTER TABLE ONLY public.class_class
	DROP CONSTRAINT class_class_relation_id_fkey;

ALTER TABLE ONLY public.class_class
	DROP CONSTRAINT class_class_user_id_fkey;

ALTER TABLE ONLY public.class_class__history ALTER COLUMN class_a SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class__history ALTER COLUMN class_b SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_class__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance ALTER COLUMN class_id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.class_instance
	DROP CONSTRAINT class_instance_user_id_fkey;

ALTER TABLE ONLY public.class_instance
	DROP CONSTRAINT class_instance_id_pkey;

ALTER TABLE ONLY public.class_instance
	ADD CONSTRAINT class_instance_pkey PRIMARY KEY (id);

ALTER TABLE ONLY public.class_instance__history ALTER COLUMN class_id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance ALTER COLUMN class_instance_a SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance ALTER COLUMN class_instance_a DROP NOT NULL;

ALTER TABLE ONLY public.class_instance_class_instance ALTER COLUMN class_instance_b SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance ALTER COLUMN class_instance_b DROP NOT NULL;

ALTER TABLE ONLY public.class_instance_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.class_instance_class_instance
	DROP CONSTRAINT class_instance_class_instance_user_id_fkey;

ALTER TABLE ONLY public.class_instance_class_instance__history ALTER COLUMN class_instance_a SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance__history ALTER COLUMN class_instance_b SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.class_instance_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.concept ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.concept ALTER COLUMN id DROP DEFAULT;

ALTER TABLE ONLY public.concept ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.concept
	DROP CONSTRAINT concept_project_id_fkey;

ALTER TABLE ONLY public.concept
	DROP CONSTRAINT concept_user_id_fkey;

ALTER TABLE ONLY public.concept__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.connector_class_instance ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.connector_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.connector_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.connector_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.connector_class_instance
	DROP CONSTRAINT connector_class_instance_class_instance_id_fkey;

ALTER TABLE ONLY public.connector_class_instance
	DROP CONSTRAINT connector_class_instance_connector_id_fkey;

ALTER TABLE ONLY public.connector_class_instance
	ADD CONSTRAINT connector_class_instance_connector_id_fkey FOREIGN KEY (connector_id) REFERENCES connector(id) ON DELETE CASCADE;

ALTER TABLE ONLY public.connector_class_instance
	DROP CONSTRAINT connector_class_instance_project_id_fkey;

ALTER TABLE ONLY public.connector_class_instance
	DROP CONSTRAINT connector_class_instance_relation_id_fkey;

ALTER TABLE ONLY public.connector_class_instance
	DROP CONSTRAINT connector_class_instance_user_id_fkey;

ALTER TABLE ONLY public.connector_class_instance__history ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.connector_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.connector_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.log ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.log ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.log
	DROP CONSTRAINT log_project_id_fkey;

ALTER TABLE ONLY public.log
	DROP CONSTRAINT log_user_id_fkey;

ALTER TABLE ONLY public.point_class_instance ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.point_class_instance
	DROP CONSTRAINT point_class_instance_class_instance_id_fkey;

ALTER TABLE ONLY public.point_class_instance
	DROP CONSTRAINT point_class_instance_point_id_fkey;

ALTER TABLE ONLY public.point_class_instance
	DROP CONSTRAINT point_class_instance_project_id_fkey;

ALTER TABLE ONLY public.point_class_instance
	DROP CONSTRAINT point_class_instance_relation_id_fkey;

ALTER TABLE ONLY public.point_class_instance
	ADD CONSTRAINT point_class_instance_sa_id FOREIGN KEY (point_id) REFERENCES point(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.point_class_instance
	DROP CONSTRAINT point_class_instance_user_id_fkey;

ALTER TABLE ONLY public.point_class_instance
	ADD CONSTRAINT point_connector_class_instance_id_fkey FOREIGN KEY (class_instance_id) REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.point_class_instance__history ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_connector ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_connector ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_connector ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.point_connector
	DROP CONSTRAINT point_connector_connector_id_fkey;

ALTER TABLE ONLY public.point_connector
	ADD CONSTRAINT point_connector_connector_id_fkey FOREIGN KEY (connector_id) REFERENCES connector(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.point_connector
	DROP CONSTRAINT point_connector_point_id_fkey;

ALTER TABLE ONLY public.point_connector
	DROP CONSTRAINT point_connector_project_id_fkey;

ALTER TABLE ONLY public.point_connector
	DROP CONSTRAINT point_connector_relation_id_fkey;

ALTER TABLE ONLY public.point_connector
	ADD CONSTRAINT point_connector_sa_id FOREIGN KEY (point_id) REFERENCES point(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.point_connector
	DROP CONSTRAINT point_connector_user_id_fkey;

ALTER TABLE ONLY public.point_connector__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.point_connector__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.region_of_interest_class_instance ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.region_of_interest_class_instance ALTER COLUMN class_instance_id DROP NOT NULL;

ALTER TABLE ONLY public.region_of_interest_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.region_of_interest_class_instance ALTER COLUMN region_of_interest_id DROP NOT NULL;

