girder 5.0.5.dev12__tar.gz → 5.0.5.dev18__tar.gz

{girder-5.0.5.dev12/girder.egg-info → girder-5.0.5.dev18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: girder
-Version: 5.0.5.dev12
+Version: 5.0.5.dev18
 Summary: Web-based data management platform
 Home-page: https://girder.readthedocs.org
 Author: Kitware, Inc.
@@ -20,9 +20,9 @@ Requires-Dist: cheroot!=11.0.0,!=11.1.1
 Requires-Dist: CherryPy
 Requires-Dist: click
 Requires-Dist: click-plugins
-Requires-Dist: dogpile.cache<1.4
+Requires-Dist: dogpile.cache
 Requires-Dist: filelock
-Requires-Dist: girder-worker>=5.0.0a5
+Requires-Dist: girder-worker>=5
 Requires-Dist: jsonschema
 Requires-Dist: Mako
 Requires-Dist: packaging

{girder-5.0.5.dev12 → girder-5.0.5.dev18}/docs/configuration.rst

@@ -4,39 +4,20 @@ Configuration
 .. _configuration:
 
 In many cases, Girder will work with default configuration whether installed via
-pip or from a source checkout or tarball. That said, the Girder config file can
-be set at the following locations (ordered by precedent):
-
-#. The path specified by the environment variable ``GIRDER_CONFIG``.
-#. ~/.girder/girder.cfg
-#. /etc/girder.cfg
+pip or from a source checkout or tarball. To compy with 12-factor application principles, Girder settings are controlled via environment variables.
 
 Settings
 --------
 
 Girder settings are specific key-value pairs that control system behavior.
-There are two ways to change Girder settings.
-
-Via the Web API / front-end web site
-....................................
-
-System settings can be set and retrieved using the web API endpoint at ``/api/v1/system/setting``.
-Most of them are exposed via the web UI under **Admin console** -> **System configuration**.
-When setting the values through the web API endpoint, they will be interpreted as JSON.
-
-.. note:: Modifying setting values via the web API is officially deprecated, as it violates the
-   `Twelve-Factor App <https://12factor.net/>`_  principle of storing configuration in the
-   environment. Setting values should instead be set via environment variables as documented below.
-
-
+Many of these settings can be queried or viewed using the web API endpoint at ``/api/v1/system/setting`` or via the web UI under **Admin console** -> **System configuration**.
 
 .. _configuration_via_env:
 
 Via the environment
 ...................
 
-Any system setting can be controlled via environment variables as well. To do so, find the
-key of the setting and apply the following transformation:
+Any system setting can be controlled via environment variables as well. To do so, find the key of the setting and apply the following transformation:
 
 * transform all ``.`` characters in the key to ``_``
 * convert it to uppercase
@@ -46,8 +27,7 @@ Whatever value you set for that environment variable will be parsed as JSON and
 If the value cannot be parsed as JSON, its raw string value will be used instead. For example, to set
 the setting named ``"core.brand_name"``, you'd use ``GIRDER_SETTING_CORE_BRAND_NAME='My brand name'``
 
-Settings set through environment variables will override any setting value that is set in the database
-via the web API.
+Settings set through environment variables will override any setting value that is set in the database.
 
 The full list of system settings available in Girder core can be seen in the file
 ``girder/girder/settings.py``, under the ``SettingKey`` class. Plugins may add additional settings

{girder-5.0.5.dev12 → girder-5.0.5.dev18}/docs/list_env_settings.py

@@ -433,7 +433,8 @@ def main():
     for env_var in sorted(seen_settings.keys()):
         key, component, repo_label, path = seen_settings[env_var]
         desc = get_desc(env_var)
-        print(f'| `{env_var}` | `{key}` | {component} | {repo_label} | `{path}` | {desc}')
+        print(f'| <a class="girder_env" id="{env_var}" href="#{env_var}">`{env_var}`</a> | '
+              f'`{key}` | {component} | {repo_label} | `{path}` | {desc}')
 
     print('\n## Direct Environment Variables\n')
     print('| Environment Variable | Component | Repo | Source File | Description |')
@@ -443,7 +444,8 @@ def main():
         desc = get_desc(env_var)
         if exclude_name_pattern and exclude_name_pattern.search(env_var):
             continue
-        print(f'| `{env_var}` | {component} | {repo_label} | `{path}` | {desc} |')
+        print(f'| <a class="girder_env" id="{env_var}" href="#{env_var}">`{env_var}`</a> | '
+              f'{component} | {repo_label} | `{path}` | {desc} |')
 
 
 if __name__ == '__main__':

