Merge pull request #3395 from IQSS/v4.5.1

V4.5.1

doc/shib/shib.md

@@ -6,8 +6,6 @@ FIXME: merge with what's in the Installation Guide: http://guides.dataverse.org/
 
 ## Set up a valid SSL cert
 
-See also notes on setting up the SSL cert for https://apitest.dataverse.org at https://github.com/IQSS/dataverse/tree/master/scripts/deploy/apitest.dataverse.org
-
 ### Create a private key
 
     [root@dvn-vm3 ~]# openssl genrsa -out /root/cert/shibtest.dataverse.org.key 2048

doc/sphinx-guides/source/admin/index.rst

@@ -13,9 +13,8 @@ These "superuser" tasks are managed via the new page called the Dashboard. A use
 Contents:
 
 .. toctree::
-   :maxdepth: 2
 
-  harvestclients
-  harvestserver
-  metadataexport
-  timers
+   harvestclients
+   harvestserver
+   metadataexport
+   timers

doc/sphinx-guides/source/api/dataaccess.rst

@@ -60,11 +60,11 @@ Multiple File ("bundle") download
 Returns the files listed, zipped. 
 
 Parameters: 
-~~~~~~~~~~
+~~~~~~~~~~~
 none.
 
 "All Formats" bundled access for Tabular Files. 
-----------------------------------------------
+-----------------------------------------------
 
 ``/api/access/datafile/bundle/$id``
 
@@ -78,7 +78,7 @@ It returns a zipped bundle that contains the data in the following formats:
 * File citation, in Endnote and RIS formats. 
 
 Parameters: 
-~~~~~~~~~~
+~~~~~~~~~~~
 none.
 
 Data Variable Metadata Access

doc/sphinx-guides/source/api/index.rst

@@ -11,16 +11,15 @@ interoperate with the Dataverse to utilize our
 APIs. In 4.0, we require to get a token, by simply registering for a Dataverse account, before using our APIs 
 (We are considering making some of the APIs completely public in the future - no token required - if you use it only a few times).
 
-Rather than using a production installation of Dataverse, API users should use http://apitest.dataverse.org for testing.
+Rather than using a production installation of Dataverse, API users are welcome to use http://demo.dataverse.org for testing.
 
 Contents:
 
 .. toctree::
-   :maxdepth: 2
 
-  sword
-  search
-  dataaccess
-  native-api
-  client-libraries
-  apps
+   sword
+   search
+   dataaccess
+   native-api
+   client-libraries
+   apps

