Change project's status to project_status | Add ngi_report and de…

[glrs]

This pull request includes several changes to the YggdrasilDocument class in lib/couchdb/document.py. These changes focus on improving the handling of project status, sample management, and delivery information. The most important changes include renaming and restructuring project-level fields, adding new methods for sample and delivery management, and updating project status logic.

Project-level fields and restructuring:

• Renamed status to project_status and added initialization for ngi_report and delivery_info fields with default values. ([[1]](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL38-R56), [[2]](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL59-R80), [[3]](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL76-R104))

Sample management improvements:

• Modified add_sample method to set default values for start_time and QC, and added delivered field. ([[1]](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL92-R114), [[2]](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL125-R172))
• Added get_sample method to retrieve a specific sample by its ID. ([lib/couchdb/document.pyL125-R172](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL125-R172))
• Enhanced update_sample_status method to handle more statuses and log errors if the sample is not found. ([lib/couchdb/document.pyL141-R235](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL141-R235))
• Added methods set_sample_qc_status and mark_sample_as_delivered to update sample QC status and mark samples as delivered, respectively. ([lib/couchdb/document.pyL141-R235](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL141-R235))

Project status logic updates:

• Refactored update_project_status and check_project_completion methods to improve project status handling and ensure consistent updates. ([[1]](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL141-R235), [[2]](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL203-R354))

NGI report and delivery information management:

• Added methods add_ngi_report_entry, add_delivery_entry, get_delivery_status, and set_delivery_status to manage NGI reports and delivery information. ([lib/couchdb/document.pyL203-R354](https://github.com/NationalGenomicsInfrastructure/Yggdrasil/pull/38/files#diff-201fc53ce0b6c824f9bcc19ecfa639daa862338f6aebddd3fb8b31105a82d5fdL203-R354))…livery support methods | several improvements