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|
-- written for Postgres 9.6 with OSSP extension for UUIDs -- ... but actually runs on Postgres 10 in qa/production
CREATE EXTENSION IF NOT EXISTS "uuid-ossp";
-- uuid_generate_v1mc: timestamp ordered, random MAC address
-- uuid_generate_v4: totally random
-- NB: could use LIKE clause, or "composite types"
CREATE TABLE editor (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
username TEXT NOT NULL UNIQUE,
is_admin BOOLEAN NOT NULL DEFAULT false,
active_editgroup_id UUID -- REFERENCES( editgroup(id) via ALTER below
);
CREATE TABLE editgroup (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
extra_json JSON,
editor_id UUID REFERENCES editor(id) NOT NULL,
description TEXT
);
ALTER TABLE editor
ADD CONSTRAINT editor_editgroupid_fkey FOREIGN KEY (active_editgroup_id)
REFERENCES editgroup(id);
CREATE TABLE changelog (
id BIGSERIAL PRIMARY KEY,
editgroup_id UUID REFERENCES editgroup(id) NOT NULL,
timestamp TIMESTAMP WITHOUT TIME ZONE DEFAULT now() NOT NULL
);
-- for "is this editgroup merged" queries
CREATE INDEX changelog_editgroup_idx ON changelog(editgroup_id);
-------------------- Creators -----------------------------------------------
CREATE TABLE creator_rev (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
extra_json JSON,
display_name TEXT NOT NULL,
given_name TEXT,
surname TEXT,
orcid TEXT
-- TODO: aliases/alternatives
-- TODO: sortable name?
);
-- Could denormalize a "is_live" flag into revision tables, to make indices
-- more efficient
CREATE INDEX creator_rev_orcid_idx ON creator_rev(orcid) WHERE orcid IS NOT NULL;
CREATE TABLE creator_ident (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
is_live BOOL NOT NULL DEFAULT false,
rev_id UUID REFERENCES creator_rev(id),
redirect_id UUID REFERENCES creator_ident(id)
);
CREATE INDEX creator_ident_rev_idx ON creator_ident(rev_id);
CREATE TABLE creator_edit (
id BIGSERIAL PRIMARY KEY,
editgroup_id UUID REFERENCES editgroup(id) NOT NULL,
ident_id UUID REFERENCES creator_ident(id) NOT NULL,
rev_id UUID REFERENCES creator_rev(id),
redirect_id UUID REFERENCES creator_ident(id),
extra_json JSON
);
CREATE INDEX creator_edit_idx ON creator_edit(editgroup_id);
-------------------- Containers --------------------------------------------
CREATE TABLE container_rev (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
extra_json JSON,
name TEXT NOT NULL,
publisher TEXT,
issnl TEXT, -- TODO: varchar
abbrev TEXT,
coden TEXT
);
CREATE INDEX container_rev_issnl_idx ON container_rev(issnl) WHERE issnl IS NOT NULL;
CREATE TABLE container_ident (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
is_live BOOL NOT NULL DEFAULT false,
rev_id UUID REFERENCES container_rev(id),
redirect_id UUID REFERENCES container_ident(id)
);
CREATE INDEX container_ident_rev_idx ON container_ident(rev_id);
CREATE TABLE container_edit (
id BIGSERIAL PRIMARY KEY,
editgroup_id UUID REFERENCES editgroup(id) NOT NULL,
ident_id UUID REFERENCES container_ident(id) NOT NULL,
rev_id UUID REFERENCES container_rev(id),
redirect_id UUID REFERENCES container_ident(id),
extra_json JSON
);
CREATE INDEX container_edit_idx ON container_edit(editgroup_id);
-------------------- Files -------------------------------------------------
CREATE TABLE file_rev (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
extra_json JSON,
size BIGINT,
sha1 TEXT, -- TODO: varchar or bytes
sha256 TEXT, -- TODO: varchar or bytes
