Merge pull request #1 from IQSS/8639-experimental

abujeda · web-flow · commit bbd9393419a6 · 2022-07-20T22:35:52.000+01:00
make comp workflow block experimental, other suggestions IQSS#8639
diff --git a/doc/sphinx-guides/source/user/appendix.rst b/doc/sphinx-guides/source/user/appendix.rst
@@ -8,13 +8,18 @@ Additional documentation complementary to the User Guide.
 .. contents:: |toctitle|
 	:local:
 
+.. _metadata-references:
+
 Metadata References
 ======================
 
 The Dataverse Project is committed to using standard-compliant metadata to ensure that a Dataverse installation's
 metadata can be mapped easily to standard metadata schemas and be exported into JSON
 format (XML for tabular file metadata) for preservation and interoperability.
 
+Supported Metadata
+~~~~~~~~~~~~~~~~~~
+
 Detailed below are what metadata schemas we support for Citation and Domain Specific Metadata in the Dataverse Project:
 
 - `Citation Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodHFEWGpoa19ia3pldEFyVFR0aFVGa0E#gid=0>`__: compliant with `DDI Lite <http://www.ddialliance.org/specification/ddi2.1/lite/index.html>`_, `DDI 2.5 Codebook <http://www.ddialliance.org/>`__, `DataCite 3.1 <http://schema.datacite.org/meta/kernel-3.1/doc/DataCite-MetadataKernel_v3.1.pdf>`__, and Dublin Core's `DCMI Metadata Terms <http://dublincore.org/documents/dcmi-terms/>`__ (`see .tsv version <https://github.com/IQSS/dataverse/blob/master/scripts/api/data/metadatablocks/citation.tsv>`__). Language field uses `ISO 639-1 <https://www.loc.gov/standards/iso639-2/php/English_list.php>`__ controlled vocabulary.
@@ -26,6 +31,15 @@ Detailed below are what metadata schemas we support for Citation and Domain Spec
   `Virtual Observatory (VO) Discovery and Provenance Metadata <http://perma.cc/H5ZJ-4KKY>`__ (`see .tsv version <https://github.com/IQSS/dataverse/blob/master/scripts/api/data/metadatablocks/astrophysics.tsv>`__).
 - `Life Sciences Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodHFEWGpoa19ia3pldEFyVFR0aFVGa0E#gid=2>`__: based on `ISA-Tab Specification <https://isa-specs.readthedocs.io/en/latest/isamodel.html>`__, along with controlled vocabulary from subsets of the `OBI Ontology <http://bioportal.bioontology.org/ontologies/OBI>`__ and the `NCBI Taxonomy for Organisms <http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/>`__ (`see .tsv version <https://github.com/IQSS/dataverse/blob/master/scripts/api/data/metadatablocks/biomedical.tsv>`__).
 - `Journal Metadata <https://docs.google.com/spreadsheets/d/13HP-jI_cwLDHBetn9UKTREPJ_F4iHdAvhjmlvmYdSSw/edit#gid=8>`__: based on the `Journal Archiving and Interchange Tag Set, version 1.2 <https://jats.nlm.nih.gov/archiving/tag-library/1.2/chapter/how-to-read.html>`__ (`see .tsv version <https://github.com/IQSS/dataverse/blob/master/scripts/api/data/metadatablocks/journals.tsv>`__).
+
+Experimental Metadata
+~~~~~~~~~~~~~~~~~~~~~
+
+Unlike supported metadata, experimental metadata is not enabled by default in a new Dataverse installation. Feedback via any `channel <https://dataverse.org/contact>`_ is welcome!
+
 - `Computational Workflow Metadata <https://docs.google.com/spreadsheets/d/13HP-jI_cwLDHBetn9UKTREPJ_F4iHdAvhjmlvmYdSSw/edit#gid=447508596>`__: adapted from `Bioschemas Computational Workflow Profile, version 1.0 <https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE>`__ and `Codemeta <https://codemeta.github.io/terms/>`__ (`see .tsv version <https://github.com/IQSS/dataverse/blob/master/scripts/api/data/metadatablocks/computationalworkflow.tsv>`__).
 
+See Also
+~~~~~~~~
+
 See also the `Dataverse Software 4.0 Metadata Crosswalk: DDI, DataCite, DC, DCTerms, VO, ISA-Tab <https://docs.google.com/spreadsheets/d/10Luzti7svVTVKTA-px27oq3RxCUM-QbiTkm8iMd5C54/edit?usp=sharing>`__ document and the :doc:`/admin/metadatacustomization` section of the Admin Guide.
diff --git a/doc/sphinx-guides/source/user/dataset-management.rst b/doc/sphinx-guides/source/user/dataset-management.rst
@@ -162,13 +162,13 @@ BagIt Support
 
 BagIt is a set of hierarchical file system conventions designed to support disk-based storage and network transfer of arbitrary digital content. It offers several benefits such as integration with digital libraries, easy implementation, and transfer validation. See `the Wikipedia article <https://en.wikipedia.org/wiki/BagIt>`__ for more information.
 