ALTER TABLE ONLY public.region_of_interest_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.region_of_interest_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.region_of_interest_class_instance
	DROP CONSTRAINT region_of_interest_class_instance_class_instance_id_fkey;

ALTER TABLE ONLY public.region_of_interest_class_instance
	ADD CONSTRAINT region_of_interest_class_instance_class_instance_id_fkey FOREIGN KEY (class_instance_id) REFERENCES class_instance(id);

ALTER TABLE ONLY public.region_of_interest_class_instance
	DROP CONSTRAINT region_of_interest_class_instance_project_id_fkey;

ALTER TABLE ONLY public.region_of_interest_class_instance
	DROP CONSTRAINT region_of_interest_class_instance_region_of_interest_id_fkey;

ALTER TABLE ONLY public.region_of_interest_class_instance
	DROP CONSTRAINT region_of_interest_class_instance_relation_id_fkey;

ALTER TABLE ONLY public.region_of_interest_class_instance
	DROP CONSTRAINT region_of_interest_class_instance_user_id_fkey;

ALTER TABLE ONLY public.region_of_interest_class_instance__history ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.region_of_interest_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.region_of_interest_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.relation ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.relation ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.relation
	DROP CONSTRAINT relation_project_id_fkey;

ALTER TABLE ONLY public.relation
	DROP CONSTRAINT relation_user_id_fkey;

ALTER TABLE ONLY public.relation
	DROP CONSTRAINT relation_id_pkey;

ALTER TABLE ONLY public.relation
	ADD CONSTRAINT relation_pkey PRIMARY KEY (id);

ALTER TABLE ONLY public.relation__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.relation_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.relation_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.relation_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.relation_instance
	DROP CONSTRAINT relation_instance_project_id_fkey;

ALTER TABLE ONLY public.relation_instance
	DROP CONSTRAINT relation_instance_relation_id_fkey;

ALTER TABLE ONLY public.relation_instance
	DROP CONSTRAINT relation_instance_user_id_fkey;

ALTER TABLE ONLY public.relation_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.relation_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.restriction ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.restriction ALTER COLUMN restricted_link_id SET DATA TYPE integer;

ALTER TABLE ONLY public.restriction ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.restriction
	ADD CONSTRAINT restricted_link_fkey FOREIGN KEY (restricted_link_id) REFERENCES class_class(id);

ALTER TABLE ONLY public.restriction
	DROP CONSTRAINT restriction_project_id_fkey;

ALTER TABLE ONLY public.restriction
	DROP CONSTRAINT restriction_restricted_link_id_fkey;

ALTER TABLE ONLY public.restriction
	DROP CONSTRAINT restriction_user_id_fkey;

ALTER TABLE ONLY public.restriction__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.restriction__history ALTER COLUMN restricted_link_id SET DATA TYPE integer;

ALTER TABLE ONLY public.review ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.review ALTER COLUMN review_time DROP DEFAULT;

ALTER TABLE ONLY public.review ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.review ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.review
	ADD CONSTRAINT review_reviewer_id_refs_id FOREIGN KEY (reviewer_id) REFERENCES auth_user(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.review
	DROP CONSTRAINT review_skeleton_id_fkey;

ALTER TABLE ONLY public.review
	ADD CONSTRAINT review_skeleton_id_refs_id FOREIGN KEY (skeleton_id) REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.review
	DROP CONSTRAINT review_treenode_id_fkey;

ALTER TABLE ONLY public.review
	DROP CONSTRAINT review_user_id_fkey;

ALTER TABLE ONLY public.review
	ADD CONSTRAINT treenode_id_fkey FOREIGN KEY (treenode_id) REFERENCES treenode(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.review__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.review__history ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.skeleton_origin ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.skeleton_origin
	ADD CONSTRAINT skeleton_origin_data_source_id_fkey FOREIGN KEY (data_source_id) REFERENCES data_source(id) ON DELETE CASCADE;

ALTER TABLE ONLY public.skeleton_origin
	DROP CONSTRAINT skeleton_origin_data_source_id_fkey1;

ALTER TABLE ONLY public.skeleton_origin
	ADD CONSTRAINT skeleton_origin_project_id_fkey FOREIGN KEY (project_id) REFERENCES project(id) ON DELETE CASCADE;

ALTER TABLE ONLY public.skeleton_origin
	DROP CONSTRAINT skeleton_origin_project_id_fkey1;

ALTER TABLE ONLY public.skeleton_origin
	ADD CONSTRAINT skeleton_origin_skeleton_id_fkey FOREIGN KEY (skeleton_id) REFERENCES class_instance(id) ON DELETE CASCADE;

ALTER TABLE ONLY public.skeleton_origin
	DROP CONSTRAINT skeleton_origin_skeleton_id_fkey1;

ALTER TABLE ONLY public.skeleton_origin
	ADD CONSTRAINT skeleton_origin_user_id_fkey FOREIGN KEY (user_id) REFERENCES auth_user(id);

ALTER TABLE ONLY public.skeleton_origin
	DROP CONSTRAINT skeleton_origin_user_id_fkey1;

ALTER TABLE ONLY public.skeleton_origin__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_class_instance ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_class_instance ALTER COLUMN class_instance_id DROP NOT NULL;

