Merge pull request #7 from IQSS/develop

Update develop from IQSS

doc/sphinx-guides/source/admin/dataverses-datasets.rst

@@ -72,3 +72,8 @@ Send Dataset metadata to PID provider
 Forces update to metadata provided to the PID provider of a published dataset. Only accessible to superusers. ::
 
     curl -H "X-Dataverse-key: $API_TOKEN" -X POST http://$SERVER/api/datasets/$dataset-id/modifyRegistrationMetadata
+
+Make Metadata Updates Without Changing Dataset Version
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As a superuser, click "Update Current Version" when publishing. (This option is only available when a 'Minor' update would be allowed.)

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

@@ -87,7 +87,7 @@ original        "Saved Original", the proprietary (SPSS, Stata, R, etc.) file fr
 
 
 "All Formats" bundled download for Tabular Files. 
------------------------------------------------
+-------------------------------------------------
 
 ``/api/access/datafile/bundle/$id``
 

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

@@ -24,7 +24,7 @@ Example: ``curl https://demo.dataverse.org/api/info/metrics/downloads``
 To-Month
 --------
 
-Returns a count of various objects in dataverse up to a specified month ``$YYYY-DD`` in YYYY-MM format (i.e. ``2018-01``)::
+Returns a count of various objects in dataverse up to a specified month ``$YYYY-DD`` in YYYY-MM format (e.g. ``2018-01``)::
 
     GET https://$SERVER/api/info/metrics/$type/toMonth/$YYYY-DD
 
@@ -36,7 +36,7 @@ Example: ``curl https://demo.dataverse.org/api/info/metrics/dataverses/toMonth/2
 Past Days
 ---------
 
-Returns a count of various objects in dataverse for the past ``$days`` (i.e. ``30``):: 
+Returns a count of various objects in dataverse for the past ``$days`` (e.g. ``30``):: 
 
     GET https://$SERVER/api/info/metrics/$type/pastDays/$days
 
@@ -45,8 +45,8 @@ Returns a count of various objects in dataverse for the past ``$days`` (i.e. ``3
 Example: ``curl https://demo.dataverse.org/api/info/metrics/datasets/pastDays/30``
 
 
-Dataverse Specific Commands
----------------------------
+Dataverse Specific Metrics
+--------------------------
 
 By Subject
 ~~~~~~~~~~~~~~~
@@ -64,18 +64,41 @@ Returns the number of dataverses by each category::
     GET https://$SERVER/api/info/metrics/dataverses/byCategory
 
 
-Dataset Specific Commands
--------------------------
+Dataset Specific Metrics
+------------------------
 
 By Subject
-~~~~~~~~~~~~~~~
+~~~~~~~~~~
 
 Returns the number of datasets by each subject::
 
     GET https://$SERVER/api/info/metrics/datasets/bySubject
 
+
+By Subject, and to Month
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Returns the number of datasets by each subject, and up to a specified month ``$YYYY-DD`` in YYYY-MM format (e.g. ``2018-01``)::
+
+    GET https://$SERVER/api/info/metrics/datasets/bySubject/toMonth/$YYYY-DD
+
+Example: ``curl https://demo.dataverse.org/api/info/metrics/datasets/bySubject/toMonth/2018-01``
+
 .. |CORS| raw:: html
 
       <span class="label label-success pull-right">
         CORS
-      </span>
+      </span>
+
+
+Metric Query Parameters
+-----------------------
+
+To further tailor your metric, query parameters can be provided.
+
+dataLocation
+~~~~~~~~~~~~
+
+Specifies whether the metric should query ``local`` data, ``remote`` data (e.g. harvested), or ``all`` data when getting results. Only works for dataset metrics.
+
+Example: ``curl https://demo.dataverse.org/api/info/metrics/datasets/?dataLocation=remote``

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

@@ -372,7 +372,7 @@ For these deletes your JSON file must include an exact match of those dataset fi
 Publish a Dataset
 ~~~~~~~~~~~~~~~~~
 
-Publishes the dataset whose id is passed. If this is the first version of the dataset, its version number will be set to ``1.0``. Otherwise, the new dataset version number is determined by the most recent version number and the ``type`` parameter. Passing ``type=minor`` increases the minor version number (2.3 is updated to 2.4). Passing ``type=major`` increases the major version number (2.3 is updated to 3.0). ::
+Publishes the dataset whose id is passed. If this is the first version of the dataset, its version number will be set to ``1.0``. Otherwise, the new dataset version number is determined by the most recent version number and the ``type`` parameter. Passing ``type=minor`` increases the minor version number (2.3 is updated to 2.4). Passing ``type=major`` increases the major version number (2.3 is updated to 3.0). Superusers can pass ``type=updatecurrent`` to update metadata without changing the version number::
 
     POST http://$SERVER/api/datasets/$id/actions/:publish?type=$type&key=$apiKey
 

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

@@ -85,7 +85,11 @@ https://demo.dataverse.org/api/search?q=trees
                     "file_content_type":"image/png",
                     "size_in_bytes":8361,
                     "md5":"0386269a5acb2c57b4eade587ff4db64",
-                    "dataset_citation":"Spruce, Sabrina, 2016, \"Spruce Goose\", http://dx.doi.org/10.5072/FK2/NFSEHG, Root Dataverse, V1"
+                    "file_persistent_id": "doi:10.5072/FK2/XTT5BV/PCCHV7",
+                    "dataset_name": "Dataset One",
+                    "dataset_id": "32",
+                    "dataset_persistent_id": "doi:10.5072/FK2/XTT5BV",
+                    "dataset_citation":"Spruce, Sabrina, 2016, \"Spruce Goose\", http://dx.doi.org/10.5072/FK2/XTT5BV, Root Dataverse, V1"
                 },
                 {
                     "name":"Birds",

doc/sphinx-guides/source/conf.py

@@ -65,9 +65,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '4.10.1'
+version = '4.11'
 # The full version, including alpha/beta/rc tags.
-release = '4.10.1'
+release = '4.11'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

