modware-import

modware-import

Cli application for importing dictybase data.

Table of Contents

• Components
  • Data Importer
  • Mock gRPC Server for Feature Annotation Service
• Documentation
• Misc Badges

Components

Data Importer

Cli application for importing dictybase data.

Mock gRPC Server for Feature Annotation Service

A command-line mock gRPC server that implements the FeatureAnnotationService for integration testing of gRPC clients.

Features

• ✅ All 8 gRPC Methods Implemented:

  • CreateFeatureAnnotation - Create new feature annotations
  • GetFeatureAnnotation - Retrieve annotations by ID
  • UpdateFeatureAnnotation - Update existing annotations
  • DeleteFeatureAnnotation - Delete annotations (soft delete or purge)
  • AddTag - Add tags to annotations
  • UpdateTag - Update existing tags
  • RemoveTag - Remove tags from annotations
  • ListFeatureAnnotationsByPubmedId - Query by PubMed ID
  • ListFeatureAnnotationsByDOI - Query by DOI

• ✅ Thread-Safe In-Memory Storage with indexes for efficient lookups

• ✅ Realistic Mock Data - Pre-loaded with 5 sample feature annotations

• ✅ Comprehensive Validation - Email format, DOI patterns, required fields

• ✅ CLI Interface with configurable port, logging, and TLS

• ✅ gRPC Reflection enabled for debugging with tools like grpcurl

• ✅ Graceful Shutdown with signal handling

Quick Start

# Build the server
cd cmd/mock-grpc-server
go build -o mock-grpc-server .

# Run with default settings (port 9000)
./mock-grpc-server

# Run with custom settings
./mock-grpc-server --port 9001 --log-level debug

NAME:
   mock-grpc-server - Mock gRPC server for feature annotation service integration testing

USAGE:
   mock-grpc-server [global options]

GLOBAL OPTIONS:
   --port value, -p value       Server port (default: 9000) [$GRPC_PORT]
   --log-level value, -l value  Log level (debug, info, warn, error) (default: "info") [$LOG_LEVEL]
   --tls, -t                    Enable TLS (default: false) [$TLS_ENABLED]
   --help, -h                   show help

Testing with grpcurl

The server has gRPC reflection enabled, so you can use grpcurl to explore and test the API:

# List available services
grpcurl -plaintext localhost:9000 list

# List methods for FeatureAnnotationService
grpcurl -plaintext localhost:9000 list dictybase.feature_annotation.FeatureAnnotationService

# Get a feature annotation (using pre-loaded mock data)
grpcurl -plaintext -d '{"id": "DDB_G0267398"}' localhost:9000 dictybase.feature_annotation.FeatureAnnotationService/GetFeatureAnnotation

# Create a new feature annotation
grpcurl -plaintext -d '{
  "type": "gene",
  "id": "TEST_001",
  "attributes": {
    "name": "testGene",
    "publications": ["10.1000/test.2023.001"],
    "pubmed": ["12345678"]
  },
  "created_by": "test@dictybase.org"
}' localhost:9000 dictybase.feature_annotation.FeatureAnnotationService/CreateFeatureAnnotation

# List annotations by PubMed ID
grpcurl -plaintext -d '{"id": "12345678"}' localhost:9000 dictybase.feature_annotation.FeatureAnnotationService/ListFeatureAnnotationsByPubmedId

Pre-loaded Mock Data

The server starts with 5 realistic feature annotations:

1. actA (DDB_G0267398) - Actin gene with cytoskeleton function
2. myoB (DDB_G0275199) - Myosin II heavy chain B with motor activity
3. pakA (DDB_G0282525) - P21-activated kinase A with kinase activity
4. rasG (DDB_G0283471) - Ras protein G with GTPase activity
5. discoidin1 (DDB_G0291234) - Discoidin with carbohydrate binding

Each annotation includes:

• Realistic gene names and synonyms
• Valid DOI and PubMed ID references
• Tag properties with functions and cellular locations
• Database cross-references (DbLinks)
• Proper timestamps and user information

Architecture

Mock gRPC Server
├── CLI Interface (urfave/cli v2)
├── FeatureAnnotationService (8 methods)
├── In-Memory Storage Layer
│   ├── Thread-Safe Maps
│   └── Indexes (ID, Name, PubmedID, DOI)
└── Validation & Mock Data Generation

Feature Annotation CLI

A command-line application for managing feature annotations.

load-feature-annotation

This subcommand loads feature annotations from an ArangoDB instance into the feature annotation service via gRPC.

Usage:

featureannotation load-feature-annotation [command options]

Options:

load-csv-to-arangodb

This subcommand updates an ArangoDB collection from a CSV file.

Usage:

featureannotation load-csv-to-arangodb [command options]

Options:

gene-updater

This subcommand updates gene annotations by stripping HTML from properties and using a gRPC API.

Usage:

featureannotation gene-updater [command options]

Options:

gene-product-updater

This subcommand updates gene products from a legacy database to the feature annotation service.

Usage:

featureannotation gene-product-updater [command options]

Options:

Documentation

• Importer
• k8s
• Feature Annotation CLI

Misc Badges