Poseidon version cli for validate and jannocoalesce

src-executables/Main-trident.hs

@@ -273,7 +273,7 @@ serveOptParser = ServeOptions <$> parseArchiveConfig
 jannocoalesceOptParser :: OP.Parser JannoCoalesceOptions
 jannocoalesceOptParser = JannoCoalesceOptions <$> parseJannocoalSourceSpec
                                               <*> parseJannocoalTargetFile
-                                              <*> parseJannocoalOutSpec
+                                              <*> parseJannocoalOutFile
                                               <*> parseJannocoalJannoColumns
                                               <*> parseJannocoalOverride
                                               <*> parseJannocoalSourceKey

src/Poseidon/CLI/Jannocoalesce.hs

@@ -10,6 +10,8 @@ import           Poseidon.Package         (PackageReadOptions (..),
                                            defaultPackageReadOptions,
                                            getJointJanno,
                                            readPoseidonPackageCollection)
+import           Poseidon.PoseidonVersion (VersionedFile (..),
+                                           latestPoseidonVersion)
 import           Poseidon.Utils           (PoseidonException (..), PoseidonIO,
                                            logDebug, logInfo, logWarning)
 
@@ -22,13 +24,12 @@ import qualified Data.HashMap.Strict      as HM
 import qualified Data.IORef               as R
 import           Data.List                ((\\))
 import           Data.Text                (pack, replace, unpack)
-import           Poseidon.PoseidonVersion (latestPoseidonVersion)
 import           System.Directory         (createDirectoryIfMissing)
 import           System.FilePath          (takeDirectory)
 import           Text.Regex.TDFA          ((=~))
 
 -- the source can be a single janno file, or a set of base directories as usual.
-data JannoSourceSpec = JannoSourceSingle FilePath | JannoSourceBaseDirs [FilePath]
+data JannoSourceSpec = JannoSourceSingle VersionedFile | JannoSourceBaseDirs [FilePath]
 
 data CoalesceJannoColumnSpec =
       AllJannoColumns
@@ -37,8 +38,8 @@ data CoalesceJannoColumnSpec =
 
 data JannoCoalesceOptions = JannoCoalesceOptions
     { _jannocoalesceSource           :: JannoSourceSpec
-    , _jannocoalesceTarget           :: FilePath
-    , _jannocoalesceOutSpec          :: Maybe FilePath -- Nothing means "in place"
+    , _jannocoalesceTarget           :: VersionedFile
+    , _jannocoalesceOutFile          :: FilePath
     , _jannocoalesceJannoColumns     :: CoalesceJannoColumnSpec
     , _jannocoalesceOverwriteColumns :: Bool
     , _jannocoalesceSourceKey        :: String -- by default set to "Poseidon_ID"
@@ -47,9 +48,9 @@ data JannoCoalesceOptions = JannoCoalesceOptions
     }
 
 runJannocoalesce :: JannoCoalesceOptions -> PoseidonIO ()
-runJannocoalesce (JannoCoalesceOptions sourceSpec target outSpec fields overwrite sKey tKey maybeStrip) = do
+runJannocoalesce (JannoCoalesceOptions sourceSpec (VersionedFile targetPV targetPath) outPath fields overwrite sKey tKey maybeStrip) = do
     JannoRows sourceRows <- case sourceSpec of
-        JannoSourceSingle sourceFile -> readJannoFile latestPoseidonVersion [] sourceFile
+        JannoSourceSingle (VersionedFile sourcePV sourcePath) -> readJannoFile sourcePV [] sourcePath
         JannoSourceBaseDirs sourceDirs -> do
             let pacReadOpts = defaultPackageReadOptions {
                       _readOptIgnoreChecksums      = True
@@ -58,11 +59,10 @@ runJannocoalesce (JannoCoalesceOptions sourceSpec target outSpec fields overwrit
                     , _readOptOnlyLatest           = True
                 }
             getJointJanno <$> readPoseidonPackageCollection pacReadOpts sourceDirs
-    JannoRows targetRows <- readJannoFile latestPoseidonVersion [] target
+    JannoRows targetRows <- readJannoFile targetPV [] targetPath
 
     newJanno <- makeNewJannoRows sourceRows targetRows fields overwrite sKey tKey maybeStrip
 
