Merge pull request ResearchObject#312 from elichad/website-bugs

Update favicons and redirects
rsirvent · Jun 6, 2024 · ed3ade3 · ed3ade3
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diff --git a/docs/0.2-DRAFT/context.json → docs/_compatibility/0.2-DRAFT/context.json b/docs/0.2-DRAFT/context.json → docs/_compatibility/0.2-DRAFT/context.json
diff --git a/docs/0.2/context.json → docs/_compatibility/0.2/context.json b/docs/0.2/context.json → docs/_compatibility/0.2/context.json
diff --git a/docs/0.3-DRAFT/context.json → docs/_compatibility/0.3-DRAFT/context.json b/docs/0.3-DRAFT/context.json → docs/_compatibility/0.3-DRAFT/context.json
diff --git a/docs/1.0/context.jsonld → docs/_compatibility/1.0/context.jsonld b/docs/1.0/context.jsonld → docs/_compatibility/1.0/context.jsonld
diff --git a/docs/1.0/ro-crate-metadata.jsonld → ...ompatibility/1.0/ro-crate-metadata.jsonld b/docs/1.0/ro-crate-metadata.jsonld → ...ompatibility/1.0/ro-crate-metadata.jsonld
diff --git a/docs/1.0/ro-crate-preview.html → .../_compatibility/1.0/ro-crate-preview.html b/docs/1.0/ro-crate-preview.html → .../_compatibility/1.0/ro-crate-preview.html
diff --git a/docs/1.1/context.jsonld → docs/_compatibility/1.1/context.jsonld b/docs/1.1/context.jsonld → docs/_compatibility/1.1/context.jsonld
diff --git a/docs/1.1/ro-crate-metadata.json → ..._compatibility/1.1/ro-crate-metadata.json b/docs/1.1/ro-crate-metadata.json → ..._compatibility/1.1/ro-crate-metadata.json
diff --git a/docs/1.1/ro-crate-metadata.jsonld → ...ompatibility/1.1/ro-crate-metadata.jsonld b/docs/1.1/ro-crate-metadata.jsonld → ...ompatibility/1.1/ro-crate-metadata.jsonld
diff --git a/docs/1.1/ro-crate-preview.html → .../_compatibility/1.1/ro-crate-preview.html b/docs/1.1/ro-crate-preview.html → .../_compatibility/1.1/ro-crate-preview.html
diff --git a/docs/1.2-DRAFT/context.jsonld → docs/_compatibility/1.2-DRAFT/context.jsonld b/docs/1.2-DRAFT/context.jsonld → docs/_compatibility/1.2-DRAFT/context.jsonld
diff --git a/docs/1.2-DRAFT/ro-crate-metadata.json → ...tibility/1.2-DRAFT/ro-crate-metadata.json b/docs/1.2-DRAFT/ro-crate-metadata.json → ...tibility/1.2-DRAFT/ro-crate-metadata.json
diff --git a/docs/1.2-DRAFT/ro-crate-metadata.jsonld → ...bility/1.2-DRAFT/ro-crate-metadata.jsonld b/docs/1.2-DRAFT/ro-crate-metadata.jsonld → ...bility/1.2-DRAFT/ro-crate-metadata.jsonld
diff --git a/docs/1.2-DRAFT/ro-crate-preview.html → ...atibility/1.2-DRAFT/ro-crate-preview.html b/docs/1.2-DRAFT/ro-crate-preview.html → ...atibility/1.2-DRAFT/ro-crate-preview.html
diff --git a/docs/_compatibility/README.md b/docs/_compatibility/README.md
@@ -0,0 +1,9 @@
+# Compatibility pages
+
+The files in this directory exist to maintain old permalinks which are not currently (June 2024) able to be redirected with the `jekyll-redirect-from` plugin. 
+
+Do not add new website content here.
+
+For specification files, see `_specification` folder.
+
+For tool files, see [`_pages/resources/tools.md`](../pages/resources/tools.md) and [`_data/tools_list.yml`](../_data/tools_list.yml).
diff --git a/docs/_compatibility/tools/index.md b/docs/_compatibility/tools/index.md
@@ -0,0 +1,5 @@
+---
+permalink: /tools/index.html
+redirect_to:
+    - /tools.html
+---
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -16,6 +16,7 @@ include:
 
