Issue 48298: Align API Filter Operators (#60)

Author: RosalineP

CHANGELOG.md

@@ -1,8 +1,14 @@
 # The LabKey Remote API Library for Java - Change Log
 
-## version 5.3.0-SNAPSHOT
+## version 5.4.0-SNAPSHOT
 *Released*: TBD
-* Update to Gradle 8.2.1 and adjust away from deprecated syntax
+
+## version 5.3.0
+*Released*: 7 September 2023
+* Update to Gradle 8.3 and adjust away from deprecated syntax
+* Add Ontology and Lineage filter type operators
+* Add `TotpManager`, a simple helper that generates TOTP one-time passwords
+* Update Commons Codec, HttpCore, and Gradle Plugins versions
 
 ## version 5.2.0
 *Released*: 3 May 2023

build.gradle

@@ -71,7 +71,7 @@ repositories {
 
 group "org.labkey.api"
 
-version "5.3.0-SNAPSHOT"
+version "5.4.0-SNAPSHOT"
 
 dependencies {
     api "org.json:json:${jsonObjectVersion}"

gradle.properties

@@ -7,15 +7,15 @@ artifactory_contextUrl=https://labkey.jfrog.io/artifactory
 sourceCompatibility=17
 targetCompatibility=17
 
-gradlePluginsVersion=1.41.0
+gradlePluginsVersion=1.41.2
 
-commonsCodecVersion=1.15
+commonsCodecVersion=1.16.0
 commonsLoggingVersion=1.2
 
 hamcrestVersion=1.3
 
 httpclient5Version=5.2.1
-httpcore5Version=5.2.1
+httpcore5Version=5.2.2
 
 jsonObjectVersion=20230618
 

gradle/wrapper/gradle-wrapper.jar

@@ -1,6 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
 networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradle/wrapper/gradle-wrapper.properties

@@ -130,10 +130,13 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.

gradlew

@@ -30,9 +30,10 @@ public enum Operator
         // WARNING: Keep in sync and in order with all other client apis and docs:
         // - server: CompareType.java
         // - java: Filter.java
-        // - js: Filter.js
+        // - js: Types.ts
         // - R: makeFilter.R, makeFilter.Rd
-        // - Python & Perl don't have a filter operator enum
+        // - Python: query.py
+        // - Perl doesn't have a filter operator enum
 
         //
         // These operators require a data value
@@ -90,7 +91,22 @@ public enum Operator
         //
 
         Q("Search", "q", "Q", true),
-        WHERE("Where", "where", "WHERE", true)
+        WHERE("Where", "where", "WHERE", true),
+
+        //
+        // Ontology operators
+        //
+
+        ONTOLOGY_IN_SUBTREE("Is In Subtree", "concept:insubtree", "ONTOLOGY_IN_SUBTREE", true),
+        ONTOLOGY_NOT_IN_SUBTREE("Is Not In Subtree", "concept:notinsubtree", "ONTOLOGY_NOT_IN_SUBTREE", true),
+
+        //
+        // Lineage operators
+        //
+
+        EXP_CHILD_OF("Is Child Of", "exp:childof", "EXP_CHILD_OF", true),
+        EXP_PARENT_OF("Is Parent Of", "exp:parentof", "EXP_PARENT_OF", true),
+        EXP_LINEAGE_OF("In The Lineage Of", "exp:lineageof", "EXP_LINEAGE_OF", true)
         ;
 
         private static final Map<String, Operator> _programmaticNameToOperator = Arrays.stream(Operator.values())

src/org/labkey/remoteapi/query/Filter.java

@@ -0,0 +1,14 @@
+/*
+ * Copyright (c) 2019 Sam Stevens
+ *
+ * Licensed under the MIT License
+ *
+ * https://github.com/samdjstevens v1.7.1
+ */
+package org.labkey.remoteapi.totp;
+
+public class CodeGenerationException extends Exception {
+    public CodeGenerationException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}

