Merge remote-tracking branch 'remotes/origin/develop' into 3980-valid…

…ation-messages-java
IQSS · Jul 5, 2018 · c121806 · c121806
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diff --git a/conf/docker-aio/1prep.sh b/conf/docker-aio/1prep.sh
@@ -22,5 +22,6 @@ mvn package
 cd scripts/installer
 make clean
 make
+mkdir -p ../../conf/docker-aio/dv/install
 cp dvinstall.zip ../../conf/docker-aio/dv/install/
 
diff --git a/conf/docker-aio/testscripts/install b/conf/docker-aio/testscripts/install
@@ -15,7 +15,7 @@ export SMTP_SERVER=localhost
 export MEM_HEAP_SIZE=2048
 export GLASSFISH_DOMAIN=domain1
 cd scripts/installer
-cp pgdriver/postgresql-8.4-703.jdbc4.jar $GLASSFISH_ROOT/glassfish/lib
+cp pgdriver/postgresql-42.2.2.jar $GLASSFISH_ROOT/glassfish/lib
 #cp ../../conf/jhove/jhove.conf $GLASSFISH_ROOT/glassfish/domains/$GLASSFISH_DOMAIN/config/jhove.conf
 cp /opt/dv/testdata/jhove.conf $GLASSFISH_ROOT/glassfish/domains/$GLASSFISH_DOMAIN/config/jhove.conf
 cp /opt/dv/testdata/jhoveConfig.xsd $GLASSFISH_ROOT/glassfish/domains/$GLASSFISH_DOMAIN/config/jhoveConfig.xsd

