Merge recent refactorings and bug fixes

Dockerfile

@@ -16,6 +16,7 @@ RUN mvn dependency:go-offline -B || true
 
 # Copy source code
 COPY treebase-core/src treebase-core/src
+COPY treebase-core/lib treebase-core/lib
 COPY treebase-web/src treebase-web/src
 COPY treebase-web/lib treebase-web/lib
 COPY oai-pmh_data_provider oai-pmh_data_provider
@@ -45,8 +46,13 @@ COPY --from=builder /build/treebase-web/target/treebase-web.war /usr/local/tomca
 RUN curl -o /usr/local/tomcat/lib/postgresql.jar \
     https://jdbc.postgresql.org/download/postgresql-42.7.7.jar
 
-# Create a directory for Mesquite (placeholder)
-RUN mkdir -p /usr/local/mesquite
+# Create a directory for Mesquite and copy the headless Mesquite library
+# The treebase-core/lib folder contains the headless Mesquite distribution with:
+# - mesquite/ - Mesquite core classes
+# - headless/ - Headless AWT implementation
+# - com/apple/ - Apple API stubs (required by Mesquite even on non-Mac platforms)
+# - Other supporting libraries
+COPY --from=builder /build/treebase-core/lib /usr/local/mesquite
 
 # Set environment variables for Tomcat
 # Java 17 compatibility flags based on GitHub Actions workflow

Dockerfile.dev

@@ -19,6 +19,8 @@ RUN curl -o /usr/local/tomcat/lib/postgresql.jar \
     https://jdbc.postgresql.org/download/postgresql-42.7.7.jar
 
 # Create Mesquite directory placeholder
+# Note: In development mode, the entrypoint script will copy
+# the Mesquite library from the mounted /app/treebase-core/lib
 RUN mkdir -p /usr/local/mesquite
 
 # Set up environment variables

WEB_UI_ANALYSIS.md

@@ -416,9 +416,6 @@ styles/
 | `autocomplete.js` | 3.7KB | Autocomplete widget | High - Prototype-dependent |
 | `menuExpandable.js` | 6.1KB | Expandable menu navigation | Medium - Pure JS possible |
 | `ajaxProgress.js` | 1KB | Progress indicators | Medium - Uses DWR |
-| `d3.phylogram.js` | 12KB | D3-based tree rendering | Low - Uses D3 v7 |
-| `newick.js` | 3.2KB | Newick format parsing | Low - Pure JavaScript |
-| `sha1.js` | 4.4KB | SHA1 hashing | Low - Pure JavaScript |
 | `googleAnalytics.js` | 3.4KB | Analytics integration | Low - Standard GA |
 | `multiFileUpload.js` | 1KB | File upload handling | Medium |
 | `xp_progress.js` | 2.5KB | Progress bars | Medium |

