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@djbrooke djbrooke released this Jun 14, 2019

This release adds the ability to filter and sort the files in a dataset, better recognition and categorization of file types, accessibility enhancements, and a new API to load language packs in support of internationalization.

For the complete list of issues, see the 4.15 milestone in Github.

For help with upgrading, installing, or general questions please post to the Dataverse Google Group or email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. In an effort to prevent accidental duplicate accounts, user spoofing, or other username-based confusion, this release introduces a database constraint that no longer allows usernames that are exactly the same but use different capitalization, e.g. Bob11 vs. bob11. You may need to do some cleanup before upgrading to deal with existing usernames like this.

To check whether you have any usernames like this that need cleaning up, run the case insensitive duplicate queries from our Useful Queries doc.

Once you identify the usernames that need cleaning up, you should use either Merge User Accounts (if it’s the same person) or Change User Identifier (if they are different people). After the cleanup you can safely upgrade without issue.

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. A new version of file type detection software, Jhove, is added in this release. It requires an update of its configuration file: jhove.conf. Download the new configuration file from the Dataverse release page on GitHub, or from the source tree at https://github.com/IQSS/dataverse/blob/master/conf/jhove/jhove.conf, and place it in <GLASSFISH_DOMAIN_DIRECTORY>/config/. For example: /usr/local/glassfish4/glassfish/domains/domain1/config/jhove.conf.

Important: If your Glassfish installation directory is different from /usr/local/glassfish4, make sure to edit the header of the config file, to reflect the correct location.

  1. Deploy this version.
  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.15.war
  1. Restart glassfish

  2. Replace Solr schema.xml, optionally replace solrconfig.xml to allow sorting and filtering on the file page
    -stop solr instance (service solr stop, depending on solr installation/OS, see http://guides.dataverse.org/en/4.15/installation/prerequisites.html#solr-init-script)
    -replace schema.xml , optionallyreplace solrconfig.xml

cp /tmp/dvinstall/schema.xml /usr/local/solr/solr-7.3.0/server/solr/collection1/conf
cp /tmp/dvinstall/solrconfig.xml /usr/local/solr/solr-7.3.0/server/solr/collection1/conf
-start solr instance (service solr start, depending on solr/OS)
  1. Kick off in place reindex
    http://guides.dataverse.org/en/4.15/admin/solr-search-index.html#reindex-in-place
curl -X DELETE http://localhost:8080/api/admin/index/timestamps
curl http://localhost:8080/api/admin/index/continue
  1. Redetect file types using the new Redetect File Types API:

https://github.com/IQSS/dataverse/blob/develop/doc/sphinx-guides/source/api/native-api.rst#id31

Assets 5

@kcondon kcondon released this May 10, 2019 · 259 commits to master since this release

This release adds OpenAIRE-compliant exports, an option on the Dashboard for superusers to move datasets, and expanded analytics options.

For the complete list of issues, see the 4.14 milestone in Github.

For help with upgrading, installing, or general questions please post to the Dataverse Google Group or email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Deploy this version.
  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.14.war
  1. Restart glassfish
Assets 4

@djbrooke djbrooke released this Apr 22, 2019 · 460 commits to master since this release

This release adds a file tree view at the Dataset level and adds a new API for file level metadata edits. It also reverts an API change from the previous release.

For the complete list of issues, see the 4.13 milestone in Github.

For help with upgrading, installing, or general questions please post to the Dataverse Google Group or email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Upgrade your version of PostgreSQL to at least 9.3. Version 9.6 is recommended.

  2. NOTE for Dataverse Installations running OpenStack Swift:

Now all Swift properties have been migrated to domain.xml, no longer needing to maintain a separate swift.properties file, and offering better governability and performance. Furthermore, now the Swift credential's password is stored using create-password-alias, which encrypts the password so that it does not appear in plain text on domain.xml.

In order to migrate to these new configuration settings, please visit http://guides.dataverse.org/en/4.13/installation/config.html#swift-storage

  1. Deploy this version.
  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.13.war
  1. Restart glassfish
Assets 4

@djbrooke djbrooke released this Apr 1, 2019 · 641 commits to master since this release

Note: Before using the User Management APIs on Shibboleth or OAuth users, we recommend upgrading to the 4.14 release or later, which will contain the fix for issue #5811. If you have renamed users and are experiencing issues, please contact support@dataverse.org.

This release adds User Management APIs, the ability to edit the hierarchy of files in a dataset, backend support for Make Data Count, and guidance on best practices for making datasets appear in search engines.

