Commit eb248441 authored by Mael NICOLAS's avatar Mael NICOLAS

fetch and search ok, need to do an xml parser and a function to connect the two routes

parents
.stack-work/
pubMedCrawler.cabal
*~
\ No newline at end of file
# Changelog for pubMedCrawler
## Unreleased changes
Copyright Author name here (c) 2019
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
* Neither the name of Author name here nor the names of other
contributors may be used to endorse or promote products derived
from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# pubMedCrawler
import Distribution.Simple
main = defaultMain
{-# LANGUAGE OverloadedStrings #-}
module Main where
import PUBMED.Client
import Network.HTTP.Client (newManager)
import Network.HTTP.Client.TLS (tlsManagerSettings)
import Servant.Client (runClientM, mkClientEnv, BaseUrl(..), Scheme(..))
main :: IO ()
main = do
manager' <- newManager tlsManagerSettings
res <- runClientM
(fetch (Just "pubmed") ["31059770", "31059556"])
(mkClientEnv manager' $ BaseUrl Https "eutils.ncbi.nlm.nih.gov" 443 "entrez/eutils")
case res of
(Left err) -> print err
(Right ok) -> print ok
name: pubMedCrawler
version: 0.1.0.0
github: "githubuser/pubMedCrawler"
license: BSD3
author: "Author name here"
maintainer: "example@example.com"
copyright: "2019 Author name here"
extra-source-files:
- README.md
- ChangeLog.md
# Metadata used when publishing your package
# synopsis: Short description of your package
# category: Web
# 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.
description: Please see the README on GitHub at <https://github.com/githubuser/pubMedCrawler#readme>
dependencies:
- base >= 4.7 && < 5
- servant
- servant-client
- text
- bytestring
- xml-conduit
- http-client
- http-client-tls
- http-media
library:
source-dirs: src
executables:
pubMedCrawler-exe:
main: Main.hs
source-dirs: app
ghc-options:
- -threaded
- -rtsopts
- -with-rtsopts=-N
dependencies:
- pubMedCrawler
tests:
pubMedCrawler-test:
main: Spec.hs
source-dirs: test
ghc-options:
- -threaded
- -rtsopts
- -with-rtsopts=-N
dependencies:
- pubMedCrawler
module Lib
( someFunc
) where
someFunc :: IO ()
someFunc = putStrLn "someFunc"
{-# LANGUAGE TypeOperators #-}
{-# LANGUAGE DataKinds #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE MultiParamTypeClasses #-}
module PUBMED.Client where
import Servant.API
import Servant.Client
import Data.Proxy (Proxy(..))
import Data.ByteString.Lazy (ByteString)
import qualified Network.HTTP.Media as M
import qualified Data.Text as T
data DB = PUBMED
newtype BsXml = BsXml ByteString
deriving (Show)
instance Accept BsXml where
contentType _ = "text" M.// "xml"
instance MimeUnrender BsXml BsXml where
mimeUnrender _ = Right . BsXml
type PUBMEDAPI =
"esearch.fcgi"
-- :> QueryParam "db" DB
-- not mandatory since the base db is pubmed
:> QueryParam "term" T.Text
:> Get '[BsXml] BsXml
:<|>
"efetch.fcgi"
:> QueryParam "db" T.Text
:> QueryParams "id" T.Text
:> Get '[BsXml] BsXml
pubmedApi :: Proxy PUBMEDAPI
pubmedApi = Proxy
search :: Maybe T.Text
-> ClientM BsXml
fetch :: Maybe T.Text
-> [T.Text]
-> ClientM BsXml
search :<|> fetch = client pubmedApi
# This file was automatically generated by 'stack init'
#
# Some commonly used options have been documented as comments in this file.
# For advanced use and comprehensive documentation of the format, please see:
# https://docs.haskellstack.org/en/stable/yaml_configuration/
# Resolver to choose a 'specific' stackage snapshot or a compiler version.
# A snapshot resolver dictates the compiler version and the set of packages
# to be used for project dependencies. For example:
#
# resolver: lts-3.5
# resolver: nightly-2015-09-21
# resolver: ghc-7.10.2
#
# The location of a snapshot can be provided as a file or url. Stack assumes
# a snapshot provided as a file might change, whereas a url resource does not.
#
# resolver: ./custom-snapshot.yaml
# resolver: https://example.com/snapshots/2018-01-01.yaml
resolver: lts-13.13
# User packages to be built.
# Various formats can be used as shown in the example below.
#
# packages:
# - some-directory
# - https://example.com/foo/bar/baz-0.0.2.tar.gz
# - location:
# git: https://github.com/commercialhaskell/stack.git
# commit: e7b331f14bcffb8367cd58fbfc8b40ec7642100a
# - location: https://github.com/commercialhaskell/stack/commit/e7b331f14bcffb8367cd58fbfc8b40ec7642100a
# subdirs:
# - auto-update
# - wai
packages:
- .
# Dependency packages to be pulled from upstream that are not in the resolver
# using the same syntax as the packages field.
# (e.g., acme-missiles-0.3)
# extra-deps: []
# Override default flag values for local packages and extra-deps
# flags: {}
# Extra package databases containing global packages
# extra-package-dbs: []
# Control whether we use the GHC we find on the path
# system-ghc: true
#
# Require a specific version of stack, using version ranges
# require-stack-version: -any # Default
# require-stack-version: ">=1.9"
#
# Override the architecture used by stack, especially useful on Windows
# arch: i386
# arch: x86_64
#
# Extra directories used by stack for building
# extra-include-dirs: [/path/to/dir]
# extra-lib-dirs: [/path/to/dir]
#
# Allow a newer minor version of GHC than the snapshot specifies
# compiler-check: newer-minor
main :: IO ()
main = putStrLn "Test suite not yet implemented"
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