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{% endtrans %} {%- endif %} {%- endif %} From aed167bd7db866bd72fb0c17dd7931043b648e74 Mon Sep 17 00:00:00 2001 From: kuhlaid <41551429+kuhlaid@users.noreply.github.com> Date: Fri, 29 Jul 2022 12:25:38 -0400 Subject: [PATCH 02/10] Update docsdataverse_org.css Adding style to highlight current page in the menu --- doc/sphinx-guides/source/_static/docsdataverse_org.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/_static/docsdataverse_org.css b/doc/sphinx-guides/source/_static/docsdataverse_org.css index e4afe89e217..da4ba06ddd4 100755 --- a/doc/sphinx-guides/source/_static/docsdataverse_org.css +++ b/doc/sphinx-guides/source/_static/docsdataverse_org.css @@ -68,7 +68,7 @@ a.headerlink { #sidebar.bs-sidenav { background-color: #f8d5b8; } -#sidebar.bs-sidenav .nav > li > a:hover, #sidebar.bs-sidenav .nav > li > a:focus { +#sidebar.bs-sidenav .nav > li > a:hover, #sidebar.bs-sidenav .nav > li > a:focus, #sidebar.bs-sidenav .nav > li > a.current { background-color: #fbf4c5; border-right: 1px solid #dbd8e0; text-decoration: none; From 10bc4646bc9f52f557959fdda43c6a206d60d276 Mon Sep 17 00:00:00 2001 From: kuhlaid <41551429+kuhlaid@users.noreply.github.com> Date: Fri, 29 Jul 2022 13:30:20 -0400 Subject: [PATCH 03/10] Update dataset-semantic-metadata-api.rst Switching @context from a link to inline literal since this text should not link to anything --- .../source/developers/dataset-semantic-metadata-api.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/developers/dataset-semantic-metadata-api.rst b/doc/sphinx-guides/source/developers/dataset-semantic-metadata-api.rst index 7abae535276..85a44da48c6 100644 --- a/doc/sphinx-guides/source/developers/dataset-semantic-metadata-api.rst +++ b/doc/sphinx-guides/source/developers/dataset-semantic-metadata-api.rst @@ -74,7 +74,7 @@ To delete metadata for a Dataset, send a json-ld representation of the fields to curl -X PUT -H X-Dataverse-key:$API_TOKEN -H 'Content-Type: application/ld+json' -d '{"https://dataverse.org/schema/core#restrictions":"No restrictions"}' "$SERVER_URL/api/datasets/:persistentId/metadata/delete?persistentId=$DATASET_PID" -Note, this example uses the term URI directly rather than adding an '@context' element. You can use either form in any of these API calls. +Note, this example uses the term URI directly rather than adding an ``@context`` element. You can use either form in any of these API calls. You should expect a 200 ("OK") response indicating whether a draft Dataset version was created or an existing draft was updated. From 0893d172f72e87803da00b183f4ad1d6da67b280 Mon Sep 17 00:00:00 2001 From: kuhlaid <41551429+kuhlaid@users.noreply.github.com> Date: Fri, 29 Jul 2022 17:07:32 -0400 Subject: [PATCH 04/10] Update native-api.rst Changing openprovenance.org to use the https (because the site seems to only be using HTTPS and the HTTP URL is not redirecting to the HTTPS URL and is breaking page) --- doc/sphinx-guides/source/api/native-api.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/api/native-api.rst b/doc/sphinx-guides/source/api/native-api.rst index cbf9e6c9128..1f85ee02825 100644 --- a/doc/sphinx-guides/source/api/native-api.rst +++ b/doc/sphinx-guides/source/api/native-api.rst @@ -2513,7 +2513,7 @@ The fully expanded example above (without environment variables) looks like this curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X POST "https://demo.dataverse.org/api/files/:persistentId/prov-freeform?persistentId=doi:10.5072/FK2/AAA000" -H "Content-type:application/json" --upload-file provenance.json -See a sample JSON file :download:`file-provenance.json <../_static/api/file-provenance.json>` from http://openprovenance.org (c.f. Huynh, Trung Dong and Moreau, Luc (2014) ProvStore: a public provenance repository. At 5th International Provenance and Annotation Workshop (IPAW'14), Cologne, Germany, 09-13 Jun 2014. pp. 275-277). +See a sample JSON file :download:`file-provenance.json <../_static/api/file-provenance.json>` from https://openprovenance.org (c.f. Huynh, Trung Dong and Moreau, Luc (2014) ProvStore: a public provenance repository. At 5th International Provenance and Annotation Workshop (IPAW'14), Cologne, Germany, 09-13 Jun 2014. pp. 275-277). Delete Provenance JSON for an uploaded file ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From 1d5ec876de31a7bcb06b7a8bf78895a00e469852 Mon Sep 17 00:00:00 2001 From: kuhlaid <41551429+kuhlaid@users.noreply.github.com> Date: Sun, 31 Jul 2022 20:35:38 -0400 Subject: [PATCH 05/10] Update index.rst Removing index links because they no longer link to anything --- doc/sphinx-guides/source/index.