Integrate the latest SR2 build

This makes the necessary changes to use the latest SR2 version and,
as such, implements support for the new bookmark views. Bookmarks
go through the same system as Readium 1, and the bookmark data
structure has been extended with chapter index and progress
information. Unfortunately, until Readium 1 is removed from the
codebase, we can't make the bookmark data structures as nice as they
could be (currently, every field is optional!).

Affects: https://jira.nypl.org/browse/SIMPLY-2796

.editorconfig

@@ -2,3 +2,11 @@
 indent_size=2
 insert_final_newline=true
 disabled_rules=import-ordering
+
+[*.gradle]
+indent_size=2
+insert_final_newline=true
+
+[*.java]
+indent_size=2
+insert_final_newline=true

build.gradle

@@ -23,21 +23,17 @@ buildscript {
     classpath "androidx.navigation:navigation-safe-args-gradle-plugin:$nav_version"
     classpath "biz.aQute.bnd:biz.aQute.bnd.gradle:4.3.1"
     classpath "com.nabilhachicha:android-native-dependencies:0.1.2"
-    classpath "com.vanniktech:gradle-android-junit-jacoco-plugin:0.15.0"
     classpath "digital.wup:android-maven-publish:3.6.3"
-    classpath "io.codearte.gradle.nexus:gradle-nexus-staging-plugin:0.21.2"
   }
 }
 
 plugins {
   id "com.github.ben-manes.versions" version "0.27.0"
-  id "com.vanniktech.android.junit.jacoco" version "0.15.0"
   id "ru.vyarus.animalsniffer" version "1.5.0"
 
   // Deprecated: Migrate to maven-publish.
   //             https://developer.android.com/studio/build/maven-publish-plugin
   id "digital.wup.android-maven-publish" version "3.6.3"
-  id "io.codearte.nexus-staging" version "0.21.2"
 }
 
 ext {
@@ -82,18 +78,10 @@ ext {
   }
 
   nyplAudioBookAPIVersion = "5.0.0"
+  nyplR2Version = "0.0.5"
 }
 
 subprojects {
-  // Force version 1.0.2 of appcompat. A bug in 1.1.0 causes a crash on API 21.
-  //
-  // https://issuetracker.google.com/issues/141132133#comment42
-  //
-  // TODO: Remove once appcompat:1.2.0 is available.
-  configurations.all {
-    resolutionStrategy.force 'androidx.appcompat:appcompat:1.0.2'
-  }
-
   //
   // We currently have transitive dependencies that specify dependencies on newer versions
   // of SLF4J. These are subtly incompatible with Logback-Android, and it will be a while before
@@ -107,14 +95,15 @@ subprojects {
 ext.libraries = [
   androidAsync                     : "com.koushikdutta.async:androidasync:2.2.1",
   androidXActivity                 : "androidx.activity:activity:1.1.0",
-  androidXAppCompat                : "androidx.appcompat:appcompat:1.0.2",
+  androidXAppCompat                : "androidx.appcompat:appcompat:1.2.0-rc01",
   androidXCardView                 : "androidx.cardview:cardview:1.0.0",
   androidXConstraintLayout         : "androidx.constraintlayout:constraintlayout:1.1.3",
   androidXCore                     : "androidx.core:core:1.1.0",
   androidXFragmentTesting          : "androidx.fragment:fragment-testing:1.1.0",
   androidXLegacyPreferenceV14      : "androidx.legacy:legacy-preference-v14:1.0.0",
   androidXLegacySupport            : "androidx.legacy:legacy-support-v4:1.0.0",
   androidXLifecycle                : "androidx.lifecycle:lifecycle-extensions:2.1.0",
+  androidXLifecycleViewmodel       : "androidx.lifecycle:lifecycle-viewmodel:2.1.0",
   androidXPaging                   : "androidx.paging:paging-runtime-ktx:2.1.0",
   androidXPreference               : "androidx.preference:preference-ktx:1.1.0",
   androidXRecyclerView             : "androidx.recyclerview:recyclerview:1.1.0",
@@ -139,8 +128,8 @@ ext.libraries = [
   jacksonKotlin                    : "com.fasterxml.jackson.module:jackson-module-kotlin:2.9.9",
   javaxAnnotationAPI               : "javax.annotation:javax.annotation-api:1.2-b01",
   jcipAnnotations                  : "com.github.stephenc.jcip:jcip-annotations:1.0-1",
-  jodahExpiringMap                 : "net.jodah:expiringmap:0.4.3",
   jodaTime                         : "joda-time:joda-time:2.9.9",
+  jodahExpiringMap                 : "net.jodah:expiringmap:0.4.3",
   junit                            : "junit:junit:4.12",
   kotlinStdlib                     : "org.jetbrains.kotlin:kotlin-stdlib-jdk7:$kotlin_version",
   leakCanary                       : "com.squareup.leakcanary:leakcanary-android:2.1",
@@ -164,22 +153,16 @@ ext.libraries = [
   nyplDRMCore                      : "org.librarysimplified.drm:org.librarysimplified.drm.core:1.1.1",
   nyplPDFAPI                       : "edu.umn.minitex.pdf:edu.umn.minitex.pdf.api:0.1.0",
   nyplPDFViewer                    : "edu.umn.minitex.pdf:edu.umn.minitex.pdf.pdfviewer:0.1.0",
+  nyplR2API                        : "org.librarysimplified.r2:org.librarysimplified.r2.vanilla:${nyplR2Version}",
+  nyplR2Vanilla                    : "org.librarysimplified.r2:org.librarysimplified.r2.api:${nyplR2Version}",
+  nyplR2Views                      : "org.librarysimplified.r2:org.librarysimplified.r2.views:${nyplR2Version}",
   picasso                          : "com.squareup.picasso:picasso:2.71828",
   readium                          : "org.librarysimplified:org.librarysimplified.readium:0.30.0",
   readiumSharedJS                  : "org.librarysimplified:org.librarysimplified.readium.shared_js:0.30.0",
   rxjava2                          : "io.reactivex.rxjava2:rxjava:2.1.13",
-  slf4j                            : "org.slf4j:slf4j-api:1.7.25"
+  slf4j                            : "org.slf4j:slf4j-api:1.7.25",
 ]
 