md5 TEXT, -- TODO: varchar or bytes
url TEXT, -- TODO: URL table
mimetype TEXT
);
CREATE INDEX file_rev_sha1_idx ON file_rev(sha1) WHERE sha1 IS NOT NULL;
CREATE INDEX file_rev_md5_idx ON file_rev(md5) WHERE md5 IS NOT NULL;
CREATE INDEX file_rev_sha256_idx ON file_rev(sha256) WHERE sha256 IS NOT NULL;
CREATE TABLE file_ident (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
is_live BOOL NOT NULL DEFAULT false,
rev_id UUID REFERENCES file_rev(id),
redirect_id UUID REFERENCES file_ident(id)
);
CREATE INDEX file_ident_rev_idx ON file_ident(rev_id);
CREATE TABLE file_edit (
id BIGSERIAL PRIMARY KEY,
editgroup_id UUID REFERENCES editgroup(id) NOT NULL,
ident_id UUID REFERENCES file_ident(id) NOT NULL,
rev_id UUID REFERENCES file_rev(id),
redirect_id UUID REFERENCES file_ident(id),
extra_json JSON
);
CREATE INDEX file_edit_idx ON file_edit(editgroup_id);
-------------------- Release -----------------------------------------------
CREATE TABLE release_rev (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
extra_json JSON,
work_ident_id UUID NOT NULL, -- FOREIGN KEY; see ALRTER below
container_ident_id UUID REFERENCES container_ident(id),
title TEXT NOT NULL,
release_type TEXT, -- TODO: enum
release_status TEXT, -- TODO: enum
release_date DATE,
doi TEXT,
isbn13 TEXT,
volume TEXT,
issue TEXT,
pages TEXT,
publisher TEXT, -- for books, NOT if container exists
language TEXT -- primary language of the work's fulltext; RFC1766/ISO639-1
-- TODO: identifier table?
);
CREATE INDEX release_rev_doi_idx ON release_rev(doi) WHERE doi IS NOT NULL;
CREATE INDEX release_rev_isbn13_idx ON release_rev(isbn13) WHERE isbn13 IS NOT NULL;
CREATE INDEX release_rev_work_idx ON release_rev(work_ident_id) WHERE work_ident_id IS NOT NULL;
CREATE TABLE release_ident (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
is_live BOOL NOT NULL DEFAULT false,
rev_id UUID REFERENCES release_rev(id),
redirect_id UUID REFERENCES release_ident(id)
);
CREATE INDEX release_ident_rev_idx ON release_ident(rev_id);
CREATE TABLE release_edit (
id BIGSERIAL PRIMARY KEY,
editgroup_id UUID REFERENCES editgroup(id) NOT NULL,
ident_id UUID REFERENCES release_ident(id) NOT NULL,
rev_id UUID REFERENCES release_rev(id),
redirect_id UUID REFERENCES release_ident(id),
extra_json JSON
);
CREATE INDEX release_edit_idx ON release_edit(editgroup_id);
-------------------- Works --------------------------------------------------
CREATE TABLE work_rev (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
extra_json JSON,
);
CREATE TABLE work_ident (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
is_live BOOL NOT NULL DEFAULT false,
rev_id UUID REFERENCES work_rev(id),
redirect_id UUID REFERENCES work_ident(id)
);
CREATE INDEX work_ident_rev_idx ON work_ident(rev_id);
CREATE TABLE work_edit (
id BIGSERIAL PRIMARY KEY,
editgroup_id UUID REFERENCES editgroup(id) NOT NULL,
ident_id UUID REFERENCES work_ident(id) NOT NULL,
rev_id UUID REFERENCES work_rev(id),
redirect_id UUID REFERENCES work_ident(id),
extra_json JSON
);
CREATE INDEX work_edit_idx ON work_edit(editgroup_id);
ALTER TABLE release_rev
ADD CONSTRAINT release_containeridentid_fkey FOREIGN KEY (work_ident_id)
REFERENCES work_ident(id);
-------------------- Inter-Entity Relations
CREATE TABLE release_contrib (
id BIGSERIAL PRIMARY KEY,
release_rev UUID REFERENCES release_rev(id) NOT NULL,
creator_ident_id UUID REFERENCES creator_ident(id),
role TEXT, -- TODO: enum?