girder-5.0.5.dev18/docs/list_env_settings.yaml

@@ -0,0 +1,97 @@
+# This yaml file has descriptions of _some_ of the environment variables to
+# augment the data shown in the auto-generated table
+GIRDER_SETTING_CORE_BRAND_NAME: >-
+  The name of the application displayed in the UI header and title. Default is "Girder".
+
+GIRDER_SETTING_CORE_CACHE_ENABLED: >-
+  Whether to enable short-term caching of database queries. Set to "true" or "false".  This can speed up
+
+GIRDER_SETTING_CORE_CACHE_CONFIG: >-
+  A JSON dictionary configuring the caching system. Use keys like:
+  `cache.global.backend` for the cache backend,
+  `cache.global.expiration_time` for timeout in seconds,
+  `cache.request.backend` for request-specific caching.
+
+GIRDER_SETTING_CORE_CORS_ALLOW_ORIGIN: >-
+  CORS header specifying which origins are allowed to access the API. Use * for all or specify domains.
+
+GIRDER_SETTING_CORE_CORS_ALLOW_METHODS: >-
+  CORS header listing allowed HTTP methods (GET, POST, PUT, DELETE, etc.).
+
+GIRDER_SETTING_CORE_CORS_ALLOW_HEADERS: >-
+  CORS header specifying which headers are allowed in requests.
+
+GIRDER_SETTING_CORE_CORS_EXPOSE_HEADERS: >-
+  CORS header listing headers that should be exposed to the client.
+
+GIRDER_SETTING_CORE_REGISTRATION_POLICY: >-
+  Controls user registration policy. Values: "open", "admin", or "closed".
+
+GIRDER_SETTING_CORE_EMAIL_VERIFICATION: >-
+  Whether email verification is required for new accounts. Set to "true" or "false".
+
+GIRDER_SETTING_CORE_ENABLE_PASSWORD_LOGIN: >-
+  Whether password-based login is enabled. Set to "true" or "false".
+
+GIRDER_SETTING_CORE_SMTP_HOST: >-
+  SMTP server hostname for sending emails.
+
+GIRDER_SETTING_CORE_SMTP_PORT: >-
+  SMTP server port number.
+
+GIRDER_SETTING_CORE_SMTP_USERNAME: >-
+  SMTP authentication username.
+
+GIRDER_SETTING_CORE_SMTP_PASSWORD: >-
+  SMTP authentication password.
+
+GIRDER_SETTING_CORE_SMTP_ENCRYPTION: >-
+  SMTP encryption method. Values: "none", "ssl", or "tls".
+
+GIRDER_SETTING_USER_QUOTA_DEFAULT_USER_QUOTA: >-
+  Default storage quota for new users in bytes.
+
+GIRDER_SETTING_USER_QUOTA_DEFAULT_COLLECTION_QUOTA: >-
+  Default storage quota for new collections in bytes.
+
+GIRDER_WORKER_DOCKER_RUN_OPTIONS: >-
+  A JSON dictionary of values to pass to all dockers that are created by Girder Worker.  For instance, you could always mount a specific directory and pass an environment variable like so: `{"volumes": ["/some/cache:/root/.cache"], "environment": {"CACHE_AVAILABLE": "1"}}`.  If the value is not a valid JSON dictionary it is ignored.  Keys of `detach` and `tty` are ignored.
+
+GIRDER_SETTING_CORE_COOKIE_LIFETIME: >-
+  The lifetime of authentication cookies in days. Default is 180.
+
+GIRDER_SETTING_CORE_COOKIE_DOMAIN: >-
+  The domain for which authentication cookies are valid. An empty string means cookies are valid for the entire domain.  You might set this if Girder is proxied to a path within the domain.
+
+GIRDER_SETTING_CORE_SERVER_ROOT: >-
+  The base URL path where Girder is mounted. Use this for reverse proxy setups.  This is prefixed to "api/v1".
+
+GIRDER_SETTING_CORE_FILEHANDLE_MAX_SIZE: >-
+  Maximum size in bytes that is read from files internally.  Controls for some memory usage. Default is 16MB (1024 * 1024 * 16).
+
+GIRDER_SETTING_CORE_UPLOAD_MINIMUM_CHUNK_SIZE: >-
+  Minimum chunk size for file uploads in bytes. Default is 5MB (1024 * 1024 * 5).
+
+GIRDER_HOST: >-
+  Hostname or IP address to bind the server to. Use '0.0.0.0' to bind to all interfaces.
+
+GIRDER_PORT: >-
+  Port number the server should listen on. Default is 8080.
+
+GIRDER_MONGO_URI: >-
+  MongoDB connection string including authentication details if needed.  Default is "mongodb://localhost:27017".
+
+GIRDER_MONGO_REPLICA_SET: >-
+  MongoDB replica set name for connecting to a replica set cluster.  It is probably better to include this as part of the URI.
+
+GIRDER_THREAD_POOL: >-
+  Number of threads in the CherryPy thread pool. Adjust based on server capacity.  Default is 100.
+
+GIRDER_WORKER_BROKER: >-
+  URL for the Celery message broker (e.g., redis://localhost:6379/0).
+
+GIRDER_WORKER_BACKEND: >-
+  URL for the Celery result backend (e.g., redis://localhost:6379/0).
+
+GIRDER_WORKER_JOB_GC_SCOPE: >-
+  A comma-separated list of extra default scopes for worker jobs.  For instance to allow jobs to schedule and check on other jobs, set this to "jobs.rest.create_job,jobs.rest.list_job"

{girder-5.0.5.dev12 → girder-5.0.5.dev18}/docs/migration-guide.rst

@@ -244,6 +244,17 @@ Then, build the core front-end application with the desired base path:
 With that variable set in your environment, the Girder core web client will now be served under
 ``/new_root/`` rather than ``/``.
 