-    let outPath = maybe target id outSpec
     logInfo $ "Writing to file (directory will be created if missing): " ++ outPath
     liftIO $ do
         createDirectoryIfMissing True (takeDirectory outPath)

src/Poseidon/CLI/OptparseApplicativeParsers.hs

@@ -24,6 +24,7 @@ import           Poseidon.GenotypeData      (GenoDataSource (..),
                                              GenotypeFileSpec (..),
                                              GenotypeOutFormatSpec (..),
                                              SNPSetSpec (..))
+import           Poseidon.PoseidonVersion
 import           Poseidon.ServerClient      (AddColSpec (..),
                                              ArchiveEndpoint (..))
 import           Poseidon.Utils             (ErrorLength (..), LogMode (..),
@@ -37,7 +38,7 @@ import           Control.Applicative        ((<|>))
 import qualified Data.ByteString.Char8      as Bchs
 import           Data.List                  (intercalate)
 import           Data.List.Split            (splitOn)
-import           Data.Version               (Version)
+import           Data.Version               (Version, makeVersion)
 import qualified Options.Applicative        as OP
 import           SequenceFormats.Plink      (PlinkPopNameMode (PlinkPopNameAsBoth, PlinkPopNameAsFamily, PlinkPopNameAsPhenotype))
 import           System.FilePath            (splitExtension, splitExtensions,
@@ -434,18 +435,33 @@ parseInPoseidonYamlFile = OP.strOption (
     OP.metavar "FILE" <>
     OP.help "Path to a POSEIDON.yml file.")
 
-parseInJannoFile :: OP.Parser FilePath
-parseInJannoFile = OP.strOption (
+parseInJannoFile :: OP.Parser VersionedFile
+parseInJannoFile = VersionedFile <$> parsePoseidonVersion "pvJanno" <*> OP.strOption (
     OP.long "janno" <>
     OP.metavar "FILE" <>
     OP.help "Path to a .janno file.")
 
-parseInSSFile :: OP.Parser FilePath
-parseInSSFile = OP.strOption (
+parseInSSFile :: OP.Parser VersionedFile
+parseInSSFile = VersionedFile <$> parsePoseidonVersion "pvSSF" <*> OP.strOption (
     OP.long "ssf" <>
     OP.metavar "FILE" <>
     OP.help "Path to a .ssf file.")
 
+parsePoseidonVersion :: String -> OP.Parser PoseidonVersion
+parsePoseidonVersion longName = OP.option (OP.eitherReader parsePV) (
+    OP.long longName <>
+    OP.metavar "VERSION" <>
+    OP.help "Poseidon version (e.g. 2.7.1)." <>
+    OP.value latestPoseidonVersion <>
+    OP.showDefaultWith showPoseidonVersion)
+  where
+    parsePV s = case readVersion s of
+        Just v -> if PoseidonVersion v `elem` validPoseidonVersions
+                  then Right (PoseidonVersion v)
+                  else Left $ "must be one of " ++ intercalate ", " (map showPoseidonVersion validPoseidonVersions)
+        Nothing -> Left "invalid version string"
+    readVersion = fmap makeVersion . traverse readMaybe . splitOn "."
+
 parseInBibFile :: OP.Parser FilePath
 parseInBibFile = OP.strOption (
     OP.long "bib" <>
@@ -879,31 +895,34 @@ parseMaybeArchiveName = OP.option (Just <$> OP.str) (
 
 parseJannocoalSourceSpec :: OP.Parser JannoSourceSpec
 parseJannocoalSourceSpec = parseJannocoalSingleSource <|> (JannoSourceBaseDirs <$> parseBasePaths)
-  where
-    parseJannocoalSingleSource = OP.option (JannoSourceSingle <$> OP.str) (
-        OP.long "sourceFile" <>
-        OP.short 's' <>
-        OP.metavar "FILE" <>
-        OP.help "The source .janno file."
-        )
-
-parseJannocoalTargetFile :: OP.Parser FilePath
-parseJannocoalTargetFile = OP.strOption (
+    where
+        parseJannocoalSingleSource :: OP.Parser JannoSourceSpec
+        parseJannocoalSingleSource =
+            JannoSourceSingle <$> (VersionedFile <$> parsePoseidonVersion "pvSource" <*> OP.strOption (
+                OP.long "sourceFile" <>
+                OP.short 's' <>
+                OP.metavar "FILE" <>
+                OP.help "The source .janno file."
+                ))
+
+parseJannocoalTargetFile :: OP.Parser VersionedFile
+parseJannocoalTargetFile = VersionedFile <$> parsePoseidonVersion "pvTarget" <*> OP.strOption (
     OP.long "targetFile" <>
     OP.short 't' <>
     OP.metavar "FILE" <>
     OP.help "The target .janno file to fill."
     )
 
