modware-stock

README

modware-stock

dictyBase API server to manage biological stocks. The API server supports gRPC protocol for data exchange.

Usage

NAME:
   modware-stock - cli for modware-stock microservice

USAGE:
   modware-stock [global options] command [command options] [arguments...]

VERSION:
   1.0.0

COMMANDS:
     start-server  starts the modware-stock microservice with grpc backends
     help, h       Shows a list of commands or help for one command

GLOBAL OPTIONS:
   --log-format value  format of the logging out, either of json or text. (default: "json")
   --log-level value   log level for the application (default: "error")
   --help, -h          show help
   --version, -v       print the version

Subcommand

NAME:
   modware-stock start-server - starts the modware-stock microservice with grpc backends

USAGE:
   modware-stock start-server [command options] [arguments...]

OPTIONS:
   --port value                            tcp port at which the server will be available (default: "9560")
   --stock-collection value                arangodb collection for storing biological stocks (default: "stock")
   --stockprop-collection value            arangodb collection for storing stock properties (default: "stockprop")
   --stock-key-generator-collection value  arangodb collection for generating unique IDs (default: "stock_key_generator")
   --stock-type-edge value                 arangodb edge collection for connecting stocks to their types (strain or plasmid) (default: "stock_type")
   --parent-strain-edge value              arangodb edge collection for connecting strains to their parent (default: "parent_strain")
   --stockproptype-graph value             arangodb named graph for managing relations between stocks and their properties (default: "stockprop_type")
   --strain2parent-graph value             arangodb named graph for managing relations between strains and their parents (default: "strain2parent")
   --reflection, --ref                     flag for enabling server reflection
   --arangodb-pass value, --pass value     arangodb database password [$ARANGODB_PASS]
   --arangodb-database value, --db value   arangodb database name [$ARANGODB_DATABASE]
   --arangodb-user value, --user value     arangodb database user [$ARANGODB_USER]
   --arangodb-host value, --host value     arangodb database host (default: "arangodb") [$ARANGODB_SERVICE_HOST]
   --arangodb-port value                   arangodb database port (default: "8529") [$ARANGODB_SERVICE_PORT]
   --is-secure                             flag for secured or unsecured arangodb endpoint
   --nats-host value                       nats messaging server host [$NATS_SERVICE_HOST]
   --nats-port value                       nats messaging server port [$NATS_SERVICE_PORT]

Default Names

Collections

• stock
• stockprop
• stock_key_generator

Edge Collections

• parent_strain
• stock_type

Graphs

• stockprop_type
• strain2parent

API

gRPC

The protocol buffer definitions and service apis are documented here.

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