path: root/rust/migrations/2018-05-12-001226_init/up.sql

-- 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                  BIGSERIAL PRIMARY KEY,
    username            TEXT NOT NULL UNIQUE,
    is_admin            BOOLEAN NOT NULL DEFAULT false,
    active_editgroup_id BIGINT -- REFERENCES( editgroup(id) via ALTER below
);

CREATE TABLE editgroup (
    id                  BIGSERIAL PRIMARY KEY,
    extra_json          JSON,
    editor_id           BIGSERIAL 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        BIGINT 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                  BIGSERIAL PRIMARY KEY,
    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              BIGINT 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        BIGINT REFERENCES editgroup(id) NOT NULL,
    ident_id            UUID REFERENCES creator_ident(id) NOT NULL,
    rev_id              BIGINT 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                  BIGSERIAL PRIMARY KEY,
    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              BIGINT 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        BIGINT REFERENCES editgroup(id) NOT NULL,
    ident_id            UUID REFERENCES container_ident(id) NOT NULL,
    rev_id              BIGINT 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                  BIGSERIAL PRIMARY KEY,
    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              BIGINT 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        BIGINT REFERENCES editgroup(id) NOT NULL,
    ident_id            UUID REFERENCES file_ident(id) NOT NULL,
    rev_id              BIGINT 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                  BIGSERIAL PRIMARY KEY,
    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              BIGINT 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        BIGINT REFERENCES editgroup(id) NOT NULL,
    ident_id            UUID REFERENCES release_ident(id) NOT NULL,
    rev_id              BIGINT 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                  BIGSERIAL PRIMARY KEY,
    extra_json          JSON,

    -- not even a work, for now
    work_type           TEXT, -- TODO: enum?
    primary_release_id  UUID REFERENCES release_ident(id)
);

CREATE TABLE work_ident (
    id                  UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
    is_live             BOOL NOT NULL DEFAULT false,
    rev_id              BIGINT 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        BIGINT REFERENCES editgroup(id) NOT NULL,
    ident_id            UUID REFERENCES work_ident(id) NOT NULL,
    rev_id              BIGINT 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         BIGSERIAL 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             BIGSERIAL 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                BIGSERIAL 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 (username, is_admin) VALUES
    ('admin', true),
    ('demo-user', true),
    ('claire', false);

INSERT INTO editgroup (editor_id, description) VALUES
    (1, 'first edit ever!'),
    (1, 'another one!'),
    (3, 'user edit'),
    (2, 'uncommited edit'),
    (1, 'journal edit'),
    (1, 'another journal edit');

INSERT INTO editor (username, is_admin, active_editgroup_id) VALUES
    ('bnewbold', true, 4);

INSERT INTO changelog (editgroup_id) VALUES
    (1),
    (2),
    (3),
    (4),
    (5);

INSERT INTO container_rev (name, publisher, issnl, abbrev, coden) VALUES
    ('MySpace Blog', null, null, null, null),
    ('Journal of Trivial Results', 'bogus publishing group', '1234-5678', 'Triv. Res.', 'CDNXYZ'),
    ('PLOS Medicine', 'Public Library of Science', '1549-1277', 'PLoS med.', null);

INSERT INTO container_ident (id, is_live, rev_id, redirect_id) VALUES
    ('00000000-0000-0000-1111-000000000001', true, 1, null),
    ('00000000-0000-0000-1111-000000000002', true, 2, null),
    ('00000000-0000-0000-1111-000000000003', true, 3, null);

INSERT INTO container_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
    ('00000000-0000-0000-1111-000000000001', 1, null, 4),
    ('00000000-0000-0000-1111-000000000002', 2, null, 5),
    ('00000000-0000-0000-1111-000000000002', 3, null, 5);

INSERT INTO creator_rev (display_name, given_name, surname, orcid) VALUES
    ('Grace Hopper', null, null, null),
    ('Christine Moran', 'Christine', 'Moran', '0000-0003-2088-7465'),
    ('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, 1, null),
    ('00000000-0000-0000-2222-000000000002', true, 2, null),
    ('00000000-0000-0000-2222-000000000003', true, 3, null),
    ('00000000-0000-0000-2222-000000000004', false, 2, null);

