Upgrade TypeScript to v6 (#236)

Upgrade TypeScript to v6 as well as update other packages at the same
time.

Author: AlexJSully

README.md

@@ -107,17 +107,17 @@ We aim to make this tool as perfect as possible but unfortunately, there may be
 
 ## Documentation
 
-For comprehensive documentation, see the [`docs/`](docs/) folder:
+For comprehensive documentation, see the [docs](docs/index.md):
 
 - [**Getting Started**](docs/index.md) - Complete overview and setup guide
-- [**Architecture**](docs/architecture/) - Technical architecture and design decisions
-- [**Usage Examples**](docs/usage/examples/) - Detailed usage examples and troubleshooting
-- [**API Reference**](docs/usage/api/) - Complete API documentation
-- [**Contributing**](docs/contributing/) - Development setup and contribution guidelines
+- [**Architecture**](docs/architecture/index.md) - Technical architecture and processing flow
+- [**Usage Guide**](docs/usage/index.md) - Setup, run, and troubleshooting workflows
+- [**API Reference**](docs/usage/api/index.md) - Module-level function documentation
+- [**Contributing**](CONTRIBUTING.md) - Development setup and contribution guidelines
 
 ## License
 
-[GLP-2.0](LICENSE.md)
+[GNU GPL v2.0](LICENSE.md)
 
 ## Maintenance Mode
 

docs/architecture/dependencies.md

@@ -4,7 +4,7 @@ This project makes use of the following open-source dependencies and APIs:
 
 ## Open Source Dependencies
 
-The following open-source packages are used in this project. For a complete and up-to-date list, see the `package.json` file in the project root.
+The following open-source packages are used in this project. For a complete and up-to-date list, see [`package.json`](../../package.json) in the project root.
 
 - axios
 - throttled-queue

docs/architecture/index.md

@@ -157,7 +157,7 @@ graph LR
 
 **XML Structure Navigation (PMC ID extraction):**
 
-The parser locates the PMC identifier in the article front matter (see implementation: [`src/processor/parseFigures.ts`](../src/processor/parseFigures.ts)).
+The parser locates the PMC identifier in the article front matter (see implementation: [`src/processor/parseFigures.ts`](../../src/processor/parseFigures.ts)).
 
 ```xml
 <pmc-articleset>
@@ -173,15 +173,15 @@ The parser locates the PMC identifier in the article front matter (see implement
 
 ### 5. Download Module (`src/processor/downloadArticlePackage.ts`)
 
-Downloads a complete PMC article package (.tar.gz) and extracts image files. The implementation fetches a package URL from the OA Web Service API, downloads the archive, extracts media, and selects the highest-priority image format per basename before copying results to the output directory (see implementation: [`src/processor/downloadArticlePackage.ts`](../src/processor/downloadArticlePackage.ts)).
+Downloads a complete PMC article package (.tar.gz) and extracts image files. The implementation fetches a package URL from the OA Web Service API, downloads the archive, extracts media, and selects the highest-priority image format per basename before copying results to the output directory (see implementation: [`src/processor/downloadArticlePackage.ts`](../../src/processor/downloadArticlePackage.ts)).
 
 Key implementation behaviors (implementation proof):
 
-- Fetches OA package metadata via the OA API and converts FTP links to HTTPS (see [`src/processor/fetchPackageUrl.ts`](../src/processor/fetchPackageUrl.ts)).
-- Downloads the package archive and extracts it to a temporary directory (see [`src/processor/downloadArticlePackage.ts`](../src/processor/downloadArticlePackage.ts)).
-- Groups files by basename and keeps the highest-priority extension using the `IMAGE_EXTENSIONS` priority map (see [`src/constants.ts`](../src/constants.ts)).
+- Fetches OA package metadata via the OA API and converts FTP links to HTTPS (see [`src/processor/fetchPackageUrl.ts`](../../src/processor/fetchPackageUrl.ts)).
+- Downloads the package archive and extracts it to a temporary directory (see [`src/processor/downloadArticlePackage.ts`](../../src/processor/downloadArticlePackage.ts)).
+- Groups files by basename and keeps the highest-priority extension using the `IMAGE_EXTENSIONS` priority map (see [`src/constants.ts`](../../src/constants.ts)).
 
-Console-level messages written by the implementation include `Fetching package URL for <PMCID>`, `Package downloaded. Extracting images...`, `Extracted image: <filename>`, and `Successfully extracted <N> images from package.` (see [`src/processor/downloadArticlePackage.ts`](../src/processor/downloadArticlePackage.ts)).
+Console-level messages written by the implementation include `Fetching package URL for <PMCID>`, `Package downloaded. Extracting images...`, `Extracted image: <filename>`, and `Successfully extracted <N> images from package.` (see [`src/processor/downloadArticlePackage.ts`](../../src/processor/downloadArticlePackage.ts)).
 
 ## Data Flow Architecture
 
@@ -282,14 +282,14 @@ graph TB
     H --> I[Save Cache to Disk]
 ```
 
