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Merge branch 'master' into staging

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Marius Bakke 2017-10-07 12:54:40 +02:00
parent 6a317919cf 3ae76f7f57
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26
doc/guix.texi
View File

@ -12120,6 +12120,32 @@ Additional command line options to pass to @code{memcached}.
@end table
@end deftp
@defvr {Scheme Variable} mongodb-service-type
This is the service type for @uref{https://www.mongodb.com/, MongoDB}.
The value for the service type is a @code{mongodb-configuration} object.
@end defvr
@example
(service mongodb-service-type)
@end example
@deftp {Data Type} mongodb-configuration
Data type representing the configuration of mongodb.
@table @asis
@item @code{mongodb} (default: @code{mongodb})
The MongoDB package to use.
@item @code{config-file} (default: @code{%default-mongodb-configuration-file})
The configuration file for MongoDB.
@item @code{data-directory} (default: @code{"/var/lib/mongodb"})
This value is used to create the directory, so that it exists and is
owned by the mongodb user. It should match the data-directory which
MongoDB is configured to use through the configuration file.
@end table
@end deftp
@defvr {Scheme Variable} redis-service-type
This is the service type for the @uref{https://redis.io/, Redis}
key/value store, whose value is a @code{redis-configuration} object.

10
gnu/packages/base.scm
View File

@ -883,12 +883,12 @@ the 'share/locale' sub-directory of this package.")
,@(package-arguments glibc))))
(substitute-keyword-arguments args
((#:phases phases)
`(alist-replace
'build
(lambda* (#:key outputs #:allow-other-keys)
`(modify-phases ,phases
(replace 'build
(lambda _
(zero? (system* "make" "localedata/install-locales"
"-j" (number->string (parallel-job-count)))))
(alist-delete 'install ,phases)))
"-j" (number->string (parallel-job-count))))))
(delete 'install)))
((#:configure-flags flags)
`(append ,flags
;; Use $(libdir)/locale/X.Y as is the case by default.

4
gnu/packages/bioinformatics.scm
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@ -6161,7 +6161,7 @@ SELECT or UPDATE queries to an end-point.")
(define-public vsearch
(package
(name "vsearch")
(version "2.4.4")
(version "2.5.0")
(source
(origin
(method url-fetch)
@ -6171,7 +6171,7 @@ SELECT or UPDATE queries to an end-point.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1d8a4gjwaqdv57krlr80x18mg5py1bbdiqs5m0jdn38filc9z40k"))
"1k8wf3qns4mqrsizywbkqcasqjw000m4drxsag3qd7390pwvf9kz"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin

94
gnu/packages/databases.scm
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@ -69,8 +69,10 @@
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages valgrind)
#:use-module (gnu packages xml)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
@ -355,6 +357,98 @@ and generic API, and was originally intended for use with dynamic web
applications.")
(license license:bsd-3)))
(define-public mongodb
(package
(name "mongodb")
(version "3.4.9")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/mongodb/mongo/archive/r"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0gidwyvh3bdwmk2pccgkqkaln4ysgn8iwa7ihjzllsq0rdg95045"))
(patches
(list
(search-patch "mongodb-support-unknown-linux-distributions.patch")))))
(build-system gnu-build-system)
(inputs
`(("openssl" ,openssl)
("pcre" ,pcre)
("yaml-cpp" ,yaml-cpp)
("zlib" ,zlib)
("snappy" ,snappy)
("boost" ,boost)))
(native-inputs
`(("scons" ,scons)
("python" ,python-2)
("valgrind" ,valgrind)
("perl" ,perl)))
(arguments
`(#:phases
(let ((common-options
`(;; "--use-system-tcmalloc" TODO: Missing gperftools
"--use-system-pcre"
;; TODO
;; build/opt/mongo/db/fts/unicode/string.o failed: Error 1
;; --use-system-boost
"--use-system-snappy"
"--use-system-zlib"
"--use-system-valgrind"
;; "--use-system-stemmer" TODO: Missing relevant package
"--use-system-yaml"
"--disable-warnings-as-errors"
,(format #f "--jobs=~a" (parallel-job-count))
"--ssl")))
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase
(add-after 'unpack 'scons-propagate-environment
(lambda _
;; Modify the SConstruct file to arrange for
;; environment variables to be propagated.
(substitute* "SConstruct"
(("^env = Environment\\(")
"env = Environment(ENV=os.environ, "))
#t))
(add-after 'unpack 'create-version-file
(lambda _
(call-with-output-file "version.json"
(lambda (port)
(display ,(simple-format #f "{
\"version\": \"~A\"
}" version) port)))
#t))
(replace 'build
(lambda _
(zero? (apply system*
`("scons"
,@common-options
"mongod" "mongo" "mongos")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(or (not tests?)
(zero? (apply system*
`("scons"
,@common-options
"dbtest" "unittests"))))))
(replace 'install
(lambda _
(let ((bin (string-append (assoc-ref %outputs "out") "/bin")))
(install-file "mongod" bin)
(install-file "mongos" bin)
(install-file "mongo" bin))
#t))))))
(home-page "https://www.mongodb.org/")
(synopsis "High performance and high availability document database")
(description
"Mongo is a high-performance, high availability, schema-free
document-oriented database. A key goal of MongoDB is to bridge the gap
between key/value stores (which are fast and highly scalable) and traditional
RDBMS systems (which are deep in functionality).")
(license (list license:agpl3
;; Some parts are licensed under the Apache License
license:asl2.0))))
(define-public mysql
(package
(name "mysql")