ALTER TABLE ONLY public.stack_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_class_instance ALTER COLUMN stack_id DROP NOT NULL;

ALTER TABLE ONLY public.stack_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.stack_class_instance
	DROP CONSTRAINT stack_class_instance_class_instance_id_fkey;

ALTER TABLE ONLY public.stack_class_instance
	ADD CONSTRAINT stack_class_instance_class_instance_id_fkey FOREIGN KEY (class_instance_id) REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.stack_class_instance
	DROP CONSTRAINT stack_class_instance_instance_relation_id_fkey;

ALTER TABLE ONLY public.stack_class_instance
	DROP CONSTRAINT stack_class_instance_project_id_fkey;

ALTER TABLE ONLY public.stack_class_instance
	DROP CONSTRAINT stack_class_instance_stack_id_fkey;

ALTER TABLE ONLY public.stack_class_instance
	ADD CONSTRAINT stack_class_instance_stack_id_fkey FOREIGN KEY (stack_id) REFERENCES stack(id);

ALTER TABLE ONLY public.stack_class_instance
	DROP CONSTRAINT stack_class_instance_user_id_fkey;

ALTER TABLE ONLY public.stack_class_instance__history ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_group_class_instance ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_group_class_instance ALTER COLUMN class_instance_id DROP NOT NULL;

ALTER TABLE ONLY public.stack_group_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_group_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_group_class_instance ALTER COLUMN stack_group_id DROP NOT NULL;

ALTER TABLE ONLY public.stack_group_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.stack_group_class_instance
	DROP CONSTRAINT stack_group_class_instance_class_instance_id_fkey;

ALTER TABLE ONLY public.stack_group_class_instance
	ADD CONSTRAINT stack_group_class_instance_class_instance_id_fkey FOREIGN KEY (class_instance_id) REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.stack_group_class_instance
	DROP CONSTRAINT stack_group_class_instance_project_id_fkey;

ALTER TABLE ONLY public.stack_group_class_instance
	DROP CONSTRAINT stack_group_class_instance_relation_id_fkey;

ALTER TABLE ONLY public.stack_group_class_instance
	DROP CONSTRAINT stack_group_class_instance_stack_group_id_fkey;

ALTER TABLE ONLY public.stack_group_class_instance
	ADD CONSTRAINT stack_group_class_instance_stack_group_id_fkey FOREIGN KEY (stack_group_id) REFERENCES stack_group(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.stack_group_class_instance
	DROP CONSTRAINT stack_group_class_instance_user_id_fkey;

ALTER TABLE ONLY public.stack_group_class_instance__history ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_group_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.stack_group_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.suppressed_virtual_treenode
	DROP CONSTRAINT suppressed_virtual_treenode_child_id_fkey;

ALTER TABLE ONLY public.suppressed_virtual_treenode
	ADD CONSTRAINT suppressed_vnodes_child_id_refs_id FOREIGN KEY (child_id) REFERENCES treenode(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.treenode ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode
	DROP CONSTRAINT treenode_editor_id_fkey;

ALTER TABLE ONLY public.treenode
	DROP CONSTRAINT treenode_project_id_fkey;

ALTER TABLE ONLY public.treenode
	DROP CONSTRAINT treenode_user_id_fkey;

ALTER TABLE ONLY public.treenode__history ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_class_instance ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.treenode_class_instance
	DROP CONSTRAINT treenode_class_instance_class_instance_id_fkey;

ALTER TABLE ONLY public.treenode_class_instance
	DROP CONSTRAINT treenode_class_instance_project_id_fkey;

ALTER TABLE ONLY public.treenode_class_instance
	DROP CONSTRAINT treenode_class_instance_relation_id_fkey;

ALTER TABLE ONLY public.treenode_class_instance
	DROP CONSTRAINT treenode_class_instance_treenode_id_fkey;

ALTER TABLE ONLY public.treenode_class_instance
	ADD CONSTRAINT treenode_class_instance_treenode_id_fkey FOREIGN KEY (treenode_id) REFERENCES treenode(id) ON DELETE CASCADE;

ALTER TABLE ONLY public.treenode_class_instance
	DROP CONSTRAINT treenode_class_instance_user_id_fkey;

ALTER TABLE ONLY public.treenode_class_instance__history ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_connector ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_connector ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_connector ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_connector ALTER COLUMN skeleton_id DROP NOT NULL;

ALTER TABLE ONLY public.treenode_connector ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.treenode_connector
	DROP CONSTRAINT treenode_connector_project_id_fkey;

ALTER TABLE ONLY public.treenode_connector
	DROP CONSTRAINT treenode_connector_relation_id_fkey;

ALTER TABLE ONLY public.treenode_connector
	DROP CONSTRAINT treenode_connector_skeleton_id_fkey;

ALTER TABLE ONLY public.treenode_connector
	DROP CONSTRAINT treenode_connector_user_id_fkey;

ALTER TABLE ONLY public.treenode_connector__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_connector__history ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.treenode_connector__history ALTER COLUMN skeleton_id SET DATA TYPE integer;

