14873: Upgrades 'pg' gem & solves an issue related to a new internal table.

Rails 5 includes an undocumented internal table called 'ar_internal_metadata'
used to record the environment that the current system is on, so that it can
avoid accidental database wipes when in production.
Our code iterates over the tables so this one needs to be skipped.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

diff --git a/services/api/Gemfile b/services/api/Gemfile
index 00e9ae0b068f3ff8f59637e7faf59cc56fe0758d..76b121de6faa79733da1a07b10bd02bf5bcbc822 100644 (file)
--- a/services/api/Gemfile
+++ b/services/api/Gemfile
@@ -18,15 +18,13 @@ group :test, :development do
   gem 'simplecov', '~> 0.7.1', require: false
   gem 'simplecov-rcov', require: false
   gem 'mocha', require: false
+  gem 'byebug'
 end
 
 # We need this dependency because of crunchv1
 gem 'arvados-cli'
 
-# pg is the only supported database driver.
-# Note: Rails 4.2 is not compatible with pg 1.0
-#       (See: https://github.com/rails/rails/pull/31671)
-gem 'pg', '~> 0.18'
+gem 'pg', '~> 1.0'
 
 gem 'multi_json'
 gem 'oj'

diff --git a/services/api/Gemfile.lock b/services/api/Gemfile.lock
index 0deb37e4e802fe289d631c46186db8efc87b9516..63ea79be804b81183286b3dd9e282c8c0dcc4911 100644 (file)
--- a/services/api/Gemfile.lock
+++ b/services/api/Gemfile.lock
@@ -85,6 +85,7 @@ GEM
       extlib (>= 0.9.15)
       multi_json (>= 1.0.0)
     builder (3.2.3)
+    byebug (11.0.1)
     capistrano (2.15.9)
       highline
       net-scp (>= 1.0.0)
@@ -182,7 +183,7 @@ GEM
     passenger (6.0.2)
       rack
       rake (>= 0.8.1)
-    pg (0.21.0)
+    pg (1.1.4)
     power_assert (1.1.3)
     public_suffix (3.0.3)
     rack (2.0.6)
@@ -273,6 +274,7 @@ DEPENDENCIES
   andand
   arvados (>= 1.3.1.20190301212059)
   arvados-cli
+  byebug
   database_cleaner
   factory_bot_rails
   faye-websocket
@@ -288,7 +290,7 @@ DEPENDENCIES
   omniauth-oauth2 (~> 1.1)
   optimist
   passenger
-  pg (~> 0.18)
+  pg (~> 1.0)
   rails (~> 5.0.0)
   rails-controller-testing
   rails-observers

diff --git a/services/api/db/structure.sql b/services/api/db/structure.sql
index f766f33e1b35e1f85a64aa2c5d87bf85e2bb6d0f..95c44f7f665b5d59864bf994eb041f19c3e96b7f 100644 (file)
--- a/services/api/db/structure.sql
+++ b/services/api/db/structure.sql
@@ -105,6 +105,18 @@ CREATE SEQUENCE public.api_clients_id_seq
 ALTER SEQUENCE public.api_clients_id_seq OWNED BY public.api_clients.id;
 
 
+--
+-- Name: ar_internal_metadata; Type: TABLE; Schema: public; Owner: -
+--
+
+CREATE TABLE public.ar_internal_metadata (
+    key character varying NOT NULL,
+    value character varying,
+    created_at timestamp without time zone NOT NULL,
+    updated_at timestamp without time zone NOT NULL
+);
+
+
 --
 -- Name: authorized_keys; Type: TABLE; Schema: public; Owner: -
 --
@@ -1408,6 +1420,14 @@ ALTER TABLE ONLY public.api_clients
     ADD CONSTRAINT api_clients_pkey PRIMARY KEY (id);
 
 
+--
+-- Name: ar_internal_metadata ar_internal_metadata_pkey; Type: CONSTRAINT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY public.ar_internal_metadata
+    ADD CONSTRAINT ar_internal_metadata_pkey PRIMARY KEY (key);
+
+
 --
 -- Name: authorized_keys authorized_keys_pkey; Type: CONSTRAINT; Schema: public; Owner: -
 --
@@ -2852,371 +2872,190 @@ CREATE INDEX workflows_search_idx ON public.workflows USING btree (uuid, owner_u
 
