From 7530f39dfbb0c52e62372d7707283557f97e3721 Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Tue, 26 Nov 2024 14:04:44 -0800
Subject: [PATCH 1/5] avoid stringifying value

---
 .../nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy  | 4 ++--
 wf/ids.csv                                                    | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)
 create mode 100644 wf/ids.csv

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 60ea4f7d..6510001b 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -80,8 +80,8 @@ class QuiltPackage {
     static String toJson(Map dict) {
         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("toJson.${key}: ${value.size()}")
+            String suffix = "toJson.error[${value.size()}]"
             try {
                 suffix = JsonOutput.toJson(value)
             }
diff --git a/wf/ids.csv b/wf/ids.csv
new file mode 100644
index 00000000..39f12f74
--- /dev/null
+++ b/wf/ids.csv
@@ -0,0 +1 @@
+SRR9984183
\ No newline at end of file

From 4dacfbd68eb237096befc247e2f36922e57bf862 Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Tue, 26 Nov 2024 16:27:36 -0800
Subject: [PATCH 2/5] revert value.size

---
 .../nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 6510001b..fa9b1789 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -80,8 +80,8 @@ class QuiltPackage {
     static String toJson(Map dict) {
         List<String> entries = dict.collect { key, value ->
             String prefix = JsonOutput.toJson(key)
-            log.debug("toJson.${key}: ${value.size()}")
-            String suffix = "toJson.error[${value.size()}]"
+            log.debug("toJson.${key}: ${value}")
+            String suffix = "toJson.error[${value}]"
             try {
                 suffix = JsonOutput.toJson(value)
             }

From 59376c4392a6e2e063856fe993f9e2832fc2883d Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Tue, 26 Nov 2024 17:04:15 -0800
Subject: [PATCH 3/5] Fix READONLY_URL

---
 .../src/test/nextflow/quilt/jep/QuiltPackageTest.groovy      | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy
index e3199ec9..86a38368 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy
@@ -40,7 +40,8 @@ class QuiltPackageTest extends QuiltSpecification {
 
     private final static String PACKAGE_URL = 'quilt+s3://quilt-example#package=examples%2fsmart-report@d68a7e9'
     private final static String TEST_URL = PACKAGE_URL + '&path=README.md'
-    private final static String READONLY_URL = 'quilt+s3://allencell#package=test%2ftmp&path=foo%2fbar.txt'
+    private final static String RO_FILE='&path=aics_mnist.ipynb'
+    private final static String READONLY_URL = "quilt+s3://allencell#package=aics/aics_mnist" + RO_FILE
 
     private QuiltPathFactory factory
     private QuiltPath qpath
@@ -195,7 +196,7 @@ class QuiltPackageTest extends QuiltSpecification {
         def qout = factory.parseUri(READONLY_URL)
         def opkg = qout.pkg()
         opkg.install()
-        def outPath = Paths.get(opkg.packageDest().toString(), 'foo/bar.txt')
+        def outPath = Paths.get(opkg.packageDest().toString(), RO_FILE)
         Files.writeString(outPath, "Time: ${timestamp}")
         expect:
         Files.exists(outPath)

From d318efb88f182f9263335257e0a74ba33b309cef Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:31:15 -0800
Subject: [PATCH 4/5] reproduce fetchngs error

---
 Makefile | 8 ++++++++
 VERSION  | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index cac87772..18eb40f5 100644
--- a/Makefile
+++ b/Makefile
@@ -3,11 +3,13 @@ PROJECT ?= nf-quilt
 WRITE_BUCKET ?= udp-spec
 FRAGMENT ?= &path=.
 NF_DIR ?= ../nextflow
+NF_GIT ?= $(NF_DIR)/nextflow
 NF_BIN ?= ./launch.sh
 PID ?= $$$$
 PIPELINE ?= sarek
 QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com
 VERSION ?= $(shell grep 'Plugin-Version' plugins/$(PROJECT)/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
+NXF_VER ?= $(shell cat VERSION)
 TEST_URI ?= quilt+s3://$(WRITE_BUCKET)$(QUERY)\#package=nf-quilt/dest-$(VERSION)$(FRAGMENT)
 PIPE_OUT ?=  quilt+s3://$(WRITE_BUCKET)\#package=$(PROJECT)/$(PIPELINE)
 S3_BASE = s3://$(WRITE_BUCKET)/$(PROJECT)
@@ -107,6 +109,12 @@ $(PIPELINE): $(NF_BIN) install
 	$(NF_BIN) pull nf-core/$(PIPELINE)
 	$(NF_BIN) run nf-core/$(PIPELINE) -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(PIPE_OUT)"
 
+fetchngs: $(NF_GIT)
+	NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/fetchngs -profile test,docker --input wf/ids.csv --outdir "s3://$(WRITE_BUCKET)/nf-quilt/fetchngs"
+
+nf-git-ver: $(NF_GIT)
+	NXF_VER=$(NXF_VER) $(NF_GIT) -v
+
 #
 # Show dependencies
 #
diff --git a/VERSION b/VERSION
index 27459e72..95795064 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.04.3
+24.10.2

From 646f056eb8fa8f7b63bf3bc29aaad7402f587bbd Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:59:19 -0800
Subject: [PATCH 5/5] run fetchngs locally

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 18eb40f5..aab5a542 100644
--- a/Makefile
+++ b/Makefile
@@ -110,7 +110,7 @@ $(PIPELINE): $(NF_BIN) install
 	$(NF_BIN) run nf-core/$(PIPELINE) -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(PIPE_OUT)"
 
 fetchngs: $(NF_GIT)
-	NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/fetchngs -profile test,docker --input wf/ids.csv --outdir "s3://$(WRITE_BUCKET)/nf-quilt/fetchngs"
+	NXF_VER=$(NXF_VER) $(NF_BIN) run quiltdata/fetchngs -r master -profile test,docker --input wf/ids.csv --outdir "s3://$(WRITE_BUCKET)/nf-quilt/fetchngs"
 
 nf-git-ver: $(NF_GIT)
 	NXF_VER=$(NXF_VER) $(NF_GIT) -v