For the complete list of issues, see the 4.12 milestone in Github.

For help with upgrading, installing, or general questions please post to the Dataverse Google Group or email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Upgrade your version of PostgreSQL to at least 9.3. Version 9.6 is recommended.

  2. Deploy this version.

  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.12.war
  1. Restart glassfish

  2. Replace Solr schema.xml
    -stop solr instance (service solr stop, depending on solr installation/OS, see http://guides.dataverse.org/en/4.12/installation/prerequisites.html#solr-init-script)
    -replace schema.xml

cp /tmp/dvinstall/schema.xml /usr/local/solr/solr-7.3.0/server/solr/collection1/conf
-start solr instance (service solr start, depending on solr/OS)
  1. Kick off in place reindex
    http://guides.dataverse.org/en/4.12/admin/solr-search-index.html#reindex-in-place
curl -X DELETE http://localhost:8080/api/admin/index/timestamps
curl http://localhost:8080/api/admin/index/continue
  1. If you are using Web Analytics, please review your "analytics-code.html" fragment (described in Installation Guide > Configuration > Web Analytics Code), and see if any of the script lines contain an empty "async" attribute. In the documentation provided by Google, its value is left blank
    (as in <script async src="...">). It must be set to "async" explicitly (for example, <script async="async" src="...">), otherwise it may cause problems with some pages/browsers.

A note on folder names:

In this release users are given an option to edit the folder names in the file metadata. Strict validation rules for the folder names are also introduced. Only the following characters are allowed: the alphanumerics, '_', '-', '.' and ' ' (white space). Some datafiles in your Dataverse may already have folder names saved in the database (if they were extracted from uploaded zip archives with folder structure). The following sanitizing rules will be applied to all the existing folder names in the database: any invalid characters will be replaced by the '.' character. Any sequences of dots will be further replaced with a single dot. For example, the folder name data&info/code=@137 will be converted to data.info/code.137. This update will be automatically applied to the database the first time this release is deployed.

A note on upgrading from older versions:

As of this release, Flyway database migration tool (https://flywaydb.org) has been incorporated into Dataverse. This means that going forward, installers no longer need to apply database update scripts manually. Instead your database is updated automatically the first time the new version of the application is deployed. (Note that there is no database update script to run in the upgrade checklist for this release!)

However, if you are upgrading from a version of Dataverse older than 4.11 it is still the responsibility of the installer to first upgrade the database to v4.11; since Flyway cannot handle versions prior to 4.12.

This can be achieved by manually deploying each intermediate version, between your current version and 4.11, and manually applying the database update sql scripts for the releases that have them.

As an alternative, we offer an EXPERIMENTAL database upgrade method allowing users to skip over a number of releases. E.g., it should be possible now to upgrade a Dataverse database from v4.8.6 directly to v4.12, without having to deploy the war files for the 5 releases between these 2 versions and manually running the corresponding database upgrade scripts.

The upgrade script, dbupgrade.sh is provided in the scripts/database directory of the Dataverse source tree. See the file README_upgrade_across_versions.txt for the instructions.

Assets 5

@djbrooke djbrooke released this Feb 20, 2019 · 1168 commits to master since this release

This release adds OAI-ORE and BagIT for archival submissions (development led by the Qualitative Data Repository), additional custom homepage options, custom analytics, and file hierarchy support for zip files.

For the complete list of issues, see the 4.11 milestone in Github.

For help with upgrading, installing, or general questions please post to the Dataverse Google Group or email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Install and configure Solr v7.3.1
    See http://guides.dataverse.org/en/4.11/installation/prerequisites.html#installing-solr

  2. Deploy this version.

  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.11.war
  1. Run db update script
psql -U <db user> -d <db name> -f upgrade_v4.10.1_to_v4.11.sql
  1. Restart glassfish

  2. Index all metadata

curl http://localhost:8080/api/admin/index
  1. If you have Google Analytics or Piwik analytics configured, remove the deprecated :GoogleAnalyticsCode, :PiwikAnalyticsId, :PiwikAnalyticsHost, :PiwikAnalyticsTrackerFileName settings, and use :WebAnalyticsCode. The new setting works like the custom HTML files for branding, which allows for more control of your analytics, making it easier to customize what you prefer to track. See Web Analytics Code in the Guides for more details.

A note on upgrading from older versions:

If you are upgrading from v4.x, you must upgrade to each intermediate version before installing this version with the exception of db updates as noted.

