chore: set up FOCA

.cruft.json

@@ -8,7 +8,7 @@
       "author_email": "[email protected]",
       "development_status": "1 - Planning",
       "short_description": "File handler utilizing TUS and MinIO with DRS-Filer integration.",
-      "project_name": "tus-storagehandler",
+      "project_name": "Tus-Storage-Handler",
       "project_slug": "tus_storagehandler",
       "github_username": "elixir-cloud-aai",
       "python_version": "3.11",

.github/ISSUE_TEMPLATE/general-purpose.md

@@ -46,4 +46,4 @@ bug in -->
 - Operating System and version (desktop or mobile):
 - Link to your project:
 
-[issue-tracker]: https://github.com/elixir-cloud-aai/tus-storagehandler/issues
+[issue-tracker]: https://github.com/elixir-cloud-aai/tus_storagehandler/issues

README.md

@@ -18,6 +18,7 @@ File handler utilizing TUS and MinIO with DRS-Filer integration.
 - [Basic Usage](#basic-usage)
 - [Installation](#installation)
 - [Development](#development)
+- [Environment Variables](#environment-variables)
 - [Contributing](#contributing)
 - [Code of Conduct](#code-of-conduct)
 - [Versioning](#versioning)
@@ -157,6 +158,12 @@ make u
 > **Note**: This is not the complete list of commands, run `make` to find out if
 > more have been added.
 
+## Environment Variables
+
+| **Environment Variable**|**Description**|**Usage**|**Error Handling**|
+|---|---|---|---|
+| `CSH_FOCA_CONFIG_PATH` | Specifies the path to the configuration file for the FOCA app. | The FOCA app uses this environment variable to locate the configuration file. If not set, it defaults to dev. | If the configuration file is not found at the specified or default path, a `FileNotFoundError` will be raised. |
+
 ## Contributing
 
 This project is a community effort and lives off _your_ contributions, be it in
@@ -213,4 +220,4 @@ To get in touch with us, please use one of the following routes:
 [license]: LICENSE
 [logo-elixir]: images/logo-elixir.svg
 [logo-elixir-cloud-aai]: images/logo-elixir-cloud-aai.svg
-[semver]: https://semver.org/
+[semver]: https://semver.org/

deployment/config.yaml

@@ -0,0 +1,40 @@
+server:
+    host: '0.0.0.0'
+    port: 8080
+    debug: False
+    environment: development
+    testing: False
+    use_reloader: True
+
+security:
+    auth:
+        required: True
+        add_key_to_claims: True
+        allow_expired: False
+        audience: null
+        claim_identity: sub
+        claim_issuer: iss
+        algorithms:
+          - RS256
+        validation_methods:
+          - userinfo
+          - public_key
+        validation_checks: all
+
+api:
+    specs:
+        - path: api/specs/specs.yaml
+          append: null
+          add_operation_fields:
+              x-openapi-router-controller: tus_storagehandler.api.elixircloud.csh.controllers
+          connexion:
+              strict_validation: True
+              validate_responses: False
+              options:
+                  swagger_ui: True
+                  serve_spec: True
+
+exceptions:
+    required_members: [['message'], ['code']]
+    status_member: ['code']
+    exceptions: exceptions.exceptions

docs/source/pages/tus_storagehandler.api.elixircloud.csh.rst

@@ -0,0 +1,21 @@
+tus\_storagehandler.api.elixircloud.csh package
+===============================================
+
+Submodules
+----------
+
+tus\_storagehandler.api.elixircloud.csh.controllers module
+----------------------------------------------------------
+
+.. automodule:: tus_storagehandler.api.elixircloud.csh.controllers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler.api.elixircloud.csh
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tus_storagehandler.api.elixircloud.rst

@@ -0,0 +1,18 @@
+tus\_storagehandler.api.elixircloud package
+===========================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tus_storagehandler.api.elixircloud.csh
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler.api.elixircloud
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tus_storagehandler.api.rst

@@ -0,0 +1,18 @@
+tus\_storagehandler.api package
+===============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tus_storagehandler.api.elixircloud
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler.api
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tus_storagehandler.rst

@@ -1,13 +1,29 @@
 tus\_storagehandler package
 ===========================
 
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tus_storagehandler.api
+
 Submodules
 ----------
 
-tus\_storagehandler.main module
--------------------------------
+tus\_storagehandler.app module
+------------------------------
+
+.. automodule:: tus_storagehandler.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tus\_storagehandler.exceptions module
+-------------------------------------
 
-.. automodule:: tus_storagehandler.main
+.. automodule:: tus_storagehandler.exceptions
    :members:
    :undoc-members:
    :show-inheritance: