bein (empty) → 0.1

raw patch · 8 files changed

+1124/−0 lines, 8 filesdep +Cryptodep +HDBCdep +HDBC-postgresqlsetup-changed

Dependencies added: Crypto, HDBC, HDBC-postgresql, base, bytestring, containers, convertible, directory, filepath, happstack-server, happstack-util, hdaemonize, hsyslog, mtl, network, old-locale, parsec, process, random, stm, time, unix, utf8-string, xhtml

Files

Bein/BeinClient.hs +39/−0
Bein/BeinCtl.hs +165/−0
Bein/Daemon.hs +30/−0
Bein/Minion.hs +119/−0
Bein/Web.hs +46/−0
LICENSE +674/−0
Setup.lhs +3/−0
bein.cabal +48/−0

+ Bein/BeinClient.hs view

@@ -0,0 +1,39 @@+module Main where++import Control.Monad+import Network.Socket+import System.Environment (getArgs)+import System.Exit (exitSuccess)+import System.IO (hPutStrLn, hGetLine, hFlush, Handle, IOMode(ReadWriteMode), hSetBuffering, BufferMode(LineBuffering), stdin, stdout)++help :: IO a+help = putStrLn "Usage: MutualAuthClient socketfile" >> exitSuccess++getSocketFile :: IO String+getSocketFile = do +  args <- getArgs+  case args of+    [] -> help+    [x] -> return x+    _ -> help++main :: IO b+main = do+  socketName <- getSocketFile+  s <- socket AF_UNIX Stream 0+  connect s (SockAddrUnix socketName)+  h <- socketToHandle s ReadWriteMode+  hSetBuffering h LineBuffering+  forever $ interactOnHandle h++whileM :: IO Bool -> IO () -> IO ()+whileM p v = p >>= \b -> if b then v >> whileM p v else return ()++interactOnHandle :: Handle -> IO ()    +interactOnHandle h = putStrLn "Listening." >> transput stdin h >> putStrLn "Receiving." >> transput h stdout >> interactOnHandle h++transput :: Handle -> Handle -> IO ()+transput from to = do l <- hGetLine from+                      hPutStrLn to l+                      if l == "." then hFlush to else transput from to+