ALTER TABLE ONLY public.volume_class_instance ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.volume_class_instance ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.volume_class_instance ALTER COLUMN relation_id SET DATA TYPE integer;

ALTER TABLE ONLY public.volume_class_instance ALTER COLUMN txid DROP NOT NULL;

ALTER TABLE ONLY public.volume_class_instance
	DROP CONSTRAINT volume_class_instance_class_instance_id_fkey;

ALTER TABLE ONLY public.volume_class_instance
	ADD CONSTRAINT volume_class_instance_id_fkey FOREIGN KEY (class_instance_id) REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.volume_class_instance
	DROP CONSTRAINT volume_class_instance_project_id_fkey;

ALTER TABLE ONLY public.volume_class_instance
	DROP CONSTRAINT volume_class_instance_relation_id_fkey;

ALTER TABLE ONLY public.volume_class_instance
	ADD CONSTRAINT volume_class_instance_sa_id FOREIGN KEY (volume_id) REFERENCES catmaid_volume(id) DEFERRABLE INITIALLY DEFERRED;

ALTER TABLE ONLY public.volume_class_instance
	DROP CONSTRAINT volume_class_instance_user_id_fkey;

ALTER TABLE ONLY public.volume_class_instance
	DROP CONSTRAINT volume_class_instance_volume_id_fkey;

ALTER TABLE ONLY public.volume_class_instance__history ALTER COLUMN class_instance_id SET DATA TYPE integer;

ALTER TABLE ONLY public.volume_class_instance__history ALTER COLUMN id SET DATA TYPE integer;

ALTER TABLE ONLY public.volume_class_instance__history ALTER COLUMN relation_id SET DATA TYPE integer;

CREATE INDEX catmaid_sampler_project_id_c93395a7 ON public.catmaid_sampler USING btree (project_id);

CREATE INDEX catmaid_sampler_sampler_state_id_80e7961f ON public.catmaid_sampler USING btree (sampler_state_id);

CREATE INDEX catmaid_sampler_skeleton_id_dfc98008 ON public.catmaid_sampler USING btree (skeleton_id);

CREATE INDEX catmaid_sampler_user_id_8d1c228f ON public.catmaid_sampler USING btree (user_id);

CREATE INDEX catmaid_skeleton_summary_num_imported_nodes_idx ON public.catmaid_skeleton_summary USING btree (num_imported_nodes);

CREATE INDEX catmaid_skeleton_summary_project_id_7340fa33 ON public.catmaid_skeleton_summary USING btree (project_id);

CREATE UNIQUE INDEX point_connector_project_id_uniq ON public.point_connector USING btree (project_id, point_id, connector_id, relation_id);

CREATE INDEX review_project_id ON public.review USING btree (project_id);

CREATE INDEX review_reviewer_id ON public.review USING btree (reviewer_id);

CREATE INDEX review_skeleton_id ON public.review USING btree (skeleton_id);

CREATE INDEX review_treenode_id ON public.review USING btree (treenode_id);

CREATE INDEX treenode_class_instance_class_instance_id ON public.treenode_class_instance USING btree (class_instance_id);

CREATE INDEX treenode_class_instance_project_id ON public.treenode_class_instance USING btree (project_id);

CREATE INDEX treenode_class_instance_relation_id ON public.treenode_class_instance USING btree (relation_id);

CREATE INDEX treenode_class_instance_treenode_id ON public.treenode_class_instance USING btree (treenode_id);

CREATE INDEX treenode_class_instance_user_id ON public.treenode_class_instance USING btree (user_id);

CREATE INDEX treenode_connector_connector_id ON public.treenode_connector USING btree (connector_id);

CREATE INDEX treenode_connector_creation_time_idx ON public.treenode_connector USING btree (creation_time);

CREATE INDEX treenode_connector_project_id ON public.treenode_connector USING btree (project_id);

CREATE UNIQUE INDEX treenode_connector_project_id_uniq ON public.treenode_connector USING btree (project_id, treenode_id, connector_id, relation_id);

CREATE INDEX treenode_connector_relation_id ON public.treenode_connector USING btree (relation_id);

CREATE INDEX treenode_connector_skeleton_id ON public.treenode_connector USING btree (skeleton_id);

CREATE INDEX treenode_connector_treenode_id ON public.treenode_connector USING btree (treenode_id);

CREATE INDEX treenode_connector_user_id ON public.treenode_connector USING btree (user_id);

CREATE INDEX treenode_creation_time_index ON public.treenode USING btree (creation_time);

CREATE INDEX treenode_edition_time_index ON public.treenode USING btree (edition_time);

CREATE INDEX treenode_location_x_index ON public.treenode USING btree (project_id, location_x);

CREATE INDEX treenode_location_y_index ON public.treenode USING btree (project_id, location_y);

CREATE INDEX treenode_location_z_index ON public.treenode USING btree (project_id, location_z);

CREATE INDEX treenode_parent_id ON public.treenode USING btree (parent_id);

CREATE INDEX treenode_project_id_skeleton_id_index ON public.treenode USING btree (project_id, skeleton_id);

CREATE INDEX treenode_project_id_user_id_index ON public.treenode USING btree (project_id, user_id);

