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authorBryan Newbold <bnewbold@robocracy.org>2019-01-17 10:44:38 -0800
committerBryan Newbold <bnewbold@robocracy.org>2019-01-17 10:44:38 -0800
commit24e7a7038f9f0c827a11282a5cc646117ffdfb9b (patch)
tree40227dbd1a2b652bad24c9d71f8027c20ef1b7d1 /rust/migrations
parent3ad702e413c084590505cff16f9532b236718049 (diff)
parent0a8c9a5e07213276617f06b0379a166e7fd1c100 (diff)
downloadfatcat-24e7a7038f9f0c827a11282a5cc646117ffdfb9b.tar.gz
fatcat-24e7a7038f9f0c827a11282a5cc646117ffdfb9b.zip
Merge branch 'citation-efficiency'
Manually merged conflict in: - ./TODO
Diffstat (limited to 'rust/migrations')
-rw-r--r--rust/migrations/2019-01-01-000000_init/down.sql1
-rw-r--r--rust/migrations/2019-01-01-000000_init/up.sql61
2 files changed, 36 insertions, 26 deletions
diff --git a/rust/migrations/2019-01-01-000000_init/down.sql b/rust/migrations/2019-01-01-000000_init/down.sql
index 30e712e3..e238a690 100644
--- a/rust/migrations/2019-01-01-000000_init/down.sql
+++ b/rust/migrations/2019-01-01-000000_init/down.sql
@@ -2,6 +2,7 @@
-- in opposite order as up.sql
DROP TABLE IF EXISTS release_contrib CASCADE;
+DROP TABLE IF EXISTS refs_blob CASCADE;
DROP TABLE IF EXISTS release_ref CASCADE;
DROP TABLE IF EXISTS file_rev_release CASCADE;
DROP TABLE IF EXISTS fileset_rev_release CASCADE;
diff --git a/rust/migrations/2019-01-01-000000_init/up.sql b/rust/migrations/2019-01-01-000000_init/up.sql
index b4c7a684..57f91d44 100644
--- a/rust/migrations/2019-01-01-000000_init/up.sql
+++ b/rust/migrations/2019-01-01-000000_init/up.sql
@@ -82,6 +82,12 @@ CREATE TABLE abstracts (
content TEXT NOT NULL
);
+CREATE TABLE refs_blob (
+ -- fixed size hash (in hex). TODO: switch to bytes
+ sha1 TEXT PRIMARY KEY CHECK (octet_length(sha1) = 40),
+ refs_json JSONB NOT NULL
+);
+
-------------------- Creators -----------------------------------------------
CREATE TABLE creator_rev (
id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
@@ -326,6 +332,7 @@ CREATE TABLE release_rev (
work_ident_id UUID NOT NULL, -- FOREIGN KEY; see ALRTER below
container_ident_id UUID REFERENCES container_ident(id),
+ refs_blob_sha1 TEXT REFERENCES refs_blob(sha1),
title TEXT NOT NULL,
release_type TEXT, -- TODO: enum
release_status TEXT, -- TODO: enum
@@ -436,20 +443,19 @@ 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_val INTEGER,
- key TEXT,
- extra_json JSONB, -- title, year, container_title, locator (aka, page), oci_id
- container_name TEXT,
- year INTEGER,
- title TEXT,
- locator TEXT
- -- TODO: oci_id (TEXT)
-);
-
-CREATE INDEX release_ref_rev_idx ON release_ref(release_rev);
+ index_val INTEGER NOT NULL,
+ target_release_ident_id UUID REFERENCES release_ident(id) NOT NULL,
+ -- all other fields are interned in refs_blob as JSONB
+ -- key TEXT,
+ -- extra_json JSONB, -- title, year, container_title, locator (aka, page), oci_id
+ -- container_name TEXT,
+ -- year INTEGER,
+ -- title TEXT,
+ -- locator TEXT
+ PRIMARY KEY(release_rev, index_val)
+);
+
CREATE INDEX release_ref_target_release_idx ON release_ref(target_release_ident_id);
CREATE TABLE file_rev_release (
@@ -632,10 +638,14 @@ INSERT INTO work_edit (ident_id, rev_id, redirect_id, editgroup_id, prev_rev) VA
('00000000-0000-0000-5555-000000000002', '00000000-0000-0000-5555-FFF000000002', null, '00000000-0000-0000-BBBB-000000000004', null),
('00000000-0000-0000-5555-000000000002', '00000000-0000-0000-5555-FFF000000003', null, '00000000-0000-0000-BBBB-000000000005', '00000000-0000-0000-5555-FFF000000002');
-INSERT INTO release_rev (id, work_ident_id, container_ident_id, title, release_type, release_status, release_date, release_year, doi, wikidata_qid, pmid, pmcid, isbn13, core_id, 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, null, null, null, null, null),
- ('00000000-0000-0000-4444-FFF000000002', '00000000-0000-0000-5555-000000000002', '00000000-0000-0000-1111-000000000001', 'bigger example', 'article-journal', null, '2018-01-01', 2018, '10.123/abc', 'Q55555', '54321', 'PMC555','978-3-16-148410-0', '42022773', '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', 'article-journal', 'published', '2005-08-30', 2005, '10.1371/journal.pmed.0020124', null, null, null, null, null, '2', '8', 'e124', 'Public Library of Science', 'en');
+INSERT INTO refs_blob (sha1, refs_json) VALUES
+ ('22222222c2979a62d29b18b537e50b2b093be27e', '[{}, {}, {}, {}, {"extra": {"unstructured":"citation note"}}]'),