doc/sphinx-guides/source/api/native-api.rst

@@ -89,7 +89,7 @@ Publish the Dataverse pointed by ``identifier``, which can either by the dataver
 Datasets
 ~~~~~~~~
 
-**Note** Creation of new datasets is done by ``POST``ing them onto dataverses. See dataverse section.
+**Note** Creation of new datasets is done with a ``POST`` onto dataverses. See dataverse section.
 
 **Note** In all commands below, dataset versions can be referred to as:
 
@@ -125,12 +125,12 @@ List versions of the dataset::
 Show a version of the dataset. The Dataset also include any metadata blocks the data might have::
 
   GET http://$SERVER/api/datasets/$id/versions/$versionNumber?key=$apiKey
-  
-      
+
+
 Export the metadata of the current published version of a dataset in various formats see Note below::
 
     GET http://$SERVER/api/datasets/export?exporter=ddi&persistentId=$persistentId
-  
+
     Note: Supported exporters (export formats) are ddi, oai_ddi, dcterms, oai_dc, and dataverse_json.
 
 
@@ -163,9 +163,9 @@ To revert to the default logic, use ``:publicationDate`` as the ``$datasetFieldT
 Note that the dataset field used has to be a date field::
 
     PUT http://$SERVER/api/datasets/$id/citationdate?key=$apiKey
-    
+
 Restores the default logic of the field type to be used as the citation date. Same as ``PUT`` with ``:publicationDate`` body::
-    
+
     DELETE http://$SERVER/api/datasets/$id/citationdate?key=$apiKey
 
 List all the role assignments at the given dataset::
@@ -185,7 +185,7 @@ Delete a Private URL from a dataset (if it exists)::
     DELETE http://$SERVER/api/datasets/$id/privateUrl?key=$apiKey
 
 Builtin Users
-~~~~~
+~~~~~~~~~~~~~
 
 This endopint deals with users of the built-in authentication provider. Note that users may come from other authentication services as well, such as Shibboleth.
 For this service to work, the setting ``BuiltinUsers.KEY`` has to be set, and its value passed as ``key`` to
@@ -368,18 +368,29 @@ Toggles superuser mode on the ``AuthenticatedUser`` whose ``identifier`` (withou
 
     POST http://$SERVER/api/admin/superuser/$identifier
 
+List all role assignments of a role assignee (i.e. a user or a group)::
+
+    GET http://$SERVER/api/admin/assignments/assignees/$identifier
+
+Note that ``identifier`` can contain slashes (e.g. ``&ip/localhost-users``).
+
 IpGroups
 ^^^^^^^^
 
-List all the ip groups::
+Lists all the ip groups::
 
   GET http://$SERVER/api/admin/groups/ip
 
-Adds a new ip group. POST data should specify the group in JSON format. Examples are available at ``data/ipGroup1.json``. ::
+Adds a new ip group. POST data should specify the group in JSON format. Examples are available at the ``data`` folder. Using this method, an IP Group is always created, but its ``alias`` might be different than the one appearing in the
+JSON file, to ensure it is unique. ::
 
   POST http://$SERVER/api/admin/groups/ip
 
-Returns a the group in a JSON format. ``groupIdtf`` can either be the group id in the database (in case it is numeric), or the group alias. ::
+Creates or updates the ip group ``$groupAlias``. ::
+
+    POST http://$SERVER/api/admin/groups/ip/$groupAlias
+
+Returns a the group in a JSON format. ``$groupIdtf`` can either be the group id in the database (in case it is numeric), or the group alias. ::
 
   GET http://$SERVER/api/admin/groups/ip/$groupIdtf
 

doc/sphinx-guides/source/api/search.rst

@@ -20,11 +20,11 @@ Parameters
 ==============  =======  ===========
 Name            Type     Description
 ==============  =======  ===========
-q               string   The search term or terms. Using "title:data" will search only the "title" field. "*" can be used as a wildcard either alone or adjacent to a term (i.e. "bird*"). For example, https://apitest.dataverse.org/api/search?q=title:data
-type            string   Can be either "dataverse", "dataset", or "file". Multiple "type" parameters can be used to include multiple types (i.e. ``type=dataset&type=file``). If omitted, all types will be returned.  For example, https://apitest.dataverse.org/api/search?q=*&type=dataset
-subtree         string   The identifier of the dataverse to which the search should be narrowed. The subtree of this dataverse and all its children will be searched.  For example, https://apitest.dataverse.org/api/search?q=data&subtree=birds
+q               string   The search term or terms. Using "title:data" will search only the "title" field. "*" can be used as a wildcard either alone or adjacent to a term (i.e. "bird*"). For example, https://demo.dataverse.org/api/search?q=title:data
+type            string   Can be either "dataverse", "dataset", or "file". Multiple "type" parameters can be used to include multiple types (i.e. ``type=dataset&type=file``). If omitted, all types will be returned.  For example, https://demo.dataverse.org/api/search?q=*&type=dataset
+subtree         string   The identifier of the dataverse to which the search should be narrowed. The subtree of this dataverse and all its children will be searched.  For example, https://demo.dataverse.org/api/search?q=data&subtree=birds
 sort            string   The sort field. Supported values include "name" and "date". See example under "order".
-order           string   The order in which to sort. Can either be "asc" or "desc".  For example, https://apitest.dataverse.org/api/search?q=data&sort=name&order=asc
+order           string   The order in which to sort. Can either be "asc" or "desc".  For example, https://demo.dataverse.org/api/search?q=data&sort=name&order=asc
 per_page        int      The number of results to return per request. The default is 10. The max is 1000. See :ref:`iteration example <iteration-example>`.
 start           int      A cursor for paging through search results. See :ref:`iteration example <iteration-example>`.
 show_relevance  boolean  Whether or not to show details of which fields were matched by the query. False by default. See :ref:`advanced search example <advancedsearch-example>`.
@@ -35,7 +35,7 @@ fq              string   A filter query on the search term. Multiple "fq" parame
 Basic Search Example
 --------------------
 
-https://apitest.dataverse.org/api/search?q=trees
+https://demo.dataverse.org/api/search?q=trees
 
 .. code-block:: json
 
@@ -52,26 +52,26 @@ https://apitest.dataverse.org/api/search?q=trees
                 {
                     "name":"Trees",
                     "type":"dataverse",
-                    "url":"https://apitest.dataverse.org/dataverse/trees",
-                    "image_url":"https://apitest.dataverse.org/api/access/dvCardImage/7",