-### 4. Error Recovery and Resilience
+### 4. Error Handling and Continuation
 
-The system implements multiple levels of error recovery:
+The system logs operation-level failures and continues processing subsequent species/articles:
 
-1. **Network Level**: Automatic retries with exponential backoff
-2. **API Level**: Rate limit compliance and quota management
-3. **Data Level**: Graceful handling of malformed XML or missing figures
-4. **File Level**: Directory creation and permission handling
+1. **Search failures**: `searchArticlesBySpecies` returns an empty list on request failures
+2. **Batch fetch failures**: `fetchArticleDetails` logs batch-level errors and continues with remaining batches
+3. **Package failures**: `parseFigures` logs package-level failures and continues with remaining articles
+4. **Filesystem setup**: output/cache directories are created on demand before writes
 
 ## Performance Considerations
 
@@ -321,7 +321,6 @@ graph TD
 
 - [Dependencies](./dependencies.md) - External libraries and tools used
 - [Pipelines](./pipelines.md) - Detailed workflow diagrams
-- [Design Decisions](./design-decisions.md) - Architectural choices and trade-offs
 
 ## Real-World Scenarios
 

docs/architecture/pipelines.md

@@ -24,8 +24,8 @@ graph TD
     J --> L{More Species?}
     K --> M[Fetch Article Details]
     M --> N[Parse XML Content]
-    N --> O[Extract Figure URLs]
-    O --> P[Download Figures]
+    N --> O[Download Article Package]
+    O --> P[Extract Images from Package]
     P --> Q[Update Progress Cache]
     Q --> L
 
@@ -85,7 +85,7 @@ graph TD
     F --> N
 ```
 
-### Step 3: XML Parsing and Figure Extraction
+### Step 3: XML Parsing and Package Extraction
 
 ```mermaid
 graph LR
@@ -101,16 +101,16 @@ graph LR
         F --> G[Extract Figure Elements]
     end
 
-    subgraph "Figure Processing"
-        G --> H[Process Figure Graphics]
-        H --> I[Construct Figure URLs]
-        I --> J[Validate URL Format]
-        J --> K[Add .jpg if No Extension]
+    subgraph "Article Package Processing"
+        G --> H[Resolve OA Package URL]
+        H --> I[Download .tar.gz Package]
+        I --> J[Extract Package Contents]
+        J --> K[Select Highest-Priority Image Per Basename]
     end
 
     subgraph "Download Orchestration"
         K --> L[Create Output Directory]
-        L --> M[Queue Figure Download]
+        L --> M[Copy Selected Images]
         M --> N[Update Progress]
     end
 ```
@@ -238,11 +238,7 @@ sequenceDiagram
 ### Cache Structure
 
