Merge branch 'develop' into 2594-contributing #2594

.gitignore

@@ -16,9 +16,14 @@ ehthumbs.db
 Thumbs.db
 .vagrant
 *.pyc
+*.swp
 scripts/api/py_api_wrapper/demo-data/*
 scripts/api/py_api_wrapper/test_data/*
 scripts/api/py_api_wrapper/local-data/*
 doc/sphinx-guides/build
 faces-config.NavData
 src/main/java/BuildNumber.properties
+/nbproject/
+oauth-credentials.md
+
+/src/main/webapp/oauth2/newAccount.html

PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,30 @@
+# RFI Checklist
+
+_**Before** submitting the pull request, fill out sections (1.) Related Issues and (2.) Pull Request Checklist._
+
+### 1. Related Issues
+
+_List and [link](https://guides.github.com/features/issues/#notifications) to the issues in this Pull Request._
+
+- [#### + Title HERE]
+
+---
+### 2. Pull Request Checklist
+
+- [ ]  Functionality completed as described in FRD
+- [ ]  Dependencies, risks, assumptions in FRD addressed
+- [ ]  Unit tests completed
+- [ ]  Deployment requirements identified (e.g., SQL scripts, indexing)
+- [ ]  Documentation completed
+- [ ]  All code checkins completed
+
+---
+### 3. Review Checklist
+
+_**After** the pull request has been submitted, fill out this section._
+
+- [ ]  Code review completed or waived
+- [ ]  Testing requirements completed
+- [ ]  Usability testing completed or waived
+- [ ]  Support testing completed or waived
+- [ ]  Merged with develop branch and resolved conflicts

README.md

@@ -1,7 +1,7 @@
 Dataverse 
 ==========
 
-Dataverse is an open source web application for sharing, citing, analyzing, and preserving research data (developed by the [Data Science team] (http://datascience.iq.harvard.edu/about-dataverse) at the [Institute for Quantitative Social Science] (http://iq.harvard.edu/)).
+Dataverse is an open source web application for sharing, citing, analyzing, and preserving research data (developed by the [Data Science and Products team] (http://www.iq.harvard.edu/people/people/data-science-products) at the [Institute for Quantitative Social Science] (http://iq.harvard.edu/)).
 
 Institutions and organizations can choose to install the Dataverse software for their own use. 
 In this case, the institution will be responsible for maintaining the application; installing upgrades, 

Vagrantfile

@@ -15,6 +15,11 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
       puts "OPERATING_SYSTEM environment variable not specified. Using #{operating_system} by default.\nTo specify it in bash: export OPERATING_SYSTEM=debian"
       config.vm.box_url = "http://puppet-vagrant-boxes.puppetlabs.com/centos-65-x64-virtualbox-puppet.box"
       config.vm.box = "puppet-vagrant-boxes.puppetlabs.com-centos-65-x64-virtualbox-puppet.box"
+    elsif ENV['OPERATING_SYSTEM'] == 'centos7'
+      puts "WARNING: CentOS 7 specified. Newer than what the dev team tests on."
+      config.vm.box_url = "https://atlas.hashicorp.com/puppetlabs/boxes/centos-7.2-64-puppet/versions/1.0.1/providers/virtualbox.box"
+      config.vm.box = "puppetlabs-centos-7.2-64-puppet-1.0.1-virtualbox.box"
+      standalone.vm.box = "puppetlabs-centos-7.2-64-puppet-1.0.1-virtualbox.box"
     elsif ENV['OPERATING_SYSTEM'] == 'debian'
       puts "WARNING: Debian specified. Here be dragons! https://github.com/IQSS/dataverse/issues/1059"
       config.vm.box_url = "http://puppet-vagrant-boxes.puppetlabs.com/debian-73-x64-virtualbox-puppet.box"

conf/httpd/conf.d/dataverse.conf

@@ -9,11 +9,11 @@ ProxyPassMatch ^/error-documents !
 # pass everything else to Glassfish
 ProxyPass / ajp://localhost:8009/
 