diff --git a/doc/sphinx-guides/source/_static/api/dataset-add-metadata-after-pub.json b/doc/sphinx-guides/source/_static/api/dataset-add-metadata-after-pub.json
@@ -0,0 +1,63 @@
+{
+    "fields": [
+        {
+            "typeName": "subject",
+            "value": ["Astronomy and Astrophysics"]
+        },
+        {
+            "typeName": "author",
+            "value": [
+                {
+                    "authorName": {
+                        "typeName": "authorName",
+                        "value": "Poe, Edgar Allen"
+                    }
+                    ,
+                    "authorAffiliation": {
+                        "typeName": "authorAffiliation",
+                        "value": "Baltimore Poets"
+                    }
+                },
+                {
+                    "authorName": {
+                        "typeName": "authorName",
+                        "value": "Mulligan, Hercules"
+                    }
+                    ,
+                    "authorAffiliation": {
+                        "typeName": "authorAffiliation",
+                        "value": "Sons of Liberty"
+                    }
+                }		
+            ]
+        },
+        {
+            "typeName": "producer",
+            "value": [
+                {
+                    "producerName": {
+                        "typeName": "producerName",
+                        "value": "Allen, Irwin"
+                    }
+                    ,
+                    "producerAffiliation": {
+                        "typeName": "producerAffiliation",
+                        "value": "MGM"
+                    }
+                },
+                {
+                    "producerName": {
+                        "typeName": "producerName",
+                        "value": "Spielberg, Stephen"
+                    }
+                    ,
+                    "producerAffiliation": {
+                        "typeName": "producerAffiliation",
+                        "value": "ILM"
+                    }
+                }		
+            ]
+        }
+    ]
+}
+
diff --git a/doc/sphinx-guides/source/_static/api/dataset-add-metadata.json b/doc/sphinx-guides/source/_static/api/dataset-add-metadata.json
@@ -0,0 +1,32 @@
+
+{
+"fields": [
+        {
+        "typeName": "subject",
+                "value": 
+                    ["Astronomy and Astrophysics"]
+
+        },
+        {
+          "typeName": "author",
+          "value": [
+            {
+              "authorName": {
+                "typeName": "authorName",
+                "value": "Spruce, Sabrina"
+              }, 
+               "authorAffiliation": {
+                "typeName": "authorAffiliation",
+                "value": "Cambridge, MA"
+              }
+            }
+          ]
+        },
+                {
+        "typeName": "kindOfData",
+                "value": 
+                    ["Bar Chart"]
+
+        }
+]
+}
diff --git a/doc/sphinx-guides/source/_static/api/dataset-add-single-field-metadata.json b/doc/sphinx-guides/source/_static/api/dataset-add-single-field-metadata.json
@@ -0,0 +1,6 @@
+        {
+        "typeName": "subject",
+                "value": [
+                    "Social Sciences"
+                ]
+        }
diff --git a/doc/sphinx-guides/source/_static/api/dataset-add-subject-metadata.json b/doc/sphinx-guides/source/_static/api/dataset-add-subject-metadata.json
@@ -0,0 +1,10 @@
+        {
+        "typeName": "subject",
+                "value": 
+                    ["Astronomy and Astrophysics", "Agricultural Sciences",
+"Arts and Humanities", "Physics"]
+
+        }
+
+
+
diff --git a/doc/sphinx-guides/source/_static/api/dataset-delete-author-metadata.json b/doc/sphinx-guides/source/_static/api/dataset-delete-author-metadata.json
@@ -0,0 +1,31 @@
+{
+    "fields": [
+        {
+            "typeName": "author",
+            "value": [
+                {
+                    "authorName": {
+                        "typeName": "authorName",
+                        "value": "Poe, Edgar Allen"
+                    }
+                    ,
+                    "authorAffiliation": {
+                        "typeName": "authorAffiliation",
+                        "value": "Baltimore Poets"
+                    }
+                },
+                {
+                    "authorName": {
+                        "typeName": "authorName",
+                        "value": "Mulligan, Hercules"
+                    }
+                    ,
+                    "authorAffiliation": {
+                        "typeName": "authorAffiliation",
+                        "value": "Sons of Liberty"
+                    }
+                }		
+            ]
+        }
+    ]
+}
