From 6c4ce2678d01f773a29c3820cef0051314342683 Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <ernest@quiltdata.io>
Date: Tue, 5 Nov 2024 10:26:38 -0800
Subject: [PATCH] Fix To json errors (#260)

Java has brain-dead JSON handling, and I didn't properly try/catch that
part...

---------

Co-authored-by: Dr. Ernie Prabhakar <19791+drernie@users.noreply.github.com>
---
 CHANGELOG.md                                  |  4 ++++
 .../main/nextflow/quilt/QuiltProduct.groovy   | 23 +++++++++++++------
 .../nextflow/quilt/jep/QuiltPackage.groovy    |  2 +-
 .../src/resources/META-INF/MANIFEST.MF        |  2 +-
 4 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ba2d32b7..3fca9e5c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,10 @@
 - Improve handling of dynamically-specified URIs
 - Rewrite README.md, splitting out developer documentation to README_DEV.md
 
+## [0.8.11] 2024-11-5 UNPUBLISHED
+
+- Catch *all* toJson errors
+
 ## [0.8.10] 2024-11-4 UNPUBLISHED
 
 - Ignore publish to 'home'
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
index a87c4e58..392337e2 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -207,8 +207,12 @@ ${nextflow}
 
     String writeNextflowMetadata(Map map, String suffix) {
         String filename = "nf-quilt/${suffix}.json"
-        // log.debug("writeNextflowMetadata[$suffix]: ${filename}")
-        writeString(QuiltPackage.toJson(map), pkg, filename)
+        log.debug("writeNextflowMetadata[$suffix]: ${filename}")
+        try {
+            writeString(QuiltPackage.toJson(map), pkg, filename)
+        } catch (Exception e) {
+            log.error("writeNextflowMetadata.toJson failed: ${e.getMessage()}", map)
+        }
         return filename
     }
 
@@ -227,7 +231,7 @@ ${nextflow}
             writeNextflowMetadata(params, 'params')
             params.remove('genomes')
             params.remove('test_data')
-        // printMap(params, 'params')
+            printMap(params, 'params')
         }
         Map wf = session.getWorkflowMetadata().toMap()
         String start = wf['start']
@@ -241,7 +245,7 @@ ${nextflow}
             wf.remove('complete')
             wf.remove('workflowStats')
             wf.remove('commandLine')
-            // printMap(wf, 'workflow')
+            printMap(wf, 'workflow')
             log.info("\npublishing: ${wf['runName']}")
         }
 
@@ -264,7 +268,7 @@ ${nextflow}
             log.error("setupReadme failed: ${e.getMessage()}\n{$e}", pkg.meta)
         }
         if (text != null && text.length() > 0) {
-            //log.debug("setupReadme: ${text.length()} bytes")
+            log.debug("setupReadme: ${text.length()} bytes")
             writeString(text, pkg, README_FILE)
         }
         return text
@@ -342,8 +346,13 @@ ${nextflow}
             }
         }
 
-        String qs_json = JsonOutput.toJson(quilt_summarize)
-        writeString(qs_json, pkg, SUMMARY_FILE)
+        try {
+            String qs_json = JsonOutput.toJson(quilt_summarize)
+            writeString(qs_json, pkg, SUMMARY_FILE)
+        }
+        catch (Exception e) {
+            log.error("setupSummarize.toJson failed: ${e.getMessage()}\n{$e}", SUMMARY_FILE)
+        }
         return quilt_summarize
     }
 
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
index 537305ac..60ea4f7d 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -81,7 +81,7 @@ class QuiltPackage {
         List<String> entries = dict.collect { key, value ->
             String prefix = JsonOutput.toJson(key)
             String suffix = "toJson.error: ${value}"
-            // log.debug("QuiltPackage.toJson: ${prefix} [${suffix.length()}]")
+            log.debug("QuiltPackage.toJson: ${prefix} [${suffix.length()}]")
             try {
                 suffix = JsonOutput.toJson(value)
             }
diff --git a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF b/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF
index d1ec193e..d7d518e3 100644
--- a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF
@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.quilt.QuiltPlugin
 Plugin-Id: nf-quilt
-Plugin-Version: 0.8.10
+Plugin-Version: 0.8.11
 Plugin-Provider: Quilt Data
 Plugin-Requires: >=22.10.6