 SET search_path TO "$user", public;
 
-INSERT INTO schema_migrations (version) VALUES ('20121016005009');
-
-INSERT INTO schema_migrations (version) VALUES ('20130105203021');
-
-INSERT INTO schema_migrations (version) VALUES ('20130105224358');
-
-INSERT INTO schema_migrations (version) VALUES ('20130105224618');
-
-INSERT INTO schema_migrations (version) VALUES ('20130107181109');
-
-INSERT INTO schema_migrations (version) VALUES ('20130107212832');
-
-INSERT INTO schema_migrations (version) VALUES ('20130109175700');
-
-INSERT INTO schema_migrations (version) VALUES ('20130109220548');
-
-INSERT INTO schema_migrations (version) VALUES ('20130113214204');
-
-INSERT INTO schema_migrations (version) VALUES ('20130116024233');
-
-INSERT INTO schema_migrations (version) VALUES ('20130116215213');
-
-INSERT INTO schema_migrations (version) VALUES ('20130118002239');
-
-INSERT INTO schema_migrations (version) VALUES ('20130122020042');
-
-INSERT INTO schema_migrations (version) VALUES ('20130122201442');
-
-INSERT INTO schema_migrations (version) VALUES ('20130122221616');
-
-INSERT INTO schema_migrations (version) VALUES ('20130123174514');
-
-INSERT INTO schema_migrations (version) VALUES ('20130123180224');
-
-INSERT INTO schema_migrations (version) VALUES ('20130123180228');
-
-INSERT INTO schema_migrations (version) VALUES ('20130125220425');
-
-INSERT INTO schema_migrations (version) VALUES ('20130128202518');
-
-INSERT INTO schema_migrations (version) VALUES ('20130128231343');
-
-INSERT INTO schema_migrations (version) VALUES ('20130130205749');
-
-INSERT INTO schema_migrations (version) VALUES ('20130203104818');
-
-INSERT INTO schema_migrations (version) VALUES ('20130203104824');
-
-INSERT INTO schema_migrations (version) VALUES ('20130203115329');
-
-INSERT INTO schema_migrations (version) VALUES ('20130207195855');
-
-INSERT INTO schema_migrations (version) VALUES ('20130218181504');
-
-INSERT INTO schema_migrations (version) VALUES ('20130226170000');
-
-INSERT INTO schema_migrations (version) VALUES ('20130313175417');
-
-INSERT INTO schema_migrations (version) VALUES ('20130315155820');
-
-INSERT INTO schema_migrations (version) VALUES ('20130315183626');
-
-INSERT INTO schema_migrations (version) VALUES ('20130315213205');
-
-INSERT INTO schema_migrations (version) VALUES ('20130318002138');
-
-INSERT INTO schema_migrations (version) VALUES ('20130319165853');
-
-INSERT INTO schema_migrations (version) VALUES ('20130319180730');
-
-INSERT INTO schema_migrations (version) VALUES ('20130319194637');
-
-INSERT INTO schema_migrations (version) VALUES ('20130319201431');
-
-INSERT INTO schema_migrations (version) VALUES ('20130319235957');
-
-INSERT INTO schema_migrations (version) VALUES ('20130320000107');
-
-INSERT INTO schema_migrations (version) VALUES ('20130326173804');
-
-INSERT INTO schema_migrations (version) VALUES ('20130326182917');
-
-INSERT INTO schema_migrations (version) VALUES ('20130415020241');
-
-INSERT INTO schema_migrations (version) VALUES ('20130425024459');
-
-INSERT INTO schema_migrations (version) VALUES ('20130425214427');
-
-INSERT INTO schema_migrations (version) VALUES ('20130523060112');
-
-INSERT INTO schema_migrations (version) VALUES ('20130523060213');
-
-INSERT INTO schema_migrations (version) VALUES ('20130524042319');
-
-INSERT INTO schema_migrations (version) VALUES ('20130528134100');
-
-INSERT INTO schema_migrations (version) VALUES ('20130606183519');
-