diff --git a/doc/sphinx-guides/source/_static/api/dataset-delete-author-no-match.json b/doc/sphinx-guides/source/_static/api/dataset-delete-author-no-match.json
@@ -0,0 +1,23 @@
+
+        {
+          "typeName": "author",
+          "value": [
+            {
+              "authorName": {
+                "typeName": "authorName",
+                "value": "Spruce, Sabrina"
+              }
+            },{
+                    "authorName": {
+                        "typeName": "authorName",
+                        "value": "Poe, Edgar Allen"
+                    }
+                    ,
+                    "authorAffiliation": {
+                        "typeName": "authorAffiliation",
+                        "value": "Baltimore Poets"
+                    }
+                }
+          ]
+        }               
+
diff --git a/doc/sphinx-guides/source/_static/api/dataset-delete-subject-metadata.json b/doc/sphinx-guides/source/_static/api/dataset-delete-subject-metadata.json
@@ -0,0 +1,5 @@
+        {
+        "typeName": "subject",
+                "value": 
+                    ["Astronomy and Astrophysics", "Arts and Humanities" ]
+        }
diff --git a/doc/sphinx-guides/source/_static/api/dataset-edit-metadata-sample.json b/doc/sphinx-guides/source/_static/api/dataset-edit-metadata-sample.json
@@ -0,0 +1,74 @@
+{
+    "fields": [
+        {
+            "typeName": "subject",
+            "value": ["Astronomy and Astrophysics"]
+        },
+
+        {
+            "typeName": "subtitle",
+            "value": "More Birds and Trees"
+        },
+
+        {
+            "typeName": "title",
+            "value": "Post Publish Title Change"               
+        },
+        {
+            "typeName": "author",
+            "value": [
+                {
+                    "authorName": {
+                        "typeName": "authorName",
+                        "value": "Poe, Edgar Allen"
+                    }
+                    ,
+                    "authorAffiliation": {
+                        "typeName": "authorAffiliation",
+                        "value": "Baltimore Poets"
+                    }
+                },
+                {
+                    "authorName": {
+                        "typeName": "authorName",
+                        "value": "Mulligan, Hercules"
+                    }
+                    ,
+                    "authorAffiliation": {
+                        "typeName": "authorAffiliation",
+                        "value": "Sons of Liberty"
+                    }
+                }		
+            ]
+        },
+        {
+            "typeName": "producer",
+            "value": [
+                {
+                    "producerName": {
+                        "typeName": "producerName",
+                        "value": "Allen, Irwin"
+                    }
+                    ,
+                    "producerAffiliation": {
+                        "typeName": "producerAffiliation",
+                        "value": "MGM"
+                    }
+                },
+                {
+                    "producerName": {
+                        "typeName": "producerName",
+                        "value": "Lucas, George"
+                    }
+                    ,
+                    "producerAffiliation": {
+                        "typeName": "producerAffiliation",
+                        "value": "ILM"
+                    }
+                }		
+            ]
+        }
+    ]
+}
+
+
diff --git a/doc/sphinx-guides/source/_static/api/dataset-edit-metadata-subtitle.json b/doc/sphinx-guides/source/_static/api/dataset-edit-metadata-subtitle.json
@@ -0,0 +1,8 @@
+{
+   "fields": [
+       {
+           "typeName": "subtitle",
+           "value": ["Even More Birds and Trees - Redux"]
+       }
+           ]  
+}
diff --git a/doc/sphinx-guides/source/_static/api/dataset-simple-update-metadata.json b/doc/sphinx-guides/source/_static/api/dataset-simple-update-metadata.json
@@ -0,0 +1,6 @@
+        {
+        "typeName": "subject",
+                "value": [
+                    "Social Sciences", "Mathematical Sciences"
+                ]
+        }
diff --git a/doc/sphinx-guides/source/_static/api/dataset-update-with-blank-metadata.json b/doc/sphinx-guides/source/_static/api/dataset-update-with-blank-metadata.json
@@ -0,0 +1,4 @@
+        {
+        "typeName": "title",
+                "value": ""
+        }
diff --git a/doc/sphinx-guides/source/admin/index.rst b/doc/sphinx-guides/source/admin/index.rst
@@ -18,6 +18,7 @@ These "superuser" tasks are managed via the new page called the Dashboard. A use
    harvestserver
    metadataexport
    timers
+   integrations
    geoconnect-worldmap
    user-administration
    dataverses-datasets