16
gnu/packages/linux.scm
View File

@ -367,8 +367,8 @@ It has been modified to remove all non-free binary blobs.")
(define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
(define %linux-libre-version "4.13.4")
(define %linux-libre-hash "028dww9c6x22mvd0jd87bmibqiz5lrsyynrbzka18gh39sk0v8j7")
(define %linux-libre-version "4.13.5")
(define %linux-libre-hash "1crw61x7qrijhpw0azxf9b3fra0cxq87ncni2419p0s23jfdpc4m")
(define-public linux-libre
(make-linux-libre %linux-libre-version
@ -377,14 +377,14 @@ It has been modified to remove all non-free binary blobs.")
#:configuration-file kernel-config))
(define-public linux-libre-4.9
(make-linux-libre "4.9.52"
"0zl1z13r4gg6r2sbx8mrif2cnjkjlfrswiap7wzb22jyfnlyj5nb"
(make-linux-libre "4.9.53"
"174i53cd090akbjq34dj4z00h1nyfmy3sl3fk6svcmbx6h34381h"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.4
(make-linux-libre "4.4.89"
"1bw1cma8hxcj6wi8znc4nvw1p6dlc1lgciqak6n6ijn53xdd242h"
(make-linux-libre "4.4.90"
"1sqzvz8yrcf99vhphkxp1wm2agq6q9nshxb1mkypspm8rhm11vhw"
%intel-compatible-systems
#:configuration-file kernel-config))
@ -3163,7 +3163,7 @@ and copy/paste text in the console and in xterm.")
(define-public btrfs-progs
(package
(name "btrfs-progs")
(version "4.13.1")
(version "4.13.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://kernel.org/linux/kernel/"
@ -3171,7 +3171,7 @@ and copy/paste text in the console and in xterm.")
"btrfs-progs-v" version ".tar.xz"))
(sha256
(base32
"1clavvrlkswgicqsm2yfsxqw04lsn8dra0db84jqm6j2apz80kz0"))))
"1ga8jk2hkaxpm17z3gdfrpq0i62kqpv2wm5yzbzmsj862cgk7ivm"))))
(build-system gnu-build-system)
(outputs '("out"
"static")) ; static versions of the binaries in "out"

6
gnu/packages/package-management.scm
View File

@ -78,8 +78,8 @@
;; Note: the 'update-guix-package.scm' script expects this definition to
;; start precisely like this.
(let ((version "0.13.0")
(commit "a9468b422b6df2349a3f4d1451c9302c3d77011b")
(revision 6))
(commit "8b920d707ed07a3251227f77526cf875d86a4417")
(revision 7))
(package
(name "guix")
@ -95,7 +95,7 @@
(commit commit)))
(sha256
(base32
"0bv323yp657x0a2aa2z5pp5541hjqmn908kh9jqlbdw5gpx9vg3d"))
"15phwcadkw44mr4hnv1dxzzw9an6x7sbdfzwy4iciqw6y2wckncd"))
(file-name (string-append "guix-" version "-checkout"))))
(build-system gnu-build-system)
(arguments

