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Resynced current code with origin/develop
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‎.gitignore‎

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@@ -22,3 +22,4 @@ scripts/api/py_api_wrapper/local-data/*
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doc/sphinx-guides/build
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faces-config.NavData
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src/main/java/BuildNumber.properties
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/nbproject/

JAVADOC_GUIDE.md renamed to doc/JAVADOC_GUIDE.md

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

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@@ -162,6 +162,21 @@ Restores the default logic of the field type to be used as the citation date. Sa
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DELETE http://$SERVER/api/datasets/$id/citationdate?key=$apiKey
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List all the role assignments at the given dataset::
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GET http://$SERVER/api/datasets/$id/assignments?key=$apiKey
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Create a Private URL (must be able to manage dataset permissions)::
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POST http://$SERVER/api/datasets/$id/privateUrl?key=$apiKey
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Get a Private URL from a dataset (if available)::
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GET http://$SERVER/api/datasets/$id/privateUrl?key=$apiKey
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Delete a Private URL from a dataset (if it exists)::
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DELETE http://$SERVER/api/datasets/$id/privateUrl?key=$apiKey
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Builtin Users
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~~~~~
@@ -244,6 +259,13 @@ Shibboleth Groups
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Management of Shibboleth groups via API is documented in the :doc:`/installation/shibboleth` section of the Installation Guide.
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Info
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~~~~
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For now, only the value for the ``:DatasetPublishPopupCustomText`` setting from the :doc:`/installation/config` section of the Installation Guide is exposed::
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GET http://$SERVER/api/info/settings/:DatasetPublishPopupCustomText
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Metadata Blocks
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~~~~~~~~~~~~~~~
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‎doc/sphinx-guides/source/api/sword.rst‎