index BIGINT,
raw TEXT
);
CREATE INDEX release_contrib_rev_idx ON release_contrib(release_rev);
CREATE INDEX release_contrib_creator_idx ON release_contrib(creator_ident_id);
CREATE TABLE release_ref (
id BIGSERIAL PRIMARY KEY,
release_rev UUID REFERENCES release_rev(id) NOT NULL,
target_release_ident_id UUID REFERENCES release_ident(id), -- or work?
index BIGINT,
key TEXT,
raw TEXT,
container_title TEXT,
year BIGINT,
title TEXT,
locator TEXT
);
CREATE INDEX release_ref_rev_idx ON release_ref(release_rev);
CREATE INDEX release_ref_target_release_idx ON release_ref(target_release_ident_id);
CREATE TABLE file_release (
file_rev UUID REFERENCES file_rev(id) NOT NULL,
target_release_ident_id UUID REFERENCES release_ident(id) NOT NULL,
PRIMARY KEY (file_rev, target_release_ident_id)
);
CREATE INDEX file_release_target_release_idx ON file_release(target_release_ident_id);
---------------------------------------------------------------------------
---------------------------------------------------------------------------
---------------------------------------------------------------------------
-- Fake data at the raw SQL level, for early development and testing
-- Convention:
-- * first entity is smallest possible (mostly null)
-- * second entity is rich (all fields/relations designed) but artificial
-- * third entity (and above) are realistic (real DOI, etc)
BEGIN;
INSERT INTO editor (id, username, is_admin) VALUES
('00000000-0000-0000-AAAA-000000000001', 'admin', true), -- aaaaaaaaaaaabkvkaaaaaaaaae
('00000000-0000-0000-AAAA-000000000002', 'demo-user', true), -- aaaaaaaaaaaabkvkaaaaaaaaai
('00000000-0000-0000-AAAA-000000000003', 'claire', false); -- aaaaaaaaaaaabkvkaaaaaaaaam
INSERT INTO editgroup (id, editor_id, description) VALUES
('00000000-0000-0000-BBBB-000000000001', '00000000-0000-0000-AAAA-000000000001', 'first edit ever!'), -- aaaaaaaaaaaabo53aaaaaaaaae
('00000000-0000-0000-BBBB-000000000002', '00000000-0000-0000-AAAA-000000000001', 'another one!'), -- aaaaaaaaaaaabo53aaaaaaaaai
('00000000-0000-0000-BBBB-000000000003', '00000000-0000-0000-AAAA-000000000003', 'user edit'), -- aaaaaaaaaaaabo53aaaaaaaaam
('00000000-0000-0000-BBBB-000000000004', '00000000-0000-0000-AAAA-000000000002', 'uncommited edit'), -- aaaaaaaaaaaabo53aaaaaaaaaq
('00000000-0000-0000-BBBB-000000000005', '00000000-0000-0000-AAAA-000000000001', 'journal edit'), -- aaaaaaaaaaaabo53aaaaaaaaau
('00000000-0000-0000-BBBB-000000000006', '00000000-0000-0000-AAAA-000000000001', 'another journal edit'); -- aaaaaaaaaaaabo53aaaaaaaaay
INSERT INTO editor (id, username, is_admin, active_editgroup_id) VALUES
('00000000-0000-0000-AAAA-000000000004', 'bnewbold', true, '00000000-0000-0000-BBBB-000000000004');
INSERT INTO changelog (editgroup_id) VALUES
('00000000-0000-0000-BBBB-000000000001'),
('00000000-0000-0000-BBBB-000000000002'),
('00000000-0000-0000-BBBB-000000000003'),
('00000000-0000-0000-BBBB-000000000004'),
('00000000-0000-0000-BBBB-000000000005');
INSERT INTO container_rev (id, name, publisher, issnl, abbrev, coden, extra_json) VALUES