-INSERT INTO schema_migrations (version) VALUES ('20130608053730');
-
-INSERT INTO schema_migrations (version) VALUES ('20130610202538');
-
-INSERT INTO schema_migrations (version) VALUES ('20130611163736');
-
-INSERT INTO schema_migrations (version) VALUES ('20130612042554');
-
-INSERT INTO schema_migrations (version) VALUES ('20130617150007');
-
-INSERT INTO schema_migrations (version) VALUES ('20130626002829');
-
-INSERT INTO schema_migrations (version) VALUES ('20130626022810');
-
-INSERT INTO schema_migrations (version) VALUES ('20130627154537');
-
-INSERT INTO schema_migrations (version) VALUES ('20130627184333');
-
-INSERT INTO schema_migrations (version) VALUES ('20130708163414');
-
-INSERT INTO schema_migrations (version) VALUES ('20130708182912');
-
-INSERT INTO schema_migrations (version) VALUES ('20130708185153');
-
-INSERT INTO schema_migrations (version) VALUES ('20130724153034');
-
-INSERT INTO schema_migrations (version) VALUES ('20131007180607');
-
-INSERT INTO schema_migrations (version) VALUES ('20140117231056');
-
-INSERT INTO schema_migrations (version) VALUES ('20140124222114');
-
-INSERT INTO schema_migrations (version) VALUES ('20140129184311');
-
-INSERT INTO schema_migrations (version) VALUES ('20140317135600');
-
-INSERT INTO schema_migrations (version) VALUES ('20140319160547');
-
-INSERT INTO schema_migrations (version) VALUES ('20140321191343');
-
-INSERT INTO schema_migrations (version) VALUES ('20140324024606');
-
-INSERT INTO schema_migrations (version) VALUES ('20140325175653');
-
-INSERT INTO schema_migrations (version) VALUES ('20140402001908');
-
-INSERT INTO schema_migrations (version) VALUES ('20140407184311');
-
-INSERT INTO schema_migrations (version) VALUES ('20140421140924');
-
-INSERT INTO schema_migrations (version) VALUES ('20140421151939');
-
-INSERT INTO schema_migrations (version) VALUES ('20140421151940');
-
-INSERT INTO schema_migrations (version) VALUES ('20140422011506');
-
-INSERT INTO schema_migrations (version) VALUES ('20140423132913');
-
-INSERT INTO schema_migrations (version) VALUES ('20140423133559');
-
-INSERT INTO schema_migrations (version) VALUES ('20140501165548');
-
-INSERT INTO schema_migrations (version) VALUES ('20140519205916');
-
-INSERT INTO schema_migrations (version) VALUES ('20140527152921');
-
-INSERT INTO schema_migrations (version) VALUES ('20140530200539');
-
-INSERT INTO schema_migrations (version) VALUES ('20140601022548');
-
-INSERT INTO schema_migrations (version) VALUES ('20140602143352');
-
-INSERT INTO schema_migrations (version) VALUES ('20140607150616');
-
-INSERT INTO schema_migrations (version) VALUES ('20140611173003');
-
-INSERT INTO schema_migrations (version) VALUES ('20140627210837');
-
-INSERT INTO schema_migrations (version) VALUES ('20140709172343');
-
-INSERT INTO schema_migrations (version) VALUES ('20140714184006');
-
-INSERT INTO schema_migrations (version) VALUES ('20140811184643');
-
-INSERT INTO schema_migrations (version) VALUES ('20140817035914');
-
-INSERT INTO schema_migrations (version) VALUES ('20140818125735');
-
-INSERT INTO schema_migrations (version) VALUES ('20140826180337');
-
-INSERT INTO schema_migrations (version) VALUES ('20140828141043');
-
-INSERT INTO schema_migrations (version) VALUES ('20140909183946');
-
-INSERT INTO schema_migrations (version) VALUES ('20140911221252');
-
-INSERT INTO schema_migrations (version) VALUES ('20140918141529');
-
-INSERT INTO schema_migrations (version) VALUES ('20140918153541');
-