-parseJannocoalOutSpec :: OP.Parser (Maybe FilePath)
-parseJannocoalOutSpec = OP.option (Just <$> OP.str) (
+parseJannocoalOutFile :: OP.Parser FilePath
+parseJannocoalOutFile = OP.strOption (
     OP.long "outFile" <>
     OP.short 'o' <>
     OP.metavar "FILE" <>
-    OP.value Nothing <>
     OP.showDefault <>
-    OP.help "An optional file to write the results to. \
-            \If not specified, change the target file in place."
+    OP.help ("File path to write the result to. Can be identical to --targetFile to overwrite the \
+             \target file in place. Note that trident only writes .janno files in the \
+             \latest Poseidon version it supports, so in this case v" ++
+             showPoseidonVersion latestPoseidonVersion ++ ".")
     )
 
 parseJannocoalJannoColumns :: OP.Parser CoalesceJannoColumnSpec

src/Poseidon/CLI/Validate.hs

@@ -27,7 +27,7 @@ import qualified Data.ByteString.Char8     as Bchs
 import           Data.List                 (groupBy, intercalate, sortOn)
 import           Data.Yaml                 (decodeEither')
 import           Poseidon.EntityTypes      (IndividualInfo (..))
-import           Poseidon.PoseidonVersion  (latestPoseidonVersion)
+import           Poseidon.PoseidonVersion  (VersionedFile (..))
 import           System.Exit               (exitFailure, exitSuccess)
 
 -- | A datatype representing command line options for the validate command
@@ -50,8 +50,8 @@ data ValidatePlan =
       }
     | ValPlanPoseidonYaml FilePath
     | ValPlanGeno GenotypeDataSpec
-    | ValPlanJanno FilePath
-    | ValPlanSSF FilePath
+    | ValPlanJanno VersionedFile
+    | ValPlanSSF VersionedFile
     | ValPlanBib FilePath
 
 runValidate :: ValidateOptions -> PoseidonIO ()
@@ -105,14 +105,14 @@ runValidate (ValidateOptions (ValPlanGeno geno) _ _ noExitCode _) = do
     pac <- makePseudoPackageFromGenotypeData geno
     validateGeno pac True
     conclude True noExitCode
-runValidate (ValidateOptions (ValPlanJanno path) mandatoryJannoCols _ noExitCode _) = do
+runValidate (ValidateOptions (ValPlanJanno (VersionedFile pv path)) mandatoryJannoCols _ noExitCode _) = do
     logInfo $ "Validating: " ++ path
-    (JannoRows entries) <- readJannoFile latestPoseidonVersion mandatoryJannoCols path
+    (JannoRows entries) <- readJannoFile pv mandatoryJannoCols path
     logInfo $ "All " ++ show (length entries) ++ " entries are valid"
     conclude True noExitCode
-runValidate (ValidateOptions (ValPlanSSF path) _ mandatorySSFCols noExitCode _) = do
+runValidate (ValidateOptions (ValPlanSSF (VersionedFile pv path)) _ mandatorySSFCols noExitCode _) = do
     logInfo $ "Validating: " ++ path
-    (SeqSourceRows entries) <- readSeqSourceFile latestPoseidonVersion mandatorySSFCols path
+    (SeqSourceRows entries) <- readSeqSourceFile pv mandatorySSFCols path
     logInfo $ "All " ++ show (length entries) ++ " entries are valid"
     conclude True noExitCode
 runValidate (ValidateOptions (ValPlanBib path) _ _ noExitCode _) = do

src/Poseidon/PoseidonVersion.hs

@@ -24,3 +24,6 @@ showPoseidonVersion (PoseidonVersion x) = showVersion x
 -- this is for the server
 minimalRequiredClientVersion :: Version
 minimalRequiredClientVersion = makeVersion [1, 1, 8, 5]
+
+-- and this for validate and jannocoalesce
+data VersionedFile = VersionedFile PoseidonVersion FilePath