('00000000-0000-0000-1111-FFF000000001', 'MySpace Blog', null, null, null, null, null),
('00000000-0000-0000-1111-FFF000000002', 'Journal of Trivial Results', 'bogus publishing group', '1234-5678', 'Triv. Res.', 'CDNXYZ', '{"is_oa": false, "in_doaj": false}'),
('00000000-0000-0000-1111-FFF000000003', 'PLOS Medicine', 'Public Library of Science', '1549-1277', 'PLoS med.', null, '{"is_oa": true, "in_doaj": true}');
INSERT INTO container_ident (id, is_live, rev_id, redirect_id) VALUES
('00000000-0000-0000-1111-000000000001', true, '00000000-0000-0000-1111-FFF000000001', null), -- aaaaaaaaaaaaaeiraaaaaaaaae
('00000000-0000-0000-1111-000000000002', true, '00000000-0000-0000-1111-FFF000000002', null), -- aaaaaaaaaaaaaeiraaaaaaaaai
('00000000-0000-0000-1111-000000000003', true, '00000000-0000-0000-1111-FFF000000003', null); -- aaaaaaaaaaaaaeiraaaaaaaaam
INSERT INTO container_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
('00000000-0000-0000-1111-000000000001', '00000000-0000-0000-1111-FFF000000001', null, '00000000-0000-0000-BBBB-000000000003'),
('00000000-0000-0000-1111-000000000002', '00000000-0000-0000-1111-FFF000000002', null, '00000000-0000-0000-BBBB-000000000004'),
('00000000-0000-0000-1111-000000000003', '00000000-0000-0000-1111-FFF000000003', null, '00000000-0000-0000-BBBB-000000000005');
INSERT INTO creator_rev (id, display_name, given_name, surname, orcid) VALUES
('00000000-0000-0000-2222-FFF000000001', 'Grace Hopper', null, null, null),
('00000000-0000-0000-2222-FFF000000002', 'Christine Moran', 'Christine', 'Moran', '0000-0003-2088-7465'),
('00000000-0000-0000-2222-FFF000000003', 'John P. A. Ioannidis', 'John', 'Ioannidis', '0000-0003-3118-6859');
INSERT INTO creator_ident (id, is_live, rev_id, redirect_id) VALUES
('00000000-0000-0000-2222-000000000001', true, '00000000-0000-0000-2222-FFF000000001', null), -- aaaaaaaaaaaaaircaaaaaaaaae
('00000000-0000-0000-2222-000000000002', true, '00000000-0000-0000-2222-FFF000000002', null), -- aaaaaaaaaaaaaircaaaaaaaaai
('00000000-0000-0000-2222-000000000003', true, '00000000-0000-0000-2222-FFF000000003', null), -- aaaaaaaaaaaaaircaaaaaaaaam
('00000000-0000-0000-2222-000000000004', false, '00000000-0000-0000-2222-FFF000000002', null); -- aaaaaaaaaaaaaircaaaaaaaaaq
INSERT INTO creator_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
('00000000-0000-0000-2222-000000000001', '00000000-0000-0000-2222-FFF000000001', null, '00000000-0000-0000-BBBB-000000000001'),
('00000000-0000-0000-2222-000000000002', '00000000-0000-0000-2222-FFF000000002', null, '00000000-0000-0000-BBBB-000000000002'),
('00000000-0000-0000-2222-000000000003', '00000000-0000-0000-2222-FFF000000003', null, '00000000-0000-0000-BBBB-000000000003'),
('00000000-0000-0000-2222-000000000004', '00000000-0000-0000-2222-FFF000000002', null, '00000000-0000-0000-BBBB-000000000004');
INSERT INTO file_rev (id, size, sha1, sha256, md5, url, mimetype) VALUES
('00000000-0000-0000-3333-FFF000000001', null, null, null, null, null, null),
('00000000-0000-0000-3333-FFF000000002', 4321, '7d97e98f8af710c7e7fe703abc8f639e0ee507c4', null, null, 'http://archive.org/robots.txt', 'text/plain'),