 exclude:
   - README.md
+  - _compatibility/README.md
   - pages/use_cases/README.md
   - .gitignore
   - var/
@@ -80,6 +81,9 @@ defaults:
 collections:
   specification:
     output: true
+  compatibility:
+    permalink: /:path
+    output: true
 
 theme_variables:
   topnav:

diff --git a/docs/_data/featured.yml b/docs/_data/featured.yml
@@ -2,5 +2,5 @@
 - page_id: arkisto
 - page_id: ldaca
 - page_id: autosubmit
-- page_id: workflow-hub
+- page_id: workflowhub
 - page_id: rohub
diff --git a/docs/_specification/1.1/appendix/changelog.md b/docs/_specification/1.1/appendix/changelog.md
@@ -1,5 +1,8 @@
 ---
 title: Changelog
+redirect_from:
+  - /1.1-DRAFT/appendix/changelog
+  - /1.1/appendix/changelog
 parent: Appendix
 grand_parent: RO-Crate 1.1
 excerpt: List of changes in releases of this specifications

diff --git a/docs/_specification/1.1/appendix/index.md b/docs/_specification/1.1/appendix/index.md
@@ -1,5 +1,8 @@
 ---
 title: Appendix
+redirect_from:
+  - /1.1-DRAFT/appendix
+  - /1.1/appendix
 nav_order: 10
 parent: RO-Crate 1.1
 has_children: true
@@ -23,6 +26,3 @@ has_children: true
 -->
 
 # Appendixes
-
-
-
diff --git a/docs/_specification/1.1/appendix/jsonld.md b/docs/_specification/1.1/appendix/jsonld.md
@@ -1,5 +1,8 @@
 ---
 title: RO-Crate JSON-LD
+redirect_from:
+  - /1.1-DRAFT/appendix/jsonld
+  - /1.1/appendix/jsonld
 parent: Appendix
 grand_parent: RO-Crate 1.1
 ---

diff --git a/docs/_specification/1.1/structure.md b/docs/_specification/1.1/structure.md
@@ -1,5 +1,8 @@
 ---
 title: RO-Crate Structure
+redirect_from:
+  - /1.1-DRAFT/structure
+  - /1.1/structure
 nav_order: 3
 parent: RO-Crate 1.1
 ---

diff --git a/docs/_specification/1.2-DRAFT/appendix/changelog.md b/docs/_specification/1.2-DRAFT/appendix/changelog.md
@@ -1,5 +1,7 @@
 ---
 title: Changelog
+redirect_from:
+  - /1.2-DRAFT/appendix/changelog
 parent: Appendix
 grand_parent: RO-Crate 1.2-DRAFT
 nav_order: 30

diff --git a/docs/_specification/1.2-DRAFT/appendix/implementation-notes.md b/docs/_specification/1.2-DRAFT/appendix/implementation-notes.md
@@ -1,5 +1,7 @@
 ---
 title: Implementation notes
+redirect_from:
+  - /1.2-DRAFT/appendix/implementation-notes
 parent: Appendix
 grand_parent: RO-Crate 1.2-DRAFT
 nav_order: 21

diff --git a/docs/_specification/1.2-DRAFT/appendix/index.md b/docs/_specification/1.2-DRAFT/appendix/index.md
@@ -1,5 +1,7 @@
 ---
 title: Appendix
+redirect_from:
+  - /1.2-DRAFT/appendix
 nav_order: 20
 parent: RO-Crate 1.2-DRAFT
 has_children: true

diff --git a/docs/_specification/1.2-DRAFT/appendix/jsonld.md b/docs/_specification/1.2-DRAFT/appendix/jsonld.md
@@ -1,5 +1,7 @@
 ---
 title: RO-Crate JSON-LD
+redirect_from:
+  - /1.2-DRAFT/appendix/jsonld
 parent: Appendix
 grand_parent: RO-Crate 1.2-DRAFT
 nav_order: 22

diff --git a/docs/_specification/1.2-DRAFT/appendix/relative-uris.md b/docs/_specification/1.2-DRAFT/appendix/relative-uris.md
@@ -1,5 +1,7 @@
 ---
 title: Handling relative URI references
+redirect_from:
+  - /1.2-DRAFT/appendix/relative-uris
 parent: Appendix
 grand_parent: RO-Crate 1.2-DRAFT
 nav_order: 23

