BiobaseHTTP (empty) → 1.1.0

raw patch · 8 files changed

+1318/−0 lines, 8 filesdep +BiobaseEnsembldep +HTTPdep +Taxonomysetup-changed

Dependencies added: BiobaseEnsembl, HTTP, Taxonomy, aeson, base, bytestring, conduit, either-unwrap, http-conduit, hxt, mtl, network, text, transformers

Files

Biobase/Ensembl/HTTP.hs +74/−0
Biobase/Entrez/HTTP.hs +417/−0
Biobase/Entrez/HTTPData.hs +73/−0
BiobaseHTTP.cabal +43/−0
LICENSE +675/−0
README.md +17/−0
Setup.hs +2/−0
changelog +17/−0

+ Biobase/Ensembl/HTTP.hs view

@@ -0,0 +1,74 @@+{-# LANGUAGE OverloadedStrings #-}+-- | Interface for Ensembl++module Biobase.Ensembl.HTTP (+                       startXRefSession,+                       requestGOTermsWithGeneIds,+                       requestUniProtWithGeneIds,+                       EnsemblEntry(..)+                      ) where++import Network.HTTP.Conduit+import qualified Data.ByteString.Lazy.Char8 as L8+import Network.Socket+import Data.Aeson+import Data.Either.Unwrap+import Biobase.Ensembl.REST.Types+import Control.Concurrent+import Data.Maybe+import Data.List+import qualified Data.Text as T++requestGOTermsWithGeneIds :: [T.Text] -> IO [(T.Text,[T.Text])]+requestGOTermsWithGeneIds geneIds = do+  let queryParameters = T.pack "?external_db=GO;all_levels=1;content-type=application/json"+  mapM (requestGOTermsWithGeneId queryParameters) geneIds++requestGOTermsWithGeneId :: T.Text -> T.Text -> IO (T.Text,[T.Text])+requestGOTermsWithGeneId queryParameters geneId = do+  --let protid= "AAC73113"+  responseJson <- startXRefSession queryParameters geneId+  --3/s+  threadDelay 330000+  if isRight responseJson+    then return (geneId,(extractGOTerms (fromRight responseJson)))+    else return (geneId,[])++extractGOTerms :: [EnsemblEntry] -> [T.Text]+extractGOTerms entries = goTerms+  where goEntries = filter (\a -> T.pack "GO" == fromMaybe "" (dbname a)) entries+        goTerms = map (fromJust . display_id) goEntries++requestUniProtWithGeneIds :: [T.Text] -> IO [(T.Text,T.Text)]+requestUniProtWithGeneIds geneIds = do+  let queryParameters = T.pack "?external_db=Uniprot/SWISSPROT;all_levels=1;content-type=application/json"+  mapM (requestUniProtWithGeneId queryParameters) geneIds++requestUniProtWithGeneId :: T.Text -> T.Text -> IO (T.Text,T.Text)+requestUniProtWithGeneId queryParameters geneId = do+  --let protid= "AAC73113"+  responseJson <- startXRefSession queryParameters geneId+  -- 3/s+  threadDelay 330000+  if isRight responseJson+    then return (geneId,(extractUniProtId (fromRight responseJson)))+    else return (geneId,T.empty)++extractUniProtId :: [EnsemblEntry] -> T.Text+extractUniProtId entries = uniprotName+  where uniprotEntry = find (\a -> T.pack "Uniprot/SWISSPROT" == fromMaybe "" (dbname a)) entries+        uniprotName = if isJust uniprotEntry then fromMaybe T.empty (display_id (fromJust uniprotEntry)) else T.empty++startXRefSession :: T.Text -> T.Text -> IO (Either String [EnsemblEntry])+startXRefSession queryParameters xrefId = do+  response <- withSocketsDo+      $ sendXRefQuery xrefId queryParameters+  let decodedJson = eitherDecode response :: Either String [EnsemblEntry]+  return decodedJson++--"[{\"display_id\":\"00300+2.7.2.4+1.1.1.3\",\"primary_id\":\"00300+2.7.2.4+1.1.1.3\",\"version\":\"0\",\"description\":\"\",\"dbname\":\"KEGG_Enzyme\",\"synonyms\":[],\"info_text\":\"\",\"info_type\":\"NONE\",\"db_display_name\":\"KEGG Pathway and Enzyme\"}]""++-- | Send query and return response+-- http://rest.ensemblgenomes.org/xrefs/id/AAC73113?content-type=application/json+sendXRefQuery :: T.Text -> T.Text -> IO L8.ByteString+sendXRefQuery xrefId queryParameters = simpleHttp ("http://rest.ensemblgenomes.org/xrefs/id/" ++ T.unpack xrefId ++ T.unpack queryParameters)

