3338 oauth orcid

conf/solr/4.6.0/schema.xml

@@ -298,6 +298,8 @@
    <field name="unf" type="string" stored="true" indexed="true" multiValued="false"/>
    <field name="fileSizeInBytes" type="long" stored="true" indexed="true" multiValued="false"/>
    <field name="fileMd5" type="string" stored="true" indexed="true" multiValued="false"/>
+   <field name="fileChecksumType" type="string" stored="true" indexed="true" multiValued="false"/>
+   <field name="fileChecksumValue" type="string" stored="true" indexed="true" multiValued="false"/>
    <field name="fileContentType" type="string" stored="true" indexed="true" multiValued="false"/>
    <field name="deaccessionReason" type="string" stored="true" indexed="false" multiValued="false"/>
 

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

@@ -16,11 +16,10 @@ Rather than using a production installation of Dataverse, API users are welcome
 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:
 
@@ -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

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

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

@@ -1,17 +1,17 @@
 .. _unf:
 
-====================================
+=====================================
 Universal Numerical Fingerprint (UNF)
-====================================
+=====================================
 
 Contents:
 
 .. toctree::
    :maxdepth: 2
 
-  unf-v3
-  unf-v5
-  unf-v6
+   unf-v3
+   unf-v5
+   unf-v6
 
 .. figure:: ./img/unf-diagram.png
     :align: center

doc/sphinx-guides/source/developers/unf/unf-v5.rst

@@ -10,6 +10,3 @@ UNF Version 5
 **To address this, the Project is about to release UNF Version 6. The release date is still being discussed. It may coincide with the release of Dataverse 4.0. Alternatively, the production version of DVN 3.6.3 may get upgraded to use UNF v6 prior to that. This will be announced shortly. In the process, we are solving another problem with UNF v5 - this time we've made an effort to offer very implementer-friendly documentation that describes the algorithm fully and unambiguously. So if you are interested in implementing your own version of a UNF calculator, (something we would like to encourage!) please proceed directly to the Version 6 documentation.**
 
 **Going forward, we are going to offer a preserved version of the Version 5 library and, possibly, an online UNF v5 calculator, for the purposes of validating vectors and data sets for which published Version 5 UNFs exist.**
-
------
-

doc/sphinx-guides/source/index.rst

@@ -3,10 +3,10 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Dataverse 4.5 Guides
+Dataverse 4.5.1 Guides
 ======================
 
-These guides are for the most recent version of Dataverse. For the guides for **version 4.3.1** please go `here <http://guides.dataverse.org/en/4.3.1/>`_.
+These guides are for the most recent version of Dataverse. For the guides for **version 4.5** please go `here <http://guides.dataverse.org/en/4.5/>`_.
 
 .. toctree::
   :glob:

doc/sphinx-guides/source/installation/config.rst

@@ -90,7 +90,7 @@ Persistent identifiers are a required and integral part of the Dataverse platfor
 
 JVM Options: :ref:`doi.baseurlstring`, :ref:`doi.username`, :ref:`doi.password`
 
-Database Settings: :ref:`:DoiProvider`, :ref:`:Protocol`, :ref:`:Authority`, :ref:`:DoiSeparator`
+Database Settings: :ref:`:DoiProvider <:DoiProvider>`, :ref:`:Protocol <:Protocol>`, :ref:`:Authority <:Authority>`, :ref:`:DoiSeparator <:DoiSeparator>`
 
 Please note that any datasets creating using the test configuration cannot be directly migrated and would need to be created again once a valid DOI namespace is configured.
 
@@ -104,8 +104,9 @@ Once this configuration is complete, your Dataverse installation should be ready
 JVM Options
 -----------
 
-JVM stands Java Virtual Machine and as a Java application, Glassfish can read JVM options when it is started. A number of JVM options are configured by the installer below is a complete list of the Dataverse-specific JVM options. You can inspect the configured options by running ``asadmin list-jvm-options | egrep 'dataverse|doi'
-``.
+JVM stands Java Virtual Machine and as a Java application, Glassfish can read JVM options when it is started. A number of JVM options are configured by the installer below is a complete list of the Dataverse-specific JVM options. You can inspect the configured options by running:
+
+``asadmin list-jvm-options | egrep 'dataverse|doi'``
 
 When changing values these values with ``asadmin``, you'll need to delete the old value before adding a new one, like this:
 
@@ -188,24 +189,30 @@ dataverse.dataAccess.thumbnail.pdf.limit
 
 For limiting the size of thumbnail images generated from files.
 