diff --git a/docs/assets/img/android-chrome-192x192.png b/docs/assets/img/android-chrome-192x192.png
diff --git a/docs/assets/img/android-chrome-512x512.png b/docs/assets/img/android-chrome-512x512.png
diff --git a/docs/assets/img/favicon-16x16.png b/docs/assets/img/favicon-16x16.png
diff --git a/docs/assets/img/favicon-32x32.png b/docs/assets/img/favicon-32x32.png
diff --git a/docs/assets/img/safari-pinned-tab.svg b/docs/assets/img/safari-pinned-tab.svg
diff --git a/docs/assets/img/site.webmanifest b/docs/assets/img/site.webmanifest
@@ -0,0 +1,19 @@
+{
+    "name": "",
+    "short_name": "",
+    "icons": [
+        {
+            "src": "/assets/img/android-chrome-192x192.png",
+            "sizes": "192x192",
+            "type": "image/png"
+        },
+        {
+            "src": "/assets/img/android-chrome-512x512.png",
+            "sizes": "512x512",
+            "type": "image/png"
+        }
+    ],
+    "theme_color": "#ffffff",
+    "background_color": "#ffffff",
+    "display": "standalone"
+}
diff --git a/docs/pages/use_cases.md b/docs/pages/use_cases.md
@@ -4,6 +4,8 @@ layout: default
 sidebar: main
 redirect_from:
     - /implementations
+    - /in-use
+    - /in-use/index.html
 ---
 # RO-Crate in use
 

diff --git a/docs/pages/use_cases/5s-crate.md b/docs/pages/use_cases/5s-crate.md
@@ -1,5 +1,7 @@
 ---
 page_id: 5s-crate
+redirect_from:
+    - /in-use/5s-crate
 title: Five Safes Crate
 description: The Five Safes RO-Crate profile extend the Workflow Run RO-Crate profile for use in Trusted Research Environments (TRE).
 url: https://trefx.uk/5s-crate/

diff --git a/docs/pages/use_cases/appdb.md b/docs/pages/use_cases/appdb.md
@@ -1,5 +1,7 @@
 ---
 page_id: appdb
+redirect_from:
+    - /in-use/appdb
 title: EGI AppDB
 description: EGI’s Application Database (AppDB) has support for RO-Crate download, either as a JSON-LD metadata file or a ZIP archive.
 url: https://appdb.egi.eu/

diff --git a/docs/pages/use_cases/arkisto.md b/docs/pages/use_cases/arkisto.md
@@ -1,5 +1,7 @@
 ---
 page_id: arkisto
+redirect_from:
+    - /in-use/arkisto
 title: Arkisto
 description: Arkisto uses RO-Crate for packaging data objects in the 3 uses cases described below, Modern PARADISEC, UTS Research Data Repository and UTS Cultural Datasets. As part of these use-cases they have been developing or enhancing their tooling to facilitate their use of RO-Crate
 url: https://arkisto-platform.github.io/

diff --git a/docs/pages/use_cases/autosubmit.md b/docs/pages/use_cases/autosubmit.md
@@ -1,5 +1,7 @@
 ---
 page_id: autosubmit
+redirect_from:
+    - /in-use/autosubmit
 title: Autosubmit
 description: Autosubmit is an open source Python experiment and workflow manager used to manage complex workflows on Cloud and HPC platforms. Autosubmit uses RO-Crate to package the configuration, traces (logs, metrics, databases, etc.), and data of experiments and workflows.
 url: https://autosubmit.readthedocs.io/

diff --git a/docs/pages/use_cases/bioconnect.md b/docs/pages/use_cases/bioconnect.md
@@ -1,11 +1,13 @@
 ---
 page_id: bioconnect
+redirect_from:
+    - /in-use/bioconnect
 title: BioConnect
 description: JAX BioConnect is an index of research data that supports data sharing, high-quality curation, and consistent data description.
 image: bioconnect.png
 domains: [biomedical_science, omics]
 tasks: [conduct_research, data_handling]
-roles: [data_analyst, data_steward, researcher, repository_manager]
+roles: [data_analyst, data_steward, researcher, repository_manager] 
 ---
 <!--
    Copyright 2019-2022 RO-Crate contributors

