Merge branch 'develop' into 4709-postgresql_96 IQSS#4709

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

@@ -0,0 +1,95 @@
+Integrations
+============
+
+Now that you've installed Dataverse, you might want to set up some integrations with other systems. Many of these integrations are open source and are cross listed in the :doc:`/api/apps` section of the API Guide.
+
+.. contents:: Contents:
+	:local:
+
+Getting Data In
+---------------
+
+A variety of integrations are oriented toward making it easier for your researchers to deposit data into your installation of Dataverse.
+
+Dropbox
++++++++
+
+If your researchers have data on Dropbox, you can make it easier for them to get it into Dataverse by setting the ``dataverse.dropbox.key`` JVM option described in the :doc:`/installation/config` section of the Installation Guide.
+
+Open Science Framework (OSF)
+++++++++++++++++++++++++++++
+
+The Center for Open Science's Open Science Framework (OSF) is an open source software project that facilitates open collaboration in science research across the lifespan of a scientific project. 
+
+For instructions on depositing data from OSF to your installation of Dataverse, your researchers can visit http://help.osf.io/m/addons/l/863978-connect-dataverse-to-a-project 
+
+RSpace
+++++++
+
+RSpace is an affordable and secure enterprise grade electronic lab notebook (ELN) for researchers to capture and organize data.
+
+For instructions on depositing data from RSpace to your installation of Dataverse, your researchers can visit https://www.researchspace.com/help-and-support-resources/dataverse-integration/
+
+Open Journal Systems (OJS)
+++++++++++++++++++++++++++
+
+Open Journal Systems (OJS) is a journal management and publishing system that has been developed by the Public Knowledge Project to expand and improve access to research.
+
+The OJS Dataverse Plugin adds data sharing and preservation to the OJS publication process.
+
+As of this writing only OJS 2.x is supported and instructions for getting started can be found at https://github.com/pkp/ojs/tree/ojs-stable-2_4_8/plugins/generic/dataverse
+
+If you are interested in OJS 3.x supporting deposit from Dataverse, please leave a comment on https://github.com/pkp/pkp-lib/issues/1822
+
+Analysis and Computation
+------------------------
+
+Data Explorer
++++++++++++++
+
+Data Explorer is a GUI which lists the variables in a tabular data file allowing searching, charting and cross tabulation analysis. 
+
+For installation instructions, see the :doc:`/installation/external-tools` section of the Installation Guide.
+
+TwoRavens/Zelig
++++++++++++++++
+
+TwoRavens is a web application for tabular data exploration and statistical analysis with Zelig.
+
+For installation instructions, see the :doc:`/installation/external-tools` section of the Installation Guide.
+
+WorldMap
+++++++++
+
+WorldMap helps researchers visualize and explore geospatial data by creating maps.
+
+For installation instructions, see :doc:`geoconnect-worldmap`.
+
+Compute Button
+++++++++++++++
+
+The "Compute" button is still highly experimental and has special requirements such as use of a Swift object store, but it is documented under "Setting up Compute" in the :doc:`/installation/config` section of the Installation Guide.
+
+Discoverability
+---------------
+
+Integration with `DataCite <https://datacite.org>`_ is built in to Dataverse. When datasets are published, metadata is sent to DataCite. You can futher increase the discoverability of your datasets by setting up additional integrations.
+
+OAI-PMH (Harvesting)
+++++++++++++++++++++
+
+Dataverse supports a protocol called OAI-PMH that facilitates harvesting datasets from one system into another. For details on harvesting, see the :doc:`harvestserver` section.
+
+SHARE
++++++
+
+`SHARE <http://www.share-research.org>`_ is building a free, open, data set about research and scholarly activities across their life cycle. It's possible to add and installation of Dataverse as one of the `sources <https://share.osf.io/sources>`_ they include if you contact the SHARE team.
+
+Future Integrations
+-------------------
+
+The `Dataverse roadmap <https://dataverse.org/goals-roadmap-and-releases>`_ is a good place to see integrations that the core Dataverse team is working on.
+
+The `Dev Efforts by the Dataverse Community <https://docs.google.com/spreadsheets/d/1pl9U0_CtWQ3oz6ZllvSHeyB0EG1M_vZEC_aZ7hREnhE/edit?usp=sharing>`_ spreadsheet is the best way to track integrations that are being worked on by the Dataverse community.
+
+Please help us keep this page up to date making a pull request! To get started, see the :doc:`/developers/documentation` section of the Developer Guide.