-If the repository you are using has enabled BagIt file handling, when uploading BagIt files the repository will validate the checksum values listed in each BagIt’s manifest file against the uploaded files and generate errors about any mismatches. The repository will identify a certain number of errors, such as the first five errors in each BagIt file, before reporting the errors.
+If the Dataverse installation you are using has enabled BagIt file handling, when uploading BagIt files the repository will validate the checksum values listed in each BagIt’s manifest file against the uploaded files and generate errors about any mismatches. The repository will identify a certain number of errors, such as the first five errors in each BagIt file, before reporting the errors.
 
 |bagit-image1|
 
 You can fix the errors and reupload the BagIt files.
 
-For information on how to enable and configure the BagIt file handler see the :ref:`installation guide <BagIt File Handler>`
+More information on how your admin can enable and configure the BagIt file handler can be found in the :ref:`Installation Guide <BagIt File Handler>`.
 
 .. _file-handling:
 
@@ -238,10 +238,11 @@ Computational workflows precisely describe a multi-step process to coordinate mu
 
 |cw-image1|
 
+
 FAIR Computational Workflow
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-FAIR principles (Findable, Accessible, Interoperable, Reusable) also apply to computational workflows. The FAIR Principles (https://doi.org/10.1162/dint_a_00033) apply to workflows in two areas as FAIR data and FAIR criteria for workflows as digital objects. In the FAIR data area, "*properly designed workflows contribute to FAIR data principles since they provide the metadata and provenance necessary to describe their data products, and they describe the involved data in a formalized, completely traceable way*" (https://doi.org/10.1162/dint_a_00033). Regarding the FAIR criteria for workflows as digital objects, "*workflows are research products in their own right, encapsulating methodological know-how that is to be found and published, accessed and cited, exchanged and combined with others, and reused as well as adapted*" (https://doi.org/10.1162/dint_a_00033).
+The FAIR Principles (Findable, Accessible, Interoperable, Reusable) apply to computational workflows (https://doi.org/10.1162/dint_a_00033) in two areas: as FAIR data and as FAIR criteria for workflows as digital objects. In the FAIR data area, "*properly designed workflows contribute to FAIR data principles since they provide the metadata and provenance necessary to describe their data products, and they describe the involved data in a formalized, completely traceable way*" (https://doi.org/10.1162/dint_a_00033). Regarding the FAIR criteria for workflows as digital objects, "*workflows are research products in their own right, encapsulating methodological know-how that is to be found and published, accessed and cited, exchanged and combined with others, and reused as well as adapted*" (https://doi.org/10.1162/dint_a_00033).
 
 How to Create a Computational Workflow
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -257,31 +258,35 @@ You are encouraged to review these examples when creating a computational workfl
 
 At https://workflows.community, the Workflows Community Initiative offers resources for computational workflows, such as a list of workflow systems (https://workflows.community/systems) and other workflow registries (https://workflows.community/registries). The initiative also helps organize working groups related to workflows research, development and application.
 
-How to Upload your Computational Workflow
+How to Upload Your Computational Workflow
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-When you :ref:`add a new dataset <adding-new-dataset>`, the Dataverse repository you are using may provide additional support for describing computational workflows, including Computational Workflow Metadata fields for describing your workflow and a "Workflow" tag you can apply to your workflow files.
+After you :ref:`upload your files <dataset-file-upload>`, you can apply a "Workflow" tag to your workflow files, such as your Snakemake or R Notebooks files, so that you and others can find them more easily among your deposit’s other files.
+
+|cw-image3|
+
+|cw-image4|
+
+How to Describe Your Computational Workflow
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The Dataverse installation you are using may have enabled Computational Workflow metadata fields for your use. If so, when :ref:`editing your dataset metadata <adding-new-dataset>`, you will see the fields described below.
 
 |cw-image2|
 
-The three fields are adapted from `Bioschemas Computational Workflow Profile, version 1.0 <https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE>`__ and `Codemeta <https://codemeta.github.io/terms/>`__:
+As described in the :ref:`metadata-references` section of the :doc:`/user/appendix`, the three fields are adapted from `Bioschemas Computational Workflow Profile, version 1.0 <https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE>`__ and `Codemeta <https://codemeta.github.io/terms/>`__:
 
 - **Workflow Type**: The kind of Computational Workflow, which is designed to compose and execute a series of computational or data manipulation steps in a scientific application
-- **External Code Repository URL**: A link to another public repository where the un-compiled, human-readable code and related code is also located (e.g., SVN, GitHub, GitLab, CodePlex)
+- **External Code Repository URL**: A link to another public repository where the un-compiled, human-readable code and related code is also located (e.g., GitHub, GitLab, SVN)
 - **Documentation**: A link (URL) to the documentation or text describing the Computational Workflow and its use
 
-After you :ref:`upload your files <dataset-file-upload>`, you can apply a "Workflow" tag to your workflow files, such as your Snakemake or R Notebooks files, so that you and others can find them more easily among your deposit’s other files.
-
-|cw-image3|
-
-|cw-image4|
 
 How to Search for Computational Workflows
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 If the search page of the Dataverse repository you are using includes a "Dataset Feature" facet with a Computational Workflows link, you can follow that link to find only datasets that contain computational workflows.
 