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/doc/sphinx-guides/source/index.rst b/doc/sphinx-guides/source/index.rst index f7e81756e5b..148518d2ce5 100755 --- a/doc/sphinx-guides/source/index.rst +++ b/doc/sphinx-guides/source/index.rst @@ -73,6 +73,4 @@ If you have a **security issue** to report, please email `security@dataverse.org Indices and Tables ------------------ -* :ref:`genindex` -* :ref:`modindex` * :ref:`search` From 6b9d175cd46be347c157f249e01b243f96d9824c Mon Sep 17 00:00:00 2001 From: kuhlaid <41551429+kuhlaid@users.noreply.github.com> Date: Sun, 31 Jul 2022 20:43:44 -0400 Subject: [PATCH 06/10] Update metadatacustomization.rst Fixing link to https://orcid.org --- doc/sphinx-guides/source/admin/metadatacustomization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/admin/metadatacustomization.rst b/doc/sphinx-guides/source/admin/metadatacustomization.rst index 094f310a156..2ee68ccbaa5 100644 --- a/doc/sphinx-guides/source/admin/metadatacustomization.rst +++ b/doc/sphinx-guides/source/admin/metadatacustomization.rst @@ -565,7 +565,7 @@ In general, the external vocabulary support mechanism may be a better choice for The specifics of the user interface for entering/selecting a vocabulary term and how that term is then displayed are managed by third-party Javascripts. The initial Javascripts that have been created provide auto-completion, displaying a list of choices that match what the user has typed so far, but other interfaces, such as displaying a tree of options for a hierarchical vocabulary, are possible. Similarly, existing scripts do relatively simple things for displaying a term - showing the term's name in the appropriate language and providing a link to an external URL with more information, but more sophisticated displays are possible. -Scripts supporting use of vocabularies from services supporting the SKOMOS protocol (see https://skosmos.org) and retrieving ORCIDs (from https:/orcid.org) are available https://github.com/gdcc/dataverse-external-vocab-support. (Custom scripts can also be used and community members are encouraged to share new scripts through the dataverse-external-vocab-support repository.) +Scripts supporting use of vocabularies from services supporting the SKOMOS protocol (see https://skosmos.org) and retrieving ORCIDs (from https://orcid.org) are available https://github.com/gdcc/dataverse-external-vocab-support. (Custom scripts can also be used and community members are encouraged to share new scripts through the dataverse-external-vocab-support repository.) Configuration involves specifying which fields are to be mapped, whether free-text entries are allowed, which vocabulary(ies) should be used, what languages those vocabulary(ies) are available in, and several service protocol and service instance specific parameters. These are all defined in the :ref:`:CVocConf <:CVocConf>` setting as a JSON array. Details about the required elements as well as example JSON arrays are available at https://github.com/gdcc/dataverse-external-vocab-support, along with an example metadata block that can be used for testing. From 01e1d5291b01de7bb79b329ce3ba2b9a3049ce59 Mon Sep 17 00:00:00 2001 From: kuhlaid <41551429+kuhlaid@users.noreply.github.com> Date: Sun, 31 Jul 2022 20:55:50 -0400 Subject: [PATCH 07/10] Update prerequisites.rst Fixing URL to the R Project --- doc/sphinx-guides/source/installation/prerequisites.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/sphinx-guides/source/installation/prerequisites.rst b/doc/sphinx-guides/source/installation/prerequisites.rst index 0ad3bf600c9..b7a01ea2ce8 100644 --- a/doc/sphinx-guides/source/installation/prerequisites.rst +++ b/doc/sphinx-guides/source/installation/prerequisites.rst @@ -288,11 +288,11 @@ If the installed location of the convert executable is different from ``/usr/bin (see the :doc:`config` section for more information on the JVM options) -R +The R Project for Statistical Computing - -The Dataverse Software uses `R