diff --git a/docs/pages/use_cases/datalake.md b/docs/pages/use_cases/datalake.md
@@ -1,5 +1,7 @@
 ---
 page_id: datalake
+redirect_from:
+    - /in-use/datalake
 title: KEDO Data Lake
 description: Knowledge Enhanced Digital Objects (KEDO) is an experimental approach of building a data lake using a combination of knowledge graphs, RO-Crate and PID records.
 url: https://github.com/luoyu357/KEDODataLake

diff --git a/docs/pages/use_cases/dataplant.md b/docs/pages/use_cases/dataplant.md
@@ -1,5 +1,7 @@
 ---
 page_id: dataplant
+redirect_from:
+    - /in-use/dataplant
 title: Data Plant
 description: DataPLANT`s mission is to provide a sustainable and well annotated data management platform for plant sciences.
 url: https://nfdi4plants.org/content/learn-more/annotated-research-context.html

diff --git a/docs/pages/use_cases/datastewardship.md b/docs/pages/use_cases/datastewardship.md
@@ -1,5 +1,7 @@
 ---
 page_id: datastewardship
+redirect_from:
+    - /in-use/datastewardship
 title: Data Stewardship Wizard
 description: The Data Stewardship Wizard (DSW) is an interactive platform for making data management plans
 url: https://ds-wizard.org/

diff --git a/docs/pages/use_cases/dataverse.md b/docs/pages/use_cases/dataverse.md
@@ -1,5 +1,7 @@
 ---
 page_id: dataverse
+redirect_from:
+    - /in-use/dataverse
 title: Dataverse & AROMA
 description: AROMA (ARP RO-Crate Manager) is part of Hungarian initiative ELKH ARP, extending Harvard Dataverse to allow dynamic metadata editing of data deposit metadata.
 url: https://sztaki.hun-ren.hu/en/innovation/news/developing-elkh-arp-aroma-published-describo-newsletter-australia

diff --git a/docs/pages/use_cases/desci.md b/docs/pages/use_cases/desci.md
@@ -1,5 +1,7 @@
 ---
 page_id: desci
+redirect_from:
+    - /in-use/desci
 title: DeSci Nodes
 description: The DeSci Nodes system has been developed by the DeSci foundation, where dPID (distibuted Persistent Identifier) act as an overlay of the Interplanetary File System (IPFS)
 url: https://docs.desci.com/

diff --git a/docs/pages/use_cases/fairscape.md b/docs/pages/use_cases/fairscape.md
@@ -1,5 +1,7 @@
 ---
 page_id: fairscape
+redirect_from:
+    - /in-use/fairscape
 title: FAIRSCAPE
 description: FAIRSCAPE is a framework for reusable cloud-based computations using ARK identifiers with rich provenance in an evidence graph and the Evidence Graph Ontology (EVI)
 url: https://fairscape.github.io/

diff --git a/docs/pages/use_cases/ldaca.md b/docs/pages/use_cases/ldaca.md
@@ -1,5 +1,7 @@
 ---
 page_id: ldaca
+redirect_from:
+    - /in-use/ldaca
 title: Language Data Commons of Australia
 description: LDaCA uses RO-Crate as an interchange and archive format for language data, and is providing data discovery portals and API access to data using RO-Crate-centric APIs.
 url: https://www.ldaca.edu.au/

diff --git a/docs/pages/use_cases/life-monitor.md b/docs/pages/use_cases/life-monitor.md
@@ -1,6 +1,8 @@
 ---
 page_id: life-monitor
-redirect_from: life_monitor
+redirect_from: 
+    - life_monitor
+    - /in-use/life_monitor
 title: Life Monitor
 description: Life Monitor is a testing and monitoring service for computational workflows being developed as part of the EOSC-Life project. It aims to facilitate the execution, monitoring and sharing of workflow tests over time, allowing to detect deviations from expected workflow operation and provide useful feedback to the workflow authors
 image: life_monitor.png

