[refactoring] add default-extensions to packages, some refactoring

app/Main.hs

-{-# LANGUAGE OverloadedStrings #-}
-
 module Main where
 
 import PUBMED (getMetadataWith)

crawlerPubMed.cabal

 cabal-version: 1.12
 
--- This file has been generated from package.yaml by hpack version 0.31.2.
+-- This file has been generated from package.yaml by hpack version 0.34.4.
 --
 -- see: https://github.com/sol/hpack
---
--- hash: 4bb73f43a66d509480c9a672fe457ad8be7cb2d27c8b0892e234b8ac088a2a44
 
 name:           crawlerPubMed
 version:        0.1.0.0
@@ -30,10 +28,16 @@ library
       PUBMED
       PUBMED.Client
       PUBMED.Parser
+      PUBMED.Test
   other-modules:
       Paths_crawlerPubMed
   hs-source-dirs:
       src
+  default-extensions:
+      DataKinds
+      MultiParamTypeClasses
+      OverloadedStrings
+      TypeOperators
   build-depends:
       attoparsec
     , base >=4.7 && <5
@@ -56,10 +60,13 @@ library
 
 executable crawlerPubMed-exe
   main-is: Main.hs
-  other-modules:
-      Paths_crawlerPubMed
   hs-source-dirs:
       app
+  default-extensions:
+      DataKinds
+      MultiParamTypeClasses
+      OverloadedStrings
+      TypeOperators
   ghc-options: -threaded -rtsopts -with-rtsopts=-N
   build-depends:
       attoparsec
@@ -89,6 +96,11 @@ test-suite crawlerPubMed-test
       Paths_crawlerPubMed
   hs-source-dirs:
       test
+  default-extensions:
+      DataKinds
+      MultiParamTypeClasses
+      OverloadedStrings
+      TypeOperators
   ghc-options: -threaded -rtsopts -with-rtsopts=-N
   build-depends:
       attoparsec

package.yaml

@@ -14,6 +14,12 @@ extra-source-files:
 # synopsis:            Short description of your package
 # category:            Web
 
+default-extensions:
+  - DataKinds
+  - MultiParamTypeClasses
+  - OverloadedStrings
+  - TypeOperators
+
 # To avoid duplicated efforts in documentation and dealing with the
 # complications of embedding Haddock markup inside cabal files, it is
 # common to point users to the README.md file.
@@ -51,6 +57,10 @@ executables:
     - -with-rtsopts=-N
     dependencies:
     - crawlerPubMed
+# https://stackoverflow.com/questions/67519851/multiple-files-use-the-same-module-name
+    when:
+    - condition: false
+      other-modules: Paths_crawlerPubMed
 
 tests:
   crawlerPubMed-test:
@@ -62,3 +72,4 @@ tests:
     - -with-rtsopts=-N
     dependencies:
     - crawlerPubMed
+

src/PUBMED.hs

-{-# LANGUAGE OverloadedStrings #-}
-
 module PUBMED where
 
 import Prelude hiding (takeWhile)
@@ -26,6 +24,17 @@ import qualified Data.ByteString      as DB
 import qualified Data.Text as T
 import qualified Data.List as List
 
+pmHost :: String
+pmHost = "eutils.ncbi.nlm.nih.gov"
+pmSearchPath :: String
+pmSearchPath = "entrez/eutils"
+pmPort :: Int
+pmPort = 443
+
+defaultEnv = do
+  manager' <- newManager tlsManagerSettings
+  pure $ mkClientEnv manager' $ BaseUrl Https pmHost pmPort pmSearchPath
+
 -- | API main function
 getMetadataWith :: Text -> Maybe Limit -> IO (Either Text [PubMed])
 getMetadataWith = runSimpleFindPubmedAbstractRequest
@@ -72,10 +81,10 @@ runSimpleFetchPubmedAbstractRequest ::
   [Integer]
   -> IO (Either Text [PubMed])
 runSimpleFetchPubmedAbstractRequest ids = do
-  manager' <- newManager tlsManagerSettings
+  env <- defaultEnv
   res <- runClientM
     (fetch (Just "pubmed") (Just "abstract") ids)
-    (mkClientEnv manager' $ BaseUrl Https "eutils.ncbi.nlm.nih.gov" 443 "entrez/eutils")
+    env
   case res of
     (Left err) -> pure (Left . T.pack $ show err)
     (Right (BsXml abs)) ->
@@ -89,13 +98,18 @@ runSimpleFetchPubmedAbstractRequest ids = do
 
 runSimpleFindPubmedAbstractRequest :: Text -> Maybe Limit -> IO (Either Text [PubMed])
 runSimpleFindPubmedAbstractRequest query limit =  do
-  manager' <- newManager tlsManagerSettings
+  eDocIds <- searchDocIds query limit
+  case eDocIds of
+    Left err -> pure $ Left err
+    Right docIds -> runMultipleFPAR docIds
+
+searchDocIds :: Text -> Maybe Limit -> IO (Either Text [Integer])
+searchDocIds query limit = do
+  env <- defaultEnv
   res <- runClientM
     (search (Just query) limit)
-    (mkClientEnv manager' $ BaseUrl Https "eutils.ncbi.nlm.nih.gov" 443 "entrez/eutils")
+    env
   case res of
     (Left err) -> pure (Left $ T.pack $ show err)
     (Right (BsXml docs)) -> do
-      let docIds = runParser parseDocId docs
-      runMultipleFPAR docIds
-
+      pure $ Right $ runParser parseDocId docs

src/PUBMED/Client.hs

-{-# LANGUAGE TypeOperators #-}
-{-# LANGUAGE DataKinds #-}
-{-# LANGUAGE OverloadedStrings #-}
-{-# LANGUAGE MultiParamTypeClasses #-}
-
 module PUBMED.Client where
 
 import Servant.API

src/PUBMED/Parser.hs

-{-# LANGUAGE OverloadedStrings #-}
-
 module PUBMED.Parser where
 
 import Text.XML.Stream.Parse