# Project and Data Management

A comparative-genetics project can produce many files across several analysis steps. The `Manager` package gives repository, user, project, database, raw-data, and web directories a consistent hierarchy. Its classes can create these directories from bundled Cookiecutter templates.


# Create a project layout

``` python
from OrthoEvol.Manager.management import ProjectManagement

project_manager = ProjectManagement(
    repo="comparative-genetics",
    user="researcher",
    project="receptor-family",
    research=None,
    research_type="comparative_genetics",
    new_project=True,
)
```

This code writes directories and files from a template. Before you set `new_project=True`, use an explicit destination and make sure that it is the intended location.


# See the managed directory layout

The management classes and templates use the repository hierarchy below. A constructor creates only the part selected by `new_repo`, `new_user`, `new_project`, `new_db`, `new_research`, or `new_app`. Some paths exist in the manager before a tool writes data to their directories.

``` text
<repository>/
├── docs/
├── users/
│   └── <user>/
│       ├── archive/
│       ├── databases/
│       │   ├── <project>/
│       │   ├── ITIS/
│       │   └── NCBI/
│       │       ├── blast/
│       │       │   ├── db/
│       │       │   ├── seqidlists/
│       │       │   └── windowmasker_files/
│       │       ├── pub/
│       │       │   └── taxonomy/
│       │       └── refseq/
│       │           └── release/
│       ├── index/
│       ├── log/
│       ├── manuscripts/
│       ├── other/
│       └── projects/
│           └── <project>/
│               ├── archive/
│               └── <research-type>/
│                   └── <research>/
│                       ├── data/
│                       ├── index/
│                       ├── raw_data/
│                       └── web/
│                           └── <app>/
└── web/
    ├── flask/
    ├── ftp/
    ├── shiny/
    └── wasabi/
```

The user's `databases/` directory contains project databases. They do not live inside `projects/<project>/`. The manager adds a research directory only when you supply both a research type and a research name.


# Choose what to create

| Option | Created area |
|----|----|
| `new_repo=True` | Repository-level directories and templates |
| `new_user=True` | A user's archive, database, project, and support directories |
| `new_db=True` | Database directories selected by the database configuration |
| `new_project=True` | The named project beneath the user's project hierarchy |
| `new_research=True` | The named research directory beneath its research type |
| `new_app=True` | The selected web application beneath newly created research |

These flags create content. They do not search an existing layout. Before you use a flag, supply the parent identifiers for that level. Make sure that the resolved paths are correct before you enable more than one creation flag.

The current [ProjectManagement](../reference/Manager.management.ProjectManagement.md#OrthoEvol.Manager.management.ProjectManagement) implementation handles `new_app=True` inside the `new_research=True` branch. You must also supply `research`, `research_type`, and `app`.


# Follow the project hierarchy

- [Management](../reference/Manager.management.Management.md#OrthoEvol.Manager.management.Management) maps package resources and an optional repository root.
- [RepoManagement](../reference/Manager.management.RepoManagement.md#OrthoEvol.Manager.management.RepoManagement) adds repository-wide user, documentation, and web paths.
- [UserManagement](../reference/Manager.management.UserManagement.md#OrthoEvol.Manager.management.UserManagement) adds user-specific databases, archives, projects, and raw data.
- [ProjectManagement](../reference/Manager.management.ProjectManagement.md#OrthoEvol.Manager.management.ProjectManagement) specializes the hierarchy for a research project.
- [DataMana](../reference/Manager.data_management.DataMana.md#OrthoEvol.Manager.data_management.DataMana) and the database-management classes dispatch configured data and database operations.


# Review the configuration

A managed workflow can combine Python objects with YAML configuration. Before you dispatch the workflow, make sure that the YAML structure and referenced paths are correct. Valid YAML can still name an invalid database strategy, an unavailable path, or an unsupported operation.


# Practice in a disposable project

Start with a small disposable project while you learn the hierarchy. Make sure that each manager supplies the paths required by the next class. This practice reduces the risk of writing to the wrong directory or starting a large data operation with the wrong configuration.