Merge branch 'master' into staging

6 files changed, 225 insertions, 130 deletions

diff --git a/guix/git-authenticate.scm b/guix/git-authenticate.scm
index 00d22ef479..c333717136 100644
--- a/guix/git-authenticate.scm
+++ b/guix/git-authenticate.scm
@@ -184,8 +184,11 @@ to remove '.guix-authorizations' file")
               default-authorizations)
             (throw key error)))))
 
-  (apply lset-intersection bytevector=?
-         (map commit-authorizations (commit-parents commit))))
+  (match (commit-parents commit)
+    (() default-authorizations)
+    (parents
+     (apply lset-intersection bytevector=?
+            (map commit-authorizations parents)))))
 
 (define* (authenticate-commit repository commit keyring
                               #:key (default-authorizations '()))
diff --git a/guix/git.scm b/guix/git.scm
index 1671f57d9f..0d8e617cc9 100644
--- a/guix/git.scm
+++ b/guix/git.scm
@@ -416,7 +416,9 @@ Essentially, this computes the set difference between the closure of NEW and
 that of OLD."
   (let loop ((commits (list new))
              (result '())
-             (visited (commit-closure old (list->setq excluded))))
+             (visited (fold commit-closure
+                            (setq)
+                            (cons old excluded))))
     (match commits
       (()
        (reverse result))
diff --git a/guix/import/stackage.scm b/guix/import/stackage.scm
index 14150201b5..e04073d193 100644
--- a/guix/import/stackage.scm
+++ b/guix/import/stackage.scm
@@ -122,7 +122,7 @@ included in the Stackage LTS release."
   (let ((pkgs-info (mlambda () (lts-info-packages (stackage-lts-info-fetch)))))
     (lambda* (package)
       "Return an <upstream-source> for the latest Stackage LTS release of
-PACKAGE or #f it the package is not inlucded in the Stackage LTS release."
+PACKAGE or #f if the package is not included in the Stackage LTS release."
       (let* ((hackage-name (guix-package->hackage-name package))
              (version (lts-package-version (pkgs-info) hackage-name))
              (name-version (hackage-name-version hackage-name version)))
diff --git a/guix/packages.scm b/guix/packages.scm
index 0ccd31a7a9..1e0ec41b76 100644
--- a/guix/packages.scm
+++ b/guix/packages.scm
@@ -1194,39 +1194,39 @@ and return it."
   (make-weak-key-hash-table 200))
 
 (define (input-graft store system)
-  "Return a procedure that, given a package with a graft, returns a graft, and
-#f otherwise."
-  (match-lambda
-    ((? package? package)
+  "Return a procedure that, given a package with a replacement and an output name,
+returns a graft, and #f otherwise."
+  (match-lambda*
+    (((? package? package) output)
      (let ((replacement (package-replacement package)))
        (and replacement
-            (cached (=> %graft-cache) package system
+            (cached (=> %graft-cache) package (cons output system)
                     (let ((orig (package-derivation store package system
                                                     #:graft? #f))
                           (new  (package-derivation store replacement system
                                                     #:graft? #t)))
                       (graft
                         (origin orig)
-                        (replacement new)))))))
-    (x
-     #f)))
+                        (origin-output output)
+                        (replacement new)
+                        (replacement-output output)))))))))
 
 (define (input-cross-graft store target system)
   "Same as 'input-graft', but for cross-compilation inputs."
-  (match-lambda
-    ((? package? package)
-    (let ((replacement (package-replacement package)))
-      (and replacement
-           (let ((orig (package-cross-derivation store package target system
-                                                 #:graft? #f))
-                 (new  (package-cross-derivation store replacement
-                                                 target system
-                                                 #:graft? #t)))
-             (graft
-               (origin orig)
-               (replacement new))))))
-   (_
-    #f)))
+  (match-lambda*
+    (((? package? package) output)
+     (let ((replacement (package-replacement package)))
+       (and replacement
+            (let ((orig (package-cross-derivation store package target system
+                                                  #:graft? #f))
+                  (new  (package-cross-derivation store replacement
+                                                  target system
+                                                  #:graft? #t)))
+              (graft
+                (origin orig)
+                (origin-output output)
+                (replacement new)
+                (replacement-output output))))))))
 