+.. note::
+
+   Remapping ``apps['']`` only moves the static SPA. The REST API (including Swagger at
+   ``/api/v1``) stays on its original ``/api`` mount unless you duplicate it. After the remount
+   above, and before `del info['serverRoot'].apps['']`, add:
+
+   .. code-block:: python
+
+       api_cp_app = info['serverRoot'].apps['/api']
+       info['serverRoot'].mount(api_cp_app.root, '/new_root/api', api_cp_app.config)
+
 Logging changes
 +++++++++++++++
 

girder-5.0.5.dev18/docs/static/custom.css

@@ -0,0 +1,28 @@
+body {
+  color: #000;
+}
+.rst-content code.literal {
+  color: inherit;
+}
+.full-width-section {
+  background: #FCFCFC;
+  width: calc(100vw - 320px - 3.236em);
+  max-width: none;
+  padding-bottom: 10px;
+  box-sizing: border-box;
+}
+.full-width-section .wy-table-responsive {
+  width: 100%;
+}
+.rst-content p a.girder_env {
+  overflow-wrap: revert;
+  color: inherit;
+}
+.full-width-section table td {
+  text-wrap-mode: wrap;
+}
+@media screen and (max-width: 768px) {
+  .full-width-section {
+    width: 100vw;
+  }
+}

{girder-5.0.5.dev12 → girder-5.0.5.dev18}/girder/utility/server.py

@@ -98,9 +98,16 @@ def create_app(mode: str) -> dict:
         '/': static_opts
     })
 
-    # Mount the web API
+    # Mount the web API at /api (always).
     tree.mount(apiRoot, '/api', appconf)
 
+    # When GIRDER_URL_ROOT names a public path prefix (e.g. "girder" for
+    # https://host/girder/...), mount the same API object at /<prefix>/api so
+    # /api/v1 and /<prefix>/api/v1 hit identical handlers
+    if custom_root:
+        prefix = '/' + custom_root.strip('/')
+        tree.mount(apiRoot, f'{prefix}/api', appconf)
+
     return info
 
 

{girder-5.0.5.dev12 → girder-5.0.5.dev18/girder.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: girder
-Version: 5.0.5.dev12
+Version: 5.0.5.dev18
 Summary: Web-based data management platform
 Home-page: https://girder.readthedocs.org
 Author: Kitware, Inc.
@@ -20,9 +20,9 @@ Requires-Dist: cheroot!=11.0.0,!=11.1.1
 Requires-Dist: CherryPy
 Requires-Dist: click
 Requires-Dist: click-plugins
-Requires-Dist: dogpile.cache<1.4
+Requires-Dist: dogpile.cache
 Requires-Dist: filelock
-Requires-Dist: girder-worker>=5.0.0a5
+Requires-Dist: girder-worker>=5
 Requires-Dist: jsonschema
 Requires-Dist: Mako
 Requires-Dist: packaging

{girder-5.0.5.dev12 → girder-5.0.5.dev18}/girder.egg-info/requires.txt

@@ -5,9 +5,9 @@ cheroot!=11.0.0,!=11.1.1
 CherryPy
 click
 click-plugins
-dogpile.cache<1.4
+dogpile.cache
 filelock
-girder-worker>=5.0.0a5
+girder-worker>=5
 jsonschema
 Mako
 packaging

{girder-5.0.5.dev12 → girder-5.0.5.dev18}/setup.py

@@ -35,9 +35,9 @@ installReqs = [
     'CherryPy',
     'click',
     'click-plugins',
-    'dogpile.cache<1.4',
+    'dogpile.cache',
     'filelock',
-    'girder-worker>=5.0.0a5',
+    'girder-worker>=5',
     'jsonschema',
     'Mako',
     'packaging',

girder-5.0.5.dev12/docs/list_env_settings.yaml

@@ -1,4 +0,0 @@
-# This yaml file has descriptions of _some_ of the environment variables to
-# augment the data shown in the auto-generated table
-GIRDER_WORKER_DOCKER_RUN_OPTIONS: >
-  A JSON dictionary of values to pass to all dockers that are created by Girder Worker.  For instance, you could always mount a specific directory and pass an environment variable like so: `{"volumes": ["/some/cache:/root/.cache"], "environment": {"CACHE_AVAILABLE": "1"}}`.  If the value is not a valid JSON dictionary it is ignored.  Keys of `detach` and `tty` are ignored.

girder-5.0.5.dev12/docs/static/custom.css

@@ -1,16 +0,0 @@
-body {
-  color: #000;
-}
-.rst-content code.literal {
-  color: inherit;
-}
-.full-width-section {
-  background: #FCFCFC;
-  width: 100vw;
-  max-width: none;
-  padding-bottom: 10px;
-  box-sizing: border-box;
-}
-.full-width-section .wy-table-responsive {
-  width: 100%;
-}