restore DASH-1211

CONTRIBUTORS.yaml

@@ -1557,6 +1557,10 @@ sylviamahara:
     github: false
     joined: 2022-03
 
+tb143:
+    name: Tim Beck
+    joined: 2023-09
+
 tduigou:
     name: Thomas Duigou
     email: [email protected]
@@ -1733,6 +1737,17 @@ yvanlebras:
     elixir_node: fr
 
 
+paulzierep:
+    name: Paul Zierep
+    email: [email protected]
+    orcid: 0000-0003-2982-388X
+    joined: 2023-02
+
+SNG888:
+    name: Sandra Ng
+    email: [email protected]
+    joined: 2023-07
+
 # Funders / External Entities
 carpentries:
     name: The Carpentries

_config.yml

@@ -164,7 +164,6 @@ icon-tag:
   param-select: fas fa-filter
   param-text: fas fa-pencil-alt
   param-toggle: fas fa-toggle-on
-  point-right: fa fa-hand-o-right
   pref-info: fas fa-user
   pref-password: fas fa-unlock-alt
   pref-identities: far fa-id-card-o

bin/lint.rb

@@ -684,21 +684,6 @@ def self.check_bolded_heading(contents)
     end
   end
 
-  def self.zenodo_api(contents)
-    find_matching_texts(contents, /(zenodo\.org\/api\/files\/)/)
-      .map do |idx, _text, selected|
-      ReviewDogEmitter.error(
-        path: @path,
-        idx: idx,
-        match_start: selected.begin(1),
-        match_end: selected.end(1) + 1,
-        replacement: nil,
-        message: 'The Zenodo.org/api URLs are not stable, you must use a URL of the format zenodo.org/record/..., apologies we cannot fix automatically.',
-        code: 'GTN:032'
-      )
-    end
-  end
-
   def self.fix_md(contents)
     [
       *fix_notoc(contents),
@@ -722,8 +707,7 @@ def self.fix_md(contents)
       *check_useless_box_prefix(contents),
       *check_bad_heading_order(contents),
       *check_bolded_heading(contents),
-      *snippets_too_close_together(contents),
-      *zenodo_api(contents),
+      *snippets_too_close_together(contents)
     ]
   end
 

topics/admin/tutorials/data-library/tutorial.md

@@ -206,18 +206,18 @@ We've included this file in the example data libraries repository we cloned at t
 >   description: some data
 >   synopsis: samples collected from somewhere
 > items:
-> - url: https://zenodo.org/records/582600/files/wildtype.fna
+> - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/wildtype.fna
 >   src: url
 >   ext: fasta
 >   info: https://doi.org/10.5281/zenodo.582600
 > - name: A directory
 >   description: Exome sequencing means that all protein-coding genes in a genome are
 >   items:
->   - url: https://zenodo.org/records/582600/files/mutant_R1.fastq
+>   - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R1.fastq
 >     src: url
 >     ext: fastqsanger
 >     info: https://doi.org/10.5281/zenodo.582600
->   - url: https://zenodo.org/records/582600/files/mutant_R2.fastq
+>   - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R2.fastq
 >     src: url
 >     ext: fastqsanger
 >     info: https://doi.org/10.5281/zenodo.582600

topics/assembly/tutorials/flye-assembly/tutorial.md

@@ -2,7 +2,7 @@
 layout: tutorial_hands_on
 
 title: 'Genome assembly using PacBio data'
-zenodo_link: 'https://zenodo.org/record/5702408'
+zenodo_link: 'https://zenodo.org/record/5702408#.YZUb5uvjIiU'
 tags:
   - assembly
   - pacbio
@@ -58,12 +58,12 @@ We will use long reads sequencing data: CLR (continuous long reads) from PacBio
 > <hands-on-title>Data upload from Zenodo</hands-on-title>
 >
 > 1. Create a new history for this tutorial
-> 2. Import the files from [Zenodo]({{ page.zenodo_link }})
+> 2. Import the files from [Zenodo](https://zenodo.org/record/5702408)
 >
 >    ```
->    https://zenodo.org/records/5702408/files/SRR8534473_subreads.fastq.gz
->    https://zenodo.org/records/5702408/files/SRR8534474_subreads.fastq.gz
->    https://zenodo.org/records/5702408/files/SRR8534475_subreads.fastq.gz
+>    https://zenodo.org/api/files/d010d8f1-a1fd-4366-991f-916c2f0c55db/SRR8534473_subreads.fastq.gz
+>    https://zenodo.org/api/files/d010d8f1-a1fd-4366-991f-916c2f0c55db/SRR8534474_subreads.fastq.gz
+>    https://zenodo.org/api/files/d010d8f1-a1fd-4366-991f-916c2f0c55db/SRR8534475_subreads.fastq.gz
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}

topics/contributing/tutorials/create-new-tutorial-technical/tutorial.md

@@ -264,7 +264,7 @@ items:
       description: latest
       items:
       - info: https://doi.org/10.5281/zenodo....
-        url: https://zenodo.org/records/URL/files/path/to/input
+        url: https://zenodo.org/api/files/URL/to/the/input/file
         ext: galaxy-datatype
         src: url
 ```

topics/fair/tutorials/fair-clinical/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/fair/tutorials/fair-clinical/tutorial.bib

@@ -0,0 +1,11 @@
+@article{wilkinson,
+  title={The FAIR Guiding Principles for scientific data management and stewardship},
+  author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others},
+  journal={Scientific data},
+  doi = {10.1038/sdata.2016.18},
+  volume={3},
+  number={1},
+  pages={1--9},
+  year={2016},
+  publisher={Nature Publishing Group}
+}