+ Bein/BeinCtl.hs view

@@ -0,0 +1,165 @@+-- This file is part of Bein.+--+-- Bein is free software: you can redistribute it and/or modify+-- it under the terms of the GNU General Public License as published by+-- the Free Software Foundation, either version 3 of the License, or+-- (at your option) any later version.+--    +-- Bein is distributed in the hope that it will be useful,+-- but WITHOUT ANY WARRANTY; without even the implied warranty of+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+-- GNU General Public License for more details.+--+-- You should have received a copy of the GNU General Public License+-- along with Bein.  If not, see <http://www.gnu.org/licenses/>.+++module Main where++import Data.Maybe (fromJust)+import System.FilePath+import System.Exit ( exitSuccess, exitFailure )+import System.IO ( hPutStrLn, stderr )+import System.Directory+import System.Console.GetOpt+import Database.HDBC+import Database.HDBC.PostgreSQL+import System.Environment (getArgs, getProgName)+import Bein.ShellScripting+import System.Posix.Files+import Bein.Configuration++data State = State { sqlDir :: Maybe FilePath,+                     outputFile :: Maybe FilePath,+                     verbose :: Bool } deriving (Eq,Show,Read)++defaultState :: State+defaultState = State { sqlDir = Nothing,+                       outputFile = Nothing,+                       verbose = False }++main :: IO ()+main = do (cmd,st) <- getState+          cmd st+            +getState :: IO (State -> IO (), State)+getState = do+  args <- getArgs+  case getOpt RequireOrder options args of+    (actions, [commandTxt], []) -> do opts <- foldl (>>=) (return defaultState) actions+                                      let command = parseCmd commandTxt+                                      case () of+                                        _ | (commandTxt `elem` ["init","cold-init","reload","deep-reload"]) && sqlDir opts == Nothing ->+                                          printHelpAndDie (Just "Must give an SQL source directory to init database.")+                                        _ | (commandTxt == "dump" && outputFile opts == Nothing) ->+                                          printHelpAndDie (Just "Must give a file to dump database to with -o option.")+                                        _ -> return (command,opts)+    (_, _, []) -> printHelpAndDie (Just "beinctl takes exactly one command.")+    (_, _, errs) -> printHelpAndDie (Just $ concat errs)++options :: [OptDescr (State -> IO State)]+options = [+  Option "h" ["help"]+         (NoArg (\_ -> printHelpAndDie Nothing))+         "Show help",+  Option "v" ["verbose"]+         (NoArg (\opt -> return opt { verbose = True }))+         "Be verbose.",+  Option "o" ["output"]+         (ReqArg (\arg opt -> return opt { outputFile = Just arg }) "OUTPUTFILE")+         "File to dump database to.",+  Option "d" ["sqldir"]+         (ReqArg (\arg opt -> do b <- doesDirectoryExist arg+                                 if b then return opt { sqlDir = Just arg }+                                   else printHelpAndDie (Just $ "Invalid directory: " ++ arg)) "SQLDIRECTORY")+         "Directory containing SQL source."