 ```json
-{
-	"cached_ids": ["PMC123456", "PMC789012", "PMC345678"],
-	"last_updated": "2024-01-15T10:30:00Z",
-	"species_processed": ["Arabidopsis_thaliana", "Cannabis_sativa"]
-}
+["PMC123456", "PMC789012", "PMC345678"]
 ```
 
 ## Performance Optimization Pipeline
@@ -332,10 +328,10 @@ graph TD
 [INFO] Found 1,234 articles for Arabidopsis_thaliana
 [INFO] Fetching Arabidopsis thaliana article details for batch 1-50...
 [INFO] Processing article PMC ID: PMC123456
-[INFO] Found 3 figures in the article.
-[INFO] Downloaded image: figure1.jpg
-[INFO] Downloaded image: figure2.png
-[INFO] Downloaded image: supplementary1.tiff
+[INFO] Fetching package URL for PMC123456...
+[INFO] Package downloaded. Extracting images...
+[INFO] Extracted image: figure1.jpg (priority: jpg)
+[INFO] Successfully extracted 1 images from package.
 [INFO] All IDs in Arabidopsis thaliana batch 51-100 are already cached.
 [INFO] Processing complete for Arabidopsis_thaliana
 ```

docs/faq.md

@@ -25,7 +25,6 @@ The project is open-source; consult the repository [`package.json`](../package.j
 **A:**
 
 - Node.js 20 or higher
-- npm 9 or higher
 - 2GB available disk space (recommended)
 - Stable internet connection
 
@@ -42,7 +41,7 @@ cd Publication-Figure-Retrieval
 npm ci
 
 # Run the tool
-npm start
+npm run start
 ```
 
 ### Q: Do I need an API key?
@@ -76,7 +75,7 @@ Get your API key from: <https://www.ncbi.nlm.nih.gov/account/settings/>
 
 ```bash
 # This will process all species in the configuration
-npm start
+npm run start
 ```
 
 ### Q: How do I limit the number of articles searched?
@@ -178,7 +177,7 @@ const throttle = throttledQueue(2, 2000); // Slower rate
 
 ### Q: How do I contribute to the project?
 
-**A:** See our [Contributing Guide](../contributing/index.md) for detailed instructions:
+**A:** See our [Contributing Guide](../CONTRIBUTING.md) for detailed instructions:
 
 1. Fork the repository
 2. Create a branch
@@ -230,26 +229,7 @@ console.log("Debug info:", variable);
 
 ### Q: What metadata is collected?
 
-**A:** For each article:
-
-```json
-{
-	"pmcId": "PMC1234567",
-	"title": "Article Title",
-	"authors": ["Author 1", "Author 2"],
-	"journal": "Journal Name",
-	"publicationDate": "2023-01-15",
-	"doi": "10.1000/example",
-	"figureCount": 3,
-	"figures": [
-		{
-			"caption": "Figure caption",
-			"url": "https://...",
-			"filename": "figure1.jpg"
-		}
-	]
-}
-```
+**A:** The current implementation primarily tracks progress in `build/output/cache/id.json` and writes extracted image files to per-species/per-PMCID directories. It does not currently generate a per-article metadata JSON file.
 
 ### Q: How are duplicate articles handled?
 
@@ -276,4 +256,4 @@ console.log("Debug info:", variable);
 - **With API key**: 10 requests per second
 - **Large jobs**: Contact NCBI for permission
 
-Need more help? Check our [documentation](../index.md) or [open an issue](https://github.com/AlexJSully/Publication-Figure-Retrieval/issues) on GitHub.
+Need more help? Check our [documentation](./index.md) or [open an issue](https://github.com/AlexJSully/Publication-Figure-Retrieval/issues) on GitHub.

docs/index.md

@@ -223,18 +223,12 @@ Each species entry includes aliases for better search coverage:
 }
 ```
 
-## Screenshots
-
-{INSERT SCREENSHOT HERE - Terminal output showing progress}
-{INSERT SCREENSHOT HERE - File explorer showing organized output structure}
-{INSERT SCREENSHOT HERE - Example downloaded scientific figures}
-
 ## Next Steps
 
 - [Architecture Overview](./architecture/index.md) - Understand the system design
 - [Usage Guide](./usage/index.md) - Detailed usage instructions and examples
 - [API Documentation](./usage/api/index.md) - Module and function references
-- [Contributing](./contributing/index.md) - How to contribute to the project
+- [Contributing](../CONTRIBUTING.md) - How to contribute to the project
 - [FAQ](./faq.md) - Common questions and troubleshooting
 
 ## Support