doc patches

docs/configuration.rst

@@ -340,9 +340,6 @@ at the start of the `Configuration`_ section.
   within the `themes`_ subdirectory.
 
 
-.. _themes: https://github.com/Ouranosinc/Magpie/tree/master/magpie/ui/home/static/themes
-
-
 Security Settings
 ~~~~~~~~~~~~~~~~~~~~~
 
@@ -768,18 +765,6 @@ this :term:`Authentication` procedure.
     Websites), rarely used authentication bridges by the developers could break without prior notice. If this is the
     case and you use one of the broken connectors, summit a new `issue`_.
 
-.. _OpenID: https://openid.net/
-.. _ESGF: https://esgf.llnl.gov/
-.. _DKRZ: https://esgf-data.dkrz.de
-.. _IPSL: https://www.ipsl.fr/
-.. _BADC: http://data.ceda.ac.uk/badc
-.. _CEDA: https://esgf-index1.ceda.ac.uk
-.. _LLNL: https://www.llnl.gov/
-.. _PCMDI: http://pcmdi.llnl.gov
-.. _SMHI: https://www.smhi.se
-.. _GitHub: https://developer.github.com/v3/#authentication
-.. _WSO2: https://wso2.com/
-.. _MagpieSecurity: https://github.com/Ouranosinc/Magpie/tree/master/magpie/security.py
 
 GitHub Settings
 ~~~~~~~~~~~~~~~~~

docs/installation.rst

@@ -28,8 +28,6 @@ If you want the full setup for development (including dependencies for test exec
 
 You can run the Magpie container with a ``docker-compose.yml`` for a local setup (see `docker-compose.yml.example`_)
 
-.. _`docker-compose.yml.example`: https://github.com/Ouranosinc/Magpie/tree/master/docker-compose.yml.example
-
 
 Backward Compatibility
 --------------------------

docs/permissions.rst

@@ -5,6 +5,8 @@
 Permissions
 ===========
 
+.. _permission_types:
+
 Types of Permissions
 -----------------------
 
@@ -173,7 +175,6 @@ value that implicitly retrieves the :term:`Request User` as the :term:`Context U
     some additional request-specific logic (depending on its purpose and resulting actions) for special-cases that is
     not explicitly detailed in above steps. Some of these special behaviors can be observed across the various `tests`_.
 
-.. _tests: https://github.com/Ouranosinc/Magpie/tree/master/tests
 
 Finally, it is worth further detailing the small distinction between
 :py:data:`magpie.constants.MAGPIE_LOGGED_PERMISSION` and :py:data:`magpie.constants.MAGPIE_CONTEXT_PERMISSION`,
@@ -236,7 +237,7 @@ to execute `Magpie` application. Effectively, when the active session correspond
 Example to distinguish Applied, Inherited and Effective Permissions
 --------------------------------------------------------------------------------------
 
-This section intends to provide more insight on the different :ref:`Types of Permissions` using a simplified
+This section intends to provide more insight on the different :ref:`permission_types` using a simplified
 demonstration of interaction between defined :term:`Service`, :term:`Resource`, :term:`Group`, :term:`User` and
 :term:`Permission` elements.
 
@@ -312,7 +313,7 @@ On the other hand, using ``effective`` would result in the following:
     /users/example-user/resources/resource-B1/permissions?effective=true    => [read]           (2)
     /users/example-user/resources/resource-B2/permissions?effective=true    => [read, write]    (4)
 
-In this case, :term:`Resource`s that had :term:`Permission` directly set on them :sup:`(2)`, whether through
+In this case, all :term:`Resource` entries that had :term:`Permission` directly set on them :sup:`(2)`, whether through
 :term:`User` or :term:`Group` combination, all return the exact same set of :term:`Permission`. This is because
 `Effective Permissions`_ always imply `Inherited Permissions`_ (i.e.: using both query simultaneously is redundant).
 The reason why we obtain these sets for cases :sup:`(2)` is also because there is no other :term:`Permission` applied
@@ -358,7 +359,7 @@ This query can be extremely useful to quickly answer *"does the user have any pe
 without needing to manually execute multiple successive lookup requests with all combinations of :term:`Resource`
 identifiers in the hierarchy.
 