 (define* (fold-bag-dependencies proc seed bag
                                 #:key (native? #t))
@@ -1243,26 +1243,21 @@ dependencies; otherwise, restrict to target dependencies."
                       (bag-host-inputs bag))))
         bag-host-inputs))
 
-  (define nodes
-    (match (bag-direct-inputs* bag)
-      (((labels things _ ...) ...)
-       things)))
-
-  (let loop ((nodes nodes)
+  (let loop ((inputs (bag-direct-inputs* bag))
              (result seed)
-             (visited (setq)))
-    (match nodes
+             (visited vlist-null))
+    (match inputs
       (()
        result)
-      (((? package? head) . tail)
-       (if (set-contains? visited head)
-           (loop tail result visited)
-           (let ((inputs (bag-direct-inputs* (package->bag head))))
-             (loop (match inputs
-                     (((labels things _ ...) ...)
-                      (append things tail)))
-                   (proc head result)
-                   (set-insert head visited)))))
+      (((label (? package? head) . rest) . tail)
+       (let ((output  (match rest (() "out") ((output) output)))
+             (outputs (vhash-foldq* cons '() head visited)))
+         (if (member output outputs)
+             (loop tail result visited)
+             (let ((inputs (bag-direct-inputs* (package->bag head))))
+               (loop (append inputs tail)
+                     (proc head output result)
+                     (vhash-consq head output visited))))))
       ((head . tail)
        (loop tail result visited)))))
 
@@ -1279,8 +1274,8 @@ to (see 'graft-derivation'.)"
     (let ((->graft (input-graft store system)))
       (parameterize ((%current-system system)
                      (%current-target-system #f))
-        (fold-bag-dependencies (lambda (package grafts)
-                                 (match (->graft package)
+        (fold-bag-dependencies (lambda (package output grafts)
+                                 (match (->graft package output)
                                    (#f    grafts)
                                    (graft (cons graft grafts))))
                                '()
@@ -1291,8 +1286,8 @@ to (see 'graft-derivation'.)"
         (let ((->graft (input-cross-graft store target system)))
           (parameterize ((%current-system system)
                          (%current-target-system target))
-            (fold-bag-dependencies (lambda (package grafts)
-                                     (match (->graft package)
+            (fold-bag-dependencies (lambda (package output grafts)
+                                     (match (->graft package output)
                                        (#f    grafts)
                                        (graft (cons graft grafts))))
                                    '()
diff --git a/guix/store.scm b/guix/store.scm
index 014d08aaec..9b3879b4a7 100644
--- a/guix/store.scm
+++ b/guix/store.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2019, 2020 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2020 Florian Pelz <pelzflorian@pelzflorian.de>
+;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -821,8 +822,8 @@ encoding conversion errors."
                             (locale (false-if-exception (setlocale LC_ALL))))
   ;; Must be called after `open-connection'.
 
-  (define socket
-    (store-connection-socket server))
+  (define buffered
+    (store-connection-output-port server))
 
   (unless (unspecified? use-build-hook?)
     (warn-about-deprecation #:use-build-hook? #f
@@ -831,9 +832,9 @@ encoding conversion errors."
   (let-syntax ((send (syntax-rules ()
                        ((_ (type option) ...)
                         (begin
-                          (write-arg type option socket)
+                          (write-arg type option buffered)
                           ...)))))
-    (write-int (operation-id set-options) socket)
+    (write-int (operation-id set-options) buffered)
     (send (boolean keep-failed?) (boolean keep-going?)
           (boolean fallback?) (integer verbosity))
     (when (< (store-connection-minor-version server) #x61)
@@ -896,6 +897,7 @@ encoding conversion errors."
                            `(("locale" . ,locale))
                            '()))))
         (send (string-pairs pairs))))
+    (write-buffered-output server)
     (let loop ((done? (process-stderr server)))
       (or done? (process-stderr server)))))
 