doc/technical-notes/HIBERNATE_VS_SQL_SCHEMA_ANALYSIS.md

@@ -0,0 +1,304 @@
+# Hibernate ORM vs SQL Schema Analysis
+
+This document provides a comprehensive analysis of discrepancies between the Hibernate ORM data model and the SQL-based PostgreSQL schema in TreeBASE.
+
+## Executive Summary
+
+**Finding**: There are discrepancies between the Hibernate ORM layer (source of truth) and the SQL schema instantiated by the database initialization scripts. However, switching to Hibernate-based schema generation introduces significant issues due to seed data dependencies.
+
+**Key Issues Identified**:
+1. **Missing patch in CI/CD**: Patch `0011_increase-citation-column-lengths.sql` was not included in `init_db_uptodate.pg` (now fixed)
+2. **Column length mismatches**: Several columns in the SQL schema have different lengths than defined in Hibernate (fixed by patches)
+3. **Different initialization paths**: CI/CD and Docker use different initialization approaches
+4. **Patch idempotency issues**: Some patches failed when schema already had correct types (now fixed)
+
+**Recommendation**: **Keep the SQL-based schema with patches** (Option A) rather than switching to Hibernate-based generation. See "Test Impact Analysis" section for reasoning.
+
+## Current Architecture
+
+### CI/CD Database Initialization
+- Uses `treebase-core/db/schema/init_db_uptodate.pg`
+- Applies snapshot `0000_SCHEMA_before_patches_start.sql` + `0000_DATA_before_patches_start.sql`
+- Then applies patches 0001 through 0011 sequentially
+- **Fixed**: Patch 0011 is now included
+
+### Docker Database Initialization
+- Uses `docker-compose.yml` volume mounts
+- Applies:
+  1. `docker/00-init-roles.sql` - Role initialization
+  2. `treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql` - Schema creation
+  3. `treebase-core/src/main/resources/initTreebase.sql` - Initial data
+  4. `docker/03-migration-hibernate-sequence.sql` - Hibernate sequence migration
+
+### Hibernate Configuration
+- `hibernate.hbm2ddl.auto=` (empty/disabled)
+- Uses annotation-based mapping (`@Entity`, `@Table`, `@Column`)
+- Entities defined in `org.cipres.treebase.domain.*`
+
+## Detailed Schema Discrepancies
+
+### 1. Citation Table
+
+| Column | Hibernate Definition | SQL Schema (snapshot) | SQL Schema (TBASE2_POSTGRES_CREATION) | Patch Applied |
+|--------|---------------------|----------------------|---------------------------------------|---------------|
+| `title` | VARCHAR(500) | VARCHAR(500) | VARCHAR(500) | - |
+| `abstract` | VARCHAR(10000) | VARCHAR(10000) | VARCHAR(10000) | - |
+| `keywords` | VARCHAR(1000) | VARCHAR(255) | VARCHAR(1000) | Patch 0011 |
+| `journal` | VARCHAR(500) | VARCHAR(255) | VARCHAR(500) | Patch 0011 |
+
+**Notes**: 
+- The snapshot has outdated column lengths for `keywords` (255 vs 1000) and `journal` (255 vs 500)
+- Patch 0011 fixes these in the snapshot-based initialization
+- `TBASE2_POSTGRES_CREATION.sql` already has correct values
+
+### 2. TaxonLabel Table
+
+| Column | Hibernate Definition | SQL Schema (snapshot) | Patch Applied |
+|--------|---------------------|----------------------|---------------|
+| `linked` | BOOLEAN | BOOLEAN | Patch 0010 |
+
+**Notes**: 
+- Earlier SQL had `linked` as `smallint`, but this was fixed by Patch 0010
+- Both snapshot (after patches) and TBASE2_POSTGRES_CREATION.sql now use BOOLEAN
+
+### 3. Help Table
+
+| Column | Hibernate Definition | SQL Schema |
+|--------|---------------------|------------|
+| `tag` | VARCHAR(255) (implicit) | VARCHAR(255) |
+| `helptext` | TEXT (LOB, 65536) | TEXT |
+
+**Notes**: Schema matches.
+
+### 4. PasswordResetToken Table
+
+| Column | Hibernate Definition | SQL Schema (Patch 0009) |
+|--------|---------------------|------------------------|
+| `token_id` | BIGINT (auto-increment) | BIGINT (sequence) |
+| `token` | VARCHAR(100), unique, NOT NULL | VARCHAR(100), unique, NOT NULL |
+| `user_id` | BIGINT, NOT NULL | BIGINT, NOT NULL, FK |
+| `expiry_date` | TIMESTAMP, NOT NULL | TIMESTAMP, NOT NULL |
+| `used` | BOOLEAN, NOT NULL | BOOLEAN, NOT NULL |
+
+**Notes**: 
+- Hibernate uses `@GeneratedValue(strategy = GenerationType.IDENTITY)`
+- SQL uses a sequence - these are compatible in PostgreSQL
+- Schema matches structurally
+
+### 5. AnalysisStep Table
+
+| Column | Hibernate Definition | SQL Schema (snapshot) |
+|--------|---------------------|----------------------|
+| `tb_analysisid` | Not in Hibernate entity | VARCHAR(34) |
+
+**Notes**: The SQL schema has a `tb_analysisid` column that doesn't appear to be mapped in Hibernate. This is a legacy TB1 field.
+
+### 6. MatrixRow Table (CRITICAL - LOB Type Mismatch)
+
+| Column | Hibernate Definition (Before) | Hibernate Definition (After) | SQL Schema |
+|--------|-------------------------------|------------------------------|------------|
+| `symbolstring` | `@Lob` + `@Column(length=524288)` | `@Column(columnDefinition="text")` | TEXT |
+
+**Root Cause of "Bad value for type long" Error**:
+The `@Lob` annotation on `MatrixRow.symbolString` caused Hibernate to use OID-based CLOB handling in PostgreSQL. However, the data is inserted via direct JDBC in `DiscreteMatrixJDBC.batchUpdateRowSymbol()` using `setString()`, which writes plain text. When Hibernate tried to read the data back using `getClob()`, it attempted to interpret the text data as a CLOB OID, causing the error:
+```
+PSQLException: Bad value for type long : 0002000000000000000000000-0-0000000---00-000000
+```
+
+**Solution**: Removed `@Lob` and used `@Column(columnDefinition = "text")` to ensure TEXT column type without CLOB semantics.
+
+### 7. PhyloTree Table (Preventive Fix)
+
+| Column | Hibernate Definition (Before) | Hibernate Definition (After) | SQL Schema |
+|--------|-------------------------------|------------------------------|------------|
+| `newickstring` | `@Lob` + `@Column(length=4194304)` | `@Column(columnDefinition="text")` | TEXT |
+
+**Notes**: Same pattern as MatrixRow. Removed `@Lob` to prevent potential similar issues.
+
+## Root Cause Analysis
+
+### Why Discrepancies Exist
+
+1. **Dual Maintenance**: The SQL schema and Hibernate annotations are maintained separately
+2. **Historical Evolution**: The SQL schema evolved over time with patches while Hibernate annotations were updated independently
+3. **Different Base Files**: 
+   - `TBASE2_POSTGRES_CREATION.sql` appears more aligned with Hibernate
+   - The snapshot approach uses older schema + patches
+4. **Missing Patch**: Patch 0011 wasn't added to the patch inclusion list