-apply plugin: "io.codearte.nexus-staging"
-apply plugin: "com.vanniktech.android.junit.jacoco"
-
-nexusStaging {
-  packageGroup = "org.librarysimplified"
-  numberOfRetries = 32
-  delayBetweenRetriesInMillis = 2000
-}
-
 allprojects {
   group = project.ext["GROUP"]
   version = project.ext["VERSION_NAME"]
@@ -275,7 +258,7 @@ Automatic-Module-Name: ${POM_AUTOMATIC_MODULE_NAME}
 
     default:
       throw new IllegalStateException(
-              "Unrecognized packaging type ${POM_PACKAGING} for ${project}")
+        "Unrecognized packaging type ${POM_PACKAGING} for ${project}")
   }
 
   task javadocsJar(type: Jar) {

simplified-books-api/src/main/java/org/nypl/simplified/books/api/BookChapterProgress.kt

@@ -0,0 +1,20 @@
+package org.nypl.simplified.books.api
+
+/**
+ * Progress through a specific chapter.
+ */
+
+data class BookChapterProgress(
+
+  /**
+   * The index of the chapter.
+   */
+
+  val chapterIndex: Int,
+
+  /**
+   * The progress through the chapter.
+   */
+
+  val chapterProgress: Double
+)

simplified-books-api/src/main/java/org/nypl/simplified/books/api/BookLocation.kt

@@ -0,0 +1,34 @@
+package org.nypl.simplified.books.api
+
+import java.io.Serializable
+
+/**
+ * The current page. A specific location in an EPUB is identified by a chapter index, or an
+ * *idref* and a *content CFI*. In some cases, the *content CFI*
+ * may not be present.
+ *
+ * Note: The type is [Serializable] purely because the Android API requires this
+ * in order pass values of this type between activities. We make absolutely no guarantees
+ * that serialized values of this class will be compatible with future releases.
+ */
+
+data class BookLocation(
+
+  /**
+   * The progress through the chapter, if progress is known.
+   */
+
+  val progress: BookChapterProgress?,
+
+  /**
+   * @return The content CFI, if any
+   */
+
+  val contentCFI: String?,
+
+  /**
+   * @return The IDRef
+   */
+
+  val idRef: String?
+) : Serializable

simplified-books-api/src/main/java/org/nypl/simplified/books/api/BookLocationJSON.java

@@ -23,6 +23,32 @@ private BookLocationJSON() {
     throw new UnreachableCodeException();
   }
 
+  /**
+   * Deserialize chapter progress from the given JSON node.
+   *
+   * @param jom  A JSON object mapper
+   * @param node A JSON node
+   * @return A parsed description
+   * @throws JSONParseException On parse errors
+   */
+
+  public static BookChapterProgress deserializeProgressFromJSON(
+    final ObjectMapper jom,
+    final JsonNode node)
+    throws JSONParseException {
+
+    Objects.requireNonNull(jom, "Object mapper");
+    Objects.requireNonNull(node, "JSON");
+
+    final ObjectNode obj =
+      JSONParserUtilities.checkObject(null, node);
+
+    return new BookChapterProgress(
+      JSONParserUtilities.getInteger(obj, "chapterIndex"),
+      JSONParserUtilities.getDouble(obj, "chapterProgress")
+    );
+  }
+
   /**
    * Deserialize reader book locations from the given JSON node.
    *
@@ -42,10 +68,21 @@ public static BookLocation deserializeFromJSON(
 