+ Biobase/Entrez/HTTP.hs view

@@ -0,0 +1,417 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE Arrows #-}++-- | Interface for the NCBI Entrez REST webservice.+--+--   The entrezHTTP function provides a interface to the NCBI Entrez REST service.+--+--   A series of different eutilites and databases are provided by the REST interface.+--   Response depends on the combination of eutil and database, as well requested returntype.+--   Specific combinations have wrapper functions with corresponding parsing functions included (see Usage example).+--+--   If you use this libary in a tool, please read <http://www.ncbi.nlm.nih.gov/books/NBK25497/ A General Introduction to the E-utilities> carefully and register your tool at eutilities@ncbi.nlm.nih.gov. You can append your registration info generated+--   with the included buildRegistration function to your query.+--+-- == Usage example:+--+-- Retrieve a nucleotide sequence for Escherichia coli+--+-- >  nucleotideFasta <- fetchNucleotideString "NC_000913.3" 50 1000 "+" Nothing++module Biobase.Entrez.HTTP (-- * Datatypes+                       module Biobase.Entrez.HTTPData,+                       -- * Retrieval function+                       entrezHTTP,+                       retrieveGeneSymbolFasta,+                       fetchNucleotideString,+                       retrieveElementsEntrez,+                       portionListElements,+                       -- * Parsing functions+                       readEntrezTaxonSet,+                       readEntrezSimpleTaxons,+                       readEntrezParentIds,+                       readEntrezSummaries,+                       readEntrezSearch,+                       -- * auxiliary functions+                       buildRegistration,+                       maybeBuildRegistration,+                       setStrand,+                       convertCoordinatesToStrand+                      ) where++import Network.HTTP.Conduit+import qualified Data.ByteString.Lazy.Char8 as L8+import Text.XML.HXT.Core+import Network.Socket+import Data.Maybe+import Biobase.Entrez.HTTPData+import Bio.TaxonomyData+import Network.HTTP.Base+import qualified Data.Text.Lazy as TL++-- | Send query and parse return XML+startSession :: String -> String -> String -> IO String+startSession program' database' query' = do+  requestXml <- withSocketsDo+      $ sendQuery program' database' query'+  let requestXMLString = L8.unpack requestXml+  return requestXMLString++-- | Send query and return response XML+sendQuery :: String -> String -> String -> IO L8.ByteString+sendQuery program' database' query' = simpleHttp ("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"++ program' ++ ".fcgi?" ++ "db=" ++ database' ++ "&" ++ query')++-- | Function for querying the NCBI entrez REST interface. Input EntrezHTTPQuery datatype is used to select database, program of interest and contains the query string.+--   Please note that query strings containing whitespace or special characters need to be urlencoded. The response format and content depends on the query type, the output+-- therefore provided as String.+entrezHTTP :: EntrezHTTPQuery -> IO String+entrezHTTP (EntrezHTTPQuery program' database' query') = do+  let defaultProgram = "summary"+  let defaultDatabase = "nucleotide"+  let selectedProgram = fromMaybe defaultProgram program'+  let selectedDatabase = fromMaybe defaultDatabase database'+  startSession selectedProgram selectedDatabase query'++-- | Wrapper function for eutils that accept a list of querys (e.g. a list of gene ids) that ensures that only chunks of 20 queries are sent per request. Sending to long queries otherwise results in a serverside exception.