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gargantext
crawlers
pubmed
Commits
66196687
Commit
66196687
authored
Dec 04, 2023
by
Alfredo Di Napoli
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Do not log requests by default
parent
b8d1de8c
Changes
1
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8 additions
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6 deletions
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-6
PUBMED.hs
src/PUBMED.hs
+8
-6
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src/PUBMED.hs
View file @
66196687
...
...
@@ -37,6 +37,7 @@ import qualified Data.Text.Lazy as TL
import
PUBMED.Types
import
PUBMED.ServantClientLogging
import
Control.Monad.Reader.Class
(
asks
)
pmHost
::
String
pmHost
=
"eutils.ncbi.nlm.nih.gov"
...
...
@@ -45,11 +46,12 @@ pmSearchPath = "entrez/eutils"
pmPort
::
Int
pmPort
=
443
defaultClientEnv
::
IO
ClientEnv
defaultClientEnv
::
Env
ClientEnv
defaultClientEnv
=
do
manager'
<-
newManager
tlsManagerSettings
manager'
<-
liftIO
$
newManager
tlsManagerSettings
let
env
=
mkClientEnv
manager'
$
BaseUrl
Https
pmHost
pmPort
pmSearchPath
pure
$
addLoggingToClientEnv
env
enableDebugLogs
<-
asks
enableDebugLogs
pure
$
if
enableDebugLogs
then
addLoggingToClientEnv
env
else
env
-- | API main function
getMetadataWith
::
Env
(
Either
Text
[
PubMed
])
...
...
@@ -58,8 +60,8 @@ getMetadataWith = runSimpleFindPubmedAbstractRequest Nothing
getMetadataWithC
::
Env
(
Either
ClientError
(
Maybe
Integer
,
ConduitT
()
PubMed
IO
()
))
getMetadataWithC
=
do
config
@
(
Config
{
apiKey
,
query
,
perPage
,
mWebEnv
})
<-
ask
liftIO
$
do
env
<-
defaultClientEnv
liftIO
$
do
-- First, estimate the total number of documents
eRes
<-
runClientM
(
searchWithHistory
apiKey
(
Just
query
)
Nothing
(
Just
1
)
(
Just
"y"
)
mWebEnv
)
env
pure
$
get'
config
env
(
fromMaybe
defaultPerPage
perPage
)
<$>
eRes
...
...
@@ -115,8 +117,8 @@ runSimpleFetchPubmedAbstractRequest :: [Integer]
->
Env
(
Either
Text
[
PubMed
])
runSimpleFetchPubmedAbstractRequest
ids
=
do
(
Config
{
apiKey
})
<-
ask
liftIO
$
do
env
<-
defaultClientEnv
liftIO
$
do
res
<-
runClientM
(
fetch
apiKey
(
Just
"pubmed"
)
(
Just
"abstract"
)
ids
)
env
...
...
@@ -147,8 +149,8 @@ runSimpleFindPubmedAbstractRequest offset = do
searchDocIds
::
Maybe
Offset
->
Env
(
Either
Text
[
Integer
])
searchDocIds
offset
=
do
(
Config
{
apiKey
,
query
,
perPage
,
mWebEnv
})
<-
ask
res
<-
liftIO
$
do
env
<-
defaultClientEnv
res
<-
liftIO
$
do
runClientM
(
searchWithHistory
apiKey
(
Just
query
)
offset
perPage
(
Just
"y"
)
mWebEnv
)
env
...
...
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