Merge pull request #4845 from Marie59/argo

Add tuto Argo

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,
@@ -1057,15 +1057,19 @@ def self.fix_file(path)
       possible_tests = Dir.glob("#{folder}/#{Regexp.escape(basename)}*ym*")
       possible_tests = possible_tests.grep(/#{Regexp.escape(basename)}[_-]tests?.ya?ml/)
 
+      contains_interactive_tool = contents.match(/interactive_tool_/)
+
       if possible_tests.empty?
-        results += [
-          ReviewDogEmitter.file_error(path: path,
-                                      message: 'This workflow is missing a test, which is now mandatory. Please ' \
-                                               'see [the FAQ on how to add tests to your workflows](' \
-                                               'https://training.galaxyproject.org/training-material/faqs/' \
-                                               'gtn/gtn_workflow_testing.html).',
-                                      code: 'GTN:027')
-        ]
+        if !contains_interactive_tool
+          results += [
+            ReviewDogEmitter.file_error(path: path,
+                                        message: 'This workflow is missing a test, which is now mandatory. Please ' \
+                                                 'see [the FAQ on how to add tests to your workflows](' \
+                                                 'https://training.galaxyproject.org/training-material/faqs/' \
+                                                 'gtn/gtn_workflow_testing.html).',
+                                        code: 'GTN:027')
+          ]
+        end
       else
         # Load tests and run some quick checks:
         possible_tests.each do |test_file|
@@ -1079,9 +1083,10 @@ 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/argo_pangeo/faqs/index.md

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

topics/climate/tutorials/argo_pangeo/tutorial.bib

@@ -0,0 +1,14 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#

topics/climate/tutorials/argo_pangeo/workflows/index.md

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

topics/climate/tutorials/argo_pangeo/workflows/main_workflow.ga

@@ -0,0 +1,224 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)",
+    "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": "Analyse Argo data ",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0",
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [],
+            "label": null,
+            "name": "Argo data access",
+            "outputs": [
+                {
+                    "name": "output_argo",
+                    "type": "netcdf"
+                }
+            ],
+            "position": {
+                "left": 0,
+                "top": 54.980682128906295
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "055a934a380f",
+                "name": "argo_getdata",
+                "owner": "ecology",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"dataset\": {\"data_dataset\": \"phy\", \"__current_case__\": 0}, \"selection\": {\"data_selection\": \"space_time\", \"__current_case__\": 0, \"cardinal_1\": \"-75.0\", \"cardinal_2\": \"-45.0\", \"cardinal_3\": \"20.0\", \"cardinal_4\": \"30.0\", \"pressure_1\": \"0.0\", \"pressure_2\": \"10.0\", \"date_1\": \"2021-04\", \"date_2\": \"2021-06\"}, \"user\": \"expert\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.1.15+galaxy0",
+            "type": "tool",
+            "uuid": "6e71455c-12ce-45f8-92bb-6256311203d7",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "input": {
+                    "id": 0,
+                    "output_name": "output_argo"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "NetCDF xarray Coordinate Info",
+            "outputs": [
+                {
+                    "name": "output_dir",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 324,
+                "top": 0
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "663e6f115a76",
+                "name": "xarray_coords_info",
+                "owner": "ecology",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2022.3.0+galaxy0",
+            "type": "tool",
+            "uuid": "00cdb789-2e2b-4e17-bd8c-a6d60486de79",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+galaxy0",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "input": {
+                    "id": 0,
+                    "output_name": "output_argo"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "NetCDF xarray Metadata Info",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "tabular"
+                },
+                {
+                    "name": "info",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 324,
+                "top": 144.63333129882812
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "00de53d18b99",
+                "name": "xarray_metadata_info",
+                "owner": "ecology",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2022.3.0+galaxy0",
+            "type": "tool",
+            "uuid": "3b31d6ac-8f88-41d4-bf7c-069f3bcc5523",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "input": {
+                    "id": 0,
+                    "output_name": "output_argo"
+                },
+                "var_tab": {
+                    "id": 2,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "NetCDF timeseries Extractor",
+            "outputs": [
+                {
+                    "name": "timeseries_tabular",
+                    "type": "tabular"
+                },
+                {
+                    "name": "timeseries_plot",
+                    "type": "png"
+                }
+            ],
+            "position": {
+                "left": 626,
+                "top": 52.98333740234375
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "810820a0d45c",
+                "name": "timeseries_extraction",
+                "owner": "ecology",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"plot_title\": \"Temperature\", \"xlabel\": \"Time\", \"ylabel\": \"Temperature\", \"format_date\": \"\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"condi_datetime\": {\"datetime\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lat_name\": null, \"lat_value\": null, \"lon_name\": null, \"lon_value\": null, \"var\": \"TEMP\", \"var_tab\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2022.3.0+galaxy0",
+            "type": "tool",
+            "uuid": "27d4b2e9-d4be-4b2a-a5ba-dac7ba612688",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "4": {
+            "annotation": "",
+            "content_id": "interactive_tool_odv",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "method|infiles": {
+                    "id": 3,
+                    "output_name": "timeseries_tabular"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "ODV",
+            "outputs": [
+                {
+                    "name": "outputs_netcdf",
+                    "type": "input"
+                },
+                {
+                    "name": "outputs_all",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 933,
+                "top": 74.98333740234375
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_odv",
+            "tool_state": "{\"__input_ext\": \"tabular\", \"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": "8a270a89-447e-4ace-b3fb-cc28108ccf07",
+            "when": null,
+            "workflow_outputs": []
+        }
+    },
+    "tags": [
+        "Ocean",
+        "Pangeo",
+        "earth-system"
+    ],
+    "uuid": "623f64bf-51b2-4a7e-8985-a61e1250be1b",
+    "version": 5
+}

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.