Merge pull request #49 from quantori/feature/data-types-task0.1

feat: add extended property types

Author: bs-quantori

.github/workflows/build-and-test.yml

@@ -17,6 +17,8 @@ jobs:
   format-check:
     name: Check Code Formatting
     runs-on: ubuntu-latest
+    env:
+      AKKA_REPO_URL: ${{ secrets.AKKA_REPO_URL }}
 
     steps:
       - uses: actions/checkout@v4
@@ -39,6 +41,8 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
+    env:
+      AKKA_REPO_URL: ${{ secrets.AKKA_REPO_URL }}
 
     steps:
     - uses: actions/checkout@v4
@@ -53,5 +57,8 @@ jobs:
     - name: Setup Gradle
       uses: gradle/actions/setup-gradle@af1da67850ed9a4cedd57bfd976089dd991e2582 # v4.0.0
 
+    - name: Build API with Gradle Wrapper
+      run: ./gradlew :cqp-api:build :cqp-api:publishToMavenLocal
+
     - name: Build with Gradle Wrapper
-      run: ./gradlew build
+      run: ./gradlew build -x :cqp-api:build

ARCHITECTURE.md

@@ -91,7 +91,7 @@ The Chemical Query Platform (CQP) is an open-source framework for indexing and s
 
 ### cqp-api (Core API Module)
 
-**Version**: 0.0.16
+**Version**: 0.0.17
 
 **Purpose**: Defines interfaces, models, and abstractions for chemical structure storage and search.
 
@@ -132,7 +132,7 @@ com.quantori.cqp.api/
 
 ### cqp-storage-elasticsearch (Elasticsearch Implementation)
 
-**Version**: 0.0.14
+**Version**: 0.0.17
 
 **Purpose**: Elasticsearch implementation of CQP storage interfaces.
 
@@ -155,7 +155,7 @@ com.quantori.cqp.storage.elasticsearch/
     └── ReactionMapper.java                # Domain ↔ Elasticsearch
 ```
 
-**Dependencies**: cqp-api (0.0.16), Elasticsearch Java Client (8.6.2)
+**Dependencies**: cqp-api (0.0.17), Elasticsearch Java Client (8.6.2)
 
 ### cqp-core (Akka Actors Module - Currently Missing)
 

CONTEXT.md

@@ -6,6 +6,20 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 CQP is an open-source framework for indexing and searching within cheminformatics applications (molecules & reactions). It's built on the Akka Actors framework for scalability and supports multiple storage engines including PostgreSQL, Elasticsearch, and Apache Solr.
 
+## Package Naming Strategy
+
+**CQP Internal Code**: All code in this repository uses the `com.quantori.cqp.*` package hierarchy:
+- `com.quantori.cqp.api.model.*` - Core data models (Property, PropertyType, PropertyValue, etc.)
+- `com.quantori.cqp.core.*` - Akka actors and core framework
+- `com.quantori.cqp.storage.elasticsearch.*` - Elasticsearch storage implementation
+- `com.quantori.cqp.build.*` - Gradle build plugins
+
+**External Indigo Library**: The external Indigo Toolkit library uses `com.epam.indigo.*`:
+- `com.epam.indigo.Indigo` - Main Indigo class
+- `com.epam.indigo.IndigoObject` - Indigo molecule/reaction objects
+- `com.epam.indigo.IndigoException` - Indigo exceptions
+- **Do not change** these package references - they belong to the external library
+
 ## Project Structure
 
 This is a multi-module Gradle project with the following key modules:

Devnotes.md

@@ -1,4 +1,15 @@
 ## Build instructions
 * Download the repository
 * Let your IDE import necessary dependencies automatically or fetch them manually
-* For local repository publication Run `gradle build` task and then run `gradle publishToMavenLocal` tasks
+* For local repository publication run the following tasks
+  * `gradlew :cqp-api:build :cqp-api:publishToMavenLocal`
+  * `gradle build -x :cqp-api:build`
+  * `gradle publishToMavenLocal -x :cqp-api:publishToMavenLocal`
+
+## Repository configuration
+
+* The shared plugin reads the Akka repository URL in this order and stops at the first match:
+  1. Gradle property `AKKA_REPO_URL` (set via `gradle.properties` or `-PAKKA_REPO_URL=...`)
+  2. Gradle property `akkaRepoUrl` (legacy camelCase fallback)
+  3. Environment variable `AKKA_REPO_URL`
+* If none of the above is supplied, the build fails immediately. Obtain the secure URL/token from https://account.akka.io/ and set one of the properties/variables before running Gradle.