+  ]++printHelpAndDie :: Maybe String -> IO a+printHelpAndDie msg = do+    case msg of+      Nothing -> help >> exitSuccess+      Just m -> hPutStrLn stderr m >> help >> exitFailure+    where help = do +            programName <- getProgName+            hPutStrLn stderr (usageInfo (programName ++ " [-hvd] command") options)+            printCommands++parseCmd :: String -> (State -> IO ())+parseCmd "cold-init" = coldInitialize+parseCmd "init" = initialize+parseCmd "teardown" = teardown+parseCmd "full-teardown" = fullTeardown+parseCmd "dump" = dump+parseCmd "reload" = reload+parseCmd "deep-reload" = deepReload+parseCmd "show-config" = showConfig+parseCmd cmd = \_ -> printHelpAndDie (Just ("Unknown command: " ++ cmd))++printCommands :: IO ()+printCommands = do+  mapM_ putStrLn +    ["  where command is one of:",+     "    init            - create Bein database ready for loading",+     "    cold-init       - create Bein database from scratch, including users",+     "    teardown        - delete the Bein database",+     "    full-teardown   - delete the Bein database and all users, leaving system pristine",+     "    dump            - dump data in the database to tar archive file", +     "    reload          - same as teardown followed by init",+     "    deep-reload     - same as full-teardown followed by cold-init",+     "    show-config     - print the system configuration from the database"]+    +coldInitialize :: State -> IO ()+coldInitialize st = do+  nologin <- takeFirstM fileExist ["/sbin/nologin", "/usr/sbin/nologin"]+  systemM_ $ "useradd --system -M --user-group --shell " ++ nologin ++ " bein"+  systemM_ $ "sudo -u postgres createuser --no-superuser --login bein --no-createdb --no-createrole --no-superuser"+  initialize st+  +initialize :: State -> IO ()+initialize State { sqlDir = Nothing } = +  printHelpAndDie (Just "Cannot initialize database without SQL directory.  Set -d option.")+initialize State { sqlDir = Just d, verbose = v } = do+  let inPath p = joinPath [d,p]+      unlessVerbose p = if v then "" else p+  systemM $ "sudo -u postgres createdb --owner bein bein"+  systemM $ "sudo -u postgres createlang plpgsql bein"+  systemM $ "sudo -u postgres createlang plpythonu bein"+  systemM $ "sudo -u bein psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file " ++ inPath "core_tables.sql"+  systemM $ "sudo -u postgres psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file "++ inPath "untrusted_functions.sql"+  systemM $ "sudo -u bein psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file " ++ inPath "triggers.sql"+  systemM $ "sudo -u bein psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file " ++ inPath "utility_functions.sql"++fullTeardown :: State -> IO ()+fullTeardown st = do+  teardown st+  systemM_ $ "userdel bein"+  systemM_ $ "groupdel bein"+  systemM_ $ "sudo -u postgres dropuser bein"++teardown :: State -> IO ()+teardown _ = do+  systemM_ $ "sudo -u postgres dropdb bein"++dump :: State -> IO ()+dump st = do+  systemM_ $ "sudo -u bein pg_dump --format=t -f " ++ fromJust (outputFile st) ++ " bein"++reload :: State -> IO ()+reload st = teardown st >> initialize st++deepReload :: State -> IO ()+deepReload st = fullTeardown st >> coldInitialize st++dbCommand :: (Connection -> IO a) -> IO ()+dbCommand cmd = do conn <- connectPostgreSQL "dbname=bein"+                   _ <- cmd conn+                   commit conn++showConfig :: State -> IO ()+showConfig _ = dbCommand (\conn -> readConfiguration conn >>= putStrLn . show)++takeFirstM :: Monad m => (a -> m Bool) -> [a] -> m a+takeFirstM _ [] = fail $ "Nothing in list succeeds."+takeFirstM f (c:cs) = f c >>= \r ->+  if r then return c else takeFirstM f cs

