gnu: postgresql: Update to 10.2 [CVE-2018-{1052,1053}].

* gnu/packages/databases.scm (postgresql): Update to 10.2.

gnu: Fix and improve the mongo-tools package.

The hash of the source for this package is wrong. Most probably because the
source was changed from a tarball to a git repository without updating the
hash. Fixing this seems to break the check phase, so I rewrote that as well,
making changes to the build and install phases as needed.

* gnu/packages/databases.scm (mongo-tools)[source]: Update the hash value.
  [arguments]: Remove the different unpack path, as this isn't necessary when
  using the git repository as a source. Move the list of tools to make it
  accessible from multiple phases. Rewrite the build phase, getting it to
  install the tools in to the location the tests seem to expect to find
  them. Replace the check phase to run the tests for each tool
  individually. Add an install phase to install the tools, now that go install
  is not being run in the build phase.
  [native-inputs]: Add go-github.com-smartystreets-goconvey as a native-input
  as this is required for running the tests.

gnu: Add mongo-tools.

* gnu/packages/databases.scm (mongo-tools): New variable.

gnu: Add go-gopkg.in-mgo.v2.

* gnu/packages/databases.scm (go-gopkg.in-mgo.v2): New variable.

gnu: 4store: Update URI.

* gnu/packages/databases.scm (4store)[source, home-page]: Update URI.

gnu: mongodb: Fix indentation.

* gnu/packages/databases.scm (mongodb): Replace tabs with spaces.

gnu: mysql: Update to 5.7.21.

* gnu/packages/databases.scm (mysql): Update to 5.7.21.

gnu: Remove redundant wrapping from packages using ruby-build-system.

Now that the build system does wrapping automatically, it can be removed from
the packages that do it manually.

* gnu/packages/databases.scm (es-dump-restore)[arguments]: Remove #:phases.
* gnu/packages/ruby.scm (ruby-redcloth)[arguments]: Remove #:phases.
  (ruby-httpclient)[arguments]: Remove 'wrap-bin-httpclient from the modified
  phases.

guix: build: ruby-build-system: Install to the vendor directory

* guix/build/ruby-build-system.scm (install): Install gems to the vendor
  directory, rather than the GEM_HOME. The vendor directory does not include
  the version of ruby used to install the gem in the path, which makes it
  easier to add it to the GEM_PATH for all versions of ruby to use.
  (gem-home): Remove procedure.
* gnu/packages/ruby.scm (ruby, ruby-2.1)[native-search-paths]: Switch to
  lib/ruby/vendor_ruby.
  (ruby-1.8)[native-search-paths]: Remove native-search-paths.
  (gem-directory): Remove procedure.
  (ruby-ansi, ruby-ae)[arguments]: Remove use of gem-directory.
  (ruby-metaclass, ruby-instantiator, ruby-introspection, ruby-mocha,
  ruby-nokogiri, ruby-minitest-tu-shim, ruby-redcloth)[arguments]: Remove use
  of gem-home.
  (ruby-git, ruby-httpclient)[arguments]: Remove use of GEM_HOME.
* gnu/packages/databases.scm (es-dump-restore)[arguments]: Remove use of
  GEM_HOME.

gnu: guile-wiredtiger: Update to 0.6.3.

* gnu/package/databases.scm (guile-wiredtiger): Update to 0.6.3.
[arguments]: Enable tests; disable parallel tests; remove
'remove-bundled-dependencies' phase.
[synopsis, description]: Improve them.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>

gnu: Run some tests in the mongodb package check phase.

Previously the mongodb dbtests and unittests were only built, and not actually
run.

* gnu/packages/databases.scm (mongodb)[native-inputs]: Add python2-minimal,
  python2-pymongo and python2-pyyaml for running the resmoke.py program, and
  add tzdata as some tests fail without this.
  [arguments]: Run the tests through the resmoke.py script in the check phase,
  set TZDIR as a couple of tests seem to depend on this, add a comment about
  the resource requirements of the tests, as they require a large amount of
  disk space, and disable the async_stream_test, as it seems to hang.

gnu: Build wiredtiger with builtin compressors.

WiredTiger is used by MongoDB, and it seems to require it to be built with
builtin support for snappy compression.

* gnu/packages/databases.scm (wiredtiger)[arguments]: Replace --enable-zlib
  and --enable-snappy with --with-builtins=snappy,zlib.

gnu: python-sqlalchemy-utils: Update to 0.32.21.

* gnu/packages/databases.scm (python-sqlalchemy-utils): Update to 0.32.21.

gnu: python-sadisplay: Update to 0.4.8.

* gnu/packages/databases.scm (python-sadisplay): Update to 0.4.8.

gnu: check, databases: Use HTTPS for bitbucket.org.

* gnu/packages/check.scm (python-pytest-capturelog)[home-page]: Likewise.
* gnu/packages/databases.scm (python-alembic)[home-page]: Likewise.

gnu: python-redis: Update to 2.10.6.

* gnu/packages/databases.scm (python-redis): Update to 2.10.6.

gnu: python-alembic: Update to 0.9.6.

* gnu/packages/databases.scm (python-alembic): Update to 0.9.6.

gnu: Build wiredtiger with snappy support.

This is probably necessary to get the MongoDB package in Guix to successfully
use the Guix wiredtiger package, as MongoDB it uses wiredtiger with snappy by
default.

* gnu/packages/databases.scm (wiredtiger)[arguments]: Add --enable-snappy to
  #:configure-flags.
  [inputs]: Add snappy.

gnu: mariadb: Update to 10.1.29.

* gnu/packages/databases.scm (mariadb): Update to 10.1.29.

gnu: perl-sql-abstract: Update source uri.

* gnu/packages/databases.scm (perl-sql-abstract)[source]: Update source uri.