Hello community, here is the log from the commit of package ghc-BlastHTTP for openSUSE:Factory checked in at 2017-04-07 13:54:56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-BlastHTTP (Old) and /work/SRC/openSUSE:Factory/.ghc-BlastHTTP.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "ghc-BlastHTTP" Fri Apr 7 13:54:56 2017 rev:2 rq:483129 version:1.2.1 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-BlastHTTP/ghc-BlastHTTP.changes 2017-03-28 15:20:20.993476486 +0200 +++ /work/SRC/openSUSE:Factory/.ghc-BlastHTTP.new/ghc-BlastHTTP.changes 2017-04-07 13:55:00.301084598 +0200 @@ -1,0 +2,5 @@ +Mon Nov 14 09:34:31 UTC 2016 - [email protected] + +- Update to version 1.2.1 with cabal2obs. + +------------------------------------------------------------------- Old: ---- 1.cabal BlastHTTP-1.2.0.tar.gz New: ---- BlastHTTP-1.2.1.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-BlastHTTP.spec ++++++ --- /var/tmp/diff_new_pack.8pHuWi/_old 2017-04-07 13:55:00.908998727 +0200 +++ /var/tmp/diff_new_pack.8pHuWi/_new 2017-04-07 13:55:00.912998162 +0200 @@ -1,7 +1,7 @@ # # spec file for package ghc-BlastHTTP # -# Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2017 SUSE LINUX GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -18,14 +18,13 @@ %global pkg_name BlastHTTP Name: ghc-%{pkg_name} -Version: 1.2.0 +Version: 1.2.1 Release: 0 Summary: Libary to interface with the NCBI blast REST interface License: GPL-3.0+ Group: Development/Languages/Other Url: https://hackage.haskell.org/package/%{pkg_name} Source0: https://hackage.haskell.org/package/%{pkg_name}-%{version}/%{pkg_name}-%{version}.tar.gz -Source1: https://hackage.haskell.org/package/%{pkg_name}-%{version}/revision/1.cabal BuildRequires: ghc-Cabal-devel BuildRequires: ghc-HTTP-devel BuildRequires: ghc-biocore-devel @@ -67,7 +66,6 @@ %prep %setup -q -n %{pkg_name}-%{version} -cp -p %{SOURCE1} %{pkg_name}.cabal %build %ghc_lib_build ++++++ BlastHTTP-1.2.0.tar.gz -> BlastHTTP-1.2.1.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/BlastHTTP-1.2.0/BlastHTTP.cabal new/BlastHTTP-1.2.1/BlastHTTP.cabal --- old/BlastHTTP-1.2.0/BlastHTTP.cabal 2015-04-20 19:27:19.000000000 +0200 +++ new/BlastHTTP-1.2.1/BlastHTTP.cabal 2016-11-12 21:14:33.000000000 +0100 @@ -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. diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/BlastHTTP-1.2.0/README.md new/BlastHTTP-1.2.1/README.md --- old/BlastHTTP-1.2.0/README.md 2015-04-20 19:27:19.000000000 +0200 +++ new/BlastHTTP-1.2.1/README.md 2016-11-12 21:14:33.000000000 +0100 @@ -1,10 +1,15 @@ -BlastHTTP [](https://travis-ci.org/eggzilla/BlastHTTP) +BlastHTTP [](https://hackage.haskell.org/package/BlastHTTP) [](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: Added optionalArgument parameter to BlastHTTP datatype and removed EntrezQuery. diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/BlastHTTP-1.2.0/changelog new/BlastHTTP-1.2.1/changelog --- old/BlastHTTP-1.2.0/changelog 2015-04-20 19:27:19.000000000 +0200 +++ new/BlastHTTP-1.2.1/changelog 2016-11-12 21:14:33.000000000 +0100 @@ -1,5 +1,7 @@ -*-change-log-*- -1.0.2 Florian Eggenhofer <[email protected]> 20. April 2015 +1.2.1 Florian Eggenhofer <[email protected]> 12. November 2016 + * Changed used NCBI URL to HTTPS +1.2.0 Florian Eggenhofer <[email protected]> 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 <[email protected]> 09. October 2014 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/BlastHTTP-1.2.0/src/Bio/BlastHTTP.hs new/BlastHTTP-1.2.1/src/Bio/BlastHTTP.hs --- old/BlastHTTP-1.2.0/src/Bio/BlastHTTP.hs 2015-04-20 19:27:19.000000000 +0200 +++ new/BlastHTTP-1.2.1/src/Bio/BlastHTTP.hs 2016-11-12 21:14:33.000000000 +0100 @@ -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)