-INSERT INTO schema_migrations (version) VALUES ('20140918153705');
-
-INSERT INTO schema_migrations (version) VALUES ('20140924091559');
-
-INSERT INTO schema_migrations (version) VALUES ('20141111133038');
-
-INSERT INTO schema_migrations (version) VALUES ('20141208164553');
-
-INSERT INTO schema_migrations (version) VALUES ('20141208174553');
-
-INSERT INTO schema_migrations (version) VALUES ('20141208174653');
-
-INSERT INTO schema_migrations (version) VALUES ('20141208185217');
-
-INSERT INTO schema_migrations (version) VALUES ('20150122175935');
-
-INSERT INTO schema_migrations (version) VALUES ('20150123142953');
-
-INSERT INTO schema_migrations (version) VALUES ('20150203180223');
-
-INSERT INTO schema_migrations (version) VALUES ('20150206210804');
-
-INSERT INTO schema_migrations (version) VALUES ('20150206230342');
-
-INSERT INTO schema_migrations (version) VALUES ('20150216193428');
-
-INSERT INTO schema_migrations (version) VALUES ('20150303210106');
-
-INSERT INTO schema_migrations (version) VALUES ('20150312151136');
-
-INSERT INTO schema_migrations (version) VALUES ('20150317132720');
-
-INSERT INTO schema_migrations (version) VALUES ('20150324152204');
-
-INSERT INTO schema_migrations (version) VALUES ('20150423145759');
-
-INSERT INTO schema_migrations (version) VALUES ('20150512193020');
-
-INSERT INTO schema_migrations (version) VALUES ('20150526180251');
-
-INSERT INTO schema_migrations (version) VALUES ('20151202151426');
-
-INSERT INTO schema_migrations (version) VALUES ('20151215134304');
-
-INSERT INTO schema_migrations (version) VALUES ('20151229214707');
-
-INSERT INTO schema_migrations (version) VALUES ('20160208210629');
-
-INSERT INTO schema_migrations (version) VALUES ('20160209155729');
-
-INSERT INTO schema_migrations (version) VALUES ('20160324144017');
-
-INSERT INTO schema_migrations (version) VALUES ('20160506175108');
-
-INSERT INTO schema_migrations (version) VALUES ('20160509143250');
-
-INSERT INTO schema_migrations (version) VALUES ('20160808151559');
-
-INSERT INTO schema_migrations (version) VALUES ('20160819195557');
-
-INSERT INTO schema_migrations (version) VALUES ('20160819195725');
-
-INSERT INTO schema_migrations (version) VALUES ('20160901210110');
-
-INSERT INTO schema_migrations (version) VALUES ('20160909181442');
-
-INSERT INTO schema_migrations (version) VALUES ('20160926194129');
-
-INSERT INTO schema_migrations (version) VALUES ('20161019171346');
-
-INSERT INTO schema_migrations (version) VALUES ('20161111143147');
-
-INSERT INTO schema_migrations (version) VALUES ('20161115171221');
-
-INSERT INTO schema_migrations (version) VALUES ('20161115174218');
-
-INSERT INTO schema_migrations (version) VALUES ('20161213172944');
-
-INSERT INTO schema_migrations (version) VALUES ('20161222153434');
-
-INSERT INTO schema_migrations (version) VALUES ('20161223090712');
-
-INSERT INTO schema_migrations (version) VALUES ('20170102153111');
-
-INSERT INTO schema_migrations (version) VALUES ('20170105160301');
-
-INSERT INTO schema_migrations (version) VALUES ('20170105160302');
-
-INSERT INTO schema_migrations (version) VALUES ('20170216170823');
-
-INSERT INTO schema_migrations (version) VALUES ('20170301225558');
-
-INSERT INTO schema_migrations (version) VALUES ('20170319063406');
-
-INSERT INTO schema_migrations (version) VALUES ('20170328215436');
-
-INSERT INTO schema_migrations (version) VALUES ('20170330012505');
-
-INSERT INTO schema_migrations (version) VALUES ('20170419173031');
-