@@ -1108,13 +1110,14 @@ path."
            ;; We don't use the 'operation' macro so we can pass SELECT? to
            ;; 'write-file'.
            (record-operation 'add-to-store)
-           (let ((port (store-connection-socket server)))
-             (write-int (operation-id add-to-store) port)
-             (write-string basename port)
-             (write-int 1 port)                   ;obsolete, must be #t
-             (write-int (if recursive? 1 0) port)
-             (write-string hash-algo port)
-             (write-file file-name port #:select? select?)
+           (let ((port (store-connection-socket server))
+                 (buffered (store-connection-output-port server)))
+             (write-int (operation-id add-to-store) buffered)
+             (write-string basename buffered)
+             (write-int 1 buffered)                   ;obsolete, must be #t
+             (write-int (if recursive? 1 0) buffered)
+             (write-string hash-algo buffered)
+             (write-file file-name buffered #:select? select?)
              (write-buffered-output server)
              (let loop ((done? (process-stderr server)))
                (or done? (loop (process-stderr server))))
@@ -1220,13 +1223,14 @@ an arbitrary directory layout in the store without creating a derivation."
         ;; We don't use the 'operation' macro so we can use 'write-file-tree'
         ;; instead of 'write-file'.
         (record-operation 'add-to-store/tree)
-        (let ((port (store-connection-socket server)))
-          (write-int (operation-id add-to-store) port)
-          (write-string basename port)
-          (write-int 1 port)                      ;obsolete, must be #t
-          (write-int (if recursive? 1 0) port)
-          (write-string hash-algo port)
-          (write-file-tree basename port
+        (let ((port (store-connection-socket server))
+              (buffered (store-connection-output-port server)))
+          (write-int (operation-id add-to-store) buffered)
+          (write-string basename buffered)
+          (write-int 1 buffered)                      ;obsolete, must be #t
+          (write-int (if recursive? 1 0) buffered)
+          (write-string hash-algo buffered)
+          (write-file-tree basename buffered
                            #:file-type+size file-type+size
                            #:file-port file-port
                            #:symlink-target symlink-target
@@ -1644,17 +1648,19 @@ the list of store paths to delete.  IGNORE-LIVENESS? should always be
 #f.  MIN-FREED is the minimum amount of disk space to be freed, in
 bytes, before the GC can stop.  Return the list of store paths delete,
 and the number of bytes freed."
-  (let ((s (store-connection-socket server)))
-    (write-int (operation-id collect-garbage) s)
-    (write-int action s)
-    (write-store-path-list to-delete s)
-    (write-arg boolean #f s)                      ; ignore-liveness?
-    (write-long-long min-freed s)
-    (write-int 0 s)                               ; obsolete
+  (let ((s (store-connection-socket server))
+        (buffered (store-connection-output-port server)))
+    (write-int (operation-id collect-garbage) buffered)
+    (write-int action buffered)
+    (write-store-path-list to-delete buffered)
+    (write-arg boolean #f buffered)                      ; ignore-liveness?
+    (write-long-long min-freed buffered)
+    (write-int 0 buffered)                               ; obsolete
     (when (>= (store-connection-minor-version server) 5)
       ;; Obsolete `use-atime' and `max-atime' parameters.
-      (write-int 0 s)
-      (write-int 0 s))
+      (write-int 0 buffered)
+      (write-int 0 buffered))
+    (write-buffered-output server)
 
     ;; Loop until the server is done sending error output.
     (let loop ((done? (process-stderr server)))
@@ -1711,10 +1717,12 @@ is raised if the set of paths read from PORT is not signed (as per
 
