Merge remote-tracking branch 'origin/304-dev-pubmed-api-not-in-toml' into dev

bin/gargantext-cli/CLI/Ini.hs

@@ -76,8 +76,7 @@ convertConfigs ini@(Ini.GargConfig { .. }) iniMail nlpConfig connInfo =
                                                    , _jc_max_docs_scrapers = _gc_max_docs_scrapers
                                                    , _jc_js_job_timeout = _gc_js_job_timeout
                                                    , _jc_js_id_timeout = _gc_js_id_timeout }
-                    , _gc_apis = CTypes.APIsConfig { _ac_pubmed_api_key = _gc_pubmed_api_key
-                                                   , _ac_epo_api_url = _gc_epo_api_url
+                    , _gc_apis = CTypes.APIsConfig { _ac_epo_api_url = _gc_epo_api_url
                                                    , _ac_scrapyd_url }
                     , _gc_log_level = LevelDebug
                     }

devops/docker/Caddyfile

+# http disables automatic https
+http://localhost:8108 {
+	root * /srv/purescript-gargantext/dist
+	file_server
+}
+

devops/docker/docker-compose.yaml

@@ -3,7 +3,6 @@ version: '3'
 services:
   caddy:
     image: caddy:alpine
-    network: host
     ports:
       - 8108:8108
     volumes:

gargantext-settings.toml_toModify

@@ -59,9 +59,6 @@ data_filepath = FILEPATH_TO_CHANGE
 
 [apis]
 
-[apis.pubmed]
-api_key = ENTER_PUBMED_API_KEY
-
 [apis.epo]
 api_url = EPO_API_URL
 

src/Gargantext/Core/AsyncUpdates/CentralExchange.hs

@@ -29,7 +29,8 @@ import Gargantext.Core.AsyncUpdates.CentralExchange.Types
 import Gargantext.Core.Config.Types (NotificationsConfig(..))
 import Gargantext.Prelude
 import Gargantext.System.Logging (LogLevel(..), withLogger, logMsg)
-import Nanomsg (Pull(..), Push(..), bind, connect, recv, sendNonblocking, withSocket)
+import Nanomsg (Pull(..), Push(..), bind, connect, recv, send, withSocket)
+import System.Timeout (timeout)
     
 {-
 
@@ -74,7 +75,8 @@ gServer (NotificationsConfig { .. }) = do
             Just _ujp@(UpdateJobProgress _s) -> do
               -- logMsg ioLogger DEBUG $ "[central_exchange] " <> show ujp
               -- send the same message that we received
-              void $ sendNonblocking s_dispatcher r
+              -- void $ sendNonblocking s_dispatcher r
+              void $ timeout 100_000 $ send s_dispatcher r
             Just (UpdateTreeFirstLevel node_id) -> do
               logMsg ioLogger INFO $ "[central_exchange] update tree: " <> show node_id
               -- putText $ "[central_exchange] sending that to the dispatcher: " <> show node_id
@@ -92,7 +94,8 @@ gServer (NotificationsConfig { .. }) = do
               -- gargantext-server but maybe it can be a separate
               -- process, independent of the server.
               -- send the same message that we received
-              void $ sendNonblocking s_dispatcher r
+              -- void $ sendNonblocking s_dispatcher r
+              void $ timeout 100_000 $ send s_dispatcher r
             _ -> logMsg ioLogger DEBUG $ "[central_exchange] unknown message"
       
 
@@ -104,4 +107,6 @@ notify (NotificationsConfig { _nc_central_exchange_connect }) ceMessage = do
       let str = Aeson.encode ceMessage
       withLogger () $ \ioLogger ->
         logMsg ioLogger DEBUG $ "[central_exchange] sending: " <> (T.unpack $ TE.decodeUtf8 $ BSL.toStrict str)
-      void $ sendNonblocking s $ BSL.toStrict str
+      -- err <- sendNonblocking s $ BSL.toStrict str
+      -- putText $ "[notify] err: " <> show err
+      void $ timeout 100_000 $ send s $ BSL.toStrict str

src/Gargantext/Core/Config/Types.hs

@@ -15,7 +15,6 @@ TODO-SECURITY: Critical
 
 module Gargantext.Core.Config.Types
   ( APIsConfig(..)
-  , ac_pubmed_api_key
   , ac_epo_api_url
   , ac_scrapyd_url
   , CORSOrigin(..)
@@ -299,13 +298,11 @@ makeLenses ''JobsConfig
 
 
 data APIsConfig =
-  APIsConfig { _ac_pubmed_api_key :: !Text
-             , _ac_epo_api_url    :: !Text
+  APIsConfig { _ac_epo_api_url    :: !Text
              , _ac_scrapyd_url    :: !BaseUrl }
   deriving (Generic, Show)
 instance FromValue APIsConfig where
   fromValue = parseTableFromValue $ do
-    _ac_pubmed_api_key <- reqKeyOf "pubmed" $ parseTableFromValue $ reqKey "api_key"
     _ac_epo_api_url <- reqKeyOf "epo" $ parseTableFromValue $ reqKey "api_url"
     scrapyd_url <- reqKeyOf "scrapyd" $ parseTableFromValue $ reqKey "url"
     _ac_scrapyd_url <-
@@ -316,8 +313,7 @@ instance FromValue APIsConfig where
 instance ToValue APIsConfig where
   toValue = defaultTableToValue
 instance ToTable APIsConfig where
-  toTable (APIsConfig { .. }) = table [ "pubmed" .= table [ "api_key" .= _ac_pubmed_api_key ]
-                                      , "epo" .= table [ "api_url" .= _ac_epo_api_url ]
+  toTable (APIsConfig { .. }) = table [ "epo" .= table [ "api_url" .= _ac_epo_api_url ]
                                       , "scrapyd" .= table [ "url" .= showBaseUrl _ac_scrapyd_url ]
                                       ]