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

@@ -1,7 +1,7 @@
 Apps
 ====
 
-The introduction of Dataverse APIs has fostered the development of apps that are listed at http://dataverse.org/integrations
+The introduction of Dataverse APIs has fostered the development of apps that are listed at http://dataverse.org/integrations and the :doc:`/admin/integrations` section of the Admin Guide.
 
 The apps below are open source, demonstrating how to use Dataverse APIs. Some of these apps (and others) are built on :doc:`/api/client-libraries` that are available for Dataverse APIs.
 
@@ -26,17 +26,15 @@ OJS
 
 The Open Journal Systems (OJS) Dataverse Plugin adds data sharing and preservation to the OJS publication process.
 
-https://github.com/pkp/ojs/tree/ojs-stable-2_4_6/plugins/generic/dataverse
+https://github.com/pkp/ojs/tree/ojs-stable-2_4_8/plugins/generic/dataverse
 
 Python
 ------
 
 OSF
 ~~~
 
-Allows you to view, download, and upload files to and from a Dataverse dataset from an Open Science Framework (OSF) project: https://osf.io/getting-started/#dataverse
-
-https://github.com/CenterForOpenScience/osf.io/tree/master/website/addons/dataverse
+Allows you to view, download, and upload files to and from a Dataverse dataset from an Open Science Framework (OSF) project: https://github.com/CenterForOpenScience/osf.io/tree/develop/addons/dataverse
 
 GeoConnect
 ~~~~~~~~~~

doc/sphinx-guides/source/conf.py

@@ -64,9 +64,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '4.8.6'
+version = '4.9'
 # The full version, including alpha/beta/rc tags.
-release = '4.8.6'
+release = '4.9'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/sphinx-guides/source/developers/making-releases.rst

@@ -14,7 +14,7 @@ Before tagging, ensure the version number has been incremented to the milestone
 - doc/sphinx-guides/source/conf.py
 - doc/sphinx-guides/source/versions.rst 
 
-.. Here's an example commit where all three files were updated at once: https://github.com/IQSS/dataverse/commit/813b66a6077e8f94026a8db5320cceffefc10e11
+Here's an example commit where all three files were updated at once: https://github.com/IQSS/dataverse/commit/99e23f96ec362ac2f524cb5cd80ca375fa13f196
 
 Merge "develop" into "master"
 -----------------------------

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

@@ -440,6 +440,11 @@ Administration of Your Dataverse Installation
 
 Now that you're live you'll want to review the :doc:`/admin/index` for more information about the ongoing administration of a Dataverse installation.
 
+Setting Up Integrations
++++++++++++++++++++++++
+
+Before going live, you might want to consider setting up integrations to make it easier for your users to deposit or explore data. See the :doc:`/admin/integrations` section of the Admin Guide for details.
+
 JVM Options
 -----------
 

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

@@ -82,6 +82,8 @@ There are a number of optional components you may choose to install or configure
 - OAuth2: an authentication system described in :doc:`oauth2`.
 - Geoconnect: a system that allows users to create maps from geospatial files, described in :doc:`geoconnect`.
 
+See also the :doc:`/admin/integrations` section of the Admin Guide.
+
 System Requirements
 -------------------
 

doc/sphinx-guides/source/versions.rst

@@ -5,7 +5,8 @@ Dataverse Guides Versions
 
 This list provides a way to refer to previous versions of the Dataverse guides, which we still host. In order to learn more about the updates delivered from one version to another, visit the `Releases <https://github.com/IQSS/dataverse/releases>`__ page in our GitHub repo.
 
-- 4.8.6
+- 4.9
+- `4.8.6 </en/4.8.6/>`__
 - `4.8.5 </en/4.8.5/>`__
 - `4.8.4 </en/4.8.4/>`__
 - `4.8.3 </en/4.8.3/>`__

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>edu.harvard.iq</groupId>
     <artifactId>dataverse</artifactId>
-    <version>4.8.6</version>
+    <version>4.9</version>
     <packaging>war</packaging>
 