55
gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch Normal file
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@ -0,0 +1,55 @@
From e724bb7018a482640c4f194f88b554af2c59d76e Mon Sep 17 00:00:00 2001
From: Mark Benvenuto <mark.benvenuto@mongodb.com>
Date: Wed, 20 Sep 2017 11:50:02 -0400
Subject: [PATCH] SERVER-30857 Support unknown Linux distributions
---
src/mongo/rpc/metadata/client_metadata.cpp | 6 ------
src/mongo/util/processinfo_linux.cpp | 9 ++++++---
2 files changed, 6 insertions(+), 9 deletions(-)
diff --git a/src/mongo/rpc/metadata/client_metadata.cpp b/src/mongo/rpc/metadata/client_metadata.cpp
index 845a315dd74..a959a4e31e9 100644
--- a/src/mongo/rpc/metadata/client_metadata.cpp
+++ b/src/mongo/rpc/metadata/client_metadata.cpp
@@ -302,9 +302,6 @@ void ClientMetadata::serializePrivate(StringData driverName,
StringData osArchitecture,
StringData osVersion,
BSONObjBuilder* builder) {
- invariant(!driverName.empty() && !driverVersion.empty() && !osType.empty() && !osName.empty() &&
- !osArchitecture.empty() && !osVersion.empty());
-
BSONObjBuilder metaObjBuilder(builder->subobjStart(kMetadataDocumentName));
{
@@ -347,9 +344,6 @@ Status ClientMetadata::serializePrivate(StringData driverName,
StringData osVersion,
StringData appName,
BSONObjBuilder* builder) {
- invariant(!driverName.empty() && !driverVersion.empty() && !osType.empty() && !osName.empty() &&
- !osArchitecture.empty() && !osVersion.empty());
-
if (appName.size() > kMaxApplicationNameByteLength) {
return Status(ErrorCodes::ClientMetadataAppNameTooLarge,
str::stream() << "The '" << kApplication << "." << kName
diff --git a/src/mongo/util/processinfo_linux.cpp b/src/mongo/util/processinfo_linux.cpp
index c3debf377bd..c2813b026b0 100644
--- a/src/mongo/util/processinfo_linux.cpp
+++ b/src/mongo/util/processinfo_linux.cpp
@@ -376,10 +376,13 @@ class LinuxSysHelper {
if ((nl = name.find('\n', nl)) != string::npos)
// stop at first newline
name.erase(nl);
- // no standard format for name and version. use kernel version
- version = "Kernel ";
- version += LinuxSysHelper::readLineFromFile("/proc/sys/kernel/osrelease");
+ } else {
+ name = "unknown";
}
+
+ // There is no standard format for name and version so use the kernel version.
+ version = "Kernel ";
+ version += LinuxSysHelper::readLineFromFile("/proc/sys/kernel/osrelease");
}
/**

89
gnu/services/databases.scm
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@ -44,6 +44,14 @@
memcached-configuration-udp-port
memcached-configuration-additional-options
<mongodb-configuration>
mongodb-configuration
mongodb-configuration?
mongodb-configuration-mongodb
mongodb-configuration-config-file
mongodb-configuration-data-directory
mongodb-service-type
mysql-service
mysql-service-type
mysql-configuration
@ -262,6 +270,87 @@ and stores the database cluster in @var{data-directory}."
(const %memcached-accounts))))
(default-value (memcached-configuration))))
;;;
;;; MongoDB
;;;
(define %default-mongodb-configuration-file
(plain-file
"mongodb.yaml"
"# GNU Guix: MongoDB default configuration file
processManagement:
pidFilePath: /var/run/mongodb/pid
storage:
dbPath: /var/lib/mongodb
"))
(define-record-type* <mongodb-configuration>
mongodb-configuration make-mongodb-configuration
mongodb-configuration?
(mongodb mongodb-configuration-mongodb
(default mongodb))
(config-file mongodb-configuration-config-file
(default %default-mongodb-configuration-file))
(data-directory mongodb-configuration-data-directory
(default "/var/lib/mongodb")))
(define %mongodb-accounts
(list (user-group (name "mongodb") (system? #t))
(user-account
(name "mongodb")
(group "mongodb")
(system? #t)
(comment "Mongodb server user")
(home-directory "/var/lib/mongodb")
(shell (file-append shadow "/sbin/nologin")))))
(define mongodb-activation
(match-lambda
(($ <mongodb-configuration> mongodb config-file data-directory)
#~(begin
(use-modules (guix build utils))
(let ((user (getpwnam "mongodb")))
(for-each
(lambda (directory)
(mkdir-p directory)
(chown directory
(passwd:uid user) (passwd:gid user)))
'("/var/run/mongodb" #$data-directory)))))))
(define mongodb-shepherd-service
(match-lambda
(($ <mongodb-configuration> mongodb config-file data-directory)
(shepherd-service
(provision '(mongodb))
(documentation "Run the Mongodb daemon.")
(requirement '(user-processes loopback))
(start #~(make-forkexec-constructor
`(,(string-append #$mongodb "/bin/mongod")
"--config"
,#$config-file)
#:user "mongodb"
#:group "mongodb"
#:pid-file "/var/run/mongodb/pid"
#:log-file "/var/log/mongodb.log"))
(stop #~(make-kill-destructor))))))
(define mongodb-service-type
(service-type
(name 'mongodb)
(description "Run the MongoDB document database server.")
(extensions
(list (service-extension shepherd-root-service-type
(compose list
mongodb-shepherd-service))
(service-extension activation-service-type
mongodb-activation)
(service-extension account-service-type
(const %mongodb-accounts))))
(default-value
(mongodb-configuration))))
;;;
;;; MySQL.