-INSERT INTO schema_migrations (version) VALUES ('20170419173712');
-
-INSERT INTO schema_migrations (version) VALUES ('20170419175801');
-
-INSERT INTO schema_migrations (version) VALUES ('20170628185847');
-
-INSERT INTO schema_migrations (version) VALUES ('20170704160233');
-
-INSERT INTO schema_migrations (version) VALUES ('20170706141334');
-
-INSERT INTO schema_migrations (version) VALUES ('20170824202826');
-
-INSERT INTO schema_migrations (version) VALUES ('20170906224040');
-
-INSERT INTO schema_migrations (version) VALUES ('20171027183824');
-
-INSERT INTO schema_migrations (version) VALUES ('20171208203841');
-
-INSERT INTO schema_migrations (version) VALUES ('20171212153352');
-
-INSERT INTO schema_migrations (version) VALUES ('20180216203422');
-
-INSERT INTO schema_migrations (version) VALUES ('20180228220311');
-
-INSERT INTO schema_migrations (version) VALUES ('20180313180114');
-
-INSERT INTO schema_migrations (version) VALUES ('20180501182859');
-
-INSERT INTO schema_migrations (version) VALUES ('20180514135529');
-
-INSERT INTO schema_migrations (version) VALUES ('20180607175050');
-
-INSERT INTO schema_migrations (version) VALUES ('20180608123145');
-
-INSERT INTO schema_migrations (version) VALUES ('20180806133039');
-
-INSERT INTO schema_migrations (version) VALUES ('20180820130357');
-
-INSERT INTO schema_migrations (version) VALUES ('20180820132617');
-
-INSERT INTO schema_migrations (version) VALUES ('20180820135808');
-
-INSERT INTO schema_migrations (version) VALUES ('20180824152014');
-
-INSERT INTO schema_migrations (version) VALUES ('20180824155207');
-
-INSERT INTO schema_migrations (version) VALUES ('20180904110712');
-
-INSERT INTO schema_migrations (version) VALUES ('20180913175443');
-
-INSERT INTO schema_migrations (version) VALUES ('20180915155335');
-
-INSERT INTO schema_migrations (version) VALUES ('20180917200000');
-
-INSERT INTO schema_migrations (version) VALUES ('20180917205609');
-
-INSERT INTO schema_migrations (version) VALUES ('20180919001158');
-
-INSERT INTO schema_migrations (version) VALUES ('20181001175023');
-
-INSERT INTO schema_migrations (version) VALUES ('20181004131141');
-
-INSERT INTO schema_migrations (version) VALUES ('20181005192222');
-
-INSERT INTO schema_migrations (version) VALUES ('20181011184200');
-
-INSERT INTO schema_migrations (version) VALUES ('20181213183234');
+INSERT INTO "schema_migrations" (version) VALUES
+('20121016005009'),
+('20130105203021'),
+('20130105224358'),
+('20130105224618'),
+('20130107181109'),
+('20130107212832'),
+('20130109175700'),
+('20130109220548'),
+('20130113214204'),
+('20130116024233'),
+('20130116215213'),
+('20130118002239'),
+('20130122020042'),
+('20130122201442'),
+('20130122221616'),
+('20130123174514'),
+('20130123180224'),
+('20130123180228'),
+('20130125220425'),
+('20130128202518'),
+('20130128231343'),
+('20130130205749'),
+('20130203104818'),
+('20130203104824'),
+('20130203115329'),
+('20130207195855'),
+('20130218181504'),
+('20130226170000'),
+('20130313175417'),
+('20130315155820'),
+('20130315183626'),
+('20130315213205'),
+('20130318002138'),
+('20130319165853'),
+('20130319180730'),
+('20130319194637'),
+('20130319201431'),
+('20130319235957'),
+('20130320000107'),
+('20130326173804'),
+('20130326182917'),
+('20130415020241'),
+('20130425024459'),
+('20130425214427'),
+('20130523060112'),
+('20130523060213'),
+('20130524042319'),
+('20130528134100'),
+('20130606183519'),
+('20130608053730'),
+('20130610202538'),
