BlastHTTP 1.0.0 → 1.0.1

raw patch · 2 files changed

+11/−14 lines, 2 files

Files

• BlastHTTP.cabal +1/−1
• src/Bio/BlastHTTP.hs +10/−13

@@ -7,7 +7,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.0.0+version:             1.0.1 synopsis:            Libary to interface with the NCBI blast REST interface description:         Searches for a provided nucleotide or protein sequence with the NCBI Blast REST service and returns a blast result in xml format as BlastResult datatype.                       .

@@ -84,16 +84,14 @@   return (Right resultXML)  -- | Check if job results are ready and then retrieves results-checkSessionStatus :: String -> Int -> IO (Either String BlastResult)-checkSessionStatus rid counter = do-    let counter2 = counter + 1-    let counter2string = show counter2+checkSessionStatus :: String -> IO (Either String BlastResult)+checkSessionStatus rid = do     threadDelay 60000000     status <- retrieveSessionStatus rid-    waitOrRetrieve status rid counter2+    waitOrRetrieve status rid  -waitOrRetrieve :: String -> String -> Int -> IO (Either String BlastResult)-waitOrRetrieve status rid counter+waitOrRetrieve :: String -> String -> IO (Either String BlastResult)+waitOrRetrieve status rid    | "Status=READY" `isInfixOf` status = retrieveResult rid   | "Status=FAILURE" `isInfixOf` status = do       let exceptionMessage = "Search $rid failed; please report to blast-help at ncbi.nlm.nih.gov.\n"@@ -101,14 +99,14 @@   | "Status=UNKNOWN" `isInfixOf` status = do       let exceptionMessage = "Search $rid expired.\n"       return (Left exceptionMessage)-  | otherwise = checkSessionStatus rid counter+  | otherwise = checkSessionStatus rid  -- | Sends Query and retrieves result on reaching READY status, will return exeption message if no query sequence has been provided -performQuery :: String -> String -> Maybe SeqData -> Maybe String -> Int -> IO (Either String BlastResult)                               -performQuery program database querySequenceMaybe optionalArgumentMaybe counter+performQuery :: String -> String -> Maybe SeqData -> Maybe String -> IO (Either String BlastResult)                               +performQuery program database querySequenceMaybe optionalArgumentMaybe   | isJust querySequenceMaybe = do       rid <- startSession program database (L8.unpack (unSD (fromJust querySequenceMaybe))) optionalArgumentMaybe-     checkSessionStatus rid counter+     checkSessionStatus rid   | otherwise = do       let exceptionMessage = "Error - no query sequence provided"      return (Left exceptionMessage)@@ -118,12 +116,11 @@ -- optionalArguments is attached to the query as is .e.g: "&ALIGNMENTS=250" blastHTTP :: BlastHTTPQuery -> IO (Either String BlastResult) blastHTTP (BlastHTTPQuery program database querySequence optionalArguments) = do-  let counter = 1   let defaultProgram = "blastn"   let defaultDatabase = "refseq_genomic"                     let selectedProgram = fromMaybe defaultProgram program   let selectedDatabase = fromMaybe defaultDatabase database  -  performQuery selectedProgram selectedDatabase querySequence entrezQuery optionalArguments+  performQuery selectedProgram selectedDatabase querySequence optionalArguments