Metadata

All objects

All metadata objects support the following fields:

Field	Supported values	Description
created*	Date	Date of creation
updated*	Date	Date of last update

* Mandatory

Projects

The following metadata fields are recognized by different interfaces for Projects:

Project Features

Metadata with additional information and features about the project:

Field	Supported values	Description
comments	String	Free-form comments
description	String	Free-form description
name*	Name	Name‡

* Mandatory

Project System Metadata

Metadata entries automatically set by MiGA:

Field	Supported values	Description
datasets*	Array of String	List of datasets in the project
type*	String	Type

* Mandatory

‡ By default the base name of the project path

Project Flags

Metadata entries that trigger specific behaviors in MiGA:

Field	Supported values	Description
ref_project	Path	Project with reference taxonomy {1}
db_proj_dir	Path	Directory containing database projects {1} {2}
tax_pvalue	Float [0,1]	Max p-value to transfer taxonomy (def: 0.1)
haai_p	String	hAAI engine {3} (def: fastaai)
aai_p	String	AAI engine {3} (def: diamond)
ani_p	String	ANI engine {3} (def: fastani)
max_try	Integer	Max number of task attempts (def: 10)
aai_save_rbm	Boolean	Should RBMs be saved for OGS analysis?
ogs_identity	Float [0,100]	Min RBM identity for OGS (def: 80)
clean_ogs	Boolean	If false, keeps ABC (clades only)
run_clades	Boolean	Should clades be estimated from distances?
gsp_ani	Float [0,100]	ANI limit to propose gsp clades (def: 95)
gsp_aai	Float [0,100]	AAI limit to propose gsp clades (def: 90)
gsp_metric	String	Metric to propose clades: ani (def), aai
ess_coll	String	Collection of essential genes to use {4}
min_qual	Float (or 'no')	Min. genome quality (or no filter; def: 25)
distances_checkpoint	Integer	Comparisons before storing data (def: 10)

{1} This path can either be absolute or relative to the project's path

{2} This is the location of the databases used by db_project. If not set, it is assumed to be the parent folder of the current project

{3} Supported values: blast, blat, diamond (only for hAAI and AAI), fastani (only for ANI), no (only for hAAI), and fastaai (only for hAAI)

{4} One of: dupont_2012 (default), or lee_2019

Project Hooks

Additionally, hooks can be defined for projects as arrays of arrays containing the action name and the arguments (if any). For example, one can define:

on_processing_ready: [
  ['run_cmd', 'date > {{project}}/ALL_DONE.txt'],
  ['run_cmd', 'sendmail ...']
]

or

on_add_dataset: [
  ['run_cmd', 'echo {{object}} > {{project}}/LATEST_DATASET.txt']
]

Supported events:

• on_create(): When created

• on_load(): When loaded

• on_save(): When saved

• on_add_dataset(object): When a dataset is added, with name object

• on_unlink_dataset(object): When dataset with name object is unlinked

• on_result_ready(object): When any result is ready, with key object

• on_result_ready_{result}(): When result is ready

• on_processing_ready(): When processing is complete

Supported hooks:

• run_lambda(lambda, args...)

• run_cmd(cmd)

Datasets

The following metadata fields are recognized by different interfaces for Datasets:

Dataset Features

Metadata with additional information and features about the dataset:

Field	Supported values	Description
tax	MiGA::Taxonomy	Taxonomy of the dataset
quality	String	Description of genome quality
trna_count	Integer	Number of tRNA elements detected
trna_aa	Integer	Number of distinct AA with tRNA elements
dprotologue	String	Taxonumber in the Digital Protologue DB
ncbi_tax_id	String	Linking ID(s) {1} for NCBI Taxonomy
ncbi_nuccore	String	Linking ID(s) {1} for NCBI Nucleotide
ncbi_asm	String	Linking ID(s) {1} for NCBI Assembly
ebi_embl	String	Linking ID(s) {1} for EBI EMBL
ebi_ena	String	Linking ID(s) {1} for EBI ENA
web_assembly	String	URL to download assembly
web_assembly_gz	String	URL to download gzipped assembly
see_also	String	Link(s) {1} in the format text:url
is_type	Boolean	If it is type material
is_ref_type	Boolean	If it is reference material {2}
type_rel	String	Relationship to type material
suspect	Array(String)	Flags indicating a suspect dataset

{1} Multiple values can be provided separated by commas or colons

{2} This is not a valid type, but it represents the closest available dataset to material that is unavailable and unlikely to ever become available. See also Federhen, 2015, NAR

Dataset System Metadata

Metadata entries automatically set by MiGA:

Field	Supported values	Description
type*	String	Type
ref	Boolean	Reference
inactive	Boolean	If auto-processing should stop
metadata_only	Boolean	Dataset with metadata but without input data
status	String	Proc. status: complete, incomplete, inactive
_step	String	For internal control of processing
_try_step	Integer	For internal control of processing
user	String	Deprecated

* Mandatory

Dataset Flags

Metadata entries that trigger specific behaviors in MiGA:

Field	Supported values	Description
run_step	Boolean	Forces running or not step
db_project	Path	Project to use as database {1}
dist_req	Array of String	Run distances against these datasets {2}

{1} By default, it uses its own project as database. The path can be absolute or relative to the parent folder of the project

{2} When searching best-matching datasets, include these datasets even if they are not visited using the medoid tree

Dataset Hooks

Additionally, hooks can be defined for datasets as arrays of arrays containing the action name and the arguments. See above (project hooks) for examples.

Supported events:

• on_load(): When loaded

• on_save(): When saved

• on_remove(): When removed

• on_inactivate(): When inactivated

• on_activate(): When activated

• on_result_ready(object): When any result is ready, with key object

• on_result_ready_{result}(): When result is ready

• on_preprocessing_ready(): When preprocessing is complete

Supported hooks:

• run_lambda(lambda, args...)

• clear_run_counts()

• run_cmd(cmd)