src/org/labkey/remoteapi/totp/CodeGenerationException.java

@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) 2019 Sam Stevens
+ *
+ * Licensed under the MIT License
+ *
+ * https://github.com/samdjstevens v1.7.1
+ */
+package org.labkey.remoteapi.totp;
+
+import org.apache.commons.codec.binary.Base32;
+
+import javax.crypto.Mac;
+import javax.crypto.spec.SecretKeySpec;
+import java.security.InvalidKeyException;
+import java.security.InvalidParameterException;
+import java.security.NoSuchAlgorithmException;
+
+public class CodeGenerator
+{
+    private final HashingAlgorithm algorithm;
+    private final int digits;
+
+    public CodeGenerator(HashingAlgorithm algorithm, int digits) {
+        if (algorithm == null) {
+            throw new InvalidParameterException("HashingAlgorithm must not be null.");
+        }
+        if (digits < 1) {
+            throw new InvalidParameterException("Number of digits must be higher than 0.");
+        }
+
+        this.algorithm = algorithm;
+        this.digits = digits;
+    }
+
+    public String generate(String key, long counter) throws CodeGenerationException {
+        try {
+            byte[] hash = generateHash(key, counter);
+            return getDigitsFromHash(hash);
+        } catch (Exception e) {
+            throw new CodeGenerationException("Failed to generate code. See nested exception.", e);
+        }
+    }
+
+    /**
+     * Generate a HMAC-SHA1 hash of the counter number.
+     */
+    private byte[] generateHash(String key, long counter) throws InvalidKeyException, NoSuchAlgorithmException {
+        byte[] data = new byte[8];
+        long value = counter;
+        for (int i = 8; i-- > 0; value >>>= 8) {
+            data[i] = (byte) value;
+        }
+
+        // Create a HMAC-SHA1 signing key from the shared key
+        Base32 codec = new Base32();
+        byte[] decodedKey = codec.decode(key);
+        SecretKeySpec signKey = new SecretKeySpec(decodedKey, algorithm.getHmacAlgorithm());
+        Mac mac = Mac.getInstance(algorithm.getHmacAlgorithm());
+        mac.init(signKey);
+
+        // Create a hash of the counter value
+        return mac.doFinal(data);
+    }
+
+    /**
+     * Get the n-digit code for a given hash.
+     */
+    private String getDigitsFromHash(byte[] hash) {
+        int offset = hash[hash.length - 1] & 0xF;
+
+        long truncatedHash = 0;
+
+        for (int i = 0; i < 4; ++i) {
+            truncatedHash <<= 8;
+            truncatedHash |= (hash[offset + i] & 0xFF);
+        }
+
+        truncatedHash &= 0x7FFFFFFF;
+        truncatedHash %= Math.pow(10, digits);
+
+        // Left pad with 0s for a n-digit code
+        return String.format("%0" + digits + "d", truncatedHash);
+    }
+}

src/org/labkey/remoteapi/totp/CodeGenerator.java

@@ -0,0 +1,32 @@
+/*
+ * Copyright (c) 2019 Sam Stevens
+ *
+ * Licensed under the MIT License
+ *
+ * https://github.com/samdjstevens v1.7.1
+ */
+
+package org.labkey.remoteapi.totp;
+
+public enum HashingAlgorithm {
+
+    SHA1("HmacSHA1", "SHA1"), //default
+    SHA256("HmacSHA256", "SHA256"),
+    SHA512("HmacSHA512", "SHA512");
+
+    private final String hmacAlgorithm;
+    private final String friendlyName;
+
+    HashingAlgorithm(String hmacAlgorithm, String friendlyName) {
+        this.hmacAlgorithm = hmacAlgorithm;
+        this.friendlyName = friendlyName;
+    }
+
+    public String getHmacAlgorithm() {
+        return hmacAlgorithm;
+    }
+
+    public String getFriendlyName() {
+        return friendlyName;
+    }
+}

src/org/labkey/remoteapi/totp/HashingAlgorithm.java

@@ -0,0 +1,16 @@
+/*
+ * Copyright (c) 2019 Sam Stevens
+ *
+ * Licensed under the MIT License
+ *
+ * https://github.com/samdjstevens v1.7.1
+ */
+package org.labkey.remoteapi.totp;
+
+import java.time.Instant;
+
+public class TimeProvider {
+    public long getTime() throws RuntimeException {
+        return Instant.now().getEpochSecond();
+    }
+}

src/org/labkey/remoteapi/totp/TimeProvider.java

@@ -0,0 +1,20 @@
+package org.labkey.remoteapi.totp;
+
+public class TotpManager
+{
+    // Generate a TOTP one-time password based on the default parameters (30 second time step, 6 digits, SHA1)
+    public static String generateCode(String secretKey) throws CodeGenerationException
+    {
+        return generateCode(secretKey, 30, 6, HashingAlgorithm.SHA1);
+    }
+
+    // Generate a TOTP one-time password using custom parameters
+    public static String generateCode(String secretKey, int timeStep, int digits, HashingAlgorithm hashingAlgorithm) throws CodeGenerationException
+    {
+        TimeProvider timeProvider = new TimeProvider();
+        long currentBucket = Math.floorDiv(timeProvider.getTime(), timeStep);
+        CodeGenerator codeGenerator = new CodeGenerator(hashingAlgorithm, digits);
+
+        return codeGenerator.generate(secretKey, currentBucket);
+    }
+}