-<Location /shib.xhtml>
-  AuthType shibboleth
-  ShibRequestSetting requireSession 1
-  require valid-user
-</Location>
+#<Location /shib.xhtml>
+#  AuthType shibboleth
+#  ShibRequestSetting requireSession 1
+#  require valid-user
+#</Location>
 
 ErrorDocument 503 /error-documents/503.html
 Alias /error-documents /var/www/dataverse/error-documents

conf/solr/4.6.0/schema.xml

@@ -249,6 +249,8 @@
    <field name="discoverableBy" type="string" stored="true" indexed="true" multiValued="true"/>
 
    <field name="dvObjectType" type="string" stored="true" indexed="true" multiValued="false"/>
+   <field name="metadataSource" type="string" stored="true" indexed="true" multiValued="false"/>
+   <field name="isHarvested" type="boolean" stored="true" indexed="true" multiValued="false"/>
 
    <field name="dvName" type="text_en" stored="true" indexed="true" multiValued="false"/>
    <field name="dvAffiliation" type="text_en" stored="true" indexed="true" multiValued="false"/>
@@ -290,11 +292,14 @@
    <field name="parentName" type="string" stored="true" indexed="false" multiValued="false"/>
    <field name="parentCitation" type="string" stored="true" indexed="false" multiValued="false"/>
    <field name="citation" type="string" stored="true" indexed="false" multiValued="false"/>
+   <field name="citationHtml" type="string" stored="true" indexed="false" multiValued="false"/>
    <field name="identifier" type="string" stored="true" indexed="true" multiValued="false"/>
    <field name="persistentUrl" type="string" stored="true" indexed="false" multiValued="false"/>
    <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"/>
 
@@ -348,6 +353,7 @@
    <field name="accessToSources" type="text_en" multiValued="false" stored="true" indexed="true"/>
    <field name="actionsToMinimizeLoss" type="text_en" multiValued="false" stored="true" indexed="true"/>
    <field name="alternativeTitle" type="text_en" multiValued="false" stored="true" indexed="true"/>
+   <field name="alternativeURL" type="text_en" multiValued="false" stored="true" indexed="true"/>
    <field name="astroFacility" type="text_en" multiValued="true" stored="true" indexed="true"/>
    <field name="astroInstrument" type="text_en" multiValued="true" stored="true" indexed="true"/>
    <field name="astroObject" type="text_en" multiValued="true" stored="true" indexed="true"/>
@@ -642,6 +648,7 @@
    <copyField source="accessToSources" dest="text" maxChars="3000"/>
    <copyField source="actionsToMinimizeLoss" dest="text" maxChars="3000"/>
    <copyField source="alternativeTitle" dest="text" maxChars="3000"/>
+   <copyField source="alternativeURL" dest="text" maxChars="3000"/>
    <copyField source="astroFacility" dest="text" maxChars="3000"/>
    <copyField source="astroInstrument" dest="text" maxChars="3000"/>
    <copyField source="astroObject" dest="text" maxChars="3000"/>

doc/Architecture/update-user-account-info.puml

@@ -0,0 +1,28 @@
+@startuml
+actor user
+participant DataverseUserPage as page
+participant "provider: AuthenticationProvider" as prv
+participant AuthenticationServiceBean as authSvc
+user --> page: HTTP GET
+== page init ==
+...
+page -> authSvc : lookupProvider(session.user)
+activate authSvc
+page <-- authSvc: provider
+deactivate authSvc
+...
+
+== Can Update User? ==
+page -> prv: isUserInfoUpdateAllowed()
+activate prv
+page <-- prv: true/false
+deactivate prv
+...
+
+== Save User ==
+user --> page: save()
+page -> page: udi = createUserDisplayInfo()
+page -> prv: updateUserInfo( udi )
+page -> authSvc: updateAuthentictedUser( session.user, udi )
+
+@enduml