INSERT INTO creator_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
    ('00000000-0000-0000-2222-000000000001', 1, null, 1),
    ('00000000-0000-0000-2222-000000000002', 2, null, 2),
    ('00000000-0000-0000-2222-000000000003', 3, null, 3),
    ('00000000-0000-0000-2222-000000000004', 2, null, 4);

INSERT INTO file_rev (size, sha1, sha256, md5, url, mimetype) VALUES
    (null, null, null, null, null, null),
    (4321, '7d97e98f8af710c7e7fe703abc8f639e0ee507c4', null, null, 'http://archive.org/robots.txt', 'text/plain'),
    (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, 1, null),
    ('00000000-0000-0000-3333-000000000002', true, 2, null),
    ('00000000-0000-0000-3333-000000000003', true, 3, null);

INSERT INTO file_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
    ('00000000-0000-0000-3333-000000000001', 1, null, 4),
    ('00000000-0000-0000-3333-000000000002', 2, null, 5),
    ('00000000-0000-0000-3333-000000000003', 3, null, 5);

INSERT INTO work_rev (work_type, primary_release_id) VALUES
    (null, null),
    ('pre-print', null),
    ('journal-article', null);

INSERT INTO work_ident (id, is_live, rev_id, redirect_id) VALUES
    ('00000000-0000-0000-5555-000000000001', true, 1, null),
    ('00000000-0000-0000-5555-000000000002', true, 2, null),
    ('00000000-0000-0000-5555-000000000003', true, 3, null);

INSERT INTO work_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
    ('00000000-0000-0000-5555-000000000001', 1, null, 4),
    ('00000000-0000-0000-5555-000000000002', 2, null, 5),
    ('00000000-0000-0000-5555-000000000002', 3, null, 5);

INSERT INTO release_rev (work_ident_id, container_ident_id, title, release_type, release_status, release_date, doi, isbn13, volume, issue, pages, publisher, language) VALUES
    ('00000000-0000-0000-5555-000000000001',                                   null,  'example title',              null, null,        null, null,         null,  null,  null, null, null, null),
    ('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'),
    ('00000000-0000-0000-5555-000000000003', '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, 1, null),
    ('00000000-0000-0000-4444-000000000002', true, 2, null),
    ('00000000-0000-0000-4444-000000000003', true, 3, null);

INSERT INTO release_edit (ident_id, rev_id, redirect_id, editgroup_id) VALUES
    ('00000000-0000-0000-4444-000000000001', 1, null, 4),
    ('00000000-0000-0000-4444-000000000002', 2, null, 5),
    ('00000000-0000-0000-4444-000000000003', 3, null, 5);

INSERT INTO release_contrib (release_rev, creator_ident_id, raw, role, index) VALUES
    (2, null, null, null, null),
    (2, '00000000-0000-0000-2222-000000000002', 'some contrib', 'editor', 4),
    (3, '00000000-0000-0000-2222-000000000003', 'John P. A. Ioannidis', 'author', 0);

INSERT INTO release_ref (release_rev, target_release_ident_id, index, raw) VALUES
    (2, null, null, null),
    (2, '00000000-0000-0000-4444-000000000001', 4, 'citation note'),
    (3, null, 0, 'Ioannidis JP, Haidich AB, Lau J. Any casualties in the clash of randomised and observational evidence? BMJ. 2001;322:879–880'),
    (3, 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.'),
    (3, null, 2, 'Vandenbroucke JP. When are observational studies as credible as randomised trials? Lancet. 2004;363:1728–1731.'),
    (3, null, 3, 'Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: A multiple random validation strategy. Lancet. 2005;365:488–492.'),
    (3, null, 4, 'Ioannidis JPA, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. Replication validity of genetic association studies. Nat Genet. 2001;29:306–309.'),
    (3, 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
    (2, '00000000-0000-0000-4444-000000000002'),
    (3, '00000000-0000-0000-4444-000000000003');

COMMIT;