diff options
| -rw-r--r-- | doc/guix.texi | 26 | ||||
| -rw-r--r-- | gnu/packages/base.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/databases.scm | 94 | ||||
| -rw-r--r-- | gnu/packages/linux.scm | 16 | ||||
| -rw-r--r-- | gnu/packages/package-management.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch | 55 | ||||
| -rw-r--r-- | gnu/services/databases.scm | 89 | ||||
| -rw-r--r-- | gnu/system.scm | 15 | ||||
| -rw-r--r-- | gnu/tests/databases.scm | 86 | ||||
| -rw-r--r-- | tests/import-utils.scm | 5 | ||||
| -rw-r--r-- | tests/uuid.scm | 2 |
12 files changed, 382 insertions, 28 deletions
diff --git a/doc/guix.texi b/doc/guix.texi index f0a59a6b4b..c10fc649d1 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -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. 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)))) diff --git a/tests/import-utils.scm b/tests/import-utils.scm index 3d8d2c698d..f4bbd335b9 100644 --- a/tests/import-utils.scm +++ b/tests/import-utils.scm @@ -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") diff --git a/tests/uuid.scm b/tests/uuid.scm index 68676f775d..91a3482490 100644 --- a/tests/uuid.scm +++ b/tests/uuid.scm @@ -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) |