test/PoseidonGoldenTests/GoldenTestsRunCommands.hs

@@ -39,6 +39,8 @@ import           Poseidon.GenotypeData      (GenoDataSource (..),
                                              GenotypeFileSpec (..),
                                              GenotypeOutFormatSpec (..),
                                              SNPSetSpec (..))
+import           Poseidon.PoseidonVersion   (VersionedFile (..),
+                                             latestPoseidonVersion)
 import           Poseidon.ServerClient      (AddColSpec (..),
                                              ArchiveEndpoint (..))
 import           Poseidon.Utils             (LogMode (..), TestMode (..),
@@ -346,10 +348,14 @@ testPipelineValidate testDir checkFilePath = do
             }
     } & run 6
     validateOpts1 {
-          _validatePlan = ValPlanJanno $ testPacsDir </> "Schiffels_2016" </> "Schiffels_2016.janno"
+          _validatePlan = ValPlanJanno $ VersionedFile
+              latestPoseidonVersion
+              (testPacsDir </> "Schiffels_2016" </> "Schiffels_2016.janno")
     } & run 7
     validateOpts1 {
-          _validatePlan = ValPlanSSF $ testPacsDir </> "Schiffels_2016" </> "ena_table.ssf"
+          _validatePlan = ValPlanSSF $ VersionedFile
+              latestPoseidonVersion
+              (testPacsDir </> "Schiffels_2016" </> "ena_table.ssf")
     } & run 8
     validateOpts1 {
           _validatePlan = ValPlanBib $ testPacsDir </> "Schiffels_2016" </> "sources.bib"
@@ -1416,9 +1422,11 @@ testPipelineJannocoalesce :: FilePath -> FilePath -> IO ()
 testPipelineJannocoalesce testDir checkFilePath = do
     -- simple coalesce
     let jannocoalesceOpts1 = JannoCoalesceOptions {
-            _jannocoalesceSource           = JannoSourceSingle "test/testDat/testJannoFiles/normal.janno",
-            _jannocoalesceTarget           = "test/testDat/testJannoFiles/minimal.janno",
-            _jannocoalesceOutSpec          = Just (testDir </> "jannocoalesce" </> "target1.janno"),
+            _jannocoalesceSource           = JannoSourceSingle $ VersionedFile latestPoseidonVersion
+                                             "test/testDat/testJannoFiles/normal.janno",
+            _jannocoalesceTarget           = VersionedFile latestPoseidonVersion
+                                             "test/testDat/testJannoFiles/minimal.janno",
+            _jannocoalesceOutFile          = testDir </> "jannocoalesce" </> "target1.janno",
             _jannocoalesceJannoColumns     = AllJannoColumns,
             _jannocoalesceOverwriteColumns = False,
             _jannocoalesceSourceKey        = "Poseidon_ID",
@@ -1430,9 +1438,11 @@ testPipelineJannocoalesce testDir checkFilePath = do
         ]
     -- only coalesce certain columns (--includeColumns)
     let jannocoalesceOpts2 = JannoCoalesceOptions {
-            _jannocoalesceSource           = JannoSourceSingle "test/testDat/testJannoFiles/normal.janno",
-            _jannocoalesceTarget           = "test/testDat/testJannoFiles/minimal.janno",
-            _jannocoalesceOutSpec          = Just (testDir </> "jannocoalesce" </> "target2.janno"),
+            _jannocoalesceSource           = JannoSourceSingle $ VersionedFile latestPoseidonVersion
+                                             "test/testDat/testJannoFiles/normal.janno",
+            _jannocoalesceTarget           = VersionedFile latestPoseidonVersion
+                                             "test/testDat/testJannoFiles/minimal.janno",
+            _jannocoalesceOutFile          = testDir </> "jannocoalesce" </> "target2.janno",
             _jannocoalesceJannoColumns     = IncludeJannoColumns ["Latitude", "Longitude"],
             _jannocoalesceOverwriteColumns = False,
             _jannocoalesceSourceKey        = "Poseidon_ID",
@@ -1444,9 +1454,11 @@ testPipelineJannocoalesce testDir checkFilePath = do
         ]
     -- do not coalesce certain columns (--excludeColumns)
     let jannocoalesceOpts3 = JannoCoalesceOptions {
-            _jannocoalesceSource           = JannoSourceSingle "test/testDat/testJannoFiles/normal.janno",
-            _jannocoalesceTarget           = "test/testDat/testJannoFiles/minimal.janno",
-            _jannocoalesceOutSpec          = Just (testDir </> "jannocoalesce" </> "target3.janno"),
+            _jannocoalesceSource           = JannoSourceSingle $ VersionedFile latestPoseidonVersion
+                                             "test/testDat/testJannoFiles/normal.janno",
+            _jannocoalesceTarget           = VersionedFile latestPoseidonVersion
+                                             "test/testDat/testJannoFiles/minimal.janno",
+            _jannocoalesceOutFile          = testDir </> "jannocoalesce" </> "target3.janno",
             _jannocoalesceJannoColumns     = ExcludeJannoColumns ["Latitude", "Longitude"],
             _jannocoalesceOverwriteColumns = False,
             _jannocoalesceSourceKey        = "Poseidon_ID",