diff --git a/doc/sphinx-guides/source/api/native-api.rst b/doc/sphinx-guides/source/api/native-api.rst
@@ -247,7 +247,7 @@ Update Metadata For a Dataset
 
 Updates the metadata for a dataset. If a draft of the dataset already exists, the metadata of that draft is overwritten; otherwise, a new draft is created with this metadata.
 
-You cannot currently target a specific field such as the title of a dataset and only update that one field. Instead, you must download a JSON representation of the dataset, edit the JSON you download, and then send the updated JSON to the Dataverse server.
+You must download a JSON representation of the dataset, edit the JSON you download, and then send the updated JSON to the Dataverse server.
 
 For example, after making your edits, your JSON file might look like :download:`dataset-update-metadata.json <../_static/api/dataset-update-metadata.json>` which you would send to Dataverse like this::
 
@@ -263,6 +263,29 @@ Now that the resulting JSON file only contains the ``metadataBlocks`` key, you c
 
 Now that you've made edits to the metadata in your JSON file, you can send it to Dataverse as described above.
 
+Edit Dataset Metadata
+~~~~~~~~~~~~~~~~~~~~~
+
+Alternatively to replacing an entire dataset version with its JSON representation you may add data to dataset fields that are blank or accept multiple values with the following ::
+
+    curl -H "X-Dataverse-key: $API_TOKEN" -X PUT $SERVER_URL/api/datasets/:persistentId/editMetadata/?persistentId=$PID --upload-file dataset-add-metadata.json    
+
+You may also replace existing metadata in dataset fields with the following (adding the parameter replace=true)   ::
+
+    curl -H "X-Dataverse-key: $API_TOKEN" -X PUT $SERVER_URL/api/datasets/:persistentId/editMetadata?persistentId=$PID&replace=true --upload-file dataset-update-metadata.json
+    
+For these edits your JSON file need only include those dataset fields which you would like to edit. A sample JSON file may be downloaded here: :download:`dataset-edit-metadata-sample.json <../_static/api/dataset-edit-metadata-sample.json>` 
+
+Delete Dataset Metadata
+~~~~~~~~~~~~~~~~~~~~~
+
+You may delete some of the metadata of a dataset version by supplying a file with a JSON representation of dataset fields that you would like to delete with the following ::
+
+    curl -H "X-Dataverse-key: $API_TOKEN" -X PUT $SERVER_URL/api/datasets/:persistentId/deleteMetadata/?persistentId=$PID --upload-file dataset-delete-author-metadata.json    
+    
+For these deletes your JSON file must include an exact match of those dataset fields which you would like to delete. A sample JSON file may be downloaded here: :download:`dataset-delete-author-metadata.json <../_static/api/dataset-delete-author-metadata.json>` 
+
+
 Publish a Dataset
 ~~~~~~~~~~~~~~~~~
 

diff --git a/doc/sphinx-guides/source/conf.py b/doc/sphinx-guides/source/conf.py
@@ -64,9 +64,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '4.9'
+version = '4.9.1'
 # The full version, including alpha/beta/rc tags.
-release = '4.9'
+release = '4.9.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/sphinx-guides/source/developers/testing.rst b/doc/sphinx-guides/source/developers/testing.rst
@@ -87,6 +87,13 @@ Unfortunately, the term "integration tests" can mean different things to differe
 - Integration tests operate on an installation of Dataverse that is running and able to talk to both PostgreSQL and Solr.
 - Integration tests are written using REST Assured.
 
+Running the full API test suite using Docker
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To run the full suite of integration tests on your laptop, we recommend using the "all in one" Docker configuration described in ``conf/docker-aio/readme.txt`` in the root of the repo.
+
+Alternatively, you can run tests against Glassfish running on your laptop by following the "getting set up" steps below.
+
 Getting Set Up to Run REST Assured Tests
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -168,7 +175,7 @@ Once installed, you may run commands with ``mvn [options] [<goal(s)>] [<phase(s)
 
   ``mvn test -Dtest=FileMetadataIT -Ddataverse.test.baseurl='http://localhost:8080'``
 
-To run the full suite of integration tests on your laptop, we recommend using the "all in one" Docker configuration described in ``conf/docker-aio/readme.txt``.
+To see the full list of tests used by the Docker option mentioned above, see :download:`run-test-suite.sh <../../../../conf/docker-aio/run-test-suite.sh>`.
 
 Load/Performance Testing
 ------------------------

diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
@@ -338,6 +338,8 @@ The name of your root dataverse is the brand of your installation of Dataverse a
 
 Downloadable sample HTML and CSS files are provided below which you can edit as you see fit. It's up to you to create a directory in which to store these files, such as ``/var/www/dataverse`` in the examples below.
 
+You may also want to look at samples at https://github.com/shlake/LibraDataHomepage from community member Sherry Lake as well as her poster from the Dataverse Community Meeting 2018 called "Branding Your Local Dataverse": https://github.com/IQSS/dataverse/files/2128735/UVaHomePage.pdf
+
 A simpler option to brand and customize your installation is to utilize the dataverse theme, which each dataverse has, that allows you to change colors, add a logo, tagline or website link to the dataverse header section of the page. Those options are outlined in the :doc:`/user/dataverse-management` section of the User Guide.
 
 Custom Homepage