('00000000-0000-0000-3333-FFF000000003', 255629, '3f242a192acc258bdfdb151943419437f440c313', 'ffc1005680cb620eec4c913437dfabbf311b535cfe16cbaeb2faec1f92afc362', 'f4de91152c7ab9fdc2a128f962faebff', 'http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable', 'application/pdf');
INSERT INTO file_ident (id, is_live, rev_id, redirect_id) VALUES
('00000000-0000-0000-3333-000000000001', true, '00000000-0000-0000-3333-FFF000000001', null), -- aaaaaaaaaaaaamztaaaaaaaaae
('00000000-0000-0000-3333-000000000002', true, '00000000-0000-0000-3333-FFF000000002', null), -- aaaaaaaaaaaaamztaaaaaaaaai
('00000000-0000-0000-3333-000000000003', true, '00000000-0000-0000-3333-FFF000000003', null); -- aaaaaaaaaaaaamztaaaaaaaaam
INSERT INTO file_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
('00000000-0000-0000-3333-000000000001', '00000000-0000-0000-3333-FFF000000001', null, '00000000-0000-0000-BBBB-000000000003'),
('00000000-0000-0000-3333-000000000002', '00000000-0000-0000-3333-FFF000000002', null, '00000000-0000-0000-BBBB-000000000004'),
('00000000-0000-0000-3333-000000000003', '00000000-0000-0000-3333-FFF000000003', null, '00000000-0000-0000-BBBB-000000000005');
INSERT INTO work_rev (id) VALUES
('00000000-0000-0000-5555-FFF000000001'),
('00000000-0000-0000-5555-FFF000000002'),
('00000000-0000-0000-5555-FFF000000003');
INSERT INTO work_ident (id, is_live, rev_id, redirect_id) VALUES
('00000000-0000-0000-5555-000000000001', true, '00000000-0000-0000-5555-FFF000000001', null), -- aaaaaaaaaaaaavkvaaaaaaaaae
('00000000-0000-0000-5555-000000000002', true, '00000000-0000-0000-5555-FFF000000002', null), -- aaaaaaaaaaaaavkvaaaaaaaaai
('00000000-0000-0000-5555-000000000003', true, '00000000-0000-0000-5555-FFF000000003', null); -- aaaaaaaaaaaaavkvaaaaaaaaam
INSERT INTO work_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
('00000000-0000-0000-5555-000000000001', '00000000-0000-0000-5555-FFF000000001', null, '00000000-0000-0000-BBBB-000000000003'),
('00000000-0000-0000-5555-000000000002', '00000000-0000-0000-5555-FFF000000002', null, '00000000-0000-0000-BBBB-000000000004'),
('00000000-0000-0000-5555-000000000002', '00000000-0000-0000-5555-FFF000000003', null, '00000000-0000-0000-BBBB-000000000005');
INSERT INTO release_rev (id, work_ident_id, container_ident_id, title, release_type, release_status, release_date, doi, isbn13, volume, issue, pages, publisher, language) VALUES
('00000000-0000-0000-4444-FFF000000001', '00000000-0000-0000-5555-000000000001', null, 'example title', null, null, null, null, null, null, null, null, null, null),
('00000000-0000-0000-4444-FFF000000002', '00000000-0000-0000-5555-000000000002', '00000000-0000-0000-1111-000000000001', 'bigger example', 'journal-article', null,'2018-01-01', '10.123/abc', '99999-999-9-X', '12', 'IV', '5-9', 'bogus publishing group', 'cn'),
('00000000-0000-0000-4444-FFF000000003', '00000000-0000-0000-5555-000000000003', '00000000-0000-0000-1111-000000000003', 'Why Most Published Research Findings Are False', 'journal-article', 'published', '2005-08-30', '10.1371/journal.pmed.0020124', null, '2', '8', 'e124', 'Public Library of Science', 'en');