     <name>dataverse</name>

scripts/api/data/metadatablocks/citation.tsv

@@ -4,7 +4,7 @@
 	title	Title	Full title by which the Dataset is known.	Enter title...	text	0		TRUE	FALSE	FALSE	FALSE	TRUE	TRUE		citation
 	subtitle	Subtitle	A secondary title used to amplify or state certain limitations on the main title.		text	1		FALSE	FALSE	FALSE	FALSE	FALSE	FALSE		citation
 	alternativeTitle	Alternative Title	A title by which the work is commonly referred, or an abbreviation of the title.		text	2		FALSE	FALSE	FALSE	FALSE	FALSE	FALSE		citation
-	alternativeURL	Alternative URL	A URL where the dataset can be viewed, such as a personal or project website.  	Enter full URL, starting with http://	url	3		FALSE	FALSE	FALSE	FALSE	FALSE	FALSE		citation
+	alternativeURL	Alternative URL	A URL where the dataset can be viewed, such as a personal or project website.  	Enter full URL, starting with http://	url	3	<a href="#VALUE" target="_blank">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE		citation
 	otherId	Other ID	Another unique identifier that identifies this Dataset (e.g., producer's or another repository's number).		none	4	:	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE		citation
 	otherIdAgency	Agency	Name of agency which generated this identifier.		text	5	#VALUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	otherId	citation
 	otherIdValue	Identifier	Other identifier that corresponds to this Dataset.		text	6	#VALUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	otherId	citation
@@ -24,23 +24,23 @@
 	keyword	Keyword	Key terms that describe important aspects of the Dataset.		none	20		FALSE	FALSE	TRUE	FALSE	TRUE	FALSE		citation
 	keywordValue	Term	Key terms that describe important aspects of the Dataset. Can be used for building keyword indexes and for classification and retrieval purposes. A controlled vocabulary can be employed. The vocab attribute is provided for specification of the controlled vocabulary in use, such as LCSH, MeSH, or others. The vocabURI attribute specifies the location for the full controlled vocabulary.		text	21	#VALUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	keyword	citation
 	keywordVocabulary	Vocabulary	For the specification of the keyword controlled vocabulary in use, such as LCSH, MeSH, or others.		text	22	(#VALUE)	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	keyword	citation
-	keywordVocabularyURI	Vocabulary URL	Keyword vocabulary URL points to the web presence that describes the keyword vocabulary, if appropriate. Enter an absolute URL where the keyword vocabulary web site is found, such as http://www.my.org.	Enter full URL, starting with http://	url	23	<a href="#VALUE">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	keyword	citation
+	keywordVocabularyURI	Vocabulary URL	Keyword vocabulary URL points to the web presence that describes the keyword vocabulary, if appropriate. Enter an absolute URL where the keyword vocabulary web site is found, such as http://www.my.org.	Enter full URL, starting with http://	url	23	<a href="#VALUE" target="_blank">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	keyword	citation
 	topicClassification	Topic Classification	The classification field indicates the broad important topic(s) and subjects that the data cover. Library of Congress subject terms may be used here.  		none	24		FALSE	FALSE	TRUE	FALSE	FALSE	FALSE		citation
 	topicClassValue	Term	Topic or Subject term that is relevant to this Dataset.		text	25	#VALUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	topicClassification	citation
 	topicClassVocab	Vocabulary	Provided for specification of the controlled vocabulary in use, e.g., LCSH, MeSH, etc.		text	26	(#VALUE)	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	topicClassification	citation
-	topicClassVocabURI	Vocabulary URL	Specifies the URL location for the full controlled vocabulary.	Enter full URL, starting with http://	url	27	<a href="#VALUE">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	topicClassification	citation
+	topicClassVocabURI	Vocabulary URL	Specifies the URL location for the full controlled vocabulary.	Enter full URL, starting with http://	url	27	<a href="#VALUE" target="_blank">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	topicClassification	citation
 	publication	Related Publication	Publications that use the data from this Dataset.		none	28		FALSE	FALSE	TRUE	FALSE	TRUE	FALSE		citation
 	publicationCitation	Citation	The full bibliographic citation for this related publication.		textbox	29	#VALUE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	publication	citation
 	publicationIDType	ID Type	The type of digital identifier used for this publication (e.g., Digital Object Identifier (DOI)).		text	30	#VALUE: 	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	publication	citation
 	publicationIDNumber	ID Number	The identifier for the selected ID type.		text	31	#VALUE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	publication	citation
-	publicationURL	URL	Link to the publication web page (e.g., journal article page, archive record page, or other).	Enter full URL, starting with http://	url	32	<a href="#VALUE">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	publication	citation