-You can also use the "Workflow Type" facet, if the Dataverse repository uses it, to find datasets that contain certain types of computational workflows, such as workflows written in Common Workflow Language files or Jupyter Notebooks.
+You can also search on the "Workflow Type" facet, if the Dataverse installation has the field enabled, to find datasets that contain certain types of computational workflows, such as workflows written in Common Workflow Language files or Jupyter Notebooks.
 
 |cw-image5|
 
diff --git a/scripts/api/data/metadatablocks/computational_workflow.tsv b/scripts/api/data/metadatablocks/computational_workflow.tsv
@@ -2,7 +2,7 @@
 	computationalworkflow		Computational Workflow Metadata
 #datasetField	name	title	description	watermark	 fieldType	displayOrder	displayFormat	advancedSearchField	allowControlledVocabulary	allowmultiples	facetable	displayoncreate	required	parent	metadatablock_id	termURI
 	workflowType	Computational Workflow Type	The kind of Computational Workflow, which is designed to compose and execute a series of computational or data manipulation steps in a scientific application		text	0		TRUE	TRUE	TRUE	TRUE	TRUE	FALSE		computationalworkflow
-	workflowCodeRepository	External Code Repository URL	A link to the repository where the un-compiled, human readable code and related code is located (e.g. SVN, GitHub, CodePlex, institutional GitLab instance)	https://...	url	1		FALSE	FALSE	TRUE	FALSE	TRUE	FALSE		computationalworkflow
+	workflowCodeRepository	External Code Repository URL	A link to the repository where the un-compiled, human readable code and related code is located (e.g. GitHub, GitLab, SVN)	https://...	url	1		FALSE	FALSE	TRUE	FALSE	TRUE	FALSE		computationalworkflow
 	workflowDocumentation	Documentation	A link (URL) to the documentation or text describing the Computational Workflow and its use		textbox	2		FALSE	FALSE	TRUE	FALSE	TRUE	FALSE		computationalworkflow
 #controlledVocabulary	DatasetField	Value	identifier	displayOrder
 	workflowType	Common Workflow Language (CWL)	workflowtype_cwl	1
@@ -18,4 +18,4 @@
 	workflowType	Makefile	workflowtype_makefile	11
 	workflowType	Other Python-based workflow	workflowtype_otherpython	12
 	workflowType	Other R-based workflow	workflowtype_otherrbased	13
-	workflowType	Other	workflowtype_other	100
+	workflowType	Other	workflowtype_other	100
diff --git a/scripts/api/setup-datasetfields.sh b/scripts/api/setup-datasetfields.sh
@@ -7,5 +7,4 @@ curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @da
 curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @data/metadatablocks/astrophysics.tsv -H "Content-type: text/tab-separated-values"
 curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @data/metadatablocks/biomedical.tsv -H "Content-type: text/tab-separated-values"
 curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @data/metadatablocks/journals.tsv -H "Content-type: text/tab-separated-values"
-curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @data/metadatablocks/computational_workflow.tsv -H "Content-type: text/tab-separated-values"
 
diff --git a/src/main/java/propertyFiles/computationalworkflow.properties b/src/main/java/propertyFiles/computationalworkflow.properties
@@ -5,7 +5,7 @@ datasetfieldtype.workflowType.title=Workflow Type
 datasetfieldtype.workflowType.description=The kind of Computational Workflow, which is designed to compose and execute a series of computational or data manipulation steps in a scientific application
 datasetfieldtype.workflowType.watermark=
 datasetfieldtype.workflowCodeRepository.title=External Code Repository URL
-datasetfieldtype.workflowCodeRepository.description=A link to another public repository where the un-compiled, human-readable code and related code is also located (e.g., SVN, GitHub, GitLab, CodePlex)
+datasetfieldtype.workflowCodeRepository.description=A link to another public repository where the un-compiled, human-readable code and related code is also located (e.g., GitHub, GitLab, SVN)
 datasetfieldtype.workflowCodeRepository.watermark=https://...
 datasetfieldtype.workflowDocumentation.title=Documentation
 datasetfieldtype.workflowDocumentation.description=A link (URL) to the documentation or text describing the Computational Workflow and its use
