Flask CLI

Flask CLI documentation.

Setup

At launch time, the app uses tables defined in SetupService.FILE_NAME_TO_DB_TABLE_MAP to perform an INSERT... ON DUPLICATE KEY UPDATE

setup_service = get_setup_service()
setup_service.upsert_all()

These tables (rna_type, modomics, method, taxonomy, ncbi_taxa, assembly, assembly_version, annotation, and annotation_version) allow to define base options for project creation, and establish a standard terminology for the application. The import format is CSV, and the header must match the column names (including id) from the corresponding database table, e.g. ncbi_taxa.csv

id,name,short_name,taxonomy_id
9606,Homo sapiens,H. sapiens,8128e900
10090,Mus musculus,M. musculus,8128e900

The upsert can be done for one model/table at a time, or forced with

flask setup [OPTIONS]

For OPTIONS, use the --help flag, e.g. flask setup --help.

To manage assemblies or annotations, use

flask assembly [OPTIONS]

flask annotation [OPTIONS] --source [ensembl|gtrnadb] TAXID

Project and data management

Projects are added with

flask project [OPTIONS] REQUEST_UUID

A user is automatically associated with a project upon creation using the email address given in the template associated with the REQUEST_UUID. After project creation, dataset can be added with

flask dataset [OPTIONS] --assembly INTEGER --annotation [ensembl|gtrnadb] --modification INTEGER --organism INTEGER --technology INTEGER FILENAME SMID TITLE

Dataset upload is normally done via POST request upon login to the running application, accessible through User menu > Data > Dataset upload. These steps, except user-project association, can be done all at once with

flask batch [OPTIONS] --annotation [ensembl|gtrnadb] INPUT_DIRECTORY [REQUEST_UUIDS]...

The note from the standard project metadata template must contain the dataset file name and title as follows: file=filename.bedrmod, title=title. All bedRMod files must be under INPUT_DIRECTORY.

To facilitate batch upload, project templates can be created from a tabulated list of datasets with

flask metadata [OPTIONS] --title TEXT --summary TEXT --surname TEXT --forename TEXT --institution TEXT --email TEXT DATASET_CSV

For a detailed description of DATASET_CSV format, use the --help flag, e.g. flask metadata --help.

A new selection can be added with

flask selection [OPTIONS] --rna TEXT --modification TEXT --taxid INTEGER --cto TEXT --method-id TEXT --technology TEXT

Permissions can be updated with

flask permission [OPTIONS] USERNAME SMID

If required, a project and all associated data can be removed with

flask delete [OPTIONS] SMID

To force update the charts, run

flask sunburst-update [OPTIONS]