+retrieveElementsEntrez :: [a] -> ([a] -> IO b) -> IO [b]+retrieveElementsEntrez listElements retrievalfunction = do+  let splits = portionListElements listElements 20+  mapM retrievalfunction splits++-- Auxiliary function for retrieveElementsEntrez+portionListElements :: [a] -> Int -> [[a]]+portionListElements listElements elementsPerSplit+  | not (null listElements) = filter (not . null) result+  | otherwise = []+  where (heads,xs) = splitAt elementsPerSplit listElements+        result = heads:portionListElements xs elementsPerSplit++---------------------------------------+-- Parsing functions++-- | Read entrez fetch for taxonomy database into a simplyfied datatype+-- Result of e.g: http://eutils.ncbi.nlm.nih.+readEntrezTaxonSet :: String -> [Taxon]+readEntrezTaxonSet = runLA (xreadDoc >>> parseEntrezTaxonSet)++parseEntrezTaxonSet :: ArrowXml a => a XmlTree Taxon+parseEntrezTaxonSet = atTag "TaxaSet" >>> getChildren >>>+  proc entrezTaxons -> do+  _taxons <- parseEntrezTaxon -< entrezTaxons+  returnA -< _taxons++parseEntrezTaxon :: ArrowXml a => a XmlTree Taxon+parseEntrezTaxon = (isElem >>> hasName "Taxon") >>>+  proc entrezTaxon -> do+    _taxonomyId <- getChildren >>> (isElem >>> hasName  "TaxId") >>> getChildren >>> getText -< entrezTaxon+    _scientificName <- getChildren >>> (isElem >>> hasName "ScientificName") >>> getChildren >>> getText -< entrezTaxon+    _parentTaxonomyId <- getChildren >>> (isElem >>> hasName "ParentTaxId") >>> getChildren >>> getText -< entrezTaxon+    _rank <- getChildren >>> (isElem >>> hasName "Rank") >>> getChildren >>> getText -< entrezTaxon+    _divison <- getChildren >>> (isElem >>> hasName "Division") >>> getChildren >>> getText -< entrezTaxon+    _geneticCode <- parseTaxonGeneticCode  -< entrezTaxon+    _mitoGeneticCode  <- parseTaxonMitoGeneticCode -< entrezTaxon+    _lineage <- getChildren >>> atTag "Lineage" >>> getChildren >>> getText -< entrezTaxon+    _lineageEx <- parseTaxonLineageEx -< entrezTaxon+    _createDate <- getChildren >>> (isElem >>> hasName "CreateDate") >>> getChildren >>> getText -< entrezTaxon+    _updateDate <- getChildren >>> (isElem >>> hasName "UpdateDate") >>> getChildren >>> getText -< entrezTaxon+    _pubDate <- getChildren >>> (isElem >>> hasName "PubDate") >>> getChildren >>> getText -< entrezTaxon+    returnA -< Taxon {+      taxonTaxId = read _taxonomyId :: Int,+      taxonScientificName = _scientificName,+      taxonParentTaxId = read _parentTaxonomyId :: Int,+      taxonRank = read _rank :: Rank,+      division = _divison,+      geneticCode = _geneticCode,+      mitoGeneticCode = _mitoGeneticCode,+      lineage = _lineage,+      lineageEx = _lineageEx,+      createDate = _createDate,+      updateDate = _updateDate,+      pubDate = _pubDate+    }++parseTaxonGeneticCode :: ArrowXml a => a XmlTree TaxGenCode+parseTaxonGeneticCode = getChildren >>> atTag "GeneticCode" >>>+  proc geneticcode -> do+  _gcId <- atTag "GCId" >>> getChildren >>> getText -< geneticcode+  _gcName <- atTag "GCName" >>> getChildren >>> getText -< geneticcode+  returnA -< TaxGenCode {+    geneticCodeId = read _gcId :: Int,+    abbreviation = Nothing,+    geneCodeName = _gcName,+    cde = [],+    starts = []+    }++parseTaxonMitoGeneticCode :: ArrowXml a => a XmlTree TaxGenCode+parseTaxonMitoGeneticCode = getChildren >>> atTag "MitoGeneticCode" >>>+  proc mitogeneticcode -> do+  _mgcId <- atTag "MGCId" >>> getChildren >>> getText -< mitogeneticcode+  _mgcName <- atTag "MGCName" >>> getChildren >>> getText -< mitogeneticcode+  returnA -< TaxGenCode {+    geneticCodeId = read _mgcId :: Int,+    abbreviation = Nothing,+    geneCodeName = _mgcName,+    cde = [],+    starts = []+    }++parseTaxonLineageEx :: ArrowXml a => a XmlTree [LineageTaxon]+parseTaxonLineageEx = getChildren >>> atTag "LineageEx" >>>+  proc taxonLineageEx -> do+  _lineageEx <- listA parseLineageTaxon -< taxonLineageEx+  returnA -< _lineageEx++parseLineageTaxon :: ArrowXml a => a XmlTree LineageTaxon+parseLineageTaxon = getChildren >>> atTag "Taxon" >>>+  proc lineageTaxon -> do+  _lineageTaxId <- atTag "TaxId" >>> getChildren >>> getText -< lineageTaxon+  _lineageScienticName <- atTag "ScientificName" >>> getChildren >>> getText -< lineageTaxon+  _lineageRank <- atTag "Rank" >>> getChildren >>> getText -< lineageTaxon+  returnA -< LineageTaxon {+    lineageTaxId = read _lineageTaxId :: Int,+    lineageScienticName = _lineageScienticName,+    lineageRank = read _lineageRank :: Rank+    }++-- | Read entrez fetch for taxonomy database into a simplyfied datatype+-- Result of e.g: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1406860+readEntrezSimpleTaxons :: String -> [SimpleTaxon]+readEntrezSimpleTaxons = runLA (xreadDoc >>> parseEntrezSimpleTaxons)++parseEntrezSimpleTaxons :: ArrowXml a => a XmlTree SimpleTaxon+parseEntrezSimpleTaxons = getChildren >>> atTag "Taxon" >>>+  proc entrezSimpleTaxon -> do+  simple_TaxId <- atTag "TaxId" >>> getChildren >>> getText -< entrezSimpleTaxon+  simple_ScientificName <- atTag "ScientificName" >>> getChildren >>> getText -< entrezSimpleTaxon+  simple_ParentTaxId <- atTag "ParentTaxId" >>> getChildren >>> getText -< entrezSimpleTaxon+  simple_Rank <- atTag "Rank" >>> getChildren >>> getText -< entrezSimpleTaxon+  returnA -< SimpleTaxon {+    simpleTaxId = read simple_TaxId :: Int,+    simpleScientificName = TL.pack simple_ScientificName,+    simpleParentTaxId = read simple_ParentTaxId :: Int,+    simpleRank = read simple_Rank :: Rank+    }++readEntrezParentIds :: String -> [Int]+readEntrezParentIds = runLA (xreadDoc >>> parseEntrezParentTaxIds)++parseEntrezParentTaxIds :: ArrowXml a => a XmlTree Int+parseEntrezParentTaxIds = getChildren >>> atTag "Taxon" >>>+  proc entrezSimpleTaxon -> do+  simple_ParentTaxId <- atTag "ParentTaxId" >>> getChildren >>> getText -< entrezSimpleTaxon+  returnA -< read simple_ParentTaxId :: Int++-- | Read entrez summary from internal haskell string+readEntrezSummaries :: String -> [EntrezSummary]+readEntrezSummaries = runLA (xreadDoc >>> parseEntrezSummaries)++-- | Parse entrez summary result+parseEntrezSummaries :: ArrowXml a => a XmlTree EntrezSummary+parseEntrezSummaries = atTag "eSummaryResult" >>>+  proc entrezSummary -> do+  document_Summaries <- listA parseEntrezDocSums -< entrezSummary+  returnA -< EntrezSummary {+    documentSummaries = document_Summaries+    }++-- |+parseEntrezDocSums :: ArrowXml a => a XmlTree EntrezDocSum+parseEntrezDocSums = atTag "DocSum" >>>+  proc entrezDocSum -> do+  summary_Id <- atTag "Id" >>> getChildren >>> getText -< entrezDocSum+  summary_Items <- listA parseSummaryItems -< entrezDocSum+  returnA -< EntrezDocSum {+    summaryId = summary_Id,+    summaryItems = summary_Items+    }++-- |+parseSummaryItems :: ArrowXml a => a XmlTree SummaryItem+parseSummaryItems = atTag "Item" >>>+  proc summaryItem -> do+  item_Name <- getAttrValue "Name" -< summaryItem+  item_Type <- getAttrValue "Type" -< summaryItem+  item_Content <- getText <<< getChildren -< summaryItem+  returnA -< SummaryItem {+    itemName = item_Name,+    itemType = item_Type,+    itemContent = item_Content+    }++-- | Read entrez summary from internal haskell string+readEntrezSearch :: String -> [EntrezSearch]+readEntrezSearch = runLA (xreadDoc >>> parseEntrezSearch)++-- | Parse entrez search result+parseEntrezSearch :: ArrowXml a => a XmlTree EntrezSearch+parseEntrezSearch = atTag "eSearchResult" >>>+  proc entrezSearch -> do+  _count <- atTag "Count" >>> getChildren >>> getText -< entrezSearch+  _retMax <- atTag "RetMax" >>> getChildren >>> getText -< entrezSearch+  _retStart <- atTag "RetStart" >>> getChildren >>> getText -< entrezSearch+  _searchIds <- atTag "IdList" >>> listA parseSearchId -< entrezSearch+  _translationStack <- listA parseTranslationStack -< entrezSearch+  _queryTranslation <- atTag "QueryTranslation" >>> getChildren >>> getText -< entrezSearch+  returnA -< EntrezSearch {+    count = readInt _count,+    retMax = readInt _retMax,+    retStart = readInt _retStart,+    searchIds = _searchIds,+    translationStack = _translationStack,+    queryTranslation = _queryTranslation+    }++-- | Parse entrez TranslationStack+parseSearchId :: ArrowXml a => a XmlTree Int+parseSearchId = atTag "Id" >>>+  proc entrezSearchId -> do+  searchId <- getChildren >>> getText -< entrezSearchId+  returnA -< (readInt searchId)++-- | Parse entrez TranslationStack+parseTranslationStack :: ArrowXml a => a XmlTree TranslationStack+parseTranslationStack = atTag "TranslationStack" >>>+  proc entrezTranslationStack -> do+  _termSets <- listA parseTermSet -< entrezTranslationStack+  _operation <- atTag "OP" >>> getChildren >>> getText -< entrezTranslationStack+  returnA -< TranslationStack {+    termSets = _termSets,+    operation = _operation+    }++-- | Parse entrez TermSet+parseTermSet :: ArrowXml a => a XmlTree TermSet+parseTermSet = atTag "TermSet" >>>+  proc entrezTermSet -> do+  _term <- atTag "Term" >>> getChildren >>> getText -< entrezTermSet+  _field <- atTag "Field" >>> getChildren >>> getText -< entrezTermSet+  _termCount <- atTag "Count" >>> getChildren >>> getText -< entrezTermSet+  _explode <- atTag "Explode" >>> getChildren >>> getText -< entrezTermSet+  returnA -< TermSet {+    term = _term,+    field = _field,+    termCount = readInt _termCount,+    explode = _explode+    }++-- | Read entrez summary from internal haskell string+readEntrezGeneSummaries :: String -> [EntrezGeneSummary]+readEntrezGeneSummaries = runLA (xreadDoc >>> parseEntrezGeneSummaries)++-- | Parse entrez summary result+parseEntrezGeneSummaries :: ArrowXml a => a XmlTree EntrezGeneSummary+parseEntrezGeneSummaries = atTag "eSummaryResult" >>> getChildren >>> atTag "DocumentSummarySet" >>>+  proc entrezSummary -> do+  _geneSummaries <- listA parseEntrezGeneDocSums -< entrezSummary+  returnA -< EntrezGeneSummary {+    geneSummaries = _geneSummaries+    }++-- |+parseEntrezGeneDocSums :: ArrowXml a => a XmlTree EntrezGeneDocSummary+parseEntrezGeneDocSums = atTag "DocumentSummary" >>>+  proc entrezDocSum -> do+  _geneId <- atTag "Name" >>> getChildren >>> getText -< entrezDocSum+  _geneName <- atTag "Description" >>> getChildren >>> getText -< entrezDocSum+  _geneStatus <- atTag "Status" >>> getChildren >>> getText -< entrezDocSum+  _geneCurrentID <- atTag "CurrentID" >>> getChildren >>> getText -< entrezDocSum+  _geneGeneticSource <- atTag "GeneticSource" >>> getChildren >>> getText -< entrezDocSum+  _geneOtherAliases <- atTag "OtherAliases" >>> getChildren >>> getText -< entrezDocSum+  _geneGenomicInfo <- parseEntrezGenomicInfo -< entrezDocSum+  returnA -< EntrezGeneDocSummary {+    geneId = _geneId,+    geneName = _geneName,+    geneStatus = _geneStatus,+    geneCurrentID = _geneCurrentID,+    geneGeneticSource = _geneGeneticSource,+    geneOtherAliases = _geneOtherAliases,+    geneGenomicInfo = _geneGenomicInfo+    }++parseEntrezGenomicInfo :: ArrowXml a => a XmlTree EntrezGenomicInfo+parseEntrezGenomicInfo = atTag "GenomicInfo" >>> getChildren >>> atTag "GenomicInfoType" >>>+  proc entrezGenomicInfo -> do+  _chrAccVer <- atTag "ChrAccVer" >>> getChildren >>> getText -< entrezGenomicInfo+  _chrStart <- atTag "ChrStart" >>> getChildren >>> getText -< entrezGenomicInfo+  _chrStop <- atTag "ChrStop" >>> getChildren >>> getText -< entrezGenomicInfo+  _exonCount <- atTag "ExonCount" >>> getChildren >>> getText -< entrezGenomicInfo+  returnA -< EntrezGenomicInfo {+    chrAccVer = _chrAccVer,+    chrStart  = readInt _chrStart,+    chrStop = readInt _chrStop,+    exonCount = readInt _exonCount+    }+++-- | gets all subtrees with the specified tag name+atTag :: ArrowXml a =>  String -> a XmlTree XmlTree+atTag tag = deep (isElem >>> hasName tag)++---------------------------------------+-- Retrieval functions++-- | Retrieve sequence for gene symbol (e.g. yhfA) from accession number (e.g. NC_000913.3) and if available entrez registration (toolname,devemail)+retrieveGeneSymbolFasta :: String -> String -> Maybe (String,String) -> IO String+retrieveGeneSymbolFasta genesymbol accession registrationInfo = do+  let query1 = EntrezHTTPQuery (Just "esearch") (Just "gene") ("term=" ++ genesymbol ++ urlEncode ("[Gene Name] AND " ++ accession ++ "[Nucleotide Accession]"))+  --print query1+  uniqueidresponse <- entrezHTTP query1+  --print uniqueidresponse+  let uniqueid = head (searchIds (head (readEntrezSearch uniqueidresponse)))+  let query2 = EntrezHTTPQuery (Just "esummary") (Just "gene") ("id=" ++ show uniqueid)+  summaryresponse <- entrezHTTP query2+  --print summaryresponse+  let parsedSummary = head (geneSummaries (head (readEntrezGeneSummaries summaryresponse)))+  let accessionVersion = chrAccVer (geneGenomicInfo parsedSummary)+  let seqStart = chrStart (geneGenomicInfo parsedSummary)+  let seqStop = chrStop (geneGenomicInfo parsedSummary)+  let strand = convertCoordinatesToStrand seqStart seqStop+  fetchNucleotideString accessionVersion seqStart seqStop strand registrationInfo+++-- | Fetches sequence strings from the nucleotide database. nucleotideId can be a NCBI accession number or gene id.+--   Strand is 1 in case of plus strand (forward) or 2 minus (reverse) strand, the setStrand function can be used for conversion.+fetchNucleotideString :: String -> Int -> Int -> Int -> Maybe (String,String) -> IO String+fetchNucleotideString nucleotideId seqStart seqStop strand maybeRegistrationInfo = do+  let registrationInfo = maybeBuildRegistration maybeRegistrationInfo+  let program' = Just "efetch"+  let database' = Just "nucleotide"+  let query' = "id=" ++ nucleotideId ++ "&seq_start=" ++ show seqStart ++ "&seq_stop=" ++ show seqStop ++ "&rettype=fasta" ++ "&strand=" ++ show strand ++ registrationInfo+  let entrezQuery = EntrezHTTPQuery program' database' query'+  entrezHTTP entrezQuery++convertCoordinatesToStrand :: Int -> Int -> Int+convertCoordinatesToStrand start end+  | start <= end = 1+  | otherwise = 2++setStrand :: String -> Int+setStrand strandString+  | strandString == "+" = 1+  | strandString == "-" = 2+  | strandString == "forward" = 1+  | strandString == "reverse" = 2+  | strandString == "Forward" = 1+  | strandString == "Reverse" = 2+  | strandString == "plus" = 1+  | strandString == "false" = 2+  | strandString == "Plus" = 1+  | strandString == "False" = 2+  | otherwise = 1++readInt :: String -> Int+readInt = read++-- | Builds Entrez registration String if present+maybeBuildRegistration :: Maybe (String,String) -> String+maybeBuildRegistration maybeRegistration+  | isJust maybeRegistration = buildRegistration toolname developeremail+  | otherwise = ""+  where registration = fromJust maybeRegistration+        toolname = fst registration+        developeremail = snd registration++-- | Builds Entrez registration String that has to be appended to query key+buildRegistration :: String -> String -> String+buildRegistration toolname developeremail = "&tool=" ++ toolname ++ "&email=" ++ developeremail