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SWORD_ stands for "Simple Web-service Offering Repository Deposit" and is a "profile" of AtomPub (`RFC 5023`_) which is a RESTful API that allows non-Dataverse software to deposit files and metadata into a Dataverse installation. :ref:`client-libraries` are available in Python, Java, R, Ruby, and PHP.
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Introduced in Dataverse Network (DVN) `3.6 <http://guides.dataverse.org/en/3.6.2/dataverse-api-main.html#data-deposit-api>`_, the SWORD API was formerly known as the "Data Deposit API" and ``data-deposit/v1`` appeared in the URLs. For backwards compatibility these URLs will continue to work (with deprecation warnings). Due to architectural changes and security improvements (especially the introduction of API tokens) in Dataverse 4.0, a few backward incompatible changes were necessarily introduced and for this reason the version has been increased to ``v1.1``. For details, see :ref:`incompatible`.
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Introduced in Dataverse Network (DVN) `3.6 <http://guides.dataverse.org/en/3.6.2/dataverse-api-main.html#data-deposit-api>`_, the SWORD API was formerly known as the "Data Deposit API" and ``data-deposit/v1`` appeared in the URLs. For backwards compatibility these URLs continue to work (with deprecation warnings). Due to architectural changes and security improvements (especially the introduction of API tokens) in Dataverse 4.0, a few backward incompatible changes were necessarily introduced and for this reason the version has been increased to ``v1.1``. For details, see :ref:`incompatible`.
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Dataverse implements most of SWORDv2_, which is specified at http://swordapp.github.io/SWORDv2-Profile/SWORDProfile.html . Please reference the `SWORDv2 specification`_ for expected HTTP status codes (i.e. 201, 204, 404, etc.), headers (i.e. "Location"), etc. For a quick introduction to SWORD, the two minute video at http://cottagelabs.com/news/intro-to-sword-2 is recommended.
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As a profile of AtomPub, XML is used throughout SWORD. As of Dataverse 4.0 datasets can also be created via JSON using the "native" API.
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As a profile of AtomPub, XML is used throughout SWORD. As of Dataverse 4.0 datasets can also be created via JSON using the "native" API. SWORD is limited to the dozen or so fields listed below in the crosswalk, but the native API allows you to populate all metadata fields available in Dataverse.
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.. _SWORD: http://en.wikipedia.org/wiki/SWORD_%28protocol%29
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Backward incompatible changes
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-----------------------------
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For better security, usernames and passwords are no longer accepted. The use of an API token is required.
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For better security than in DVN 3.x, usernames and passwords are no longer accepted. The use of an API token is required.
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In addition, differences in Dataverse 4.0 have lead to a few minor backward incompatible changes in the Dataverse implementation of SWORD, which are listed below. Old ``v1`` URLs should continue to work but the ``Service Document`` will contain a deprecation warning and responses will contain ``v1.1`` URLs. See also :ref:`known-issues`.
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Differences in Dataverse 4 from DVN 3.x lead to a few minor backward incompatible changes in the Dataverse implementation of SWORD, which are listed below. Old ``v1`` URLs should continue to work but the ``Service Document`` will contain a deprecation warning and responses will contain ``v1.1`` URLs. See also :ref:`known-issues`.
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- Newly required fields when creating/editing datasets for compliance with the `Joint Declaration for Data Citation principles <http://thedata.org/blog/joint-declaration-data-citation-principles-and-dataverse>`_.
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New features as of v1.1
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-----------------------
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- Dataverse 4.0 supports API tokens and they must be used rather that a username and password. In the ``curl`` examples below, you will see ``curl -u $API_TOKEN:`` showing that you should send your API token as the username and nothing as the password. For example, ``curl -u 54b143b5-d001-4254-afc0-a1c0f6a5b5a7:``.
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- Dataverse 4 supports API tokens and they must be used rather that a username and password. In the ``curl`` examples below, you will see ``curl -u $API_TOKEN:`` showing that you should send your API token as the username and nothing as the password. For example, ``curl -u 54b143b5-d001-4254-afc0-a1c0f6a5b5a7:``.
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- Dataverses can be published via SWORD
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- SWORD operations no longer require "admin" permission. In order to use any SWORD operation in DVN 3.x, you had to be "admin" on a dataverse (the container for your dataset) and similar rules were applied in Dataverse 4.4 and earlier (the ``EditDataverse`` permission was required). The SWORD API has now been fully integrated with the Dataverse 4 permission model such that any action you have permission to perform in the GUI or "native" API you are able to perform via SWORD. This means that even a user with a "Contributor" role can operate on datasets via SWORD. Note that users with the "Contributor" role do not have the ``PublishDataset`` permission and will not be able publish their datasets via any mechanism, GUI or API.
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- Datasets versions will only be increased to the next minor version (i.e. 1.1) rather than a major version (2.0) if possible. This depends on the nature of the change.
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- Dataverses can be published via SWORD.
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- Datasets versions will only be increased to the next minor version (i.e. 1.1) rather than a major version (2.0) if possible. This depends on the nature of the change. Adding or removing, a file, for example, requires a major version bump.
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- "Author Affiliation" can now be populated with an XML attribute. For example: <dcterms:creator affiliation="Coffee Bean State University">Stumptown, Jane</dcterms:creator>
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Retrieve SWORD service document
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The service document enumerates the dataverses ("collections" from a SWORD perspective) the user can deposit data into. The "collectionPolicy" element for each dataverse contains the Terms of Use.
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The service document enumerates the dataverses ("collections" from a SWORD perspective) the user can deposit data into. The "collectionPolicy" element for each dataverse contains the Terms of Use. Any user with an API token can use this API endpoint. Institution-wide Shibboleth groups are not respected because membership in such a group can only be set via a browser.
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``curl -u $API_TOKEN: https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/service-document``
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Create a dataset with an Atom entry
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To create a dataset, you must have the "Dataset Creator" role (the ``AddDataset`` permission) on a dataverse. Practically speaking, you should first retrieve the service document to list the dataverses into which you are authorized to deposit data.
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``curl -u $API_TOKEN: --data-binary "@path/to/atom-entry-study.xml" -H "Content-Type: application/atom+xml" https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/collection/dataverse/$DATAVERSE_ALIAS``
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Example Atom entry (XML)
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.. literalinclude:: sword-atom-entry.xml
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Dublin Core Terms (DC Terms) Qualified Mapping - Dataverse DB Element Crosswalk
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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+-----------------------------+----------------------------------------------+--------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+
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|DC (terms: namespace) | Dataverse DB Element | Required | Note |
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+=============================+==============================================+==============+=============================================================================================================================================================+
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List datasets in a dataverse
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You must have permission to add datasets in a dataverse (the dataverse should appear in the service document) to list the datasets inside. Institution-wide Shibboleth groups are not respected because membership in such a group can only be set via a browser.
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``curl -u $API_TOKEN: https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/collection/dataverse/$DATAVERSE_ALIAS``
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You must have ``EditDataset`` permission (Contributor role or above such as Curator or Admin) on the dataset to add files.
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``curl -u $API_TOKEN: --data-binary @path/to/example.zip -H "Content-Disposition: filename=example.zip" -H "Content-Type: application/zip" -H "Packaging: http://purl.org/net/sword/package/SimpleZip" https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/edit-media/study/doi:TEST/12345``
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You must have ``ViewUnpublishedDataset`` permission (Contributor role or above such as Curator or Admin) on the dataset to view its Atom entry.
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Contains data citation (bibliographicCitation), alternate URI (persistent URI of study), edit URI, edit media URI, statement URI.
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Contains title, author, feed of file entries, latestVersionState, locked boolean, updated timestamp.
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You must have ``EditDataset`` permission (Contributor role or above such as Curator or Admin) on the dataset to delete files.
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Replacing metadata for a dataset
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Please note that **ALL** metadata (title, author, etc.) will be replaced, including fields that can not be expressed with "dcterms" fields.
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Please note that **ALL** metadata (title, author, etc.) will be replaced, including fields that can not be expressed with "dcterms" fields. You must have ``EditDataset`` permission (Contributor role or above such as Curator or Admin) on the dataset to replace metadata.
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``curl -u $API_TOKEN: --upload-file "path/to/atom-entry-study2.xml" -H "Content-Type: application/atom+xml" https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/edit/study/doi:TEST/12345``
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You must have the ``DeleteDatasetDraft`` permission (Contributor role or above such as Curator or Admin) on the dataset to delete it. Please note that if the dataset has never been published you will be able to delete it completely but if the dataset has already been published you will only be able to delete post-publication drafts, never a published version.
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``curl -u $API_TOKEN: -i -X DELETE https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/edit/study/doi:TEST/12345``
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This API endpoint is the same as the "list datasets in a dataverse" endpoint documented above and the same permissions apply but it is documented here separately to point out that you can look for a boolean called ``dataverseHasBeenReleased`` to know if a dataverse has been released, which is required for publishing a dataset.
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``curl -u $API_TOKEN: https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/collection/dataverse/$DATAVERSE_ALIAS``
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The ``cat /dev/null`` and ``--data-binary @-`` arguments are used to send zero-length content to the API, which is required by the upstream library to process the ``In-Progress: false`` header.
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The ``cat /dev/null`` and ``--data-binary @-`` arguments are used to send zero-length content to the API, which is required by the upstream library to process the ``In-Progress: false`` header. You must have the ``PublishDataverse`` permission (Admin role) on the dataverse to publish it.
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``cat /dev/null | curl -u $API_TOKEN: -X POST -H "In-Progress: false" --data-binary @- https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/edit/dataverse/$DATAVERSE_ALIAS``
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The ``cat /dev/null`` and ``--data-binary @-`` arguments are used to send zero-length content to the API, which is required by the upstream library to process the ``In-Progress: false`` header. You must have the ``PublishDataset`` permission (Curator or Admin role) on the dataset to publish it.
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``cat /dev/null | curl -u $API_TOKEN: -X POST -H "In-Progress: false" --data-binary @- https://$HOSTNAME/dvn/api/data-deposit/v1.1/swordv2/edit/study/doi:TEST/12345``
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- Potential mismatch between the dataverses ("collections" from a SWORD perspective) the user can deposit data into in returned by the Service Document and which dataverses the user can actually deposit data into. This is due to an incomplete transition from the old DVN 3.x "admin-only" style permission checking to the new permissions system in Dataverse 4.0 ( https://github.com/IQSS/dataverse/issues/1070 ). The mismatch was reported at https://github.com/IQSS/dataverse/issues/1443
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- Should see all the fields filled in for a dataset regardless of what the parent dataverse specifies: https://github.com/IQSS/dataverse/issues/756
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- Inefficiency in constructing the ``Service Document``: https://github.com/IQSS/dataverse/issues/784
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- Inefficiency in constructing the list of datasets: https://github.com/IQSS/dataverse/issues/784
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- Deleting a file from a published version (not a draft) creates a draft but doesn't delete the file: https://github.com/IQSS/dataverse/issues/2464
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Roadmap
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-------
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- The Service Document does not honor groups within groups: https://github.com/IQSS/dataverse/issues/3056
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These are features we'd like to add in the future:
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- Should see all the fields filled in for a dataset regardless of what the parent dataverse specifies: https://github.com/IQSS/dataverse/issues/756
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- Implement SWORD 2.0 Profile 6.4: https://github.com/IQSS/dataverse/issues/183
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- SWORD 2.0 Profile 6.4 "Retrieving the content" has not been implemented: https://github.com/IQSS/dataverse/issues/183
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- Support deaccessioning via API: https://github.com/IQSS/dataverse/issues/778
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- Deaccessioning via API is not supported (it was in DVN 3.x): https://github.com/IQSS/dataverse/issues/778
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- Let file metadata (i.e. description) be specified during zip upload: https://github.com/IQSS/dataverse/issues/723
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‎doc/sphinx-guides/source/installation/config.rst‎