15
gnu/system.scm
View File

@ -231,6 +231,14 @@ directly by the user."
(kernel-arguments boot-parameters-kernel-arguments)
(initrd boot-parameters-initrd))
(define (ensure-not-/dev device)
"If DEVICE starts with a slash, return #f. This is meant to filter out
Linux device names such as /dev/sda, and to preserve GRUB device names and
file system labels."
(if (and (string? device) (string-prefix? "/" device))
#f
device))
(define (read-boot-parameters port)
"Read boot parameters from PORT and return the corresponding
<boot-parameters> object or #f if the format is unrecognized."
@ -243,11 +251,6 @@ directly by the user."
((? string? device)
device)))
(define (ensure-not-/dev device)
(if (and (string? device) (string-prefix? "/" device))
#f
device))
(match (read port)
(('boot-parameters ('version 0)
('label label) ('root-device root)
@ -939,7 +942,7 @@ kernel arguments for that derivation to <boot-parameters>."
(operating-system-user-kernel-arguments os)))
(initrd initrd)
(bootloader-name bootloader-name)
(store-device (fs->boot-device store))
(store-device (ensure-not-/dev (fs->boot-device store)))
(store-mount-point (file-system-mount-point store))))))
(define (device->sexp device)

86
gnu/tests/databases.scm
View File

@ -25,9 +25,11 @@
#:use-module (gnu services)
#:use-module (gnu services databases)
#:use-module (gnu services networking)
#:use-module (gnu packages databases)
#:use-module (guix gexp)
#:use-module (guix store)
#:export (%test-memcached))
#:export (%test-memcached
%test-mongodb))
(define %memcached-os
(simple-operating-system
@ -121,3 +123,85 @@
(name "memcached")
(description "Connect to a running MEMCACHED server.")
(value (run-memcached-test))))
(define %mongodb-os
(operating-system
(inherit
(simple-operating-system
(dhcp-client-service)
(service mongodb-service-type)))
(packages (cons* mongodb
%base-packages))))
(define* (run-mongodb-test #:optional (port 27017))
"Run tests in %MONGODB-OS, forwarding PORT."
(define os
(marionette-operating-system
%mongodb-os
#:imported-modules '((gnu services herd)
(guix combinators))))
(define vm
(virtual-machine
(operating-system os)
(memory-size 1024)
(disk-image-size (* 1024 (expt 2 20)))
(port-forwardings `((27017 . ,port)))))
(define test
(with-imported-modules '((gnu build marionette))
#~(begin
(use-modules (srfi srfi-11) (srfi srfi-64)
(gnu build marionette)
(ice-9 popen)
(ice-9 rdelim))
(define marionette
(make-marionette (list #$vm)))
(mkdir #$output)
(chdir #$output)
(test-begin "mongodb")
(test-assert "service running"
(marionette-eval
'(begin
(use-modules (gnu services herd))
(match (start-service 'mongodb)
(#f #f)
(('service response-parts ...)
(match (assq-ref response-parts 'running)
((pid) (number? pid))))))
marionette))
(test-eq "test insert"
0
(system* (string-append #$mongodb "/bin/mongo")
"test"
"--eval"
"db.testCollection.insert({data: 'test-data'})"))
(test-equal "test find"
"test-data"
(let* ((port (open-pipe*
OPEN_READ
(string-append #$mongodb "/bin/mongo")
"test"
"--quiet"
"--eval"
"db.testCollection.findOne().data"))
(output (read-line port))
(status (close-pipe port)))
output))
(test-end)
(exit (= (test-runner-fail-count (test-runner-current)) 0)))))
(gexp->derivation "mongodb-test" test))
(define %test-mongodb
(system-test
(name "mongodb")
(description "Connect to a running MONGODB server.")
(value (run-mongodb-test))))

5
tests/import-utils.scm
View File

@ -43,7 +43,10 @@
(test-assert "alist->package with simple source"
(let* ((meta '(("name" . "hello")
("version" . "2.10")
("source" . "mirror://gnu/hello/hello-2.10.tar.gz")
("source" .
;; Use a 'file://' URI so that we don't cause a download.
,(string-append "file://"
(search-path %load-path "guix.scm")))
("build-system" . "gnu")
("home-page" . "https://gnu.org")
("synopsis" . "Say hi")

2
tests/uuid.scm
View File

@ -57,7 +57,7 @@
"1234-ABCD"
(uuid->string (uuid "1234-abcd" 'fat32)))
(test-equal "uuid=?"
(test-assert "uuid=?"
(and (uuid=? (uuid-bytevector (uuid "1234-abcd" 'fat32))
(uuid "1234-abcd" 'fat32))
(uuid=? (uuid "1234-abcd" 'fat32)