-.. _permission_modifiers::
+.. _permission_modifiers:
 
 Permissions Definition and Modifiers
 --------------------------------------
@@ -483,4 +484,4 @@ Therefore, it can be noted that all API responses that contain details about per
 
 It can be noted that the JSON representation also provides a fourth ``type`` parameter which serves as indicative
 detail about the kind of :term:`Permission` being displayed, in attempt to reduce the ambiguity described in
-:ref:`Types of Permissions`.
+:ref:`permission_types`.

docs/references.rst

@@ -18,10 +18,29 @@
 .. _Waitress: https://github.com/Pylons/waitress
 .. _Ziggurat-Foundations: https://github.com/ergo/ziggurat_foundations
 
+.. external providers
+.. _OpenID: https://openid.net/
+.. _ESGF: https://esgf.llnl.gov/
+.. _DKRZ: https://esgf-data.dkrz.de
+.. _IPSL: https://www.ipsl.fr/
+.. _BADC: http://data.ceda.ac.uk/badc
+.. _CEDA: https://esgf-index1.ceda.ac.uk
+.. _LLNL: https://www.llnl.gov/
+.. _PCMDI: http://pcmdi.llnl.gov
+.. _SMHI: https://www.smhi.se
+.. _GitHub: https://developer.github.com/v3/#authentication
+.. _WSO2: https://wso2.com/
+
 .. file/source references
+.. _configuration: configuration.rst
 .. _constants.py: https://github.com/Ouranosinc/Magpie/tree/master/magpie/constants.py
+.. _`docker-compose.yml.example`: https://github.com/Ouranosinc/Magpie/tree/master/docker-compose.yml.example
+.. _magpie-con: https://github.com/Ouranosinc/Magpie/tree/master/magpie-cron
 .. _magpie.env.example: https://github.com/Ouranosinc/Magpie/tree/master/env/magpie.env.example
 .. _magpie.ini: https://github.com/Ouranosinc/Magpie/tree/master/config/magpie.ini
+.. _MagpieSecurity: https://github.com/Ouranosinc/Magpie/tree/master/magpie/security.py
 .. _permissions.cfg: https://github.com/Ouranosinc/Magpie/tree/master/config/permissions.cfg
 .. _postgres.env.example: https://github.com/Ouranosinc/Magpie/tree/master/env/postgres.env.example
 .. _providers.cfg: https://github.com/Ouranosinc/Magpie/tree/master/config/permissions.cfg
+.. _themes: https://github.com/Ouranosinc/Magpie/tree/master/magpie/ui/home/static/themes
+.. _tests: https://github.com/Ouranosinc/Magpie/tree/master/tests

docs/services.rst

@@ -1,9 +1,6 @@
 .. _services:
 .. include:: references.rst
 
-.. employ the permissions as base for this chapter to ease reading by shorter reference definitions
-.. py:currentmodule:: magpie.permissions
-
 ===========
 Services
 ===========
@@ -25,7 +22,7 @@ Therefore, they can be listed and searched for either using ``/services`` API ro
 On top of any :term:`Resource`'s metadata, a :term:`Service` provides specific information about its location, its
 remote synchronization method (if any), and its exposed endpoint. Another important detail about the :term:`Service`
 is its ``type``. This will not only dictate its purpose, but also define the whole schema of allowed :term:`Resource`
-under it (if any), as well as every one of their :ref:`Allowed Permissions`.
+under it (if any), as well as every one of their :term:`Allowed Permissions`.
 
 The final distinction between a :term:`Service` and generic :term:`Resource` is their position in the hierarchy. Only
 :term:`Service`-specialized :term:`Resource` (literally ``resource_type = "service"``) are allowed to be placed at the
@@ -89,6 +86,9 @@ On top of the above methods, the following attributes must be defined.
 Available Services
 -------------------
 
+.. employ the permissions as base for this section to ease reading by shorter reference definitions
+.. py:currentmodule:: magpie.permissions
+
 .. seealso::
     Module :py:mod:`magpie.services` contains the implementation of every :term:`Service` presented below.
 
@@ -148,7 +148,7 @@ each sub-:term:`Resource` as presented below.
 
 Every :class:`magpie.models.Route` as well as the :term:`Service` itself can have the :term:`Permission` based on the
 HTTP method of the incoming request. All :class:`Access` and :class:`Scope` modifiers are also supported for highly
-customizable :term:`ACL` combinations. See `permission_modifiers`_ for further details.
+customizable :term:`ACL` combinations. See :ref:`permission_modifiers` for further details.
 
 ServiceTHREDDS
 ~~~~~~~~~~~~~~~~~~~~~

docs/utilities.rst

@@ -37,8 +37,6 @@ Available helpers:
       - | Synchronizes local and remote resources based on `Magpie` service's ``sync-type`` methodology.
         | See also `magpie-con`_.
 
-.. _configuration: configuration.rst
-.. _magpie-con: https://github.com/Ouranosinc/Magpie/tree/master/magpie-cron
 
 For convenience, a generic CLI ``magpie_helper`` is also provided which allows calling each of the other helper
 operations as *mode*. You can therefore do as follows.