+
+### The Two Initialization Paths
+
+```
+CI/CD Path:
+  snapshot → patches (0001-0011) → final schema
+
+Docker Path:
+  TBASE2_POSTGRES_CREATION.sql → initTreebase.sql → final schema
+```
+
+These paths should produce equivalent schemas but use different mechanisms.
+
+## Recommendations
+
+### Option A: Continue with SQL-Based Schema (RECOMMENDED)
+**Pros**:
+- Known working approach - all tests pass
+- Explicit control over schema
+- Migration scripts for production
+- Seed data loading order is controlled
+
+**Cons**:
+- Dual maintenance burden
+- Potential for drift between Hibernate and SQL
+- Requires diligent patch management
+
+**Action Items**:
+1. ✅ Add patch 0011 to `init_db_uptodate.pg` (DONE)
+2. ✅ Make patches idempotent (DONE)
+3. Consider creating a new schema snapshot that includes all patches
+4. Consider adding `hibernate.hbm2ddl.auto=validate` in production
+
+### Option B: Switch to Hibernate-Based Schema Generation
+**Pros**:
+- Single source of truth (Hibernate entities)
+- No impedance mismatch
+- Automatic schema updates with `hbm2ddl.auto=update`
+
+**Cons**:
+- ❌ **NOT VIABLE** - 21 test failures/errors (see Test Impact Analysis)
+- Requires significant refactoring of seed data loading
+- Risk of data loss in production if not carefully managed
+- Less control over exact DDL
+
+### Option C: Hybrid Approach
+**Strategy**: Use Hibernate for tests/development, SQL for production
+
+**Status**: Not recommended due to:
+- Seed data dependency issues
+- Would require rewriting test data setup
+- Maintenance burden of two approaches
+
+## Test Impact Analysis
+
+### Actual Test Results
+
+#### SQL-Based Schema (Current Approach)
+**Result**: ✅ All tests pass
+```
+Tests run: 301, Failures: 0, Errors: 0, Skipped: 43
+BUILD SUCCESS
+```
+
+#### Hibernate-Based Schema (`hbm2ddl.auto=create`)
+**Result**: ❌ 12 failures, 9 errors
+```
+Tests run: 301, Failures: 12, Errors: 9, Skipped: 53
+BUILD FAILURE
+```
+
+**Failed Tests (Missing Seed Data)**:
+- `ItemDefinitionDAOTest.testFindByDescription`
+- `ItemDefinitionDAOTest.testFindPredefinedItemDefinition`
+- `MatrixDAOTest.testfindKindByDescription`
+- `MatrixDataTypeDAOTest.testFindByDescription`
+- `AlgorithmDAOTest.testFinalAllUniqueAlgorithmDescriptions`
+- `StudyStatusDAOTest.testFindStatusInProgress/Published/Ready`
+- `PhyloTreeDAOTest.testFindTypeByDescription/findKindByDescription/findQualityByDescription`
+- `SubmissionServiceImplTest.testProcessNexusFile`
+
+**Error Tests (Foreign Key Violations)**:
+- `EnvironmentTest.testGetGeneratedKey` - null value in column violation
+- `EnvironmentTest.testSelectFromInsert` - null value in column violation
+- `MatrixServiceImplTest.testAddDelete` - NullPointerException (missing service beans)
+- `AnalysisServiceImplTest.testAddDelete` - NullPointerException
+- `StudyServiceImplTest.*` - Multiple NullPointerExceptions
+
+### Root Cause Analysis
+
+The test failures with Hibernate-based schema generation are caused by:
+
+1. **Missing Seed Data**: Hibernate creates empty tables. Tests expect pre-populated reference data for:
+   - `ItemDefinition` (predefined item definitions)
+   - `MatrixDataType` (DNA, RNA, Protein, etc.)
+   - `StudyStatus` (In Progress, Ready, Published)
+   - `TreeType`, `TreeKind`, `TreeQuality`
+   - `Algorithm` (reference algorithm types)
+   - `User`, `Person` (test user accounts)
+
+2. **Foreign Key Ordering**: When loading `initTreebase.sql` after Hibernate schema creation:
+   - Hibernate creates FK constraints immediately
+   - SQL script inserts data in wrong order (e.g., `user` before `person`)
+   - Results in FK constraint violations
+
+3. **Schema Already Exists Errors**: 
+   - `password_reset_token` table created by Hibernate conflicts with SQL script
+
+### Conclusion
+
+**Hibernate-based schema generation is NOT suitable** for the current test setup because:
+1. Tests depend on seed data that must be loaded in a specific order
+2. The `initTreebase.sql` script was designed for SQL-based schema creation
+3. Significant refactoring of test data setup would be required
+
+**Recommendation**: Continue with **Option A (SQL-Based Schema)** with the following improvements:
+1. ✅ Keep patches idempotent (fixed in this PR)
+2. ✅ Ensure all patches are included in `init_db_uptodate.pg`
+3. Consider adding `hibernate.hbm2ddl.auto=validate` in production to catch drift
+
+### Tests to Monitor
+
+Based on the codebase, these test categories should be monitored:
+
+1. **DAO Tests** (`org.cipres.treebase.dao.*`)
+   - Test CRUD operations against database
+   - May be affected by constraint differences
+
+2. **Service Tests** (`org.cipres.treebase.service.*`)
+   - Test business logic with database
+   - Should be unaffected by schema generation method
+
+3. **Domain Tests** (`org.cipres.treebase.domain.*`)
+   - Test entity relationships
+   - May be affected by cascade/fetch settings
+
+## Implementation Plan
+
+### Phase 1: Fix Immediate Issues (COMPLETED)
+1. ✅ Add patch 0011 to `init_db_uptodate.pg`
+
+### Phase 2: Validate Current State
+1. Run full test suite with current SQL-based initialization
+2. Document any existing test failures
+
+### Phase 3: Test Hibernate-Based Initialization
+1. Create test configuration with `hbm2ddl.auto=create`
+2. Run tests to identify failures
+3. Document failures and root causes
+
+### Phase 4: Implement Chosen Strategy
+1. Based on test results, implement Option A, B, or C
+2. Update CI/CD configuration
+3. Update Docker configuration
+4. Update documentation
+
+## Appendix: Column Length Constants
+
+From `org.cipres.treebase.domain.TBPersistable`:
+
+```java
+public static final int COLUMN_LENGTH_30 = 30;
+public static final int COLUMN_LENGTH_50 = 50;
+public static final int COLUMN_LENGTH_100 = 100;
+public static final int COLUMN_LENGTH_STRING = 255;
+public static final int COLUMN_LENGTH_500 = 500;
+public static final int COLUMN_LENGTH_STRING_1K = 1000;
+public static final int COLUMN_LENGTH_STRING_NOTES = 2000;
+public static final int COLUMN_LENGTH_STRING_MAX = 5000;
+
+public static final int CITATION_TITLE_COLUMN_LENGTH = 500;
+public static final int CITATION_ABSTRACT_COLUMN_LENGTH = 10000;
+public static final int CITATION_KEYWORDS_COLUMN_LENGTH = 1000;
+public static final int CITATION_JOURNAL_COLUMN_LENGTH = 500;
+```
+
+These constants define the expected column lengths in Hibernate and should be used as the reference when comparing with SQL schemas.

