consolidate logging

deps.edn

@@ -2,29 +2,35 @@
 
  :deps
  {
-  org.clojure/clojure       {:mvn/version "1.11.0"}
+  org.clojure/clojure                       {:mvn/version "1.11.0"}
   ;; util
-  prismatic/schema          {:mvn/version "1.2.0"}    ; schema validator
-  slingshot/slingshot       {:mvn/version "0.12.2"}   ; better exception handling
-  com.cemerick/friend       {:mvn/version "0.2.3"}    ; auth library
-  cheshire/cheshire         {:mvn/version "5.10.2"}   ; fast JSON encoding (used by Ring JSON middleware)
-  potemkin/potemkin         {:mvn/version "0.4.5"}    ; utility macros & fns
+  prismatic/schema                          {:mvn/version "1.2.0"}    ; schema validator
+  slingshot/slingshot                       {:mvn/version "0.12.2"}   ; better exception handling
+  com.cemerick/friend                       {:mvn/version "0.2.3"}    ; auth library
+  cheshire/cheshire                         {:mvn/version "5.10.2"}   ; fast JSON encoding (used by Ring JSON middleware)
+  potemkin/potemkin                         {:mvn/version "0.4.5"}    ; utility macros & fns
   ;; webserver+routing
-  compojure/compojure       {:mvn/version "1.6.2"}
-  ring/ring-core            {:mvn/version "1.9.4"}
-  ring/ring-jetty-adapter   {:mvn/version "1.9.5"}
-  ring/ring-json            {:mvn/version "0.5.1"}
-  ring-cors/ring-cors       {:mvn/version "0.1.13"}
+  compojure/compojure                       {:mvn/version "1.6.2"}
+  ring/ring-core                            {:mvn/version "1.9.4"}
+  ring/ring-jetty-adapter                   {:mvn/version "1.9.5"}
+  ring/ring-json                            {:mvn/version "0.5.1"}
+  ring-cors/ring-cors                       {:mvn/version "0.1.13"}
   ;; log
-  com.taoensso/timbre       {:mvn/version "5.1.2"}
+  org.clojure/tools.logging                 {:mvn/version "1.2.4"}
+  org.apache.logging.log4j/log4j-1.2-api    {:mvn/version "2.18.0"}             ; apache logging framework
+  org.apache.logging.log4j/log4j-api        {:mvn/version "2.18.0"}             ; add compatibility with log4j 1.2
+  org.apache.logging.log4j/log4j-core       {:mvn/version "2.18.0"}             ; apache logging framework
+  org.apache.logging.log4j/log4j-jcl        {:mvn/version "2.18.0"}             ; allows the commons-logging API to work with log4j 2
+  org.apache.logging.log4j/log4j-jul        {:mvn/version "2.18.0"}             ; java.util.logging (JUL) -> Log4j2 adapter
+  org.apache.logging.log4j/log4j-slf4j-impl {:mvn/version "2.18.0"}             ; allows the slf4j API to work with log4j 2
   ;; database
-  org.clojure/java.jdbc     {:mvn/version "0.7.12"}
-  com.h2database/h2         {:mvn/version "2.1.210"}  ; H2 driver
-  org.postgresql/postgresql {:mvn/version "42.2.13"}  ; Postgres driver
-  com.mchange/c3p0          {:mvn/version "0.9.5.5"}
-  toucan/toucan             {:mvn/version "1.18.0"}
-  ;; hickory/hickory           {:mvn/version "0.7.1"} ; seems like a fater parser than enlive, but using enlive for now bc it has DOM selector
-  enlive/enlive             {:mvn/version "1.1.6"}}   ; html parser
+  org.clojure/java.jdbc                     {:mvn/version "0.7.12"}
+  com.h2database/h2                         {:mvn/version "2.1.210"}  ; H2 driver
+  org.postgresql/postgresql                 {:mvn/version "42.2.13"}  ; Postgres driver
+  com.mchange/c3p0                          {:mvn/version "0.9.5.5"}
+  toucan/toucan                             {:mvn/version "1.18.0"}
+  ;; hickory/hickory                           {:mvn/version "0.7.1"} ; seems like a fater parser than enlive, but using enlive for now bc it has DOM selector
+  enlive/enlive                             {:mvn/version "1.1.6"}}   ; html parser
 
  :aliases
  {; clj -M:dev

resources/log4j2.xml

@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Configuration>
+  <Appenders>
+    <Console name="STDOUT" target="SYSTEM_OUT" follow="true">
+      <PatternLayout pattern="%date %level %logger{2} :: %message%n%throwable">
+        <replace regex=":basic-auth \\[.*\\]" replacement=":basic-auth [redacted]"/>
+      </PatternLayout>
+    </Console>
+
+    <!-- This file appender is provided as an example -->
+    <!--
+    <RollingFile name="FILE" fileName="${logfile.path}/ubinote.log" filePattern="${logfile.path}/ubinote.log.%i">
+      <Policies>
+        <SizeBasedTriggeringPolicy size="500 MB"/>
+      </Policies>
+      <DefaultRolloverStrategy max="2"/>
+      <PatternLayout pattern="%d [%t] %-5p%c - %m%n">
+        <replace regex=":basic-auth \\[.*\\]" replacement=":basic-auth [redacted]"/>
+      </PatternLayout>
+    </RollingFile>
+    -->
+  </Appenders>
+
+  <Loggers>
+    <Logger name="ubinote" level="INFO"/>
+    <Logger name="com.mchange" level="ERROR"/>
+
+    <Root level="WARN">
+      <AppenderRef ref="STDOUT"/>
+    </Root>
+  </Loggers>
+</Configuration>

