packages feed

BlastHTTP 1.2.0 → 1.2.1

raw patch · 4 files changed

+17/−10 lines, 4 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

- Bio.BlastHTTP: database :: BlastHTTPQuery -> Maybe String
- Bio.BlastHTTP: instance Eq BlastHTTPQuery
- Bio.BlastHTTP: instance Show BlastHTTPQuery
- Bio.BlastHTTP: optionalArguments :: BlastHTTPQuery -> Maybe String
- Bio.BlastHTTP: optionalWalltime :: BlastHTTPQuery -> Maybe Int
- Bio.BlastHTTP: program :: BlastHTTPQuery -> Maybe String
- Bio.BlastHTTP: provider :: BlastHTTPQuery -> Maybe String
- Bio.BlastHTTP: querySequences :: BlastHTTPQuery -> [Sequence]
+ Bio.BlastHTTP: [database] :: BlastHTTPQuery -> Maybe String
+ Bio.BlastHTTP: [optionalArguments] :: BlastHTTPQuery -> Maybe String
+ Bio.BlastHTTP: [optionalWalltime] :: BlastHTTPQuery -> Maybe Int
+ Bio.BlastHTTP: [program] :: BlastHTTPQuery -> Maybe String
+ Bio.BlastHTTP: [provider] :: BlastHTTPQuery -> Maybe String
+ Bio.BlastHTTP: [querySequences] :: BlastHTTPQuery -> [Sequence]
+ Bio.BlastHTTP: instance GHC.Classes.Eq Bio.BlastHTTP.BlastHTTPQuery
+ Bio.BlastHTTP: instance GHC.Show.Show Bio.BlastHTTP.BlastHTTPQuery

Files

BlastHTTP.cabal view
@@ -7,7 +7,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.2.0+version:             1.2.1 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.                       .@@ -35,9 +35,9 @@   location: https://github.com/eggzilla/BlastHTTP  source-repository this-  type:     darcs-  location: https://github.com/eggzilla/BlastHTTP/tree/1.0.1-  tag:      1.0.1+  type:     git+  location: https://github.com/eggzilla/BlastHTTP/tree/1.2.1+  tag:      1.2.1  library   -- Modules exported by the library.
README.md view
@@ -1,9 +1,14 @@-BlastHTTP  [![Build Status](https://travis-ci.org/eggzilla/BlastHTTP.svg?branch=master)](https://travis-ci.org/eggzilla/BlastHTTP)+BlastHTTP  [![Hackage](https://img.shields.io/hackage/v/BlastHTTP.svg)](https://hackage.haskell.org/package/BlastHTTP) [![Build Status](https://travis-ci.org/eggzilla/BlastHTTP.svg?branch=master)](https://travis-ci.org/eggzilla/BlastHTTP) =========  Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice  Changes:++Version 1.2.0:++Added experimental support for the european bioinformatics institute blast REST interface+Added support for multiple sequences in one request  Version 1.0.0:
changelog view
@@ -1,5 +1,7 @@ -*-change-log-*--1.0.2 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 20. April 2015+1.2.1 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 12. November 2016+	* Changed used NCBI URL to HTTPS+1.2.0 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 20. April 2015 	* Added experimental support for the european bioinformatics institute blast REST interface 	* Added support for multiple sequences in one request 1.0.1 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 09. October 2014
src/Bio/BlastHTTP.hs view
@@ -97,8 +97,8 @@ -- | Send query with or without optional arguments and return response HTML sendQueryNCBI :: String -> String -> String -> Maybe String -> IO L8.ByteString sendQueryNCBI program' database' querySequences' optionalArguments'-  | isJust optionalArguments' = simpleHttp ("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&PROGRAM=" ++ program' ++ "&DATABASE=" ++ database' ++ fromJust optionalArguments' ++ "&QUERY=" ++ querySequences')-  | otherwise = simpleHttp ("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&PROGRAM=" ++ program' ++ "&DATABASE=" ++ database' ++ "&QUERY=" ++ querySequences')+  | isJust optionalArguments' = simpleHttp ("https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&PROGRAM=" ++ program' ++ "&DATABASE=" ++ database' ++ fromJust optionalArguments' ++ "&QUERY=" ++ querySequences')+  | otherwise = simpleHttp ("https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&PROGRAM=" ++ program' ++ "&DATABASE=" ++ database' ++ "&QUERY=" ++ querySequences')           -- | Retrieve session status with RID retrieveSessionStatus :: String -> String -> IO String @@ -110,7 +110,7 @@        putStrLn "EBI statusXMLString"        return statusXMLString      else do-       statusXml <- withSocketsDo $ simpleHttp ("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=" ++ rid)+       statusXml <- withSocketsDo $ simpleHttp ("https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=" ++ rid)        let statusXMLString = L8.unpack statusXml        return statusXMLString   @@ -123,7 +123,7 @@        resultXML <- parseXML statusXml        return (Right resultXML)      else do-       statusXml <- withSocketsDo $ simpleHttp ("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RESULTS_FILE=on&RID=" ++ rid ++ "&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get")+       statusXml <- withSocketsDo $ simpleHttp ("https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RESULTS_FILE=on&RID=" ++ rid ++ "&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get")        resultXML <- parseXML statusXml        return (Right resultXML)