Open eboileau opened 1 week ago
Refactor/improve CLI.
[ ] Refactor plugins to cli, etc.
[ ] Is logging-level CLI-specific configurable?
[ ] We need a new method to add selections, independently of project creation.
[ ] Do we need a method to remove projects/datasets?
[ ] Handle graceful exit on failure e.g. if annotating dataset with nonexistent taxa_id and version, see also below:
taxa_id
version
flask project with e.g. nonexistent combination of taxa_id and cto
flask project
cto
Failed to create project: (MySQLdb.IntegrityError) (1452, 'Cannot add or update a child row: a foreign key constraint fails (`scimodom`.`organism`, CONSTRAINT `fk_organism_taxa_id_ncbi_taxa` FOREIGN KEY (`taxa_id`) REFERENCES `ncbi_taxa` (`id`))') [SQL: INSERT INTO organism (taxa_id, cto) VALUES (%s, %s)] [parameters: (10900, 'Cell')] (Background on this error at: https://sqlalche.me/e/20/gkpj)... skipping t1!
FileNotFoundError: [Errno 2] No such file or directory: '/data/metadata/project_requests/bla.json'
Aims/objectives.
Refactor/improve CLI.
A clear and concise description of todo items.
[ ] Refactor plugins to cli, etc.
[ ] Is logging-level CLI-specific configurable?
[ ] We need a new method to add selections, independently of project creation.
[ ] Do we need a method to remove projects/datasets?
[ ] Handle graceful exit on failure e.g. if annotating dataset with nonexistent
taxa_idandversion, see also below:flask projectwith e.g. nonexistent combination oftaxa_idandctoFileNotFoundError: [Errno 2] No such file or directory: '/data/metadata/project_requests/bla.json'