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/Makefile

@@ -55,7 +55,7 @@ htmldeploy: html $(GUIDESDIR)
 	@echo
 	@cp -Rf build/html/* $(GUIDESDIR)
 	@echo "HTML documentation deployed to $(GUIDESDIR)."
-	@echo "It should now be available at http://<YOURHOST>:<YOURPORT>/guides."
+	@echo "It should now be available at http://<YOURHOST>:<YOURPORT>/guides/index.html"
 
 $(GUIDESDIR):
 	@mkdir -p $(GUIDESDIR) 

doc/sphinx-guides/source/_static/api/dataverse-complete.json

@@ -0,0 +1,15 @@
+{
+  "name": "Scientific Research",
+  "alias": "science",
+  "dataverseContacts": [
+    {
+      "contactEmail": "[email protected]"
+    },
+    {
+      "contactEmail": "[email protected]"
+    }
+  ],
+  "affiliation": "Scientific Research University",
+  "description": "We do all the science.",
+  "dataverseType": "LABORATORY"
+}

doc/sphinx-guides/source/_static/api/dataverse-minimal.json

@@ -0,0 +1,9 @@
+{
+  "name": "Scientific Research",
+  "alias": "science",
+  "dataverseContacts": [
+    {
+      "contactEmail": "[email protected]"
+    }
+  ]
+}

doc/sphinx-guides/source/_static/docsdataverse_org.css

@@ -1,11 +1,11 @@
-/*!
+*!
  * Start Bootstrap - Heroic Features HTML Template (http://startbootstrap.com)
  * Code licensed under the Apache License v2.0.
  * For details, see http://www.apache.org/licenses/LICENSE-2.0.
  */
 
 body {
-    padding-top: 70px; /* Required padding for .navbar-fixed-top. Remove if using .navbar-static-top. Change if height of navigation changes. */
+    padding-top: 52px; /* Required padding for .navbar-fixed-top. Remove if using .navbar-static-top. Change if height of navigation changes. */
 }
 
 .hero-spacer {
@@ -54,6 +54,13 @@ a.headerlink {
     text-decoration: none;
 }
 
+.fixedwidthplain {
+    color:#606060; 
+    font-family: Menlo, Monaco, Consolas, "Courier New", monospace; 
+}
+
+/* alternative formattings:  font-weight: bold; font-size: 110%; etc. */
+
 /* #sidebar.bs-sidenav.affix {
 	position: static;
 } REMOVED STATIC ToC */

doc/sphinx-guides/source/_static/installation/files/etc/httpd/conf.d/shibtest.dataverse.org.conf → doc/sphinx-guides/source/_static/installation/files/etc/httpd/conf.d/dataverse.example.edu.conf

@@ -1,6 +1,6 @@
 <VirtualHost *:80>
 
-ServerName shibtest.dataverse.org
+ServerName dataverse.example.edu
 
 # From https://wiki.apache.org/httpd/RewriteHTTPToHTTPS
 

doc/sphinx-guides/source/_static/installation/files/etc/httpd/conf.d/ssl.conf

@@ -75,7 +75,7 @@ SSLCryptoDevice builtin
 
 # General setup for the virtual host, inherited from global configuration
 #DocumentRoot "/var/www/html"
-ServerName shibtest.dataverse.org:443
+ServerName dataverse.example.edu:443
 
 # Use separate log files for the SSL virtual host; note that LogLevel
 # is not inherited from httpd.conf.
@@ -102,14 +102,14 @@ SSLCipherSuite ALL:!ADH:!EXPORT:!SSLv2:RC4+RSA:+HIGH:+MEDIUM:+LOW
 # the certificate is encrypted, then you will be prompted for a
 # pass phrase.  Note that a kill -HUP will prompt again.  A new
 # certificate can be generated using the genkey(1) command.
-SSLCertificateFile /etc/pki/tls/certs/shibtest.dataverse.org.crt
+SSLCertificateFile /etc/pki/tls/certs/dataverse.example.edu.crt
 