+ ('33333333c2979a62d29b18b537e50b2b093be27e', '[{"extra": {"unstructured": "Ioannidis JP, Haidich AB, Lau J. Any casualties in the clash of randomised and observational evidence? BMJ. 2001;322:879–880"}}, {"extra": {"unstructured":"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."}}, {"extra": {"unstructured":"Vandenbroucke JP. When are observational studies as credible as randomised trials? Lancet. 2004;363:1728–1731."}}, {"extra": {"unstructured":"Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: A multiple random validation strategy. Lancet. 2005;365:488–492."}}, {"extra": {"unstructured":"Ioannidis JPA, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. Replication validity of genetic association studies. Nat Genet. 2001;29:306–309."}}, {"extra": {"unstructured":"Colhoun HM, McKeigue PM, Davey Smith G. Problems of reporting genetic associations with complex outcomes. Lancet. 2003;361:865–872."}}]');
+
+INSERT INTO release_rev (id, work_ident_id, container_ident_id, title, release_type, release_status, release_date, release_year, doi, wikidata_qid, pmid, pmcid, isbn13, core_id, volume, issue, pages, publisher, language, refs_blob_sha1) VALUES
+ ('00000000-0000-0000-4444-FFF000000001', '00000000-0000-0000-5555-000000000001', null, 'example title', null, null, null, null, null, null, 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', 'article-journal', null, '2018-01-01', 2018, '10.123/abc', 'Q55555', '54321', 'PMC555','978-3-16-148410-0', '42022773', '12', 'IV', '5-9', 'bogus publishing group', 'cn', '22222222c2979a62d29b18b537e50b2b093be27e'),
+ ('00000000-0000-0000-4444-FFF000000003', '00000000-0000-0000-5555-000000000003', '00000000-0000-0000-1111-000000000003', 'Why Most Published Research Findings Are False', 'article-journal', 'published', '2005-08-30', 2005, '10.1371/journal.pmed.0020124', null, null, null, null, null, '2', '8', 'e124', 'Public Library of Science', 'en', '33333333c2979a62d29b18b537e50b2b093be27e');
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
@@ -656,15 +666,14 @@ INSERT INTO release_contrib (release_rev, creator_ident_id, raw_name, role, inde
('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_val, extra_json) VALUES
- ('00000000-0000-0000-4444-FFF000000002', null, null, null),
- ('00000000-0000-0000-4444-FFF000000002', '00000000-0000-0000-4444-000000000001', 4, '{"unstructured":"citation note"}'),
- ('00000000-0000-0000-4444-FFF000000003', null, 0, '{"unstructured": "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, '{"unstructured":"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, '{"unstructured":"Vandenbroucke JP. When are observational studies as credible as randomised trials? Lancet. 2004;363:1728–1731."}'),
- ('00000000-0000-0000-4444-FFF000000003', null, 3, '{"unstructured":"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, '{"unstructured":"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, '{"unstructured":"Colhoun HM, McKeigue PM, Davey Smith G. Problems of reporting genetic associations with complex outcomes. Lancet. 2003;361:865–872."}');
+INSERT INTO release_ref (release_rev, index_val, target_release_ident_id) VALUES
+ ('00000000-0000-0000-4444-FFF000000002', 4, '00000000-0000-0000-4444-000000000001'), -- '{"unstructured":"citation note"}'),
+ ('00000000-0000-0000-4444-FFF000000003', 0, '00000000-0000-0000-4444-000000000001'), --'{"unstructured": "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', 1, '00000000-0000-0000-4444-000000000001'), --'{"unstructured":"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', 2, '00000000-0000-0000-4444-000000000001'), --'{"unstructured":"Vandenbroucke JP. When are observational studies as credible as randomised trials? Lancet. 2004;363:1728–1731."}'),
+ ('00000000-0000-0000-4444-FFF000000003', 3, '00000000-0000-0000-4444-000000000001'), --'{"unstructured":"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', 4, '00000000-0000-0000-4444-000000000001'), --'{"unstructured":"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', 5, '00000000-0000-0000-4444-000000000001'); --'{"unstructured":"Colhoun HM, McKeigue PM, Davey Smith G. Problems of reporting genetic associations with complex outcomes. Lancet. 2003;361:865–872."}');
INSERT INTO file_rev_release (file_rev, target_release_ident_id) VALUES
('00000000-0000-0000-3333-FFF000000002', '00000000-0000-0000-4444-000000000002'),