+ Bein/Daemon.hs view

@@ -0,0 +1,30 @@+{-# LANGUAGE ScopedTypeVariables #-}+module Main where++import Control.Concurrent.QSem+import System.Posix.Daemonize (serviced,CreateDaemon(..), simpleDaemon)+import Bein.Daemon.SignalHandlers (installSignalHandlers)+import Bein.Daemon.Protocol+import Bein.Daemon.Types +import Bein.SocketHandler (listenWith)+import Control.Monad.Reader (ReaderT(..))+import Control.Concurrent.STM+import Database.HDBC.PostgreSQL+import Bein.Configuration++main :: IO ()+main = serviced $ simpleDaemon { program = beind, user = Just "bein", group = Just "bein" }++beind :: IO ()+beind = getState >>= runReaderT beind'+  where beind' = do installSignalHandlers+                    socketFile <- configField daemon_port+                    listenWith daemonProtocol socketFile++getState :: IO DaemonState  +getState = do+  conn <- connectPostgreSQL "dbname=bein"+  config <- readConfiguration conn+  configTV <- newTVarIO config+  sem <- newQSem 1+  return $ State { stDb = conn, stConfigT = configTV, stSem = sem }

+ Bein/Minion.hs view

@@ -0,0 +1,119 @@+-- Add setting status to running in db, and checking state and finalizing status when doing cleanup+module Main where++import Database.HDBC+import System.Posix.Syslog+import System.Environment (getProgName)+import Control.Monad.Reader+import Database.HDBC.PostgreSQL+import Control.Concurrent.STM+import System.Exit (ExitCode(..))+import System.Directory+import System.Posix.Signals+import System.Posix.Process+import System.FilePath.Posix (joinPath)++import Bein.Configuration+import Bein.Minion.Types+import Bein.Minion.Arguments+import Bein.SocketHandler+import Bein.Minion.Commands+import Bein.Minion.Protocol++main :: IO ()+main = do+  getSettings >>= getState >>= \st -> do+    programName <- getProgName+    withSyslog programName [PID,PERROR] DAEMON $ runReaderT main' st+      +getState :: Settings -> IO State+getState opts = do+  conn <- connectPostgreSQL "dbname=bein"+  config <- readConfiguration conn+  configTV <- newTVarIO config+  minP <- newTVarIO Nothing+  return $ State { stDb = conn, stConfigT = configTV, stSettings = opts, stMinionPid = minP }++main' :: ReaderT State IO b+main' = do +  execution >>= \e -> checkExecution e >>= \r -> case r of+    Left errors -> dieWith errors+    Right _ -> do installHandlers+                  scratchDir >>= createScratchDirectory+                  script <- execution >>= \_ -> scratchDir >>= \s -> writeScript e s+                  forkR $ minionSocket >>= listenWith minionProtocol+                  runScript script+                  forever $ return () -- Doing this requires using exitImmediately to kill the program when we're done.++checkExecution :: ExecutionID -> BeinM State (Either String ())+checkExecution ex = do+  [notFuture, isWaiting, nonemptyScript, noNullInputs] <- +    liftM (map fromSql) $ receiveOneRow $ query queryString [toSql ex]+  let errors = concat $ map snd $ filter (not.fst) $+               [(notFuture, "Execution " ++ show ex ++ " is not a future.\n"),+                (isWaiting, "Execution " ++ show ex ++ " is not waiting.\n"),+                (nonemptyScript, "Execution " ++ show ex ++ +                                 " refers to a program with an empty script.\n"),+                (noNullInputs, "Execution " ++ show ex ++ " has null inputs.\n")]+    in if (notFuture && isWaiting && nonemptyScript && noNullInputs) +         then do verboseMsgLn "Setting status to running."+                 update "update executions set status = 'running' where id=?" [toSql ex]+                 return (Right ())+         else return (Left errors)+    where queryString = "select not_future, is_waiting, nonempty_script, " ++ +                        "no_null_inputs from runnable where id = ?"++installHandlers :: BeinM State ()+installHandlers = ask >>= \s -> do +  verboseMsg "Installing handlers..."+  mapM_ ignoreSignal [sigALRM, sigPIPE, sigPOLL, sigPROF, sigUSR1, sigUSR2, sigVTALRM]+  liftIO $ installHandler sigCHLD (Catch $ runReaderT sigCHLDHandler s) (Just fullSignalSet)+  liftIO $ installHandler sigHUP (Catch $ runReaderT (cleanUp (ExitFailure 1)) s) (Just fullSignalSet)+  liftIO $ installHandler sigTERM (Catch $ runReaderT (cleanUp (ExitFailure 1)) s) (Just fullSignalSet)+  verboseMsgLn "ok"++sigCHLDHandler :: BeinM State ()+sigCHLDHandler = do+  v <- liftIO $ getAnyProcessStatus False False+  case v of+    Just (pid,status) -> do +      minionPid >>= \p -> if p /= Just pid +        then verboseMsgLn "Received sigCHLD from something besides script." >> sigCHLDHandler+        else (verboseMsgLn $ "Child exited with status " ++ show status) >> cleanUp ExitSuccess+    Nothing -> return ()+                                                  ++createScratchDirectory :: FilePath -> BeinM State ()+createScratchDirectory dir = do+  verboseMsg $ "Creating scratch directory " ++ dir ++ "..."+  (liftIO $ createDirectory dir) `catchR` +    (\e -> dieWith $ "Could not create scratch directory.\n" ++ show e)+  (liftIO $ setCurrentDirectory dir) `catchR` +    (\e -> dieWith $ "Could not set working directory.\n" ++ show e)+  verboseMsgLn "ok"++writeScript :: ExecutionID -> FilePath -> BeinM State FilePath+writeScript ex dir = do +  verboseMsg $ "Writing script to " ++ dir ++ "..."+  [lang,script] <- liftM (map fromSql) $ receiveOneRow $ query queryString [toSql ex]+  let scriptName = case lang of+        "perl" -> "script.pl"+        "r" -> "script.R"+        _ -> error "Invalid value for language."+  scriptPath <- scratchDir >>= (\d -> return $ joinPath [d,scriptName])+  liftIO $ writeFile scriptPath script+  verboseMsgLn "ok"+  return scriptPath+    where queryString = "select p.language,p.script from programs " ++ +                        "as p join executions as e on e.program=p.id where e.id=?"+                     +runScript :: FilePath -> BeinM State ()+runScript script = do+  verboseMsg $ "Running script " ++ script ++ "..."+  perlCmd <- configField perl_executable+  minionPort <- configField minion_port+  p <- liftIO $ forkProcess $ executeFile perlCmd False [script,minionPort] Nothing+  writeMinionPid p+  verboseMsgLn "ok"++