+ Biobase/Entrez/HTTPData.hs view

@@ -0,0 +1,73 @@+-- | Data structures for Entrez HTTP queries++module Biobase.Entrez.HTTPData where++-- | Input datastructure for EntrezHTTP. Program is the selected eutility (e.g efetch, esearch),+--   database is the selected Entrez database (nucleotide) and query the query string.+data EntrezHTTPQuery = EntrezHTTPQuery+  { program :: Maybe String+  , database :: Maybe String+  , query :: String+  }+  deriving (Show, Eq)++-- | Data structure for Entrez summary result+newtype EntrezSummary = EntrezSummary+  {  documentSummaries :: [EntrezDocSum]}+  deriving (Show, Eq)++data EntrezDocSum = EntrezDocSum+  {  summaryId :: String+  ,  summaryItems :: [SummaryItem]}+  deriving (Show, Eq)++data SummaryItem = SummaryItem+  { itemName :: String+  , itemType :: String+  , itemContent :: String}+  deriving (Show, Eq)++-- | Gene doc summary+newtype EntrezGeneSummary = EntrezGeneSummary+  {  geneSummaries :: [EntrezGeneDocSummary]}+  deriving (Show, Eq)++data EntrezGeneDocSummary = EntrezGeneDocSummary+  { geneId :: String+  , geneName :: String+  , geneStatus :: String+  , geneCurrentID :: String+  , geneGeneticSource :: String+  , geneOtherAliases :: String+  , geneGenomicInfo :: EntrezGenomicInfo}+  deriving (Show, Eq)++data EntrezGenomicInfo = EntrezGenomicInfo+  { chrAccVer :: String+  , chrStart :: Int+  , chrStop :: Int+  , exonCount :: Int+  }+  deriving (Show, Eq)++-- | Data structure for Entrez search result+data EntrezSearch = EntrezSearch+  { count :: Int+  , retMax :: Int+  , retStart :: Int+  , searchIds :: [Int]+  , translationStack :: [TranslationStack]+  , queryTranslation :: String}+  deriving (Show, Eq)++data TranslationStack = TranslationStack+  { termSets :: [TermSet]+  , operation :: String}+  deriving (Show, Eq)++data TermSet = TermSet+  { term :: String+  , field :: String+  , termCount :: Int+  , explode :: String}+  deriving (Show, Eq)