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Set custom text a user will view when publishing a dataset.
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Set custom text a user will view when publishing a dataset. Note that this text is exposed via the "Info" endpoint of the :doc:`/api/native-api`.
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``curl -X PUT -d "Deposit License Requirements" http://localhost:8080/api/admin/settings/:DatasetPublishPopupCustomText``
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‎doc/sphinx-guides/source/installation/shibboleth.rst‎

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.. literalinclude:: ../_static/installation/files/etc/shibboleth/shibGroupTestShib.json
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Note that institution-wide Shibboleth groups are based on the "Shib-Identity-Provider" attribute but https://github.com/IQSS/dataverse/issues/1515 tracks adding support for arbitrary attributes such as ""eduPersonScopedAffiliation", etc.
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Institution-wide Shibboleth groups are based on the "Shib-Identity-Provider" SAML attribute asserted at runtime after successful authentication with the Identity Provider (IdP) and held within the browser session rather than being persisted in the database for any length of time. It is for this reason that roles based on these groups, such as the ability to create a dataset, are not honored by non-browser interactions, such as through the SWORD API.
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To list institution-wide Shibboleth groups: ``curl http://localhost:8080/api/admin/groups/shib``
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To delete an institution-wide Shibboleth group (assuming id 1): ``curl -X DELETE http://localhost:8080/api/admin/groups/shib/1``
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Support for arbitrary attributes beyond "Shib-Identity-Provider" such as "eduPersonScopedAffiliation", etc. is being tracked at https://github.com/IQSS/dataverse/issues/1515
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Converting Local Users to Shibboleth
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