| Safe Haskell | Safe-Inferred |
|---|---|
| Language | Haskell2010 |
Poseidon.Utils
Synopsis
- data PoseidonException
- = PoseidonYamlParseException FilePath ParseException
- | PoseidonPackageException String
- | PoseidonPackageVersionException FilePath String
- | PoseidonPackageMissingVersionException FilePath
- | PoseidonIndSearchException String
- | PoseidonGenotypeException String
- | PoseidonGenotypeExceptionForward ErrorLength SomeException
- | PoseidonHttpExceptionForward HttpException
- | PoseidonFileRowException FilePath String String
- | PoseidonFileConsistencyException FilePath String
- | PoseidonCrossFileConsistencyException String String
- | PoseidonCollectionException String
- | PoseidonFileExistenceException FilePath
- | PoseidonFileChecksumException FilePath
- | PoseidonFStatsFormatException String
- | PoseidonBibTeXException FilePath String
- | PoseidonPoseidonEntityParsingException ParseError
- | PoseidonForgeEntitiesException String
- | PoseidonEmptyForgeException
- | PoseidonNewPackageConstructionException String
- | PoseidonRemoteJSONParsingException String
- | PoseidonGenericException String
- | PoseidonEmptyOutPacNameException
- | PoseidonUnequalBaseDirException FilePath FilePath FilePath
- | PoseidonServerCommunicationException String
- | PoseidonUnzipException SomeException
- | PoseidonChronicleException String
- | PoseidonGitException FilePath String
- | PoseidonCantPreserveException
- renderPoseidonException :: PoseidonException -> String
- usePoseidonLogger :: LogMode -> TestMode -> PlinkPopNameMode -> ErrorLength -> PoseidonIO a -> IO a
- testLog :: PoseidonIO a -> IO a
- type PoseidonIO = ReaderT Env IO
- envLogAction :: PoseidonIO LogA
- envInputPlinkMode :: PoseidonIO PlinkPopNameMode
- envErrorLength :: PoseidonIO ErrorLength
- data LogMode
- checkFile :: FilePath -> Maybe String -> IO ()
- getChecksum :: FilePath -> IO String
- logWarning :: String -> PoseidonIO ()
- logInfo :: String -> PoseidonIO ()
- logDebug :: String -> PoseidonIO ()
- logError :: String -> PoseidonIO ()
- type LogA = LogAction IO Message
- noLog :: LogA
- logWithEnv :: MonadIO m => LogA -> PoseidonIO () -> m ()
- padRight :: Int -> String -> String
- padLeft :: Int -> String -> String
- determinePackageOutName :: Maybe String -> FilePath -> IO String
- data PlinkPopNameMode
- data TestMode
- data Env = Env {}
- uniquePO :: Ord a => [a] -> [a]
- uniqueRO :: Ord a => [a] -> [a]
- showParsecErr :: ParseError -> String
- data ErrorLength
Documentation
data PoseidonException Source #
A Poseidon Exception data type with several concrete constructors
Constructors
| PoseidonYamlParseException FilePath ParseException | An exception to represent YAML parsing errors |
| PoseidonPackageException String | An exception to represent a logical error in a package |
| PoseidonPackageVersionException FilePath String | An exception to represent an issue with a package version |
| PoseidonPackageMissingVersionException FilePath | An exception to indicate a missing poseidonVersion field |
| PoseidonIndSearchException String | An exception to represent an error when searching for individuals or populations |
| PoseidonGenotypeException String | An exception to represent errors in the genotype data |
| PoseidonGenotypeExceptionForward ErrorLength SomeException | An exception to represent errors in the genotype data forwarded from the sequence-formats library |
| PoseidonHttpExceptionForward HttpException | An exception to represent errors in the remote data loading forwarded from simpleHttp |
| PoseidonFileRowException FilePath String String | An exception to represent errors when trying to parse the janno or seqSource file |
| PoseidonFileConsistencyException FilePath String | An exception to represent consistency errors in janno or seqSource files |
| PoseidonCrossFileConsistencyException String String | An exception to represent inconsistencies across multiple files in a package |
| PoseidonCollectionException String | An exception to represent logical issues in a poseidon package Collection |
| PoseidonFileExistenceException FilePath | An exception to represent missing files |
| PoseidonFileChecksumException FilePath | An exception to represent failed checksum tests |
| PoseidonFStatsFormatException String | An exception type to represent FStat specification errors |
| PoseidonBibTeXException FilePath String | An exception to represent errors when trying to parse the .bib file |
| PoseidonPoseidonEntityParsingException ParseError | An exception to indicate failed entity parsing |
| PoseidonForgeEntitiesException String | An exception to indicate issues in the forge selection |
| PoseidonEmptyForgeException | An exception to throw if there is nothing to be forged |
| PoseidonNewPackageConstructionException String | An exception to indicate an issue in newPackageTemplate |
| PoseidonRemoteJSONParsingException String | An exception to indicate failed remote info JSON parsing |
| PoseidonGenericException String | A catch-all for any other type of exception |
| PoseidonEmptyOutPacNameException | An exception to throw if the output package lacks a name |
| PoseidonUnequalBaseDirException FilePath FilePath FilePath | An exception to throw if genotype data files don't share a common base directory |
| PoseidonServerCommunicationException String | An exception to mark server communication errors |
| PoseidonUnzipException SomeException | An exception for unzipping issues in fetch |
| PoseidonChronicleException String | An exception for issues in chronicle |
| PoseidonGitException FilePath String | An exception for issues with git |
| PoseidonCantPreserveException | An exception for issues with --preservePyml |
Instances
| Exception PoseidonException Source # | |
Defined in Poseidon.Utils Methods toException :: PoseidonException -> SomeException # | |
| Show PoseidonException Source # | |
Defined in Poseidon.Utils Methods showsPrec :: Int -> PoseidonException -> ShowS # show :: PoseidonException -> String # showList :: [PoseidonException] -> ShowS # | |
usePoseidonLogger :: LogMode -> TestMode -> PlinkPopNameMode -> ErrorLength -> PoseidonIO a -> IO a Source #
testLog :: PoseidonIO a -> IO a Source #
Constructors
| NoLog | |
| SimpleLog | |
| DefaultLog | |
| ServerLog | |
| VerboseLog |
logWarning :: String -> PoseidonIO () Source #
logInfo :: String -> PoseidonIO () Source #
logDebug :: String -> PoseidonIO () Source #
logError :: String -> PoseidonIO () Source #
logWithEnv :: MonadIO m => LogA -> PoseidonIO () -> m () Source #
data PlinkPopNameMode #
Instances
| Show PlinkPopNameMode | |
Defined in SequenceFormats.Plink Methods showsPrec :: Int -> PlinkPopNameMode -> ShowS # show :: PlinkPopNameMode -> String # showList :: [PlinkPopNameMode] -> ShowS # | |
| Eq PlinkPopNameMode | |
Defined in SequenceFormats.Plink Methods (==) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool # (/=) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool # | |
Constructors
| Testing | |
| Production |
Constructors
| Env | |
Fields | |
showParsecErr :: ParseError -> String Source #
data ErrorLength Source #
A data type for error length settings
Instances
| Show ErrorLength Source # | |
Defined in Poseidon.Utils Methods showsPrec :: Int -> ErrorLength -> ShowS # show :: ErrorLength -> String # showList :: [ErrorLength] -> ShowS # | |