makeReadme debug

quiltdata · Oct 23, 2024 · eab05c6 · eab05c6
1 parent 06eaf21
commit eab05c6
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -78,7 +78,7 @@ ${nextflow}
 
 ### Processes
 
-`${meta['workflow']['stats']['processes']}`
+`${meta['workflow']?.get('stats')?.get('processes')}`
 '''
     private final static String DEFAULT_SUMMARIZE = '*.md,*.html,*.?sv,*.pdf,igv.json,**/multiqc_report.html'
 
@@ -239,7 +239,7 @@ ${nextflow}
             text = makeReadme()
         }
         catch (Exception e) {
-            log.error("setupReadme failed: ${e.getMessage()}", pkg.meta)
+            log.error("setupReadme failed: ${e.getMessage()}\n{$e}", pkg.meta)
         }
         if (text != null && text.length() > 0) {
             //log.debug("setupReadme: ${text.length()} bytes")
@@ -261,15 +261,17 @@ ${nextflow}
             ?.replace('nextflow.NextflowMeta(', '  - **')\
             ?.replace(')', '```')
             ?.replace(':', '**: ```')
-        String template = engine.createTemplate(raw_readme).make([
+        Map params = [
             cmd: cmd,
             meta: meta,
             msg: msg,
             nextflow: nextflow,
             now: now(),
             pkg: pkg.packageName,
-        ])
-        // log.debug("readme.template: ${template}")
+        ]
+        log.debug("makeReadme.params: ${params}")
+        String template = engine.createTemplate(raw_readme).make(params)
+        log.debug("makeReadme.template: ${template}")
         return template
     }
 

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
@@ -50,7 +50,6 @@ class QuiltProductTest extends QuiltSpecification {
             getParams() >> [outdir: url]
             isSuccess() >> success
             config >> [quilt: [metadata: [cfkey: 'cfval']], runName: 'my-run', publishing: false]
-            workflow >> [stats: [processes: 1, threads: 1]]
         }
         return new QuiltProduct(pathify, session)
     }
@@ -136,6 +135,7 @@ class QuiltProductTest extends QuiltSpecification {
         def files = defaultREADME.pkg.folder.list().sort()
 
         then:
+        false
         !defaultREADME.shouldSkip(QuiltProduct.KEY_README)
         files.size() == 1