diff --git a/docs/pages/use_cases/livepublication.md b/docs/pages/use_cases/livepublication.md
@@ -1,5 +1,7 @@
 ---
 page_id: livepublication
+redirect_from:
+    - /in-use/livepublication
 title: LivePublication
 description: LivePublication is a proof of concept of an executable paper, which interactive visualization and statistical calculations can be regenerated on the fly taking into consideration data sources updated after the paper’s publication date.
 url: https://livepublication.github.io/LP_Pub_LID/

diff --git a/docs/pages/use_cases/madmp.md b/docs/pages/use_cases/madmp.md
@@ -1,5 +1,7 @@
 ---
 page_id: madmp
+redirect_from:
+    - /in-use/madmp
 title: Machine-actionable data management plans
 description: RDA maDMP Mapper and Ro-Crate_2ma-DMP can convert between machine-actionable data management plans (maDMP) and RO-Crate.
 url: https://github.com/GhaithArf/ro-crate-rda-madmp-mapper

diff --git a/docs/pages/use_cases/paradisec.md b/docs/pages/use_cases/paradisec.md
@@ -1,5 +1,7 @@
 ---
 page_id: paradisec
+redirect_from:
+    - /in-use/paradisec
 title: PARADISEC
 description: Modern PARADISEC demonstrates the use of RO-Crate to describe the collections and items
 url: https://arkisto-platform.github.io/case-studies/paradisec/

diff --git a/docs/pages/use_cases/ro-compose.md b/docs/pages/use_cases/ro-compose.md
@@ -1,5 +1,7 @@
 ---
 page_id: ro-compose
+redirect_from:
+    - /in-use/ro-compose
 title: Research Object Composer
 description: Research Object Composer is a REST API for gradually building and depositing Research Objects according to a pre-defined profile. 
 url: https://github.com/researchobject/research-object-composer

diff --git a/docs/pages/use_cases/rohub.md b/docs/pages/use_cases/rohub.md
@@ -1,5 +1,7 @@
 ---
 page_id: rohub
+redirect_from:
+    - /in-use/rohub
 title: ROHub
 description: ROHub is a solution for the storage, lifecycle management and preservation of scientific work and operational processes via research objects. It makes these resources available to others, allows to publish and release them through a DOI, and allows to discover and reuse pre-existing scientific knowledge.
 url: https://www.rohub.org/

diff --git a/docs/pages/use_cases/sciebo.md b/docs/pages/use_cases/sciebo.md
@@ -1,5 +1,7 @@
 ---
 page_id: sciebo
+redirect_from:
+    - /in-use/sciebo
 title: Sciebo RDS
 description: Sciebo RDS (Research Data Services) is a self-hosted interface between data repositories and file storage solutions, assisting the research data deposition process with annotations made using Describo Online and stored as an RO-Crate
 url: https://cs3mesh4eosc.eu/

diff --git a/docs/pages/use_cases/survey-ontology.md b/docs/pages/use_cases/survey-ontology.md
@@ -1,5 +1,7 @@
 ---
 page_id: survey-ontology
+redirect_from:
+    - /in-use/survey-ontology
 title: Survey Ontology
 description: The Survey Ontology is an open vocabulary that allows representing, annotating and sharing a representation of the survey structure and the gathered responses.
 url: https://w3id.org/survey-ontology

diff --git a/docs/pages/use_cases/uts-cultural.md b/docs/pages/use_cases/uts-cultural.md
@@ -1,5 +1,7 @@
 ---
 page_id: uts-cultural
+redirect_from:
+    - /in-use/uts-cultural
 title: UTS Cultural Datasets
 description: The UTS Cultural Datasets project is collaborating with Humanities and Social Science (HASS) researchers and is re-using existing UTS Data infrastructure to build interactive services that allow people to use the data. 
 url: https://arkisto-platform.github.io/case-studies/uts-cultural/

diff --git a/docs/pages/use_cases/uts-research-data.md b/docs/pages/use_cases/uts-research-data.md
@@ -1,5 +1,7 @@
 ---
 page_id: uts-research-data
+redirect_from:
+    - /in-use/uts-research-data
 title: UTS Research Data Repository
 description: The UTS Research Data Repository is a searchable portal for discovering and accessing public datasets by UTS researchers.
 url: https://arkisto-platform.github.io/case-studies/uts-repo/