CREATE INDEX treenode_skeleton_id_index ON public.treenode USING btree (skeleton_id);

CREATE OR REPLACE FUNCTION public.check_treenode_connector_related_reviews(tc treenode_connector) RETURNS void
    LANGUAGE plpgsql VOLATILE
AS $$BEGIN

            -- Mark linked treenodes as unreviewed. If relation is postsynaptic,
            -- mark only one, otherwise mark all treenodes related to connector.
            IF EXISTS (SELECT 1
                         FROM relation
                         WHERE id = tc.relation_id
                           AND relation_name = 'postsynaptic_to') THEN
              DELETE FROM review WHERE treenode_id = tc.treenode_id;
            ELSE
              DELETE FROM review r
                USING treenode_connector tc2
                WHERE r.treenode_id = tc2.treenode_id
                  AND tc2.connector_id = tc.connector_id;
            END IF;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.drop_history_table(live_table regclass) RETURNS void
    LANGUAGE plpgsql VOLATILE
AS $$
    DECLARE

        -- This will contain the name of the newly created history table. No
        -- regclass is used, because the implicit table existence check on variable
        -- assignment can fail if the table has already been removed by an
        -- cascaded table drop.
        history_table_name text;

    BEGIN

        -- History tables will be named like the live table plus a '__history' suffix
        history_table_name = get_history_table_name(live_table);

        -- Cascading deleting is used to also delete child tables and triggers.
        EXECUTE format('DROP TABLE IF EXISTS %I CASCADE', history_table_name);
        EXECUTE format('DROP TRIGGER IF EXISTS %I ON %s',
            get_tracking_table_update_trigger_name(), live_table);
        EXECUTE format('DROP TRIGGER IF EXISTS %I ON %s',
            get_tracking_table_truncate_trigger_name(), live_table);
        EXECUTE format('DROP TABLE IF EXISTS %I CASCADE',
            get_tracking_table_name(live_table));

        EXECUTE format('DROP TRIGGER IF EXISTS %I ON %s',
            get_history_update_trigger_name_regular(), live_table);
        EXECUTE format('DROP TRIGGER IF EXISTS %I ON %s',
            get_history_update_trigger_name_tracking(), live_table);
        EXECUTE format('DROP FUNCTION IF EXISTS %s() CASCADE',
            get_history_update_fn_name_regular(live_table));
        EXECUTE format('DROP TRIGGER IF EXISTS %I ON %s',
            get_history_truncate_trigger_name(), live_table);

        -- Remove from created table log
        DELETE FROM catmaid_history_table cht WHERE cht.live_table = $1;
    END;
    $$;

CREATE OR REPLACE FUNCTION public.update_history_cardinality_restriction_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO cardinality_restriction__history (id,user_id,creation_time,edition_time,project_id,enabled,restricted_link_id,cardinality_type,value,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.enabled,ot.restricted_link_id,ot.cardinality_type,ot.value,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_change_request_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO change_request__history (id,user_id,creation_time,edition_time,project_id,type,description,status,recipient_id,location,treenode_id,connector_id,validate_action,approve_action,reject_action,completion_time,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.type,ot.description,ot.status,ot.recipient_id,ot.location,ot.treenode_id,ot.connector_id,ot.validate_action,ot.approve_action,ot.reject_action,ot.completion_time,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_class_class_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO class_class__history (id,user_id,creation_time,edition_time,project_id,relation_id,class_a,class_b,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.class_a,ot.class_b,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_class_instance_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO class_instance_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,class_instance_a,class_instance_b,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.class_instance_a,ot.class_instance_b,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO class_instance__history (id,user_id,creation_time,edition_time,project_id,class_id,name,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.class_id,ot.name,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_class_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO class__history (id,user_id,creation_time,edition_time,project_id,class_name,description,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.class_name,ot.description,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_concept_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO concept__history (id,user_id,creation_time,edition_time,project_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_connector_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO connector_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,connector_id,class_instance_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.connector_id,ot.class_instance_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_point_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO point_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,txid,point_id,class_instance_id,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.txid,ot.point_id,ot.class_instance_id, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_point_connector_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO point_connector__history (id,user_id,creation_time,edition_time,project_id,relation_id,txid,point_id,connector_id,confidence,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.txid,ot.point_id,ot.connector_id,ot.confidence, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_region_of_interest_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO region_of_interest_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,region_of_interest_id,class_instance_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.region_of_interest_id,ot.class_instance_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_relation_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO relation_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_relation_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO relation__history (id,user_id,creation_time,edition_time,project_id,relation_name,uri,description,isreciprocal,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_name,ot.uri,ot.description,ot.isreciprocal,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_restriction_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO restriction__history (id,user_id,creation_time,edition_time,project_id,enabled,restricted_link_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.enabled,ot.restricted_link_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_stack_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO stack_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,stack_id,class_instance_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.stack_id,ot.class_instance_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_stack_group_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO stack_group_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,txid,stack_group_id,class_instance_id,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.txid,ot.stack_group_id,ot.class_instance_id, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_treenode_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO treenode_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,treenode_id,class_instance_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.treenode_id,ot.class_instance_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_treenode_connector_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO treenode_connector__history (id,user_id,creation_time,edition_time,project_id,relation_id,treenode_id,connector_id,skeleton_id,confidence,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.treenode_id,ot.connector_id,ot.skeleton_id,ot.confidence,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_treenode_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO treenode__history (id,project_id,location_x,location_y,location_z,editor_id,user_id,creation_time,edition_time,skeleton_id,radius,confidence,parent_id,txid,sys_period,exec_transaction_id)
                SELECT ot.id,ot.project_id,ot.location_x,ot.location_y,ot.location_z,ot.editor_id,ot.user_id,ot.creation_time,ot.edition_time,ot.skeleton_id,ot.radius,ot.confidence,ot.parent_id,ot.txid, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