We now offer an EXPERIMENTAL database upgrade method allowing users to skip over a number of releases. E.g., it should be possible now to upgrade a Dataverse database from v4.8.6 directly to the current release, without having to deploy the war files for the 5 releases between these 2 versions and manually running the corresponding database upgrade scripts.

The upgrade script, dbupgrade.sh is provided in the scripts/database directory of the Dataverse source tree. See the file README_upgrade_across_versions.txt for the instructions.

Assets 5

@kcondon kcondon released this Jan 7, 2019 · 1508 commits to master since this release

This is a patch release that fixes an issue where datasets sometimes had trouble publishing when file doi minting was enabled and DataCite was configured as PID provider. This issue was a latent bug that existed in earlier versions but was revealed by a recent change in DataCite API behavior.

Thanks to Jim Myers (@qqmyers) for troubleshooting this and providing a solution!

See #5427 for more details.

Upgrade instructions from v4.10:

  1. Undeploy current war file
  2. Stop Glassfish
  3. Remove /usr/local/glassfish4/glassfish/domains/domain/generated directory
  4. Start Glassfish
  5. Deploy new war file
Assets 4

@djbrooke djbrooke released this Dec 20, 2018 · 1523 commits to master since this release

This release includes support for large data transfers and storage, a simplified upgrade process, and internationalization.

All installations will be able to use Dataverse's integration with the Data Capture Module, an optional component for deposition of large datasets (both large number of files and large file size). Specific support for large datasets includes client-side checksums, non-http uploads (currently supporting rsync via ssh), and preservation of in-place directory hierarchy. This expands Dataverse to other disciplines and allows project installations to handle large-scale data.

Administrators will be able to configure a Dataverse installation to allow datasets to be mirrored to multiple locations, allowing faster data transfers from closer locations, access to more efficient or cost effective computation, and other benefits.

Internationalization features provided by Scholar's Portal are now available in Dataverse.

Dataverse Installation Administrators will be able to upgrade from one version to another without the need to step through each incremental version.

Configuration options for custom S3 URLs of Amazon S3 compatible storage available.
See configuration documentation for details.

For the complete list of issues, see the 4.10 milestone in Github.

For help with upgrading, installing, or general questions please email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Deploy this version.
  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.10.war
  1. Run db update script
psql -U <db user> -d <db name> -f upgrade_v4.9.4_to_v4.10.sql
  1. Restart glassfish
  2. Update citation metadata block
curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @citation.tsv -H "Content-type: text/tab-separated-values"
  1. Restart glassfish
  2. Replace Solr schema.xml, optionally replace solrconfig.xml to change search results boost logic
    -stop solr instance (service solr stop, depending on solr installation/OS, see http://guides.dataverse.org/en/4.10/installation/prerequisites.html#solr-init-script)
    -replace schema.xml , optionallyreplace solrconfig.xml
cp /tmp/dvinstall/schema.xml /usr/local/solr/solr-7.3.0/server/solr/collection1/conf
cp /tmp/dvinstall/solrconfig.xml /usr/local/solr/solr-7.3.0/server/solr/collection1/conf
-start solr instance (service solr start, depending on solr/OS)
  1. Kick off in place reindex
    http://guides.dataverse.org/en/4.9.3/admin/solr-search-index.html#reindex-in-place
curl -X DELETE http://localhost:8080/api/admin/index/timestamps
curl http://localhost:8080/api/admin/index/continue
  1. Retroactively store original file size

Starting with release 4.10 the size of the saved original file (for an
ingested tabular datafile) is stored in the database. We provided the
following API that retrieve and permanently store the sizes for any
already existing saved originals:
/api/admin/datafiles/integrity/fixmissingoriginalsizes (see the
documentation note in the Native API guide, under "Datafile
Integrity").

While it's not strictly necessary to have these sizes in the database,
having them makes certain operations more efficient (primary example
is a user downloading the saved originals for multiple files/an entire
dataset etc.) Also, if present in the database, the size will be added
to the file information displayed in the output of the /api/datasets;
which can be useful for some users.

  1. Run ReExportall to generate JSON-LD exports in the new format added in 4.10: http://guides.dataverse.org/en/4.10/admin/metadataexport.html?highlight=export#batch-exports-through-the-api

A note on upgrading from older versions:

If you are upgrading from v4.x, you must upgrade to each intermediate version before installing this version with the exception of db updates as noted.

We now offer an EXPERIMENTAL database upgrade method allowing users to skip over a number of releases. E.g., it should be possible now to upgrade a Dataverse database from v4.8.6 directly to v4.10, without having to deploy the war files for the 5 releases between these 2 versions and manually running the corresponding database upgrade scripts.