+ Bein/Web.hs view

@@ -0,0 +1,46 @@+module Main where++import Bein.Web.Types+import Bein.Web.Commands+import Bein.Web.Routing+import qualified System.Posix.Daemonize as D+import Happstack.Server+import Control.Concurrent+import Control.Monad.Trans+import Control.Monad.Reader+import Control.Concurrent.STM+import Database.HDBC.PostgreSQL+import Bein.Configuration+import Network+import System.IO++main :: IO ()+main = D.serviced $ D.simpleDaemon { D.program = httpd, D.user = Just "bein", D.group = Just "bein" }++getPort :: WebState -> IO Int+getPort st = (liftIO.atomically.readTVar.configT) st >>= return.http_port++httpd :: IO ()+httpd = getState >>= \s -> do +  p <- getPort s+  runReaderT sessionExpirer s+  simpleHTTP' (\a -> runReaderT a s) (Conf p Nothing) routing++sessionExpirer :: BeinM WebState ThreadId+sessionExpirer = forkR f+  where f = do update "select remove_expired_sessions()" []+               liftIO $ threadDelay (5*60*1000000)+               f++getState :: IO WebState+getState = do+  conn <- connectPostgreSQL "dbname=bein"+  config <- readConfiguration conn+  configTV <- newTVarIO config+  sockMV <- (connectTo "" (UnixSocket (daemon_port config)) >>= \h -> do+                hSetBuffering h LineBuffering                                       +                newMVar h) `catch` (\_ -> newEmptyMVar)+  return $ WebState { stDb = conn, stConfigT = configTV, stDaemonPort = sockMV, +                      stObject = undefined, stUser = Nothing }++

+ LICENSE view

@@ -0,0 +1,674 @@+                    GNU GENERAL PUBLIC LICENSE+                       Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.++                            Preamble++  The GNU General Public License is a free, copyleft license for+software and other kinds of works.++  The licenses for most software and other practical works are designed+to take away your freedom to share and change the works.  By contrast,+the GNU General Public License is intended to guarantee your freedom to+share and change all versions of a program--to make sure it remains free+software for all its users.  We, the Free Software Foundation, use the+GNU General Public License for most of our software; it applies also to+any other work released this way by its authors.  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+ Setup.lhs view

@@ -0,0 +1,3 @@+#!/usr/bin/env runhaskell+> import Distribution.Simple+> main = defaultMain

+ bein.cabal view

@@ -0,0 +1,48 @@+name:                bein+version:             0.1+synopsis:            Bein is a provenance and workflow management system for bioinformatics.+description:         To avoid having thousands of files produced in a random way from a bunch of scripts, as is typically the case for a bioinformaticist, Bein keeps track of scripts, and their executions on various inputs.  It provides a web front end, and will integrate with LSF clusters.+category:            Application+license:             GPL-3+license-file:        LICENSE+author:              Fred Ross+maintainer:          fred.ross@epfl.ch+build-type:          Simple+Cabal-Version:       >= 1.4++Executable beinctl+  Main-is:           Bein/BeinCtl.hs+  Build-Depends:     base >= 3 && < 5, HDBC, HDBC-postgresql, process+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread+  Hs-Source-Dirs:    .+  extra-libraries:   pgport xslt xml2 pam ssl crypto krb5 com_err gssapi_krb5 z readline crypt dl m++Executable beind+  Main-is:           Bein/Daemon.hs+  Build-Depends:     base >= 3 && < 5, HDBC, HDBC-postgresql, process,+                     hdaemonize >= 0.3, hsyslog, parsec, random, unix, network,+                     convertible, stm, mtl, filepath+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread+  Hs-Source-Dirs:    .++Executable beinclient+  Main-is:           Bein/BeinClient.hs+  Build-Depends:     base >= 3 && < 5, network+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread+  Hs-Source-Dirs:    .++Executable beinminion+  Main-is:           Bein/Minion.hs+  Build-Depends:     base >= 3 && < 5, network, hsyslog, parsec, HDBC,+                     HDBC-postgresql, process, unix, stm, mtl, filepath, directory+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread+  Hs-Source-Dirs:    .++Executable beinhttpd+  Main-is:           Bein/Web.hs+  Build-Depends:     base >= 3 && < 5, HDBC, HDBC-postgresql, unix, stm, mtl, filepath,+                     directory, hsyslog, hdaemonize, happstack-server, Crypto,+                     happstack-util, containers, xhtml, time, old-locale, utf8-string,+                     bytestring+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread+  Hs-Source-Dirs:    .