 (define* (export-path server path port #:key (sign? #t))
   "Export PATH to PORT.  When SIGN? is true, sign it."
-  (let ((s (store-connection-socket server)))
-    (write-int (operation-id export-path) s)
-    (write-store-path path s)
-    (write-arg boolean sign? s)
+  (let ((s (store-connection-socket server))
+        (buffered (store-connection-output-port server)))
+    (write-int (operation-id export-path) buffered)
+    (write-store-path path buffered)
+    (write-arg boolean sign? buffered)
+    (write-buffered-output server)
     (let loop ((done? (process-stderr server port)))
       (or done? (loop (process-stderr server port))))
     (= 1 (read-int s))))
diff --git a/guix/store/database.scm b/guix/store/database.scm
index ef52036ede..ad9ca68efe 100644
--- a/guix/store/database.scm
+++ b/guix/store/database.scm
@@ -99,27 +99,76 @@ create it and initialize it as a new database."
 ;; XXX: missing in guile-sqlite3@0.1.0
 (define SQLITE_BUSY 5)
 
-(define (call-with-transaction db proc)
-  "Start a transaction with DB (make as many attempts as necessary) and run
-PROC.  If PROC exits abnormally, abort the transaction, otherwise commit the
-transaction after it finishes."
+(define (call-with-SQLITE_BUSY-retrying thunk)
+  "Call THUNK, retrying as long as it exits abnormally due to SQLITE_BUSY
+errors."
   (catch 'sqlite-error
+    thunk
+    (lambda (key who code errmsg)
+      (if (= code SQLITE_BUSY)
+          (call-with-SQLITE_BUSY-retrying thunk)
+          (throw key who code errmsg)))))
+
+
+
+(define* (call-with-transaction db proc #:key restartable?)
+  "Start a transaction with DB and run PROC.  If PROC exits abnormally, abort
+the transaction, otherwise commit the transaction after it finishes.
+RESTARTABLE? may be set to a non-#f value when it is safe to run PROC multiple
+times.  This may reduce contention for the database somewhat."
+  (define (exec sql)
+    (with-statement db sql stmt
+      (sqlite-fold cons '() stmt)))
+  ;; We might use begin immediate here so that if we need to retry, we figure
+  ;; that out immediately rather than because some SQLITE_BUSY exception gets
+  ;; thrown partway through PROC - in which case the part already executed
+  ;; (which may contain side-effects!) might have to be executed again for
+  ;; every retry.
+  (exec (if restartable? "begin;" "begin immediate;"))
+  (catch #t
     (lambda ()
-      ;; We use begin immediate here so that if we need to retry, we
-      ;; figure that out immediately rather than because some SQLITE_BUSY
-      ;; exception gets thrown partway through PROC - in which case the
-      ;; part already executed (which may contain side-effects!) would be
-      ;; executed again for every retry.
-      (sqlite-exec db "begin immediate;")
-      (let ((result (proc)))
-        (sqlite-exec db "commit;")
-        result))
-    (lambda (key who error description)
-      (if (= error SQLITE_BUSY)
-          (call-with-transaction db proc)
-          (begin
-            (sqlite-exec db "rollback;")
-            (throw 'sqlite-error who error description))))))
+      (let-values ((result (proc)))
+        (exec "commit;")
+        (apply values result)))
+    (lambda args
+      ;; The roll back may or may not have occurred automatically when the
+      ;; error was generated. If it has occurred, this does nothing but signal
+      ;; an error. If it hasn't occurred, this needs to be done.
+      (false-if-exception (exec "rollback;"))
+      (apply throw args))))
+
+(define* (call-with-savepoint db proc
+                              #:optional (savepoint-name "SomeSavepoint"))
+  "Call PROC after creating a savepoint named SAVEPOINT-NAME.  If PROC exits
+abnormally, rollback to that savepoint.  In all cases, remove the savepoint
+prior to returning."
+  (define (exec sql)
+    (with-statement db sql stmt
+      (sqlite-fold cons '() stmt)))
+
+  (dynamic-wind
+    (lambda ()
+      (exec (string-append "SAVEPOINT " savepoint-name ";")))
+    (lambda ()
+      (catch #t
+        proc
+        (lambda args
+          (exec (string-append "ROLLBACK TO " savepoint-name ";"))
+          (apply throw args))))
+    (lambda ()
+      (exec (string-append "RELEASE " savepoint-name ";")))))
+
+(define* (call-with-retrying-transaction db proc #:key restartable?)
+  (call-with-SQLITE_BUSY-retrying
+   (lambda ()
+     (call-with-transaction db proc #:restartable? restartable?))))
+
+(define* (call-with-retrying-savepoint db proc
+                                       #:optional (savepoint-name
+                                                   "SomeSavepoint"))
+  (call-with-SQLITE_BUSY-retrying
+   (lambda ()
+     (call-with-savepoint db proc savepoint-name))))
 