CREATE OR REPLACE FUNCTION public.update_history_volume_class_instance_reg() RETURNS trigger
    LANGUAGE plpgsql VOLATILE
AS $$
            BEGIN

                -- Insert new historic data into history table, based on the
                -- currently available columns in the updated table.
                INSERT INTO volume_class_instance__history (id,user_id,creation_time,edition_time,project_id,relation_id,txid,volume_id,class_instance_id,sys_period,exec_transaction_id)
                SELECT ot.id,ot.user_id,ot.creation_time,ot.edition_time,ot.project_id,ot.relation_id,ot.txid,ot.volume_id,ot.class_instance_id, tstzrange(LEAST(ot.edition_time, current_timestamp), current_timestamp), txid_current()
                FROM old_treenode ot;

                RETURN NULL;
            END;
            $$;

DROP SEQUENCE public.skeleton_origin_id_seq1;

DROP INDEX public.catmaid_sampler_project_id_idx;

DROP INDEX public.catmaid_sampler_sampler_state_id_idx;

DROP INDEX public.catmaid_sampler_skeleton_id_idx;

DROP INDEX public.catmaid_sampler_user_id_idx;

DROP INDEX public.catmaid_skeleton_summary_project_id_idx;

DROP INDEX public.class_class_name_idx;

DROP INDEX public.guardian_gr_content_ae6aec_idx;

DROP INDEX public.guardian_us_content_179ed2_idx;

DROP INDEX public.point_connector_project_id_point_id_connector_id_relation_id_un;

DROP INDEX public.review_project_id_idx;

DROP INDEX public.review_reviewer_id_idx;

DROP INDEX public.review_skeleton_id_idx;

DROP INDEX public.review_treenode_id_idx;

DROP INDEX public.treenode_class_instance_class_instance_id_idx;

DROP INDEX public.treenode_class_instance_project_id_idx;

DROP INDEX public.treenode_class_instance_relation_id_idx;

DROP INDEX public.treenode_class_instance_treenode_id_idx;

DROP INDEX public.treenode_class_instance_user_id_idx;

DROP INDEX public.treenode_connector_connector_id_idx;

DROP INDEX public.treenode_connector_creation_time_idx_idx;

DROP INDEX public.treenode_connector_project_id_idx;

DROP INDEX public.treenode_connector_project_id_treenode_id_connector_id_relation;

DROP INDEX public.treenode_connector_relation_id_idx;

DROP INDEX public.treenode_connector_skeleton_id_idx;

DROP INDEX public.treenode_connector_treenode_id_idx;

DROP INDEX public.treenode_connector_user_id_idx;

DROP INDEX public.treenode_creation_time_idx;

DROP INDEX public.treenode_edition_time_idx;

DROP INDEX public.treenode_parent_id_idx;

DROP INDEX public.treenode_project_id_location_x_idx;

DROP INDEX public.treenode_project_id_location_y_idx;

DROP INDEX public.treenode_project_id_location_z_idx;

DROP INDEX public.treenode_project_id_user_id_idx;

DROP INDEX public.treenode_skeleton_id_project_id_idx;

DROP FUNCTION public.drop_history_table_keep_data(live_table regclass);

DROP TRIGGER on_edit_cardinality_restrictions ON public.cardinality_restriction;

DROP TRIGGER on_edit_point_class_instance ON public.point_class_instance;

DROP TRIGGER on_edit_point_connector ON public.point_connector;

DROP TRIGGER on_edit_region_of_interest_class_instance ON public.region_of_interest_class_instance;

DROP TRIGGER on_stack_class_instance ON public.stack_class_instance;

DROP TRIGGER on_stack_group_class_instance ON public.stack_group_class_instance;

DROP TRIGGER on_edit_volume_class_instance ON public.volume_class_instance;

Loading branch information

tomka committed Jan 17, 2020

1 parent 4af80a5 commit c23ea2d

CHANGELOG.md

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -18,12 +18,12 @@
  
      startup, advisory locks are now used. This should make the startup of parallel

      CATMAID workers more robust.

    - The application of migration 82 might take a while to complete, because it

    - The application of migration 88-91 might take a while to complete, because it

      rewrites a potentially big table (treenode_edge). Therefore, make also sure

      that there is enough space available at the database storate location (25% of

      database data directory should be plenty). If no replication is used, setting

      the following Postgres options can speed up the process: `wal_level = minimal`,

      `archive_mode = off` and `max_wal_senders = 0`.

      the following Postgres options can speed up the process: `wal_level =

      minimal`, `archive_mode = off` and `max_wal_senders = 0`.