+('20130611163736'),
+('20130612042554'),
+('20130617150007'),
+('20130626002829'),
+('20130626022810'),
+('20130627154537'),
+('20130627184333'),
+('20130708163414'),
+('20130708182912'),
+('20130708185153'),
+('20130724153034'),
+('20131007180607'),
+('20140117231056'),
+('20140124222114'),
+('20140129184311'),
+('20140317135600'),
+('20140319160547'),
+('20140321191343'),
+('20140324024606'),
+('20140325175653'),
+('20140402001908'),
+('20140407184311'),
+('20140421140924'),
+('20140421151939'),
+('20140421151940'),
+('20140422011506'),
+('20140423132913'),
+('20140423133559'),
+('20140501165548'),
+('20140519205916'),
+('20140527152921'),
+('20140530200539'),
+('20140601022548'),
+('20140602143352'),
+('20140607150616'),
+('20140611173003'),
+('20140627210837'),
+('20140709172343'),
+('20140714184006'),
+('20140811184643'),
+('20140817035914'),
+('20140818125735'),
+('20140826180337'),
+('20140828141043'),
+('20140909183946'),
+('20140911221252'),
+('20140918141529'),
+('20140918153541'),
+('20140918153705'),
+('20140924091559'),
+('20141111133038'),
+('20141208164553'),
+('20141208174553'),
+('20141208174653'),
+('20141208185217'),
+('20150122175935'),
+('20150123142953'),
+('20150203180223'),
+('20150206210804'),
+('20150206230342'),
+('20150216193428'),
+('20150303210106'),
+('20150312151136'),
+('20150317132720'),
+('20150324152204'),
+('20150423145759'),
+('20150512193020'),
+('20150526180251'),
+('20151202151426'),
+('20151215134304'),
+('20151229214707'),
+('20160208210629'),
+('20160209155729'),
+('20160324144017'),
+('20160506175108'),
+('20160509143250'),
+('20160808151559'),
+('20160819195557'),
+('20160819195725'),
+('20160901210110'),
+('20160909181442'),
+('20160926194129'),
+('20161019171346'),
+('20161111143147'),
+('20161115171221'),
+('20161115174218'),
+('20161213172944'),
+('20161222153434'),
+('20161223090712'),
+('20170102153111'),
+('20170105160301'),
+('20170105160302'),
+('20170216170823'),
+('20170301225558'),
+('20170319063406'),
+('20170328215436'),
+('20170330012505'),
+('20170419173031'),
+('20170419173712'),
+('20170419175801'),
+('20170628185847'),
+('20170704160233'),
+('20170706141334'),
+('20170824202826'),
+('20170906224040'),
+('20171027183824'),
+('20171208203841'),
+('20171212153352'),
+('20180216203422'),
+('20180228220311'),
+('20180313180114'),
+('20180501182859'),
+('20180514135529'),
+('20180607175050'),
+('20180608123145'),
+('20180806133039'),
+('20180820130357'),
+('20180820132617'),
+('20180820135808'),
+('20180824152014'),
+('20180824155207'),
+('20180904110712'),
+('20180913175443'),
+('20180915155335'),
+('20180917200000'),
+('20180917205609'),
+('20180919001158'),
+('20181001175023'),
+('20181004131141'),
+('20181005192222'),
+('20181011184200'),
+('20181213183234'),
+('20190214214814');
 
-INSERT INTO schema_migrations (version) VALUES ('20190214214814');
 

diff --git a/services/api/lib/can_be_an_owner.rb b/services/api/lib/can_be_an_owner.rb
index 1a990e14ea09fa67d6682c9f5baf7b776a0a5c11..a970383b8714653e9621def26a404cc7e10bf48b 100644 (file)
--- a/services/api/lib/can_be_an_owner.rb
+++ b/services/api/lib/can_be_an_owner.rb
@@ -16,6 +16,7 @@ module CanBeAnOwner
       next if t == base.table_name
       next if t == 'schema_migrations'
       next if t == 'permission_refresh_lock'
+      next if t == 'ar_internal_metadata'
       klass = t.classify.constantize
       next unless klass and 'owner_uuid'.in?(klass.columns.collect(&:name))
       base.has_many(t.to_sym,