+	publicationURL	URL	Link to the publication web page (e.g., journal article page, archive record page, or other).	Enter full URL, starting with http://	url	32	<a href="#VALUE" target="_blank">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	publication	citation
 	notesText	Notes	Additional important information about the Dataset.		textbox	33		FALSE	FALSE	FALSE	FALSE	TRUE	FALSE		citation
 	language	Language	Language of the Dataset		text	34		TRUE	TRUE	TRUE	TRUE	FALSE	FALSE		citation
 	producer	Producer	Person or organization with the financial or administrative responsibility over this Dataset		none	35		FALSE	FALSE	TRUE	FALSE	FALSE	FALSE		citation
 	producerName	Name	Producer name	FamilyName, GivenName or Organization	text	36	#VALUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	producer	citation
 	producerAffiliation	Affiliation	The organization with which the producer is affiliated.		text	37	(#VALUE)	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	producer	citation
 	producerAbbreviation	Abbreviation	The abbreviation by which the producer is commonly known. (ex. IQSS, ICPSR)		text	38	(#VALUE)	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	producer	citation
-	producerURL	URL	Producer URL points to the producer's web presence, if appropriate. Enter an absolute URL where the producer's web site is found, such as http://www.my.org.  	Enter full URL, starting with http://	url	39	<a href="#VALUE">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	producer	citation
+	producerURL	URL	Producer URL points to the producer's web presence, if appropriate. Enter an absolute URL where the producer's web site is found, such as http://www.my.org.  	Enter full URL, starting with http://	url	39	<a href="#VALUE" target="_blank">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	producer	citation
 	producerLogoURL	Logo URL	URL for the producer's logo, which points to this  producer's web-accessible logo image. Enter an absolute URL where the producer's logo image is found, such as http://www.my.org/images/logo.gif.	Enter full URL for image, starting with http://	url	40	<img src="#VALUE" alt="#NAME" class="metadata-logo"/><br/>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	producer	citation
 	productionDate	Production Date	Date when the data collection or other materials were produced (not distributed, published or archived).	YYYY-MM-DD	date	41		TRUE	FALSE	FALSE	TRUE	FALSE	FALSE		citation
 	productionPlace	Production Place	The location where the data collection and any other related materials were produced.		text	42		FALSE	FALSE	FALSE	FALSE	FALSE	FALSE		citation
@@ -54,7 +54,7 @@
 	distributorName	Name	Distributor name	FamilyName, GivenName or Organization	text	50	#VALUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	distributor	citation
 	distributorAffiliation	Affiliation	The organization with which the distributor contact is affiliated.		text	51	(#VALUE)	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	distributor	citation
 	distributorAbbreviation	Abbreviation	The abbreviation by which this distributor is commonly known (e.g., IQSS, ICPSR).		text	52	(#VALUE)	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	distributor	citation
-	distributorURL	URL	Distributor URL points to the distributor's web presence, if appropriate. Enter an absolute URL where the distributor's web site is found, such as http://www.my.org.	Enter full URL, starting with http://	url	53	<a href="#VALUE">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	distributor	citation
+	distributorURL	URL	Distributor URL points to the distributor's web presence, if appropriate. Enter an absolute URL where the distributor's web site is found, such as http://www.my.org.	Enter full URL, starting with http://	url	53	<a href="#VALUE" target="_blank">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	distributor	citation
 	distributorLogoURL	Logo URL	URL of the distributor's logo, which points to this  distributor's web-accessible logo image. Enter an absolute URL where the distributor's logo image is found, such as http://www.my.org/images/logo.gif.	Enter full URL for image, starting with http://	url	54	<img src="#VALUE" alt="#NAME" class="metadata-logo"/><br/>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	distributor	citation
 	distributionDate	Distribution Date	Date that the work was made available for distribution/presentation.	YYYY-MM-DD	date	55		TRUE	FALSE	FALSE	TRUE	FALSE	FALSE		citation
 	depositor	Depositor	The person (Family Name, Given Name) or the name of the organization that deposited this Dataset to the repository.		text	56		FALSE	FALSE	FALSE	FALSE	FALSE	FALSE		citation

scripts/database/upgrades/upgrade_v4.8.6_to_v4.9.0.sql

@@ -69,3 +69,5 @@ VALUES (':Shoulder', (SELECT substring(content, strpos(content,'/')+1) || '/' fr
  SET content=(SELECT substring(content from 0 for strpos(content,'/'))
  FROM setting
  WHERE name=':Authority' and strpos(content,'/')>0) where name=':Authority';
+
+update datasetfieldtype set displayformat = '<a href="#VALUE" target="_blank">#VALUE</a>' where name in ('alternativeURL', 'keywordVocabularyURI', 'topicClassVocabURI', 'publicationURL', 'producerURL', 'distributorURL');