cqp-api/build.gradle.kts

@@ -6,7 +6,7 @@ plugins {
 
 group = "com.quantori"
 description = "Chem query platform. Storage API"
-version = "0.0.16"
+version = "0.0.17"
 
 dependencies {
     implementation("commons-codec:commons-codec:1.15")
@@ -34,4 +34,4 @@ dependencies {
     testImplementation(libs.jackson)
     testImplementation(libs.lombok)
     testAnnotationProcessor(libs.lombok)
-}
+}

cqp-api/src/main/java/com/quantori/cqp/api/model/Property.java

@@ -21,7 +21,48 @@ public Property(String name, PropertyType type) {
     this.type = type;
   }
 
+  /**
+   * Defines the supported property kinds in Chem Query Platform. Existing values must remain
+   * unchanged to keep backward compatibility with previously persisted data.
+   */
   public enum PropertyType {
-    STRING, DECIMAL, DATE
+    STRING,
+    DECIMAL,
+    DATE,
+    /**
+     * Binary payload for storing images, PDFs or other small files. Intended size limit is 10 MB per
+     * value and the binary content is transferred as byte arrays.
+     */
+    BINARY,
+    /**
+     * Timestamp value with timezone information preserved. Values are serialized as ISO-8601
+     * instants (e.g. {@code 2025-01-15T10:30:00Z}).
+     */
+    DATE_TIME,
+    /**
+     * Ordered collection of string values. This allows preserving the order in which the user
+     * provided the values (e.g. {@code ["first", "second"]}).
+     */
+    LIST,
+    /**
+     * Hyperlink that stores HTTP/HTTPS (and similar) URL references. Validation is applied on
+     * backend layers while the enum only marks the data type.
+     */
+    HYPERLINK,
+    /**
+     * Chemical structure serialized as a SMILES string. Consumers rely on Indigo toolkit for
+     * validation.
+     */
+    CHEMICAL_STRUCTURE,
+    /**
+     * Three dimensional molecular structure stored as MOL text block. This is typically used for 3D
+     * renderings and cannot be exported to legacy SDF files.
+     */
+    STRUCTURE_3D,
+    /**
+     * Sanitized HTML fragment used for rich text property rendering. Scripts and unsafe tags are
+     * expected to be removed before persisting.
+     */
+    HTML
   }
 }

cqp-api/src/main/java/com/quantori/cqp/api/model/PropertyValue.java

@@ -0,0 +1,53 @@
+package com.quantori.cqp.api.model;
+
+import java.time.Instant;
+import java.time.LocalDate;
+import java.util.List;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+/**
+ * Container for the value of a {@link Property}. Each concrete field maps to a {@link
+ * Property.PropertyType}. Only one field is expected to be non-null for a particular value.
+ */
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+@Builder
+public class PropertyValue {
+
+  /** String payload for {@link Property.PropertyType#STRING} values. */
+  private String stringValue;
+
+  /** Decimal payload for {@link Property.PropertyType#DECIMAL} values. */
+  private Double decimalValue;
+
+  /** Date payload for {@link Property.PropertyType#DATE} values. */
+  private LocalDate dateValue;
+
+  /**
+   * Binary content for {@link Property.PropertyType#BINARY} values. Typical use cases include
+   * storing images or PDF attachments (up to 10 MB).
+   */
+  private byte[] binaryValue;
+
+  /** Timestamp payload for {@link Property.PropertyType#DATE_TIME} values. */
+  private Instant dateTimeValue;
+
+  /** Ordered collection of strings for {@link Property.PropertyType#LIST} values. */
+  private List<String> listValue;
+
+  /** URL string for {@link Property.PropertyType#HYPERLINK} values. */
+  private String hyperlinkValue;
+
+  /** SMILES payload for {@link Property.PropertyType#CHEMICAL_STRUCTURE} values. */
+  private String chemicalStructureValue;
+
+  /** MOL block payload for {@link Property.PropertyType#STRUCTURE_3D} values. */
+  private String structure3DValue;
+
+  /** Sanitized HTML fragment for {@link Property.PropertyType#HTML} values. */
+  private String htmlValue;
