Update ocean variables tuto

bin/lint.rb

@@ -345,7 +345,7 @@ def self.check_bad_cite(contents)
   def self.check_bad_icon(contents)
     find_matching_texts(contents, /{%\s*icon\s+([^%]*)\s*%}/i)
       .map do |idx, _text, selected|
-      icon_key = selected[1].strip
+      icon_key = selected[1].strip.split[0]
       if jekyll_config['icon-tag'][icon_key].nil?
         ReviewDogEmitter.error(
           path: @path,
@@ -1079,9 +1079,10 @@ def self.fix_file(path)
           end
 
           test = YAML.safe_load(File.open(test_file))
+          test_plain = File.read(test_file)
           # check that for each test, the outputs is non-empty
           test.each do |test_job|
-            if test_job['outputs'].nil? || test_job['outputs'].empty?
+            if (test_job['outputs'].nil? || test_job['outputs'].empty?) && !test_plain.match(/GTN_RUN_SKIP_REASON/)
               results += [
                 ReviewDogEmitter.file_error(path: path,
                                             message: 'This workflow test does not test the contents of outputs, ' \

topics/climate/tutorials/ocean-variables/faqs/index.md

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

topics/climate/tutorials/ocean-variables/tutorial.bib

@@ -12,34 +12,7 @@
 # If you want to cite an online resourse (website etc)
 # you can use the 'online' format (see below)
 #
-# You can remove the examples below
 
-@article{Batut2018,
-  doi = {10.1016/j.cels.2018.05.012},
-  url = {https://doi.org/10.1016/j.cels.2018.05.012},
-  year = {2018},
-  month = jun,
-  publisher = {Elsevier {BV}},
-  volume = {6},
-  number = {6},
-  pages = {752--758.e1},
-  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
-           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
-           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
-           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
-           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
-           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
-           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
-  title = {Community-Driven Data Analysis Training for Biology},
-  journal = {Cell Systems}
-}
-
-@online{gtn-website,
-  author = {GTN community},
-  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
-  url = {https://training.galaxyproject.org},
-  urldate = {2021-03-24}
-}
 
 @misc{hcmrdata,
   doi = {10.13120},
@@ -51,3 +24,13 @@ @misc{hcmrdata
   year = {2022},
   copyright = {Creative Commons Attribution 4.0 International}
 }
+
+@misc{emodnet,
+  doi = {10.13120/8XM0-5M67},
+  url = {https://nodc.ogs.it/catalogs/doidetails?doi=10.13120/8xm0-5m67},
+  author = {Lipizer,  M. and Molina Jack M.,  E. and Wesslander,  K. and Fyrberg,  L. and Tsompanou,  M. and Iona,  A. and Buga,  L. and Sarbu,  G. and Gatti,  J. and Larsen M.,  M. and Giorgetti,  A.},
+  language = {en},
+  title = {EMODnet Chemistry Regional sea eutrophication data collection and Quality Control loop},
+  publisher = {OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale),  Oceanographic Section},
+  year = {2023}
+}

topics/climate/tutorials/ocean-variables/workflows/index.md

@@ -0,0 +1,3 @@
+---
+layout: workflow-list
+---

topics/climate/tutorials/ocean-variables/workflows/main_workflow-tests.yml

@@ -0,0 +1,7 @@
+# GTN_RUN_SKIP_REASON: Uses Interactive Tools
+- doc: Test outline for main_workflow.ga
+  job:
+    Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip:
+      class: File
+      location: https://github.com/fair-ease/Data-for-Galaxy-/raw/main/Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip
+  outputs: {}

topics/climate/tutorials/ocean-variables/workflows/main_workflow.ga

@@ -0,0 +1,165 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Subset data on the Mediterreanean see and extract and visualise the Phosphate variable",
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "0009-0008-0622-604X",
+            "name": "Marie Joss\u00e9",
+            "url": "https://github.com/Marie59"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "CC-BY-4.0",
+    "name": "Ocean's variables",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip"
+                }
+            ],
+            "label": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 2
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "04b96704-a567-4c94-8708-285fe2efb087",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "interactive_tool_odv",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "method|folder": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "ODV",
+            "outputs": [
+                {
+                    "name": "outputs_netcdf",
+                    "type": "input"
+                },
+                {
+                    "name": "outputs_all",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 256,
+                "top": 16
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_odv",
+            "tool_state": "{\"__input_ext\": \"zip\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"zip\", \"__current_case__\": 1, \"folder\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.6.5.1",
+            "type": "tool",
+            "uuid": "6e83d448-87de-48da-9649-95a87a23973c",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "interactive_tool_divand",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "input": {
+                    "id": 1,
+                    "output_name": "outputs_netcdf"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Interactive DIVAnd Notebooks",
+            "outputs": [
+                {
+                    "name": "output_netcdf",
+                    "type": "input"
+                },
+                {
+                    "name": "output_all",
+                    "type": "input"
+                },
+                {
+                    "name": "jupyter_notebook",
+                    "type": "ipynb"
+                }
+            ],
+            "position": {
+                "left": 515,
+                "top": 0
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_divand",
+            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.0.5",
+            "type": "tool",
+            "uuid": "aaa2c97b-cef5-4952-b21e-b4f71a7d6e3b",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "",
+            "content_id": "interactive_tool_odv",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "method|infiles": {
+                    "id": 2,
+                    "output_name": "output_netcdf"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "ODV",
+            "outputs": [
+                {
+                    "name": "outputs_netcdf",
+                    "type": "input"
+                },
+                {
+                    "name": "outputs_all",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 778,
+                "top": 87
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_odv",
+            "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"own_data\", \"__current_case__\": 0, \"infiles\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.6.5.1",
+            "type": "tool",
+            "uuid": "13277c72-e0e3-4353-9c2a-d3440ba1860e",
+            "when": null,
+            "workflow_outputs": []
+        }
+    },
+    "tags": [
+        "earth-system",
+        "Ocean"
+    ],
+    "uuid": "aacfc1b1-2c81-486d-8bed-5eeaef39a818",
+    "version": 2
+}

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

@@ -241,6 +241,16 @@ planemo test \
 
 Planemo will autodetect that the `workflow-test.yml` file and load that for the testing.
 
+### Skipping Testing in the GTN
+
+If for some reason you want to skip this workflow being tested in the GTN,
+please add a comment with `GTN_RUN_SKIP_REASON` in the `-test.yml` file stating
+the reason it is skipped.
+
+This will also exempt you from writing output tests.
+
+A good use case for this is you want to provide a working test, but the workflow takes upwards of 6 hours to execute (e.g. large download jobs.)
+
 # Creating the `data-library.yaml` (recommended)
 
 The datasets needed for a tutorial can also be integrated in the Galaxy instance inside of data libraries. These allow the datasets to be easily shared with all users of a Galaxy instance. Additionally it lets trainees avoid each re-downloading the input data.