INSERT INTO release_ident (id, is_live, rev_id, redirect_id) VALUES
('00000000-0000-0000-4444-000000000001', true, '00000000-0000-0000-4444-FFF000000001', null), -- aaaaaaaaaaaaarceaaaaaaaaae
('00000000-0000-0000-4444-000000000002', true, '00000000-0000-0000-4444-FFF000000002', null), -- aaaaaaaaaaaaarceaaaaaaaaai
('00000000-0000-0000-4444-000000000003', true, '00000000-0000-0000-4444-FFF000000003', null); -- aaaaaaaaaaaaarceaaaaaaaaam
INSERT INTO release_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
('00000000-0000-0000-4444-000000000001', '00000000-0000-0000-4444-FFF000000001', null, '00000000-0000-0000-BBBB-000000000003'),
('00000000-0000-0000-4444-000000000002', '00000000-0000-0000-4444-FFF000000002', null, '00000000-0000-0000-BBBB-000000000004'),
('00000000-0000-0000-4444-000000000003', '00000000-0000-0000-4444-FFF000000003', null, '00000000-0000-0000-BBBB-000000000005');
INSERT INTO release_contrib (release_rev, creator_ident_id, raw, role, index) VALUES
('00000000-0000-0000-4444-FFF000000002', null, null, null, null),
('00000000-0000-0000-4444-FFF000000002', '00000000-0000-0000-2222-000000000002', 'some contrib', 'editor', 4),
('00000000-0000-0000-4444-FFF000000003', '00000000-0000-0000-2222-000000000003', 'John P. A. Ioannidis', 'author', 0);
INSERT INTO release_ref (release_rev, target_release_ident_id, index, raw) VALUES
('00000000-0000-0000-4444-FFF000000002', null, null, null),
('00000000-0000-0000-4444-FFF000000002', '00000000-0000-0000-4444-000000000001', 4, 'citation note'),
('00000000-0000-0000-4444-FFF000000003', null, 0, 'Ioannidis JP, Haidich AB, Lau J. Any casualties in the clash of randomised and observational evidence? BMJ. 2001;322:879–880'),
('00000000-0000-0000-4444-FFF000000003', null, 1, 'Lawlor DA, Davey Smith G, Kundu D, Bruckdorfer KR, Ebrahim S. Those confounded vitamins: What can we learn from the differences between observational versus randomised trial evidence? Lancet. 2004;363:1724–1727.'),
('00000000-0000-0000-4444-FFF000000003', null, 2, 'Vandenbroucke JP. When are observational studies as credible as randomised trials? Lancet. 2004;363:1728–1731.'),
('00000000-0000-0000-4444-FFF000000003', null, 3, 'Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: A multiple random validation strategy. Lancet. 2005;365:488–492.'),
('00000000-0000-0000-4444-FFF000000003', null, 4, 'Ioannidis JPA, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. Replication validity of genetic association studies. Nat Genet. 2001;29:306–309.'),
('00000000-0000-0000-4444-FFF000000003', null, 5, 'Colhoun HM, McKeigue PM, Davey Smith G. Problems of reporting genetic associations with complex outcomes. Lancet. 2003;361:865–872.');
INSERT INTO file_release (file_rev, target_release_ident_id) VALUES
('00000000-0000-0000-3333-FFF000000002', '00000000-0000-0000-4444-000000000002'),
('00000000-0000-0000-3333-FFF000000003', '00000000-0000-0000-4444-000000000003');
commit;
|