 (define %default-database-file
   ;; Default location of the store database.
@@ -130,14 +179,37 @@ transaction after it finishes."
 If FILE doesn't exist, create it and initialize it as a new database."
   (call-with-database file (lambda (db) exp ...)))
 
+(define (sqlite-finalize stmt)
+  ;; As of guile-sqlite3 0.1.0, cached statements aren't reset when
+  ;; sqlite-finalize is invoked on them (see
+  ;; https://notabug.org/guile-sqlite3/guile-sqlite3/issues/12).  This can
+  ;; cause problems with automatically-started transactions, so we work around
+  ;; it by wrapping sqlite-finalize so that sqlite-reset is always called.
+  ;; This always works, because resetting a statement twice has no adverse
+  ;; effects.  We can remove this once the fixed guile-sqlite3 is widespread.
+  (sqlite-reset stmt)
+  ((@ (sqlite3) sqlite-finalize) stmt))
+
+(define (call-with-statement db sql proc)
+  (let ((stmt (sqlite-prepare db sql #:cache? #t)))
+    (dynamic-wind
+      (const #t)
+      (lambda ()
+        (proc stmt))
+      (lambda ()
+        (sqlite-finalize stmt)))))
+
+(define-syntax-rule (with-statement db sql stmt exp ...)
+  "Run EXP... with STMT bound to a prepared statement corresponding to the sql
+string SQL for DB."
+  (call-with-statement db sql
+                       (lambda (stmt) exp ...)))
+
 (define (last-insert-row-id db)
   ;; XXX: (sqlite3) currently lacks bindings for 'sqlite3_last_insert_rowid'.
   ;; Work around that.
-  (let* ((stmt   (sqlite-prepare db "SELECT last_insert_rowid();"
-                                 #:cache? #t))
-         (result (sqlite-fold cons '() stmt)))
-    (sqlite-finalize stmt)
-    (match result
+  (with-statement db "SELECT last_insert_rowid();" stmt
+    (match (sqlite-fold cons '() stmt)
       ((#(id)) id)
       (_ #f))))
 
@@ -147,13 +219,11 @@ If FILE doesn't exist, create it and initialize it as a new database."
 (define* (path-id db path)
   "If PATH exists in the 'ValidPaths' table, return its numerical
 identifier.  Otherwise, return #f."
-  (let ((stmt (sqlite-prepare db path-id-sql #:cache? #t)))
+  (with-statement db path-id-sql stmt
     (sqlite-bind-arguments stmt #:path path)
-    (let ((result (sqlite-fold cons '() stmt)))
-      (sqlite-finalize stmt)
-      (match result
-        ((#(id) . _) id)
-        (_ #f)))))
+    (match (sqlite-fold cons '() stmt)
+      ((#(id) . _) id)
+      (_ #f))))
 
