1. specify_cli-stubsy(1)
  2. specify_cli-stubsy(1)

NAME

specify_cli-stubsy - A command line interface for Specify

SYNOPSIS

specify_cli [global options] stubs [options] collection count specify_cli stubs --file count

DESCRIPTION

The stubs command creates stub records in a collection, so that catalog numbers can be printed to labels e.g. prior to mass digitizaton. The command currently only works for collection objects, and will currently only work for collections using the numeric catalog numbering scheme.

Generated catalog numbers are printed to stdout.

The number of stub records created is specified with the count argument. The target collection is provided as the collection argument. Host and database are provided using the global options --host and --database respectively. The command will generate a record set with all generated collection objects. The record set will be owned by either the Specify user (as provided via the global option --specify_user or in the database configuration file), or the Specify user provided with the --cataloger option. If no dataset name is provided using the --dataset option, the default name will be stub record set <TIMESTAMP>.

Records can be created with the following basic information (provided using command options - see below): cataloger, accession, geography/locality, taxon, preparation.

Only existing accessions and preparation types can be assigned at present. Unknown items will raise an error.

If geographic information is provided, but no locality name, the default locality name will be not cataloged, see label. This can be changed using the --locality option. Geographic information should be passed in the format Geographic Rank: Name; Geographic Subrank: Name; locality: name where locality is optional (if not given, the default locality name will be used). Only geographic names/ranks and locality names that exist in the database will can be used (unknown item will raise an error).

Taxon information is assigned as a determination. Only one determination can be given to a stub records using the command. Taxon information is provided in the format Taxon Rank: Name; Taxon Subrank: Name. Only taxonomic names that exist in the database will be accepted. Unknown items will raise an error.

Alternatively to using the options, a YAML file with all required information can be passed with the --file option. In that case, the database and collection arguments can be ommitted.

FILES

YAML files with stub record information provided using the --file option should have the general structure:

---
:stub_generator:
  :host: <hostname>
  :database: <database name>
  :collection: <collection name>
  :config: <database configuration file>
dataset_name: <record set name>
accession: <accession number>
cataloger: <specify user name>
collecting_data:
  <1st rank>: <name>
  <2nd rank>: <name>
  <3rd rank>: <name>
  :locality: <name>
default_locality_name: <name>
determination:
  <rank>: <name>
preparation:
  :type: <preparation type>
  :count: <preparation count>

Items prefixed with : in the YAML will be deserialized as Ruby symbols and need to be prefixed with : in your file. Leave any unnecessary items out. The first section :stub_generator contains connection information. When :config is left out, stubs will use the config file provided with the global option --db_config or the default file ~/.specify_dbs.rc.yaml if none provided. Likewise, :host, and :database can be provided using the global options --host and --database respectively.

If you provide the :locality under collecting data:, this will have precedence over the default_locality_name, so the latter is redundant.

OPTIONS

EXAMPLES

Create 10 blank stub records in the collection Triloites in the database Specify on localhost:

$ specify_cli -D Specify stubs Trilobites 10

Create 10 stub records determined to Asaphidae in the collection Triloites in the databaseSpecify on localhost:

$ specify_cli -D Specify stubs\n
    --taxon='Class: Trilobita; Order: Asaphida; Family: Asaphidae'\n
    Trilobites 10

Create 10 stub records for herbarium sheets in the collection Orchids in the database Specify on localhost, determined to taxon Orchidaceae:

$ specify_cli -D Specify stubs --taxon='Family: Orchidaceae'\n
    --preptype=Sheet --perpcount=1 Orchids 10

Create 10 stub records for herbarium sheets in the collection Orchids in the database Specify on localhost, determined to taxon Orchidaceae, collected in Downtown Lawrence:

$ specify_cli -D Specify stubs --taxon='Family: Orchidaceae'\n
    --geography='Country: United States, State: Kansas,\n
    County: Douglas County; locality: Downtown Lawrence'
    --preptype=Sheet --perpcount=1 Orchids 10

Create 10 stub records from a YAML file stub_details.yaml:

$ specify_cli stubs --file=stub_details.yaml 10

SPECIFY_CLI

Part of the specify_cli(1) suite

  1. August 2018
  2. specify_cli-stubsy(1)