docker-compose.yml

@@ -22,6 +22,7 @@ services:
       - ./docker/00-init-roles.sql:/docker-entrypoint-initdb.d/00-init-roles.sql
       - ./treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql:/docker-entrypoint-initdb.d/01-schema.sql
       - ./treebase-core/src/main/resources/initTreebase.sql:/docker-entrypoint-initdb.d/02-init.sql
+      - ./docker/03-migration-hibernate-sequence.sql:/docker-entrypoint-initdb.d/03-migration-hibernate-sequence.sql
     healthcheck:
       test: ["CMD-SHELL", "pg_isready -U treebase"]
       interval: 10s

docker/03-migration-hibernate-sequence.sql

@@ -0,0 +1,14 @@
+-- Migration script to add hibernate_sequence if it doesn't exist
+-- This sequence is required by Hibernate's @CollectionId annotation
+-- for generating collection_id values in sub_matrix and sub_treeblock tables
+
+DO $$
+BEGIN
+  IF NOT EXISTS (SELECT FROM pg_catalog.pg_sequences WHERE sequencename = 'hibernate_sequence') THEN
+    CREATE SEQUENCE hibernate_sequence;
+    RAISE NOTICE 'Created hibernate_sequence';
+  ELSE
+    RAISE NOTICE 'hibernate_sequence already exists';
+  END IF;
+END
+$$;