 #   Server Private Key:
 #   If the key is not combined with the certificate, use this
 #   directive to point at the key file.  Keep in mind that if
 #   you've both a RSA and a DSA private key you can configure
 #   both in parallel (to also allow the use of DSA ciphers, etc.)
-SSLCertificateKeyFile /etc/pki/tls/private/shibtest.dataverse.org.key
+SSLCertificateKeyFile /etc/pki/tls/private/dataverse.example.edu.key
 
 #   Server Certificate Chain:
 #   Point SSLCertificateChainFile at a file containing the
@@ -118,7 +118,7 @@ SSLCertificateKeyFile /etc/pki/tls/private/shibtest.dataverse.org.key
 #   the referenced file can be the same as SSLCertificateFile
 #   when the CA certificates are directly appended to the server
 #   certificate for convinience.
-SSLCertificateChainFile /etc/pki/tls/certs/shibtest.dataverse.org_server-chain.crt
+SSLCertificateChainFile /etc/pki/tls/certs/dataverse.example.edu_server-chain.crt
 
 #   Certificate Authority (CA):
 #   Set the CA certificate verification path where to find CA

doc/sphinx-guides/source/_static/installation/files/etc/init.d/glassfish

@@ -0,0 +1,44 @@
+#! /bin/sh
+# chkconfig: 2345 99 01
+# description: GlassFish App Server
+
+set -e
+
+ASADMIN=/usr/local/glassfish4/bin/asadmin
+
+case "$1" in
+  start)
+        echo -n "Starting GlassFish server: glassfish"
+        # Increase file descriptor limit:
+        ulimit -n 32768
+        # Allow "memory overcommit":
+        # (basically, this allows to run exec() calls from inside the
+        # app, without the Unix fork() call physically hogging 2X
+        # the amount of memory glassfish is already using)
+        echo 1 > /proc/sys/vm/overcommit_memory
+
+        #echo
+        #echo "GLASSFISH IS UNDER MAINTENANCE;"
+        #echo "PLEASE DO NOT USE service init script."
+        #echo
+	LANG=en_US.UTF-8; export LANG
+        $ASADMIN start-domain domain1
+        echo "."
+        ;;
+  stop)
+        echo -n "Stopping GlassFish server: glassfish"
+        #echo
+        #echo "GLASSFISH IS UNDER MAINTENANCE;"
+        #echo "PLEASE DO NOT USE service init script."
+        #echo
+
+        $ASADMIN stop-domain domain1
+        echo "."
+        ;;
+
+  *)
+        echo "Usage: /etc/init.d/glassfish {start|stop}"
+        exit 1
+esac
+
+exit 0

doc/sphinx-guides/source/_static/installation/files/etc/init.d/solr

@@ -0,0 +1,35 @@
+****
+#!/bin/sh
+
+# Starts, stops, and restarts Apache Solr.
+#
+# chkconfig: 35 92 08
+# description: Starts and stops Apache Solr
+
+SOLR_DIR="/usr/local/solr-4.6.0/example"
+JAVA_OPTIONS="-Xmx1024m -DSTOP.PORT=8079 -DSTOP.KEY=mustard -jar start.jar"
+LOG_FILE="/var/log/solr.log"
+JAVA="/usr/bin/java"
+
+case $1 in
+    start)
+        echo "Starting Solr"
+        cd $SOLR_DIR
+        $JAVA $JAVA_OPTIONS 2> $LOG_FILE &
+        ;;
+    stop)
+        echo "Stopping Solr"
+        cd $SOLR_DIR
+        $JAVA $JAVA_OPTIONS --stop
+        ;;
+    restart)
+        $0 stop
+        sleep 1
+        $0 start
+        ;;
+    *)
+        echo "Usage: $0 {start|stop|restart}" >&2
+        exit 1
+        ;;
+esac
+