featureannotation.md

Feature Annotation CLI

A command-line application for managing feature annotations with support for loading data from various sources and updating gene information.

Execution Sequence

The feature annotation subcommands should be executed in the following sequence, with all commands depending on the initial load-feature-annotation:

flowchart TD
    A["1. load-feature-annotation<br/>(Required foundation)"] --> B["1a. load-csv-to-arangodb<br/>(Optional: Update ArangoDB from CSV)"]
    A --> C["2. gene-updater<br/>(Update gene annotations)"]
    A --> D["3. gene-product-updater<br/>(Update gene products from legacy DB)"]
    A --> E["4. load-gene-product-from-csv<br/>(Load gene products from CSV)"]
    A --> F["5. load-synonyms<br/>(Load synonyms to gRPC service)"]
    
    B -.-> C
    B -.-> D
    B -.-> E
    B -.-> F
    
    style A fill:#e1f5fe,stroke:#01579b,stroke-width:3px
    style B fill:#fff3e0,stroke:#e65100,stroke-width:2px,stroke-dasharray: 5 5
    style C fill:#f3e5f5,stroke:#4a148c,stroke-width:2px
    style D fill:#e8f5e8,stroke:#1b5e20,stroke-width:2px
    style E fill:#fff8e1,stroke:#e65100,stroke-width:2px
    style F fill:#fce4ec,stroke:#880e4f,stroke-width:2px

Loading

Legend:

• Solid arrows: Required dependencies
• Dashed arrows: Optional sequence (if step 1a is executed)
• Blue: Foundation command (must run first)
• Orange: Data loading/updating commands
• Purple/Green/Pink: Processing and enhancement commands

Table of Contents

• load-feature-annotation - Load feature annotations from ArangoDB to gRPC service
• load-csv-to-arangodb - Update ArangoDB collection from CSV file
• gene-updater - Update gene annotations by stripping HTML and using gRPC
• gene-product-updater - Update gene products from legacy database
• load-gene-product-from-csv - Load gene products from CSV files
• load-synonyms - Load synonyms from ArangoDB to gRPC service

---

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:

Flag	Description	Environment Variable	Default	Required
--arangodb-user	ArangoDB user name	ARANGODB_USER		Yes
--arangodb-pass	ArangoDB password	ARANGODB_PASS		Yes
--arangodb-database	ArangoDB database name	ARANGODB_DATABASE		Yes
--arangodb-host	ArangoDB host	ARANGODB_SERVICE_HOST	arangodb	No
--arangodb-port	ArangoDB port	ARANGODB_SERVICE_PORT	8529	No
--is-secure	Use TLS for ArangoDB connection	ARANGODB_IS_SECURE	false	No
--feature-annotation-grpc-host	Feature annotation gRPC host	ANNO_FEAT_API_SERVICE_HOST	anno-feat-api	No
--feature-annotation-grpc-port	Feature annotation gRPC port	ANNO_FEAT_API_SERVICE_PORT	9250	No
--pubmed-workers	Number of pubmed fetcher workers	PUBMED_WORKERS	4	No
--grpc-workers	Number of gRPC create workers	GRPC_WORKERS	8	No

---

load-csv-to-arangodb

This subcommand updates an ArangoDB collection from a CSV file.

Usage:

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

Options:

Flag	Description	Environment Variable	Default	Required
--csv-file	Path to CSV file to load			Yes
--collection	ArangoDB collection name		featureprop	No
--delimiter	CSV delimiter character		,	No
--batch-size	Documents to update per batch		40	No
--workers	Concurrent workers for batching		4	No
--arangodb-user	ArangoDB user name	ARANGODB_USER		Yes
--arangodb-pass	ArangoDB password	ARANGODB_PASS		Yes
--arangodb-database	ArangoDB database name	ARANGODB_DATABASE		Yes
--arangodb-host	ArangoDB host	ARANGODB_SERVICE_HOST	arangodb	No
--arangodb-port	ArangoDB port	ARANGODB_SERVICE_PORT	8529	No
--is-secure	Use TLS for ArangoDB connection	ARANGODB_IS_SECURE	false	No