+                    "url":"https://demo.dataverse.org/dataverse/trees",
+                    "image_url":"https://demo.dataverse.org/api/access/dvCardImage/7",
                     "identifier":"trees",
                     "description":"A tree dataverse with some birds",
                     "published_at":"2016-05-10T12:53:38Z"
                 },
                 {
                     "name":"Chestnut Trees",
                     "type":"dataverse",
-                    "url":"https://apitest.dataverse.org/dataverse/chestnuttrees",
-                    "image_url":"https://apitest.dataverse.org/api/access/dvCardImage/9",
+                    "url":"https://demo.dataverse.org/dataverse/chestnuttrees",
+                    "image_url":"https://demo.dataverse.org/api/access/dvCardImage/9",
                     "identifier":"chestnuttrees",
                     "description":"A dataverse with chestnut trees and an oriole",
                     "published_at":"2016-05-10T12:52:38Z"
                 },
                 {
                     "name":"trees.png",
                     "type":"file",
-                    "url":"https://apitest.dataverse.org/api/access/datafile/12",
-                    "image_url":"https://apitest.dataverse.org/api/access/fileCardImage/12",
+                    "url":"https://demo.dataverse.org/api/access/datafile/12",
+                    "image_url":"https://demo.dataverse.org/api/access/fileCardImage/12",
                     "file_id":"12",
                     "description":"",
                     "published_at":"2016-05-10T12:53:39Z",
@@ -84,8 +84,8 @@ https://apitest.dataverse.org/api/search?q=trees
                 {
                     "name":"Birds",
                     "type":"dataverse",
-                    "url":"https://apitest.dataverse.org/dataverse/birds",
-                    "image_url":"https://apitest.dataverse.org/api/access/dvCardImage/2",
+                    "url":"https://demo.dataverse.org/dataverse/birds",
+                    "image_url":"https://demo.dataverse.org/api/access/dvCardImage/2",
                     "identifier":"birds",
                     "description":"A bird dataverse with some trees",
                     "published_at":"2016-05-10T12:57:27Z"
@@ -100,7 +100,7 @@ https://apitest.dataverse.org/api/search?q=trees
 Advanced Search Example
 -----------------------
 
-https://apitest.dataverse.org/api/search?q=finch&show_relevance=true&show_facets=true&fq=publicationDate:2016&subtree=birds
+https://demo.dataverse.org/api/search?q=finch&show_relevance=true&show_facets=true&fq=publicationDate:2016&subtree=birds
 
 In this example, ``show_relevance=true`` matches per field are shown. Available facets are shown with ``show_facets=true`` and of the facets is being used with ``fq=publication_date_s:2015``. The search is being narrowed to the dataverse with the identifier "birds" with the parameter ``subtree=birds``.
 
@@ -118,8 +118,8 @@ In this example, ``show_relevance=true`` matches per field are shown. Available
                 {
                     "name":"Finches",
                     "type":"dataverse",
-                    "url":"https://apitest.dataverse.org/dataverse/finches",
-                    "image_url":"https://apitest.dataverse.org/api/access/dvCardImage/3",
+                    "url":"https://demo.dataverse.org/dataverse/finches",
+                    "image_url":"https://demo.dataverse.org/api/access/dvCardImage/3",
                     "identifier":"finches",
                     "description":"A dataverse with finches",
                     "published_at":"2016-05-10T12:57:38Z",
@@ -145,7 +145,7 @@ In this example, ``show_relevance=true`` matches per field are shown. Available
                     "name":"Darwin's Finches",
                     "type":"dataset",
                     "url":"http://dx.doi.org/10.5072/FK2/G2VPE7",
-                    "image_url":"https://apitest.dataverse.org/api/access/dsCardImage/2",
+                    "image_url":"https://demo.dataverse.org/api/access/dsCardImage/2",
                     "global_id":"doi:10.5072/FK2/G2VPE7",
                     "description": "Darwin's finches (also known as the Galápagos finches) are a group of about fifteen species of passerine birds.",
                     "published_at":"2016-05-10T12:57:45Z",
@@ -224,7 +224,7 @@ Be default, up to 10 results are returned with every request (though this can be
     #!/usr/bin/env python
     import urllib2
     import json
-    base = 'https://apitest.dataverse.org'
+    base = 'https://demo.dataverse.org'
     rows = 10
     start = 0
     page = 1

doc/sphinx-guides/source/conf.py

@@ -14,6 +14,7 @@
 
 import sys
 import os
+from datetime import datetime
 sys.path.insert(0, os.path.abspath('../../'))
 import sphinx_bootstrap_theme
 
@@ -56,16 +57,16 @@
 
 # General information about the project.
 project = u'Dataverse'
-copyright = u'2016, The President & Fellows of Harvard College'
+copyright = u'%d, The President & Fellows of Harvard College' % datetime.now().year
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '4.5'
+version = '4.5.1'
 # The full version, including alpha/beta/rc tags.
-release = '4.5'
+release = '4.5.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -358,7 +359,7 @@
 epub_title = u'Dataverse'
 epub_author = u'Dataverse Team'
 epub_publisher = u'Dataverse Team'
-epub_copyright = u'2014, Dataverse Team'
+epub_copyright = u'%d, The President & Fellows of Harvard College' % datetime.now().year
 
 # The basename for the epub file. It defaults to the project name.
 #epub_basename = u'Consilience Documentation'

doc/sphinx-guides/source/developers/dev-environment.rst

@@ -7,7 +7,7 @@ Development Environment
 Assumptions
 -----------
 
-This guide assumes you are using a Mac but we do have pages for :doc:`/developers/windows` and :doc:`/developers/ubuntu`.
+This guide assumes you are using a Mac. If you are using Windows or Linux, please reach out to other developers at https://groups.google.com/forum/#!forum/dataverse-dev
 
 Requirements
 ------------

doc/sphinx-guides/source/developers/index.rst

@@ -9,17 +9,14 @@ Developer Guide
 Contents:
 
 .. toctree::
-   :maxdepth: 2
-
-  intro
-  dev-environment
-  branching-strategy
-  testing
-  documentation
-  debugging
-  coding-style
-  making-releases
-  tools
-  unf/index
-
 
+   intro
+   dev-environment
+   branching-strategy
+   testing
+   documentation
+   debugging
+   coding-style
+   making-releases
+   tools
+   unf/index