src/frontend/components/Page/View.tsx

@@ -24,14 +24,17 @@ const addHighlight = (pageId: number, selection: window.Selection, color = "red"
   // need to calculate textpos before highlight, otherwise the position will be messed up
   // when try to highlight on re-load
   const textPos = fromRange(document.body, range);
-  const highlightElements = highlightRange(range, 'span', {class: colorToCSS[color]});
-  console.log("Elements: ", highlightElements);
+  console.log("range:", range);
+  console.log("textpos:", textPos);
+  console.log("bounding: ", range.getBoundingClientRect());
+  // from this bounding => display a dom at the middle end
+  //const highlightElements = highlightRange(range, 'span', {class: colorToCSS[color]});
   // save it
-  createAnnotation(
-    {coordinate: textPos,
-      page_id: pageId})
-    .catch(err => console.error("Failed to add annotaiton: ", err));
-  return highlightElements;
+  //createAnnotation(
+  //  {coordinate: textPos,
+  //    page_id: pageId})
+  //  .catch(err => console.error("Failed to add annotaiton: ", err));
+  //return highlightElements;
 }
 
 const PageView = (props: Props) => {
@@ -43,6 +46,7 @@ const PageView = (props: Props) => {
     document.addEventListener("mouseup", () => {
       const selection = window.getSelection();
       if (!selection.isCollapsed) {
+        // open up a popover
         addHighlight(page.id, selection);
       }
     });

src/ubinote/cmd.clj

@@ -2,7 +2,7 @@
   (:require [ubinote.util.fs :as fs]
             [clojure.string :as string]
             [clojure.java.shell :refer [sh]]
-            [taoensso.timbre :as log]))
+            [clojure.tools.logging :as log]))
 
 (defn which
   "like `which` command"

src/ubinote/migration.clj

@@ -4,7 +4,7 @@
             [ubinote.config :as cfg]
             [clojure.java.jdbc :as jdbc]
             [clojure.string :as string]
-            [taoensso.timbre :as log]
+            [clojure.tools.logging :as log]
             [toucan.db :as db]))
 
 (def migrations (atom []))

src/ubinote/server/core.clj

@@ -8,9 +8,19 @@
             [compojure.route :as route]
             [compojure.core :refer [context defroutes GET]]
             [ring.util.response :refer [resource-response]]
-            [taoensso.timbre :as log]
+            [clojure.tools.logging :as log]
             [ring.adapter.jetty :refer [run-jetty]]))
 
+;; ensure we use a `BasicContextSelector` instead of a `ClassLoaderContextSelector` for log4j2. Ensures there is only
+;; one LoggerContext instead of one per classpath root. Practical effect is that now `(LogManager/getContext true)`
+;; and `(LogManager/getContext false)` will return the same (and only)
+;; LoggerContext. https://logging.apache.org/log4j/2.x/manual/logsep.html
+(System/setProperty "log4j2.contextSelector" "org.apache.logging.log4j.core.selector.BasicContextSelector")
+
+;; ensure the [[clojure.tools.logging]] logger factory is the log4j2 version (slf4j is far slower and identified first)
+(System/setProperty "clojure.tools.logging.factory" "clojure.tools.logging.impl/log4j2-factory")
+(System/setProperty "log4j2.configurationFile" "log4j2.xml")
+
 (defroutes routes
   ;; serving bundle.js this seems hacky?
   (GET "/static/js/bundle.js" [_req] (resource-response "frontend/static/js/bundle.js")) ;; inside the resources folder

src/ubinote/server/db.clj

@@ -3,7 +3,6 @@
             [clojure.java.jdbc :as jdbc]
             [clojure.java.io :as io]
             [clojure.string :as string]
-            [taoensso.timbre :as log]
             [toucan.models :as models]
             [toucan.db :as db])
   (:import java.util.Properties
@@ -91,6 +90,5 @@
   []
   (let [db-type (cfg/config-kw :un-db-type)]
     (models/set-root-namespace! 'ubinote.model)
-    ;(db/set-default-automatically-convert-dashes-and-underscores! true)
     (db/set-default-quoting-style! (db-type quoting-style))
     (db/set-default-db-connection! (db-details db-type))))

src/ubinote/server/middleware/api.clj

@@ -1,5 +1,5 @@
 (ns ubinote.server.middleware.api
-  (:require [taoensso.timbre :as log]))
+  (:require [clojure.tools.logging :as log]))
 
 (defn resp->log-level
   [{:keys [status]}]

src/ubinote/server/middleware/exceptions.clj

@@ -1,5 +1,5 @@
 (ns ubinote.server.middleware.exceptions
-  (:require [taoensso.timbre :as log]))
+  (:require [clojure.tools.logging :as log]))
 
 (defn- explain-one-schema-error
   [[k v]]

src/ubinote/server/middleware/log.clj

@@ -1,5 +1,5 @@
 (ns ubinote.server.middleware.log
-  (:require [taoensso.timbre :as log]))
+  (:require [clojure.tools.logging :as log]))
 
 (defn resp->log-level
   [{:keys [status]}]