+ BiobaseHTTP.cabal view

@@ -0,0 +1,43 @@+name:                BiobaseHTTP+version:             1.1.0+synopsis:            Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl+description:         BiobaseHTTP provides functions to interface the Bioinformatics REST services - Entrez Ensembl+                     .+                     NCBI Entrez provides multiple different databases and eutils.+                     .+                     For more information on Entrez refer to: <http://www.ncbi.nlm.nih.gov/gquery/>.+                     .+                     Information on the webservice can be found at: <http://www.ncbi.nlm.nih.gov/books/NBK25497/>.+                     If you plan to include the library in a tool, register it as explained <http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Usage_Guidelines_and_Requiremen here>.+                     .+                     Information on ENSEMBL genomes API can be found here: <http://rest.ensemblgenomes.org/>.+                     .+                     BiobaseHTTP is the successor of the deprecated EntrezHTTP library.+license:             GPL-3+license-file:        LICENSE+author:              Florian Eggenhofer+maintainer:          egg@informatik.uni-freiburg.de+copyright:           Florian Eggenhofer+homepage:	     https://github.com/eggzilla/BiobaseHTTP+category:            Bioinformatics+build-type:          Simple+cabal-version:       >=1.8+Tested-With: GHC == 8.4.3++Extra-Source-Files:+        README.md changelog++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++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+  hs-source-dirs:      .

+ LICENSE view

@@ -0,0 +1,675 @@+              GNU GENERAL PUBLIC LICENSE+                Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.++                     Preamble++  The GNU General Public License is a free, copyleft license for+software and other kinds of works.++  The licenses for most software and other practical works are designed+to take away your freedom to share and change the works.  By contrast,+the GNU General Public License is intended to guarantee your freedom to+share and change all versions of a program--to make sure it remains free+software for all its users.  We, the Free Software Foundation, use the+GNU General Public License for most of our software; it applies also to+any other work released this way by its authors.  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+ README.md view

@@ -0,0 +1,17 @@+BiobaseHTTP+[![Hackage](https://img.shields.io/hackage/v/BiobaseHTTP.svg)](https://hackage.haskell.org/package/BiobaseHTTP) [![Build Status](https://travis-ci.org/eggzilla/BiobaseHTTP.svg?branch=master)](https://travis-ci.org/eggzilla/BiobaseHTTP)+=========++BiobaseHTTP provides functions to interface the Bioinformatics REST services - Entrez Ensembl.++NCBI Entrez provides multiple different databases and eutils.++For more information on Entrez refer to: [Entrez](http://www.ncbi.nlm.nih.gov/gquery/).+ +Information on the webservice can be found at: [NCBI books](http://www.ncbi.nlm.nih.gov/books/NBK25497/).++Information on ENSEMBL genomes API can be found here: [Ensembl Genomes](http://rest.ensemblgenomes.org/).+ +If you plan to include the library in a tool, register it as explained [here](http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Usage_Guidelines_and_Requiremen).++BiobaseHTTP is the successor of the deprecated EntrezHTTP library.

+ Setup.hs view

@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain

+ changelog view

@@ -0,0 +1,17 @@+-*-change-log-*-+1.1.0 Florian Eggenhofer <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 <egg@informatik.uni-freiburg.de> 10. August 2017+	* Updated version constraints for Taxonomy+1.0.3 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 12. November 2016+	* Default NCBI URL now uses HTTPS+1.0.2 Florian Eggenhofer <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 <florian.eggenhofer@univie.ac.at> 5. January 2016+	* Fixed version constraints, added changelog+1.0.0 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 11.September 2015+	* Initial version+