From cb25669f3d622ac1cc650a4bdc2cce3e1cb778cf Mon Sep 17 00:00:00 2001
From: hujambo-dunia <michelle.savage.1@gmail.com>
Date: Thu, 25 Jul 2024 18:00:00 -0400
Subject: [PATCH 1/4] Fix for Numeric form field to allow Null min/max values
 in validation methods

---
 client/src/components/Form/Elements/FormNumber.vue | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Form/Elements/FormNumber.vue b/client/src/components/Form/Elements/FormNumber.vue
index efdd9bfbd935..e9b5d8cba604 100644
--- a/client/src/components/Form/Elements/FormNumber.vue
+++ b/client/src/components/Form/Elements/FormNumber.vue
@@ -38,11 +38,13 @@ export default {
             type: [Number, String],
             required: false,
             default: undefined,
+            validator: (prop) => typeof prop == "number" || prop === null,
         },
         max: {
             type: [Number, String],
             required: false,
             default: undefined,
+            validator: (prop) => typeof prop == "number" || prop === null,
         },
         workflowBuildingMode: {
             type: Boolean,
@@ -74,7 +76,7 @@ export default {
             return this.workflowBuildingMode ? "text" : "number";
         },
         isRangeValid() {
-            return !isNaN(this.min) && !isNaN(this.max) && this.max > this.min;
+            return typeof this.min == "number" && typeof this.max == "number" && this.max > this.min;
         },
         isInteger() {
             return this.type.toLowerCase() === "integer";
@@ -124,10 +126,15 @@ export default {
             }
         },
         isOutOfRange(value) {
-            return this.isRangeValid && (value > this.max || value < this.min);
+            /* If value=null, then value is within range. */
+            return (
+                (typeof this.max == "number" && value > this.max) || (typeof this.min == "number" && value < this.min)
+            );
         },
         showOutOfRangeWarning(value) {
-            const warningMessage = `${value} is out of ${this.min} - ${this.max} range!`;
+            const rangeDetail =
+                typeof this.max == "number" && value > this.max ? `${value} > ${this.max}` : `${value} < ${this.min}`;
+            const warningMessage = `${value} is out of range! (${rangeDetail})`;
             this.showAlert(warningMessage);
         },
         resetAlert() {

From dd902c4d28d38f09b540c40406a74fad8f291c70 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 29 Jul 2024 16:15:33 +0200
Subject: [PATCH 2/4] Add deprecation warning for csfasta

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 315525bc6183..e69935fa90c4 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -114,7 +114,11 @@
     <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
     <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="false"/>
     <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="false"/>
-    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
+    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true">
+        <upload_warning>
+          SOLID Color-Space sequence data is a rare data type. Consider selecting fasta instead.
+        </upload_warning>
+    </datatype>
     <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
     <datatype extension="gz" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>

From 68b9f64a97d6ee25f4f13e001fcf4bcd073a7d7b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 29 Jul 2024 16:20:40 +0200
Subject: [PATCH 3/4] Add deprecation warning for solexa, illumina quality
 encoding

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index e69935fa90c4..0e026b5a7b0a 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -152,6 +152,9 @@
     </datatype>
     <datatype extension="fastqsolexa" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="Solexa variant of the FASTQ format: solexa+64" description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa">
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+      <upload_warning>
+        Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
     </datatype>
     <datatype extension="fastqcssanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true" description="sequence in in color space phred scored quality values 0:93 represented by ASCII 33:126">
       <upload_warning>
@@ -161,6 +164,9 @@
     </datatype>
     <datatype extension="fastqillumina" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true" description="Sanger variant of the FASTQ format: phred+64">
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+      <upload_warning>
+        Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
     </datatype>
     <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
     <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>

From 50cf5e60b74729f3758caf2080d73bf2ab095d1e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 30 Jul 2024 11:27:00 -0400
Subject: [PATCH 4/4] Don't enable session replay by default -- we're going to
 have users opt in to this.

---
 client/src/onload/globalInits/initSentry.js | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/client/src/onload/globalInits/initSentry.js b/client/src/onload/globalInits/initSentry.js
index c5a32648bd04..9815743e8a3c 100644
--- a/client/src/onload/globalInits/initSentry.js
+++ b/client/src/onload/globalInits/initSentry.js
@@ -19,9 +19,7 @@ export const initSentry = (galaxy, config) => {
         Sentry.init({
             Vue,
             dsn: sentry_dsn_public,
-            integrations: [Sentry.browserTracingIntegration({ router }), Sentry.replayIntegration()],
-            replaysSessionSampleRate: 0,
-            replaysOnErrorSampleRate: 1.0,
+            integrations: [Sentry.browserTracingIntegration({ router })],
             release: release,
             beforeSend(event, hint) {
                 const error = hint.originalException;