Add checking for bad TRS links

EngyNasr · Apr 16, 2024 · 2554e94 · 2554e94
1 parent 8cc3b4a
commit 2554e94
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Showing 3 changed files with 21 additions and 2 deletions.
diff --git a/bin/lint.rb b/bin/lint.rb
@@ -611,6 +611,24 @@ def self.check_bad_link(contents)
     end
   end
 
+  def self.check_bad_trs_link(contents)
+    find_matching_texts(contents, /snippet faqs\/galaxy\/workflows_run_trs.md path="([^"]*)"/i)
+      .map do |idx, _text, selected|
+      path = selected[1].to_s.strip
+      if !File.exist?(path)
+        ReviewDogEmitter.error(
+          path: @path,
+          idx: idx,
+          match_start: selected.begin(0),
+          match_end: selected.end(0),
+          replacement: nil,
+          message: "The linked file (`#{path}`) could not be found.",
+          code: 'GTN:036'
+        )
+      end
+    end
+  end
+
   def self.check_looks_like_heading(contents)
     # TODO: we should remove this someday, but, we need to have a good solution
     # and we're still a ways from that.
@@ -806,6 +824,7 @@ def self.fix_md(contents)
       *snippets_too_close_together(contents),
       *zenodo_api(contents),
       *empty_alt_text(contents),
+      *check_bad_trs_link(contents),
       *nonsemantic_list(contents)
     ]
   end

diff --git a/topics/galaxy-interface/tutorials/workflow-reports/tutorial.md b/topics/galaxy-interface/tutorials/workflow-reports/tutorial.md
@@ -62,7 +62,7 @@ We will start by importing this workflow into your Galaxy account:
 >
 > 1. **Import the workflow** into Galaxy
 >
->    {% snippet faqs/galaxy/workflows_run_trs.md path="/topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.ga" title="Galaxy 101 for Everyone" %}
+>    {% snippet faqs/galaxy/workflows_run_trs.md path="topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.ga" title="Galaxy 101 for Everyone" %}
 >
 >
 {: .hands_on}

diff --git a/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.md b/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.md
@@ -256,7 +256,7 @@ In this section, you can run the RetroSynthesis Workflow more easily and fastly
 >
 > 1. Import the workflow into Galaxy
 >
->    {% snippet faqs/galaxy/workflows_run_trs.md path="topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/RetroSynthesis.ga" title="RetroSynthesis workflow" %}
+>    {% snippet faqs/galaxy/workflows_run_trs.md path="topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.ga" title="RetroSynthesis workflow" %}
 >
 > 2. Click on *Workflow* on the top menu bar of Galaxy. You will see **RetroSynthesis** workflow.
 > 3. Click on the {% icon workflow-run %} (*Run workflow*) button next to your workflow