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

@@ -8,7 +8,7 @@ Dataverse has a flexible workflow mechanism that can be used to trigger actions
 
 
 Introduction
----------
+------------
 
 Dataverse can perform two sequences of actions when datasets are published: one prior to publishing (marked by a ``PrePublishDataset`` trigger), and one after the publication has succeeded (``PostPublishDataset``). The pre-publish workflow is useful for having an external system prepare a dataset for being publicly accessed (a possibly lengthy activity that requires moving files around, uploading videos to a streaming server, etc.), or to start an approval process. A post-publish workflow might be used for sending notifications about the newly published dataset.
 
@@ -104,7 +104,7 @@ Available variables are:
 * ``releaseStatus``
 
 archiver
-+++++++
+++++++++
 
 A step that sends an archival copy of a Dataset Version to a configured archiver, e.g. the DuraCloud interface of Chronopolis. See the `DuraCloud/Chronopolis Integration documentation <http://guides.dataverse.org/en/latest/admin/integrations.html#id15>`_ for further detail.
 

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

@@ -606,7 +606,7 @@ In the Chronopolis case, since the transfer from the DuraCloud front-end to arch
 
 **PostPublication Workflow**
 
-To automate the submission of archival copies to an archive as part of publication, one can setup a Dataverse Workflow using the "archiver" workflow step - see the :doc:`developers/workflows` guide.
+To automate the submission of archival copies to an archive as part of publication, one can setup a Dataverse Workflow using the "archiver" workflow step - see the :doc:`/developers/workflows` guide.
 . The archiver step uses the configuration information discussed above including the :ArchiverClassName setting. The workflow step definition should include the set of properties defined in \:ArchiverSettings in the workflow definition.
 
 To active this workflow, one must first install a workflow using the archiver step. A simple workflow that invokes the archiver step configured to submit to DuraCloud as its only action is included in dataverse at /scripts/api/data/workflows/internal-archiver-workflow.json.

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

@@ -223,7 +223,7 @@ Solr will warn about needing to increase the number of file descriptors and max
         solr soft nofile 65000
         solr hard nofile 65000
 
-On operating systems which use systemd such as RHEL or CentOS 7, you may then add a line like LimitNOFILE=65000 to the systemd unit file, or adjust the limits on a running process using the prlimit tool::
+On operating systems which use systemd such as RHEL or CentOS 7, you may then add a line like LimitNOFILE=65000 for the number of open file descriptors and a line with LimitNPROC=65000 for the max processes to the systemd unit file, or adjust the limits on a running process using the prlimit tool::
 
         # sudo prlimit --pid pid --nofile=65000:65000
 

doc/sphinx-guides/source/versions.rst

@@ -6,8 +6,9 @@ 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.
 
-- 4.10.1
+- 4.11
 
+- `4.10.1 </en/4.10/>`__
 - `4.10 </en/4.10/>`__
 - `4.9.4 </en/4.9.4/>`__
 - `4.9.3 </en/4.9.3/>`__

local_lib/net/handle/handle/2006-06-16-generated/handle-2006-06-16-generated.pom → local_lib/net/handle/handle/8.1.1/handle-8.1.1.pom

@@ -4,5 +4,6 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>net.handle</groupId>
   <artifactId>handle</artifactId>
-  <version>2006-06-16-generated</version>
+  <version>8.1.1</version>
+  <description>POM was created from install:install-file</description>
 </project>

pom.xml

@@ -7,7 +7,7 @@
     -->
     <groupId>edu.harvard.iq</groupId>
     <artifactId>dataverse</artifactId>
-    <version>4.10.1</version>
+    <version>4.11</version>
     <packaging>war</packaging>
 
     <name>dataverse</name>
@@ -328,7 +328,7 @@
         <dependency>
             <groupId>net.handle</groupId>
             <artifactId>handle</artifactId>
-            <version>2006-06-16-generated</version>
+            <version>8.1.1</version>
         </dependency>
         <!-- UNF v5 (buggy), (temporarily) added for testing ingest against DVN v3  - L.A. -->
         <dependency>
@@ -558,6 +558,10 @@
                 <groupId>org.slf4j</groupId>
                 <artifactId>log4j-over-slf4j</artifactId>
               </exclusion>
+              <exclusion>
+                <groupId>ch.qos.logback</groupId>
+                <artifactId>logback-classic</artifactId>
+              </exclusion>
             </exclusions>
         </dependency>
         <dependency>
@@ -573,6 +577,10 @@
                 <groupId>com.amazonaws</groupId>
                 <artifactId>aws-java-sdk-sqs</artifactId>
               </exclusion>
+              <exclusion>
+                <groupId>ch.qos.logback</groupId>
+                <artifactId>logback-classic</artifactId>
+              </exclusion>
             </exclusions>
 
         </dependency>