     final ObjectNode obj =
       JSONParserUtilities.checkObject(null, node);
-
-    return BookLocation.create(
-      JSONParserUtilities.getStringOptional(obj, "contentCFI"),
-      JSONParserUtilities.getString(obj, "idref"));
+    final ObjectNode progressNode =
+      JSONParserUtilities.getObjectOrNull(obj, "progress");
+
+    final BookChapterProgress progress;
+    if (progressNode != null) {
+      progress = deserializeProgressFromJSON(jom, progressNode);
+    } else {
+      progress = null;
+    }
+
+    return new BookLocation(
+      progress,
+      JSONParserUtilities.getStringOrNull(obj, "contentCFI"),
+      JSONParserUtilities.getStringOrNull(obj, "idref")
+    );
   }
 
   /**
@@ -63,8 +100,22 @@ public static ObjectNode serializeToJSON(
     Objects.requireNonNull(description, "Description");
 
     final ObjectNode jo = jom.createObjectNode();
-    description.contentCFI().map_(cfi -> jo.put("contentCFI", cfi));
-    jo.put("idref", description.idRef());
+    final String contentCFI = description.getContentCFI();
+    if (contentCFI != null) {
+      jo.put("contentCFI", contentCFI);
+    }
+    final String idRef = description.getIdRef();
+    if (idRef != null) {
+      jo.put("idref", idRef);
+    }
+
+    final BookChapterProgress progress = description.getProgress();
+    if (progress != null) {
+      final ObjectNode progressNode = jom.createObjectNode();
+      progressNode.put("chapterIndex", progress.getChapterIndex());
+      progressNode.put("chapterProgress", progress.getChapterProgress());
+      jo.set("progress", progressNode);
+    }
     return jo;
   }
 

simplified-books-api/src/main/java/org/nypl/simplified/books/api/Bookmark.kt

@@ -1,6 +1,5 @@
 package org.nypl.simplified.books.api
 
-import com.io7m.jfunctional.Some
 import org.joda.time.LocalDateTime
 import java.io.Serializable
 import java.net.URI
@@ -48,12 +47,6 @@ data class Bookmark(
 
   val chapterTitle: String,
 
-  /**
-   * An estimate of the current chapter progress, in the range [0, 1]
-   */
-
-  val chapterProgress: Double,
-
   /**
    * An estimate of the current book progress, in the range [0, 1]
    */
@@ -73,6 +66,13 @@ data class Bookmark(
   val uri: URI?
 ) : Serializable {
 
+  /**
+   * An estimate of the current chapter progress, in the range [0, 1]
+   */
+
+  val chapterProgress: Double =
+    this.location.progress?.chapterProgress ?: 0.0
+
   /**
    * The ID of the book to which the bookmark belongs.
    */
@@ -116,11 +116,22 @@ data class Bookmark(
         val messageDigest = MessageDigest.getInstance("SHA-256")
         val utf8 = Charset.forName("UTF-8")
         messageDigest.update(book.value().toByteArray(utf8))
-        val cfiOpt = location.contentCFI()
-        if (cfiOpt is Some<String>) {
-          messageDigest.update(cfiOpt.get().toByteArray(utf8))
+
+        val chapterProgress = location.progress
+        if (chapterProgress != null) {
+          messageDigest.update(chapterProgress.chapterIndex.toString().toByteArray(utf8))
+          val truncatedProgress = String.format("%.6f", chapterProgress.chapterProgress)
+          messageDigest.update(truncatedProgress.toByteArray(utf8))
+        }
+
+        val cfi = location.contentCFI
+        if (cfi != null) {
+          messageDigest.update(cfi.toByteArray(utf8))
+        }
+        val idRef = location.idRef
+        if (idRef != null) {
+          messageDigest.update(idRef.toByteArray(utf8))
         }
-        messageDigest.update(location.idRef().toByteArray(utf8))
         messageDigest.update(kind.motivationURI.toByteArray(utf8))
 
         val digestResult = messageDigest.digest()

simplified-books-api/src/main/java/org/nypl/simplified/books/api/BookmarkJSON.kt

@@ -66,7 +66,6 @@ object BookmarkJSON {
       location = BookLocationJSON.deserializeFromJSON(objectMapper, JSONParserUtilities.getObject(node, "location")),
       time = LocalDateTime.parse(JSONParserUtilities.getString(node, "time")),
       chapterTitle = JSONParserUtilities.getString(node, "chapterTitle"),
-      chapterProgress = JSONParserUtilities.getDouble(node, "chapterProgress"),
       bookProgress = JSONParserUtilities.getDouble(node, "bookProgress"),
       uri = toNullable(JSONParserUtilities.getURIOptional(node, "uri")),
       deviceID = JSONParserUtilities.getStringDefault(node, "deviceID", null))