    - Both `configuration.py.example` and `create_configuration.py` support now the

      option `catmaid_default_enabled_tools`, which defines the list of front-end

django/applications/catmaid/control/annotation.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -682,7 +682,7 @@ def _update_neuron_annotations(project_id:Union[int,str], neuron_id,
  
                cursor.execute('''

                    UPDATE class_instance_class_instance

                    SET class_instance_a = %s, user_id = missing.u_id

                    FROM UNNEST(%s::integer[], %s::integer[]) AS missing(cici_id, u_id)

                    FROM UNNEST(%s::bigint[], %s::integer[]) AS missing(cici_id, u_id)

                    WHERE id = missing.cici_id;

                    ''', (neuron_id, cici_ids, u_ids))

    @@ -710,12 +710,12 @@ def _update_neuron_annotations(project_id:Union[int,str], neuron_id,
  
        cursor.execute("""

            UPDATE class_instance_class_instance

            SET creation_time = to_update.creation_time

            FROM UNNEST(%s::integer[], %s::timestamptz[])

            FROM UNNEST(%s::bigint[], %s::timestamptz[])

                AS to_update(cici_id, creation_time)

            WHERE id = to_update.cici_id;

            UPDATE class_instance_class_instance

            SET edition_Time = to_update.edition_time

            FROM UNNEST(%s::integer[], %s::timestamptz[])

            FROM UNNEST(%s::bigint[], %s::timestamptz[])

                AS to_update(cici_id, edition_time)

            WHERE id = to_update.cici_id;

        """, (to_update_ids,

django/applications/catmaid/control/connector.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -160,13 +160,13 @@ def _many_to_many_synapses(skids1, skids2, relation_name, project_id) -> Tuple:
  
             treenode t1,

             treenode t2,

             connector c

        WHERE tc1.skeleton_id = ANY(%(skeleton_ids_1)s::int[])

        WHERE tc1.skeleton_id = ANY(%(skeleton_ids_1)s::bigint[])

          AND tc1.connector_id = c.id

          AND tc2.skeleton_id = ANY(%(skeleton_ids_2)s::int[])

          AND tc2.skeleton_id = ANY(%(skeleton_ids_2)s::bigint[])

          AND tc1.connector_id = tc2.connector_id

          AND tc1.relation_id = %(relation_id)s

          AND (tc1.relation_id != tc2.relation_id

            OR tc1.relation_id = ANY(%(undir_rel_ids)s::int[]))

            OR tc1.relation_id = ANY(%(undir_rel_ids)s::bigint[]))

          AND tc1.id != tc2.id

          AND tc1.treenode_id = t1.id

          AND tc2.treenode_id = t2.id

    @@ -1067,7 +1067,7 @@ def get_connectors_in_bb_postgis3d(params) -> List:
  
                JOIN (

                    SELECT DISTiNCT tc2.connector_id

                    FROM treenode_connector tc2

                    JOIN UNNEST(%(skeleton_ids)s::int[]) skeleton(id)

                    JOIN UNNEST(%(skeleton_ids)s::bigint[]) skeleton(id)

                        ON tc2.skeleton_id = skeleton.id

                ) allowed_connector(id)

                    ON allowed_connector.id = c.id

django/applications/catmaid/control/label.py

-Original file line number
+Diff line change
@@ Expand Up @@
                       class_instance ci,
                       treenode_class_instance tci,
                       treenode tn,
-                      unnest(%s::text[], %s::integer[]) AS ll (name, max)
+                      unnest(%s::text[], %s::bigint[]) AS ll (name, max)
                     WHERE ci.name = ll.name
                       AND ci.project_id = %s
                       AND ci.class_id = %s
@@ Expand Down @@

django/applications/catmaid/control/landmarks.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -886,7 +886,7 @@ def get_landmark_group_locations(project_id, landmarkgroup_ids, with_names:bool=
  
                FROM (

                    SELECT pci.point_id, pci.class_instance_id, array_agg(l.name) as names

                    FROM point_class_instance pci

                    JOIN UNNEST(%(landmarkgroup_ids)s::integer[]) landmarkgroup(id)

                    JOIN UNNEST(%(landmarkgroup_ids)s::bigint[]) landmarkgroup(id)

                        ON pci.class_instance_id = landmarkgroup.id

                    LEFT JOIN point_class_instance pci_l

                        ON pci_l.point_id = pci.point_id

    @@ -936,7 +936,7 @@ def get_landmark_group_locations(project_id, landmarkgroup_ids, with_names:bool=
  
                SELECT pci.point_id, pci.class_instance_id, p.location_x,

                    p.location_y, p.location_z

                FROM point_class_instance pci

                JOIN UNNEST(%(landmarkgroup_ids)s::integer[]) landmarkgroup(id)

                JOIN UNNEST(%(landmarkgroup_ids)s::bigint[]) landmarkgroup(id)

