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-rw-r--r--gnu/packages/base.scm12
-rw-r--r--gnu/packages/bioinformatics.scm4
-rw-r--r--gnu/packages/databases.scm94
-rw-r--r--gnu/packages/linux.scm16
-rw-r--r--gnu/packages/package-management.scm6
-rw-r--r--gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch55
-rw-r--r--gnu/services/databases.scm89
-rw-r--r--gnu/system.scm15
-rw-r--r--gnu/tests/databases.scm86
9 files changed, 351 insertions, 26 deletions
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 972ffeeecb..bc745351af 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -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)
- (zero? (system* "make" "localedata/install-locales"
- "-j" (number->string (parallel-job-count)))))
- (alist-delete 'install ,phases)))
+ `(modify-phases ,phases
+ (replace 'build
+ (lambda _
+ (zero? (system* "make" "localedata/install-locales"
+ "-j" (number->string (parallel-job-count))))))
+ (delete 'install)))
((#:configure-flags flags)
`(append ,flags
;; Use $(libdir)/locale/X.Y as is the case by default.
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 95632e2f9c..f2f3b807c3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 2afc94c965..ae138796ff 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -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")
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 585b41a376..1445089a58 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -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"
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 197a7a0142..91e44ec6fe 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -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
diff --git a/gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch b/gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch
new file mode 100644
index 0000000000..6057ebeb08
--- /dev/null
+++ b/gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch
@@ -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");
+ }
+
+ /**
diff --git a/gnu/services/databases.scm b/gnu/services/databases.scm
index de1f6b8411..6a01cb1ce6 100644
--- a/gnu/services/databases.scm
+++ b/gnu/services/databases.scm
@@ -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
@@ -264,6 +272,87 @@ and stores the database cluster in @var{data-directory}."
;;;
+;;; 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.
;;;
diff --git a/gnu/system.scm b/gnu/system.scm
index 8ab4801b74..0e834ba5ed 100644
--- a/gnu/system.scm
+++ b/gnu/system.scm
@@ -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)
diff --git a/gnu/tests/databases.scm b/gnu/tests/databases.scm
index 9d9a753747..9e335b27c6 100644
--- a/gnu/tests/databases.scm
+++ b/gnu/tests/databases.scm
@@ -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))))
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-26 12:24:50 +0000