Add support for APIKey

src/PUBMED.hs

@@ -38,14 +38,14 @@ defaultEnv = do
   pure $ mkClientEnv manager' $ BaseUrl Https pmHost pmPort pmSearchPath
 
 -- | API main function
-getMetadataWith :: Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [PubMed])
+getMetadataWith :: Maybe Text -> Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [PubMed])
 getMetadataWith = runSimpleFindPubmedAbstractRequest
 
-getMetadataWithC :: Text -> Maybe Limit -> IO (Either ClientError (Maybe Integer, ConduitT () PubMed IO ()))
-getMetadataWithC query limit = do
+getMetadataWithC :: Maybe Text -> Text -> Maybe Limit -> IO (Either ClientError (Maybe Integer, ConduitT () PubMed IO ()))
+getMetadataWithC mAPIKey query limit = do
   env <- defaultEnv
   -- First, estimate the total number of documents
-  eRes <- runClientM (search (Just query) Nothing (Just 1)) env
+  eRes <- runClientM (search mAPIKey (Just query) Nothing (Just 1)) env
   pure $ get' env query limit batchSize <$> eRes
   where
     get' :: ClientEnv -> Text -> Maybe Limit -> Int -> BsXml -> (Maybe Integer, ConduitT () PubMed IO ())
@@ -53,21 +53,26 @@ getMetadataWithC query limit = do
       ( Just numResults
       , yieldMany [0..]
         .| takeC (fromInteger numPages)
-        .| concatMapMC (getPage env q perPage))
+        .| concatMapMC (getPage env mAPIKey q perPage))
       where
         numResults = fromMaybe 0 $ parseDocCount $ TL.fromStrict $ TE.decodeUtf8 $ LBS.toStrict res
         numPages = numResults `div` (fromIntegral perPage) + 1
 
-getPage :: ClientEnv -> Text -> Int -> Int -> IO [PubMed]
-getPage env q perPage pageNum = do
+getPage :: ClientEnv
+        -> Maybe Text
+        -> Text
+        -> Int
+        -> Int
+        -> IO [PubMed]
+getPage env mAPIKey q perPage pageNum = do
   let offset = fromIntegral $ pageNum * perPage
-  eDocs <- runSimpleFindPubmedAbstractRequest q (Just offset) (Just $ fromIntegral perPage)
+  eDocs <- runSimpleFindPubmedAbstractRequest mAPIKey q (Just offset) (Just $ fromIntegral perPage)
   case eDocs of
     Left err -> panic $ "[getPage] error: " <> show err
     Right docs -> do
       _ <- threadDelay 2000000 -- One seconds
       pure docs
-  
+
 -- | TODO this parser need at least one subs at the end
 -- (use endOfInput)
 removeSub :: Parser ByteString
@@ -110,7 +115,7 @@ runSimpleFetchPubmedAbstractRequest ::
 runSimpleFetchPubmedAbstractRequest ids = do
   env <- defaultEnv
   res <- runClientM
-    (fetch (Just "pubmed") (Just "abstract") ids)
+    (fetch Nothing (Just "pubmed") (Just "abstract") ids)
     env
   case res of
     (Left err) -> pure (Left . T.pack $ show err)
@@ -126,18 +131,22 @@ runSimpleFetchPubmedAbstractRequest ids = do
 --                                                pure []) :: XmlException -> IO [PubMed])
 --          Right <$> pure parsed
 
-runSimpleFindPubmedAbstractRequest :: Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [PubMed])
-runSimpleFindPubmedAbstractRequest query offset limit =  do
-  eDocIds <- searchDocIds query offset limit
+runSimpleFindPubmedAbstractRequest :: Maybe Text
+                                   -> Text
+                                   -> Maybe Integer
+                                   -> Maybe Limit
+                                   -> IO (Either Text [PubMed])
+runSimpleFindPubmedAbstractRequest mAPIKey query offset limit =  do
+  eDocIds <- searchDocIds mAPIKey query offset limit
   case eDocIds of
     Left err -> pure $ Left err
     Right docIds -> runMultipleFPAR docIds
 
-searchDocIds :: Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [Integer])
-searchDocIds query offset limit = do
+searchDocIds :: Maybe Text -> Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [Integer])
+searchDocIds mAPIKey query offset limit = do
   env <- defaultEnv
   res <- runClientM
-    (search (Just query) offset limit)
+    (search mAPIKey (Just query) offset limit)
     env
   case res of
     (Left err) -> pure (Left $ T.pack $ show err)

src/PUBMED/Client.hs

@@ -22,12 +22,14 @@ type PUBMEDAPI =
   "esearch.fcgi"
 --  :> QueryParam "db" DB
 -- not mandatory since the base db is pubmed
+  :> QueryParam "api_key" T.Text
   :> QueryParam "term" T.Text
   :> QueryParam "retstart" Integer
   :> QueryParam "retmax" Integer
   :> Get '[BsXml] BsXml
   :<|>
   "efetch.fcgi"
+  :> QueryParam "api_key" T.Text
   :> QueryParam "db" T.Text
   :> QueryParam "rettype" T.Text
   :> QueryParams "id" Integer
@@ -36,10 +38,15 @@ type PUBMEDAPI =
 pubmedApi :: Proxy PUBMEDAPI
 pubmedApi = Proxy
 
-search :: Maybe T.Text -> Maybe Integer -> Maybe Integer -> ClientM BsXml
+search :: Maybe T.Text
+       -> Maybe T.Text
+       -> Maybe Integer
+       -> Maybe Integer
+       -> ClientM BsXml
 
 fetch :: Maybe T.Text
-  -> Maybe T.Text
-  -> [Integer]
-  -> ClientM BsXml
+      -> Maybe T.Text
+      -> Maybe T.Text
+      -> [Integer]
+      -> ClientM BsXml
 search :<|> fetch = client pubmedApi