+}

cqp-api/src/test/java/com/quantori/cqp/api/model/PropertyTypeTest.java

@@ -0,0 +1,60 @@
+package com.quantori.cqp.api.model;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.time.Instant;
+import java.time.LocalDate;
+import java.util.EnumSet;
+import java.util.List;
+import org.junit.jupiter.api.Test;
+
+class PropertyTypeTest {
+
+  @Test
+  void shouldContainExtendedTypes() {
+    EnumSet<Property.PropertyType> types = EnumSet.allOf(Property.PropertyType.class);
+
+    assertThat(types)
+        .contains(
+            Property.PropertyType.BINARY,
+            Property.PropertyType.DATE_TIME,
+            Property.PropertyType.LIST,
+            Property.PropertyType.HYPERLINK,
+            Property.PropertyType.CHEMICAL_STRUCTURE,
+            Property.PropertyType.STRUCTURE_3D,
+            Property.PropertyType.HTML);
+  }
+
+  @Test
+  void shouldAllowPropertyValueAccessors() {
+    byte[] binary = new byte[] {1, 2, 3};
+    Instant timestamp = Instant.parse("2024-01-01T10:15:30Z");
+    List<String> orderedList = List.of("first", "second");
+    LocalDate date = LocalDate.of(2024, 2, 29);
+
+    PropertyValue value =
+        PropertyValue.builder()
+            .stringValue("test")
+            .decimalValue(12.34d)
+            .dateValue(date)
+            .binaryValue(binary)
+            .dateTimeValue(timestamp)
+            .listValue(orderedList)
+            .hyperlinkValue("https://example.com")
+            .chemicalStructureValue("CCO")
+            .structure3DValue("3D-MOL-DATA")
+            .htmlValue("<p>html</p>")
+            .build();
+
+    assertThat(value.getStringValue()).isEqualTo("test");
+    assertThat(value.getDecimalValue()).isEqualTo(12.34d);
+    assertThat(value.getDateValue()).isEqualTo(date);
+    assertThat(value.getBinaryValue()).containsExactly(binary);
+    assertThat(value.getDateTimeValue()).isEqualTo(timestamp);
+    assertThat(value.getListValue()).containsExactlyElementsOf(orderedList);
+    assertThat(value.getHyperlinkValue()).isEqualTo("https://example.com");
+    assertThat(value.getChemicalStructureValue()).isEqualTo("CCO");
+    assertThat(value.getStructure3DValue()).isEqualTo("3D-MOL-DATA");
+    assertThat(value.getHtmlValue()).isEqualTo("<p>html</p>");
+  }
+}

cqp-build/src/main/kotlin/com/quantori/cqp/build/CqpJavaLibraryPlugin.kt

@@ -1,5 +1,6 @@
 package com.quantori.cqp.build
 
+import org.gradle.api.GradleException
 import org.gradle.api.JavaVersion
 import org.gradle.api.Plugin
 import org.gradle.api.Project
@@ -28,10 +29,18 @@ class CqpJavaLibraryPlugin : Plugin<Project> {
 
         project.repositories {
             mavenLocal()
-            mavenCentral ()
+            mavenCentral()
+
+            val akkaRepoUrl =
+                (project.findProperty("AKKA_REPO_URL") as String?)
+                    ?: (project.findProperty("akkaRepoUrl") as String?)
+                    ?: System.getenv("AKKA_REPO_URL").takeIf { !it.isNullOrBlank() }
+                    ?: throw GradleException(
+                        "AKKA_REPO_URL is not configured. Configure the secret/property to resolve Akka artifacts.")
+
             maven {
                 name = "Akka"
-                url = project.uri("https://repo.akka.io/maven")
+                url = project.uri(akkaRepoUrl)
                 content {
                     includeGroup("com.typesafe.akka")
                     includeGroupByRegex("com\\.lightbend\\..*")
@@ -200,4 +209,4 @@ class CqpJavaLibraryPlugin : Plugin<Project> {
             }
         }
     }
-}
+}

cqp-core/build.gradle.kts

@@ -5,13 +5,13 @@ plugins {
 }
 
 description = "Chem query platform. Compound quick search"
-version = "0.0.15"
+version = "0.0.17"
 
 val akkaVersion: String = "2.9.0"
 val lightbendVersion: String = "1.5.0"
 
 dependencies {
-    implementation("com.quantori:cqp-api:0.0.16")
+    implementation("com.quantori:cqp-api:0.0.17")
 
     implementation("com.typesafe:config:1.4.2")