+.. _doi.baseurlstring:
+
 doi.baseurlstring
 +++++++++++++++++
-.. _doi.baseurlstring:
+
 As of this writing "https://ezid.cdlib.org" and "https://mds.datacite.org" are the only valid values. See also these related database settings below:
 
 - :DoiProvider
 - :Protocol
 - :Authority
 - :DoiSeparator
 
+.. _doi.username:
+
 doi.username
 ++++++++++++
-.. _doi.username:
+
 Used in conjuction with ``doi.baseurlstring``.
 
+.. _doi.password:
+
 doi.password
 ++++++++++++
-.. _doi.password:
+
 Used in conjuction with ``doi.baseurlstring``.
 
 dataverse.handlenet.admcredfile
@@ -265,30 +272,45 @@ This is the email address that "system" emails are sent from such as password re
 
 ``curl -X PUT -d "Support <support@example.edu>" http://localhost:8080/api/admin/settings/:SystemEmail``
 
+:FooterCopyright
+++++++++++++++++
+
+By default the footer says "Copyright © [YYYY]" but you can add text after the year, as in the example below.
+
+``curl -X PUT -d ", The President &#38; Fellows of Harvard College" http://localhost:8080/api/admin/settings/:FooterCopyright``
+
+.. _:DoiProvider:
+
 :DoiProvider
 ++++++++++++
-.. _:DoiProvider:
+
 As of this writing "EZID" and "DataCite" are the only valid options.
 
 ``curl -X PUT -d EZID http://localhost:8080/api/admin/settings/:DoiProvider``
 
+.. _:Protocol:
+
 :Protocol
 +++++++++
-.. _:Protocol:
+
 As of this writing "doi" is the only valid option for the protocol for a persistent ID.
 
 ``curl -X PUT -d doi http://localhost:8080/api/admin/settings/:Protocol``
 
+.. _:Authority:
+
 :Authority
 ++++++++++
-.. _:Authority:
+
 Use the DOI authority assigned to you by your DoiProvider.
 
 ``curl -X PUT -d 10.xxxx http://localhost:8080/api/admin/settings/:Authority``
 
+.. _:DoiSeparator:
+
 :DoiSeparator
 +++++++++++++
-.. _:DoiSeparator:
+
 It is recommended that you keep this as a slash ("/").
 
 ``curl -X PUT -d "/" http://localhost:8080/api/admin/settings/:DoiSeparator``
@@ -370,7 +392,9 @@ Limit the number of files in a zip that Dataverse will accept.
 :GoogleAnalyticsCode
 ++++++++++++++++++++
 
-For setting up Google Analytics for your Dataverse installation.
+Set your Google Analytics Tracking ID thusly:
+
+``curl -X PUT -d 'trackingID' http://localhost:8080/api/admin/settings/:GoogleAnalyticsCode``
 
 :SolrHostColonPort
 ++++++++++++++++++
@@ -392,7 +416,7 @@ The relative path URL to which users will be sent after signup. The default sett
 The location of your TwoRavens installation.  Activation of TwoRavens also requires the setting below, ``TwoRavensTabularView``
 
 :TwoRavensTabularView
-+++++++++++++++++++
++++++++++++++++++++++
 
 Set ``TwoRavensTabularView`` to true to allow a user to view tabular files via the TwoRavens application. This boolean affects whether a user will see the "Explore" button.
 
@@ -477,3 +501,10 @@ Host FQDN or URL of your Piwik instance before the ``/piwik.php``. Examples:
 or
 
 ``curl -X PUT -d hostname.domain.tld/stats http://localhost:8080/api/admin/settings/:PiwikAnalyticsHost``
+
+:FileFixityChecksumAlgorithm
+++++++++++++++++++++++++++++
+
+Dataverse calculates checksums for uploaded files so that users can determine if their file was corrupted via upload or download. This is sometimes called "file fixity": https://en.wikipedia.org/wiki/File_Fixity
+
+The default checksum algorithm used is MD5 and should be sufficient for establishing file fixity. "SHA-1" is an experimental alternate value for this setting.