 (define update-sql
   "UPDATE ValidPaths SET hash = :hash, registrationTime = :time, deriver =
@@ -168,22 +238,41 @@ VALUES (:path, :hash, :time, :deriver, :size)")
 doesn't exactly have... they've got something close, but it involves deleting
 and re-inserting instead of updating, which causes problems with foreign keys,
 of course. Returns the row id of the row that was modified or inserted."
-  (let ((id (path-id db path)))
-    (if id
-        (let ((stmt (sqlite-prepare db update-sql #:cache? #t)))
-          (sqlite-bind-arguments stmt #:id id
-                                 #:deriver deriver
-                                 #:hash hash #:size nar-size #:time time)
-          (sqlite-fold cons '() stmt)
-          (sqlite-finalize stmt)
-          (last-insert-row-id db))
-        (let ((stmt (sqlite-prepare db insert-sql #:cache? #t)))
-          (sqlite-bind-arguments stmt
-                                 #:path path #:deriver deriver
-                                 #:hash hash #:size nar-size #:time time)
-          (sqlite-fold cons '() stmt)             ;execute it
-          (sqlite-finalize stmt)
-          (last-insert-row-id db)))))
+
+  ;; It's important that querying the path-id and the insert/update operation
+  ;; take place in the same transaction, as otherwise some other
+  ;; process/thread/fiber could register the same path between when we check
+  ;; whether it's already registered and when we register it, resulting in
+  ;; duplicate paths (which, due to a 'unique' constraint, would cause an
+  ;; exception to be thrown). With the default journaling mode this will
+  ;; prevent writes from occurring during that sensitive time, but with WAL
+  ;; mode it will instead arrange to return SQLITE_BUSY when a write occurs
+  ;; between the start of a read transaction and its upgrading to a write
+  ;; transaction (see https://sqlite.org/rescode.html#busy_snapshot).
+  ;; Experimentally, it seems this SQLITE_BUSY will ignore a busy_timeout and
+  ;; immediately return (makes sense, since waiting won't change anything).
+
+  ;; Note that when that kind of SQLITE_BUSY error is returned, it will keep
+  ;; being returned every time we try to upgrade the same outermost
+  ;; transaction to a write transaction.  So when retrying, we have to restart
+  ;; the *outermost* write transaction.  We can't inherently tell whether
+  ;; we're the outermost write transaction, so we leave the retry-handling to
+  ;; the caller.
+  (call-with-savepoint db
+    (lambda ()
+      (let ((id (path-id db path)))
+        (if id
+            (with-statement db update-sql stmt
+              (sqlite-bind-arguments stmt #:id id
+                                     #:deriver deriver
+                                     #:hash hash #:size nar-size #:time time)
+              (sqlite-fold cons '() stmt))
+            (with-statement db insert-sql stmt
+              (sqlite-bind-arguments stmt
+                                     #:path path #:deriver deriver
+                                     #:hash hash #:size nar-size #:time time)
+              (sqlite-fold cons '() stmt)))
+        (last-insert-row-id db)))))
 
 (define add-reference-sql
   "INSERT OR REPLACE INTO Refs (referrer, reference) VALUES (:referrer, :reference);")
@@ -191,15 +280,13 @@ of course. Returns the row id of the row that was modified or inserted."
 (define (add-references db referrer references)
   "REFERRER is the id of the referring store item, REFERENCES is a list
 ids of items referred to."
-  (let ((stmt (sqlite-prepare db add-reference-sql #:cache? #t)))
+  (with-statement db add-reference-sql stmt
     (for-each (lambda (reference)
                 (sqlite-reset stmt)
                 (sqlite-bind-arguments stmt #:referrer referrer
                                        #:reference reference)
-                (sqlite-fold cons '() stmt)       ;execute it
-                (last-insert-row-id db))
-              references)
-    (sqlite-finalize stmt)))
+                (sqlite-fold cons '() stmt))
+              references)))
 
 (define* (sqlite-register db #:key path (references '())
                           deriver hash nar-size time)
@@ -354,7 +441,7 @@ Write a progress report to LOG-PORT."
   (mkdir-p db-dir)
   (parameterize ((sql-schema schema))
     (with-database (string-append db-dir "/db.sqlite") db
-      (call-with-transaction db
+      (call-with-retrying-transaction db
           (lambda ()
             (let* ((prefix   (format #f "registering ~a items" (length items)))
                    (progress (progress-reporter/bar (length items)