The upgrade script, dbupgrade.sh is provided in the scripts/database directory of the Dataverse source tree. See the file README_upgrade_across_versions.txt for the instructions.

Assets 8

@djbrooke djbrooke released this Oct 3, 2018 · 2553 commits to master since this release

This release addresses a bug introduced in 4.9.3 which prevented users from logging in with an email address (#5129).

For help with upgrading, installing, or general questions please email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Deploy this version.
  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.9.4.war
  1. Restart glassfish

If you are upgrading from v4.x, you must upgrade to each intermediate version before installing this version.

Assets 4

@djbrooke djbrooke released this Sep 28, 2018 · 2572 commits to master since this release

Note: We recommend upgrading to 4.9.4, which includes a fix for a bug that prevented users from logging in using an email address. Learn more in the 4.9.4 Release Notes.

This release is focused on expanded options for handling datasets and files in Dataverse. The dataset linking feature is now available to all users, not just superusers. It is now accessible through the UI in addition to the API. Users now have the option of downloading all files in a dataset in their original file format via the Download All button, in addition to the already available "archival format" option. Installations can now configure whether or not PIDs will be minted for files. We have also made the application more stable by addressing leaks.

For the complete list of issues, see the 4.9.3 milestone in Github.

For help with upgrading, installing, or general questions please email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Deploy this version.
  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.9.3.war
  1. Run db update script
psql -U <db user> -d <db name> -f upgrade_v4.9.2_to_v4.9.3.sql
  1. Restart glassfish
  2. Replace Solr schema.xml
    -stop solr instance (service solr stop, depending on solr installation/OS, see http://guides.dataverse.org/en/4.9.3/installation/prerequisites.html#solr-init-script)
    -replace schema.xml
cp /tmp/dvinstall/schema.xml /usr/local/solr/solr-7.3.0/server/solr/collection1/conf
-start solr instance (service solr start, depending on solr/OS)
  1. Kick off in place reindex
    http://guides.dataverse.org/en/4.9.3/admin/solr-search-index.html#reindex-in-place
curl -X DELETE http://localhost:8080/api/admin/index/timestamps
curl http://localhost:8080/api/admin/index/continue
  1. If you are running TwoRavens as part of your Dataverse installation, please find the following line in your TwoRavens app_ddi.js file:
dataurl = dataurl+"?key="+apikey+"&gbrecs=true";

(or, if you are using an older version, it may look like this:)

dataurl = dataurl+"?key="+apikey;

and change it as follows:

dataurl = dataurl+"?key="+apikey+"%26gbrecs=true";

(this ensures that the download counts are properly incremented for TwoRavens explore sessions, and eliminates the confusing "Warning: The request is not valid json. Check for special characters" messages that some users were seeing after the 4.8.6 upgrade)

If you are upgrading from v4.x, you must upgrade to each intermediate version before installing this version.

Assets 6

@kcondon kcondon released this Aug 8, 2018 · 3040 commits to master since this release

This release is focused on ingest upgrades, new import APIs, and infrastructure upgrades.
Stata 14, Stata 15, and .tsv files will now be ingested by Dataverse. New APIs will allow datasets with existing DOIs to be imported into Dataverse. Bootstrap and Primefaces, which power the Dataverse front end, have been updated.

For the complete list of issues, see the 4.9.2 milestone in Github.

For help with upgrading, installing, or general questions please email support@dataverse.org.

Installation:

If this is a new installation, please see our Installation Guide.

Upgrade:

  1. Undeploy the previous version.
  • <glassfish install path>/glassfish4/bin/asadmin list-applications
  • <glassfish install path>/glassfish4/bin/asadmin undeploy dataverse
  1. Stop glassfish and remove the generated directory, start
  • service glassfish stop
  • remove the generated directory: rm -rf <glassfish install path>glassfish4/glassfish/domains/domain1/generated
  • service glassfish start
  1. Deploy this version.
  • <glassfish install path>/glassfish4/bin/asadmin deploy <path>dataverse-4.9.2.war
  1. Run db update script
psql -U <db user> -d <db name> -f upgrade_v4.9.1_to_v4.9.2.sql
  1. Restart glassfish

If your Dataverse is configured to use R, you need to install one extra R library (haven); Dataverse is now using it to export tabular datafiles as RData. Install the package with the following R command (for example):

install.packages("haven", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )

If you are upgrading from v4.x, you must upgrade to each intermediate version before installing this version.

Assets 5
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