diff --git a/Biobase/Entrez/HTTP.hs b/Biobase/Entrez/HTTP.hs --- a/Biobase/Entrez/HTTP.hs +++ b/Biobase/Entrez/HTTP.hs @@ -41,11 +41,12 @@ import Network.HTTP.Conduit import qualified Data.ByteString.Lazy.Char8 as L8 +import qualified Data.ByteString.Char8 as B import Text.XML.HXT.Core import Network.Socket import Data.Maybe import Biobase.Entrez.HTTPData -import Bio.TaxonomyData +import Biobase.Taxonomy.Types import Network.HTTP.Base import qualified Data.Text.Lazy as TL @@ -117,17 +118,17 @@ _pubDate <- getChildren >>> (isElem >>> hasName "PubDate") >>> getChildren >>> getText -< entrezTaxon returnA -< Taxon { taxonTaxId = read _taxonomyId :: Int, - taxonScientificName = _scientificName, + taxonScientificName = (B.pack _scientificName), taxonParentTaxId = read _parentTaxonomyId :: Int, taxonRank = read _rank :: Rank, - division = _divison, + division = (B.pack _divison), geneticCode = _geneticCode, mitoGeneticCode = _mitoGeneticCode, - lineage = _lineage, + lineage = (B.pack _lineage), lineageEx = _lineageEx, - createDate = _createDate, - updateDate = _updateDate, - pubDate = _pubDate + createDate = (B.pack _createDate), + updateDate = (B.pack _updateDate), + pubDate = (B.pack _pubDate) } parseTaxonGeneticCode :: ArrowXml a => a XmlTree TaxGenCode @@ -137,10 +138,10 @@ _gcName <- atTag "GCName" >>> getChildren >>> getText -< geneticcode returnA -< TaxGenCode { geneticCodeId = read _gcId :: Int, - abbreviation = Nothing, - geneCodeName = _gcName, - cde = [], - starts = [] + abbreviation = B.empty, + geneCodeName = (B.pack _gcName), + cde = B.empty, + starts = B.empty } parseTaxonMitoGeneticCode :: ArrowXml a => a XmlTree TaxGenCode @@ -150,10 +151,10 @@ _mgcName <- atTag "MGCName" >>> getChildren >>> getText -< mitogeneticcode returnA -< TaxGenCode { geneticCodeId = read _mgcId :: Int, - abbreviation = Nothing, - geneCodeName = _mgcName, - cde = [], - starts = [] + abbreviation = B.empty, + geneCodeName = B.pack _mgcName, + cde = B.empty, + starts = B.empty } parseTaxonLineageEx :: ArrowXml a => a XmlTree [LineageTaxon] @@ -170,7 +171,7 @@ _lineageRank <- atTag "Rank" >>> getChildren >>> getText -< lineageTaxon returnA -< LineageTaxon { lineageTaxId = read _lineageTaxId :: Int, - lineageScienticName = _lineageScienticName, + lineageScienticName = (B.pack _lineageScienticName), lineageRank = read _lineageRank :: Rank } diff --git a/BiobaseHTTP.cabal b/BiobaseHTTP.cabal --- a/BiobaseHTTP.cabal +++ b/BiobaseHTTP.cabal @@ -1,5 +1,5 @@ name: BiobaseHTTP -version: 1.1.0 +version: 1.2.0 synopsis: Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl description: BiobaseHTTP provides functions to interface the Bioinformatics REST services - Entrez Ensembl . @@ -22,22 +22,22 @@ category: Bioinformatics build-type: Simple cabal-version: >=1.8 -Tested-With: GHC == 8.4.3 +Tested-With: GHC == 8.4.4, GHC == 8.6.5 Extra-Source-Files: - README.md changelog + README.md ChangeLog.md source-repository head type: git location: https://github.com/eggzilla/BiobaseHTTP source-repository this - type: darcs - location: https://github.com/eggzilla/BiobaseHTTP/tree/1.1.0 - tag: 1.1.0 + type: git + location: https://github.com/eggzilla/BiobaseHTTP/tree/1.2.0 + tag: 1.2.0 library exposed-modules: Biobase.Entrez.HTTP, Biobase.Entrez.HTTPData, Biobase.Ensembl.HTTP ghc-options: -Wall - build-depends: base >=4.5 && <5, transformers, bytestring, conduit, HTTP, http-conduit, hxt, network, mtl, Taxonomy>=1.0.3, text, aeson, either-unwrap, BiobaseEnsembl + build-depends: base >=4.5 && <5, transformers, bytestring, conduit, HTTP, http-conduit, hxt, network<=2.8.0.0, mtl, Taxonomy>=2.0.0, text, aeson, either-unwrap, BiobaseEnsembl hs-source-dirs: . diff --git a/ChangeLog.md b/ChangeLog.md new file mode 100644 --- /dev/null +++ b/ChangeLog.md @@ -0,0 +1,32 @@ +-*-change-log-*- + +### 1.2.0 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 18 November 2019 + + * Updated to Taxonomy library version 2.0.0 + +### 1.1.0 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 12 December 2018 + + * Changed library name to BiobaseHTTP + * Now using Biobase libraries + * Added functionality for Ensembl Genomes API requests + +### 1.0.4 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 10. August 2017 + + * Updated version constraints for Taxonomy + +### 1.0.3 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 12. November 2016 + + * Default NCBI URL now uses HTTPS + +### 1.0.2 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 23. October 2016 + + * Now compatible with GHC 8.0 + * Travis testing for GHC 7.6 - GHC 8.0 + +### 1.0.1 [Florian Eggenhofer](mailto:florian.eggenhofer@univie.ac.at) 5. January 2016 + + * Fixed version constraints, added changelog + +### 1.0.0 [Florian Eggenhofer](mailto:florian.eggenhofer@univie.ac.at) 11.September 2015 + + * Initial version diff --git a/changelog b/changelog deleted file mode 100644 --- a/changelog +++ /dev/null @@ -1,17 +0,0 @@ --*-change-log-*- -1.1.0 Florian Eggenhofer 12 December 2018 - * Changed library name to BiobaseHTTP - * Now using Biobase libraries - * Added functionality for Ensembl Genomes API requests -1.0.4 Florian Eggenhofer 10. August 2017 - * Updated version constraints for Taxonomy -1.0.3 Florian Eggenhofer 12. November 2016 - * Default NCBI URL now uses HTTPS -1.0.2 Florian Eggenhofer 23. October 2016 - * Now compatible with GHC 8.0 - * Travis testing for GHC 7.6 - GHC 8.0 -1.0.1 Florian Eggenhofer 5. January 2016 - * Fixed version constraints, added changelog -1.0.0 Florian Eggenhofer 11.September 2015 - * Initial version -