                    ON pci.class_instance_id = landmarkgroup.id

                JOIN point p

                    ON p.id = pci.point_id

    @@ -965,7 +965,7 @@ def make_landmark_relation_index(project_id, landmarkgroup_ids) -> Tuple[Default
  
            SELECT cici.id, lg.id, cici.relation_id, r.relation_name,

                cici.class_instance_a, cici.class_instance_b

            FROM class_instance_class_instance cici

            JOIN UNNEST(%(landmarkgroup_ids)s::integer[]) lg(id)

            JOIN UNNEST(%(landmarkgroup_ids)s::bigint[]) lg(id)

                ON lg.id = cici.class_instance_a

                OR lg.id = cici.class_instance_b

            JOIN relation r

django/applications/catmaid/control/similarity.py

-Original file line number
+Diff line change
@@ Expand Up @@
                     cursor.execute("""
                         SELECT css.skeleton_id
                         FROM catmaid_skeleton_summary css
-                        JOIN UNNEST(%(skeleton_ids)s::int[]) skeleton(id)
+                        JOIN UNNEST(%(skeleton_ids)s::bigint[]) skeleton(id)
                             ON css.skeleton_id = skeleton.id
                         WHERE project_id = %(project_id)s
                             AND cable_length >= %(min_cable)s
@@ Expand Down @@

django/applications/catmaid/control/skeleton.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1039,7 +1039,7 @@ def connectivity_counts(request:HttpRequest, project_id=None) -> JsonResponse:
  
        cursor.execute("""

            SELECT tc.skeleton_id, tc.relation_id, COUNT(tc)

            FROM treenode_connector tc

            JOIN UNNEST(%(skeleton_ids)s::int[]) skeleton(id)

            JOIN UNNEST(%(skeleton_ids)s::bigint[]) skeleton(id)

                ON skeleton.id = tc.skeleton_id

            {extra_select}

            WHERE tc.project_id = %(project_id)s

    @@ -1575,7 +1575,7 @@ def newPartner():
  
            t1.treenode_id, t2.treenode_id

        FROM treenode_connector t1,

             treenode_connector t2

        WHERE t1.skeleton_id = ANY(%s::integer[])

        WHERE t1.skeleton_id = ANY(%s::bigint[])

          AND t1.relation_id = %s

          AND t1.connector_id = t2.connector_id

          AND t1.id != t2.id

    @@ -1610,7 +1610,7 @@ def newPartner():
  
        cursor.execute('''

        SELECT skeleton_id, num_nodes

        FROM catmaid_skeleton_summary

        WHERE skeleton_id = ANY(%s::integer[])

        WHERE skeleton_id = ANY(%s::bigint[])

        GROUP BY skeleton_id

        ''', (partner_skids,))

        for row in cursor.fetchall():

    @@ -1620,7 +1620,7 @@ def newPartner():
  
        cursor.execute('''

        SELECT DISTINCT reviewer_id

        FROM review

        WHERE skeleton_id = ANY(%s::integer[])

        WHERE skeleton_id = ANY(%s::bigint[])

        ''', (partner_skids,))

        reviewers = [row[0] for row in cursor]

    @@ -1943,8 +1943,8 @@ def get_connectivity_matrix(project_id, row_skeleton_ids, col_skeleton_ids,
  
            FROM treenode_connector t1,

                 treenode_connector t2

                {extra_join}

            WHERE t1.skeleton_id = ANY(%(row_skeleton_ids)s::integer[])

              AND t2.skeleton_id = ANY(%(col_skeleton_ids)s::integer[])

            WHERE t1.skeleton_id = ANY(%(row_skeleton_ids)s::bigint[])

              AND t2.skeleton_id = ANY(%(col_skeleton_ids)s::bigint[])

              AND t1.connector_id = t2.connector_id

              AND t1.relation_id = %(pre_rel_id)s

              AND t2.relation_id = %(post_rel_id)s

    @@ -3657,7 +3657,7 @@ def skeletons_by_node_labels(request:HttpRequest, project_id=None) -> JsonRespon
  
                ON t.id = tci.treenode_id

              JOIN class_instance ci

                ON tci.class_instance_id = ci.id

              JOIN UNNEST(%(label_ids)s::int[]) label(id)

              JOIN UNNEST(%(label_ids)s::bigint[]) label(id)

                ON label.id = ci.id

              WHERE ci.project_id = %(project_id)s

                AND tci.relation_id = %(labeled_as)s

    @@ -3701,7 +3701,7 @@ def get_skeletons_in_bb(params) -> List:
  
        if skeleton_ids:

            extra_joins.append("""

                JOIN UNNEST(%(skeleton_ids)s::int[]) query_skeleton(id)

                JOIN UNNEST(%(skeleton_ids)s::bigint[]) query_skeleton(id)

                    ON query_skeleton.id = skeleton.id

            """)

django/applications/catmaid/migrations/0010_history_tracking_update.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -2243,6 +2243,7 @@ class Migration(migrations.Migration): @@
         dependencies = [
             ('catmaid', '0009_ensure_required_project_classes'),
+            ('admin', '0003_logentry_add_action_flag_choices'),
         ]
         operations = [
@@ Expand Down @@

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