---

gene-updater

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

Usage:

featureannotation gene-updater [command options]

Options:

Flag	Description	Environment Variable	Default	Required
--aql-query	AQL query to fetch gene data	AQL_QUERY	(See source)	No
--processing-workers	HTML processing workers	PROCESSING_WORKERS	4	No
--grpc-workers	gRPC update workers	GRPC_WORKERS	8	No
--arangodb-user	ArangoDB user name	ARANGODB_USER		Yes
--arangodb-pass	ArangoDB password	ARANGODB_PASS		Yes
--arangodb-database	ArangoDB database name	ARANGODB_DATABASE		Yes
--arangodb-host	ArangoDB host	ARANGODB_SERVICE_HOST	arangodb	No
--arangodb-port	ArangoDB port	ARANGODB_SERVICE_PORT	8529	No
--is-secure	Use TLS for ArangoDB connection	ARANGODB_IS_SECURE	false	No
--feature-annotation-grpc-host	Feature annotation gRPC host	ANNO_FEAT_API_SERVICE_HOST	anno-feat-api	No
--feature-annotation-grpc-port	Feature annotation gRPC port	ANNO_FEAT_API_SERVICE_PORT	9250	No

---

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:

Flag	Description	Environment Variable	Default	Required
--legacy-database	Legacy database name	LEGACY_DATABASE	cgm_ddb	No
--legacy-workers	Legacy DB query workers	LEGACY_WORKERS	4	No
--grpc-workers	gRPC update workers	GRPC_WORKERS	8	No
--arangodb-user	ArangoDB user name	ARANGODB_USER		Yes
--arangodb-pass	ArangoDB password	ARANGODB_PASS		Yes
--arangodb-database	ArangoDB database name	ARANGODB_DATABASE		Yes
--arangodb-host	ArangoDB host	ARANGODB_SERVICE_HOST	arangodb	No
--arangodb-port	ArangoDB port	ARANGODB_SERVICE_PORT	8529	No
--is-secure	Use TLS for ArangoDB connection	ARANGODB_IS_SECURE	false	No
--feature-annotation-grpc-host	Feature annotation gRPC host	ANNO_FEAT_API_SERVICE_HOST	anno-feat-api	No
--feature-annotation-grpc-port	Feature annotation gRPC port	ANNO_FEAT_API_SERVICE_PORT	9250	No

---

load-gene-product-from-csv

This subcommand loads gene products from CSV files into the feature annotation service.

Usage:

featureannotation load-gene-product-from-csv [command options]

Options:

Flag	Description	Environment Variable	Default	Required
--input, -i	One or more input CSV files with gene products			Yes
--workers	Number of concurrent workers for loading		4	No
--batch-size	Batch size for loading		100	No
--user	Email of the user running the load			Yes
--feature-annotation-grpc-host	Feature annotation gRPC host	ANNO_FEAT_API_SERVICE_HOST	anno-feat-api	No
--feature-annotation-grpc-port	Feature annotation gRPC port	ANNO_FEAT_API_SERVICE_PORT	9250	No

---

load-synonyms

This subcommand loads synonyms from ArangoDB to the feature annotation service.

Usage:

featureannotation load-synonyms [command options]

Options:

Flag	Description	Environment Variable	Default	Required
--arangodb-user	ArangoDB user name	ARANGODB_USER		Yes
--arangodb-pass	ArangoDB password	ARANGODB_PASS		Yes
--arangodb-database	ArangoDB database name	ARANGODB_DATABASE		Yes
--arangodb-host	ArangoDB host	ARANGODB_SERVICE_HOST	arangodb	No
--arangodb-port	ArangoDB port	ARANGODB_SERVICE_PORT	8529	No
--is-secure	Use TLS for ArangoDB connection	ARANGODB_IS_SECURE	false	No
--feature-annotation-grpc-host	Feature annotation gRPC host	ANNO_FEAT_API_SERVICE_HOST	anno-feat-api	No
--feature-annotation-grpc-port	Feature annotation gRPC port	ANNO_FEAT_API_SERVICE_PORT	9250	No
--grpc-workers	Number of gRPC update workers	GRPC_WORKERS	4	No