Merge branch 'hotfix/1.16.1'

Author: kathy-t

README.md

@@ -20,7 +20,7 @@ Check for broken links
 
 Open the `_build/html/index.html` in your browser!
 
-OICR affilates can view additional developer docs here: https://wiki.oicr.on.ca/display/DOC/Read+The+Docs 
+OICR partners can view additional developer docs here: https://wiki.oicr.on.ca/display/DOC/Read+The+Docs
 
 ## Writing/Maintaining docs
 Most of our docs are written in RST. A handful are written are in markdown. Both the RST and markdown documents will be rendered as HTML using the Python-based documentation manager Sphinx.

docs/assets/templates/notebooks/template-big.dockstore.yml

@@ -63,6 +63,11 @@ notebooks:
     # A value of true will automatically display the latest tag updated as default.
     # A value of false will retain the default version that has been specified via the Dockstore UI.
     latestTagAsDefault: <Boolean>
+
+    # 'enableAutoDois' is a notebook-wide setting that will affect ALL branches/tags; only set this as needed in a main branch
+    # to control whether DOIs are automatically issued for tags. Implicit default: True, can only be overridden as False
+    # A value of false will disable automatic DOIs, DOIs will only be issued on demand.
+    enableAutoDois: <Boolean>
 
     # The optional filters section allow specifying sets of Git branches and tags to include for the notebook.
     # If no filters are given, all branches and tags are included.

docs/assets/templates/notebooks/template-small.dockstore.yml

@@ -14,4 +14,4 @@ notebooks:
     authors:
       - name: <String>
         email: <String>
-    topic: <String>
+    topic: <String>

docs/assets/templates/services/template-big.dockstore.yml

@@ -33,6 +33,11 @@ service:
   # Omitting the publish setting leaves the publish-state unchanged (recommended for all non-primary branches).
   publish:
 
+  # 'enableAutoDois' is a service-wide setting that will affect ALL branches/tags; only set this as needed in a main branch
+  # to control whether DOIs are automatically issued for tags. Implicit default: True, can only be overridden as False
+  # A value of false will disable automatic DOIs, DOIs will only be issued on demand.
+  enableAutoDois: <Boolean>
+
   # These are files the Dockstore will index. They will be directly downloadable from Dockstore. Wildcards are not supported.
   files:
 

docs/assets/templates/services/template-small.dockstore.yml

@@ -20,4 +20,4 @@ service:
       targetDirectory: <String, relative path>
       files:
         <String-name-of-file>:
-          description: <String>
+          description: <String>

docs/assets/templates/workflows/template-big.dockstore.yml

@@ -65,6 +65,11 @@ workflows:
     # A value of true will automatically display the latest tag updated as default.
     # A value of false will retain the default version that has been specified via the Dockstore UI.
     latestTagAsDefault: <Boolean>
+
+    # 'enableAutoDois' is a workflow-wide setting that will affect ALL branches/tags; only set this as needed in a main branch
+    # to control whether DOIs are automatically issued for tags. Implicit default: True, can only be overridden as False
+    # A value of false will disable automatic DOIs, DOIs will only be issued on demand.
+    enableAutoDois: <Boolean>
 
     # The optional filters section allow specifying sets of Git branches and tags to include for the workflow.
     # If no filters are given, all branches and tags are included.

docs/assets/templates/workflows/template-small.dockstore.yml

@@ -9,4 +9,4 @@ workflows:
     authors:
       - name: <String>
         email: <String>
-    topic: <String>
+    topic: <String>

docs/end-user-topics/dois.rst

@@ -82,6 +82,18 @@ Automatically-generated DOIs:
 * Are editable by request to the Dockstore team
 * Will be editable via a Zenodo account in a subsequent Dockstore release
 
+If you wish to override and disable this feature, you can opt-out on a per-workflow basis by adding the following setting to your `.dockstore.yml` files
+
+.. code-block:: yaml
+
+   enableAutoDois: false
+
+
+One rare case to potentially watch out for: if your workflows are tagged with your ORCID as an author
+you may get a large number of notifications or workflows automatically added to your ORCID profile.
+This will occur outside of Dockstore if you have the `ORCID Auto-Update <https://support.datacite.org/docs/datacite-and-orcid#2-orcid-auto-update>`__ feature turned on in DataCite.
+DataCite's auto-update feature is not aware of how Zenodo groups DOIs into one overall "concept" DOI and will import each version independently.
+
 GitHub-Zenodo Generation
 ~~~~~~~~~~~~~~~~~~~~~~~~