From e4993e6d888aa4359a04ab62ea7b0875db770a79 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 14 Dec 2023 12:17:01 +0100
Subject: [PATCH 1/4] unintrusive fix for converter tests

---
 .../interval_to_bgzip_converter.xml           | 37 ++++++++++++++-----
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 52e1e8d7b98f..6bc11fb5888d 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -40,9 +40,12 @@
     <tests>
         <test>
             <param name="input1" ftype="bed" value="droPer1.bed"/>
-            <output name="output1" ftype="bgzip" value="droPer1.bgzip" decompress="true">
+            <output name="output1" ftype="bgzip" value="droPer1.bgzip">
                 <expand macro="assert_size" value="131"/>
             </output>
+            <output name="output1" ftype="bgzip" decompress="true">
+                <expand macro="assert_size" value="120"/>
+            </output>
             <assert_command>
                 <has_text text="-k1,1 -k2,2n -k3,3n"/>
             </assert_command>
@@ -50,6 +53,9 @@
         <test>
             <param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
             <output name="output1" ftype="bgzip">
+                <expand macro="assert_size" value="141"/>
+            </output>
+            <output name="output1" ftype="bgzip" decompress="true">
                 <expand macro="assert_size" value="143">
                     <has_text_matching expression="^#" negate="true"/>
                 </expand>
@@ -60,9 +66,12 @@
         </test>
         <test>
             <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>
-            <output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
+            <output name="output1" ftype="bgzip">
                 <expand macro="assert_size" value="638"/>
             </output>
+            <output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
+                <expand macro="assert_size" value="3824"/>
+            </output>
             <assert_command>
                 <has_text text="-k1,1 -k4,4n"/>
                 <has_text text="-k5,5" negate="true"/>
@@ -70,20 +79,25 @@
         </test>
         <test>
             <param name="input1" ftype="interval" value="2.interval"/>
-            <output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
+            <output name="output1" ftype="bgzip">
                 <expand macro="assert_size" value="208"/>
             </output>
+            <output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
+                <expand macro="assert_size" value="501"/>
+            </output>
             <assert_command>
                 <has_text text="-k1,1 -k2,2n -k3,3n"/>
             </assert_command>
         </test>
         <test>
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
+            <output name="output1" ftype="bgzip">
+                <expand macro="assert_size" value="321"/>
+            </output>
             <output name="output1" ftype="bgzip" decompress="true">
-                <expand macro="assert_size" value="322">
-                    <!-- will only work with https://github.com/galaxyproject/galaxy/pull/15085
-                        <has_n_lines n="3"/>
-                        <has_text_matching expression="^#" negate="true"/> -->
+                <expand macro="assert_size" value="507">
+                    <has_n_lines n="5"/>
+                    <has_text_matching expression="^#" negate="true"/>
                 </expand>
             </output>
             <assert_command>
@@ -92,9 +106,14 @@
         </test>
         <test>
             <param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
-            <output name="output1" ftype="bgzip" >
+            <output name="output1" ftype="bgzip">
+                <assert_contents>
+                    <has_size value="270" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="output1" ftype="bgzip" decompress="true">
                 <assert_contents>
-                    <has_size value="270" delta="10" />
+                    <has_size value="887"/>
                 </assert_contents>
             </output>
             <assert_command>

From dc8275cb869aac72d8d05b7f127eacd439ff831f Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 14 Dec 2023 12:20:55 +0100
Subject: [PATCH 2/4] slighly more intrusive fix

---
 .../interval_to_bgzip_converter.xml           | 22 +------------------
 1 file changed, 1 insertion(+), 21 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 6bc11fb5888d..fe1df3514d19 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -40,10 +40,7 @@
     <tests>
         <test>
             <param name="input1" ftype="bed" value="droPer1.bed"/>
-            <output name="output1" ftype="bgzip" value="droPer1.bgzip">
-                <expand macro="assert_size" value="131"/>
-            </output>
-            <output name="output1" ftype="bgzip" decompress="true">
+            <output name="output1" ftype="bgzip" value="droPer1.bgzip" decompress="true">
                 <expand macro="assert_size" value="120"/>
             </output>
             <assert_command>
@@ -52,9 +49,6 @@
         </test>
         <test>
             <param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="141"/>
-            </output>
             <output name="output1" ftype="bgzip" decompress="true">
                 <expand macro="assert_size" value="143">
                     <has_text_matching expression="^#" negate="true"/>
@@ -66,9 +60,6 @@
         </test>
         <test>
             <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="638"/>
-            </output>
             <output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
                 <expand macro="assert_size" value="3824"/>
             </output>
@@ -79,9 +70,6 @@
         </test>
         <test>
             <param name="input1" ftype="interval" value="2.interval"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="208"/>
-            </output>
             <output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
                 <expand macro="assert_size" value="501"/>
             </output>
@@ -91,9 +79,6 @@
         </test>
         <test>
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="321"/>
-            </output>
             <output name="output1" ftype="bgzip" decompress="true">
                 <expand macro="assert_size" value="507">
                     <has_n_lines n="5"/>
@@ -106,11 +91,6 @@
         </test>
         <test>
             <param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
-            <output name="output1" ftype="bgzip">
-                <assert_contents>
-                    <has_size value="270" delta="10"/>
-                </assert_contents>
-            </output>
             <output name="output1" ftype="bgzip" decompress="true">
                 <assert_contents>
                     <has_size value="887"/>

From 07bf0d6955fdbdd04c4e33b790a2b0b840209abe Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 14 Dec 2023 14:50:11 +0100
Subject: [PATCH 3/4] Also fix test of the vcf_to_vcf_bgzip_converter

---
 lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
index 41617707e2b9..f6ebadcf1d34 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
@@ -17,7 +17,7 @@
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
             <output name="output1" ftype="vcf_bgzip" value="vcf_bgzip_to_maf_in.vcf_bgzip" decompress="true">
                 <assert_contents>
-                    <has_size value="717" delta="10"/>
+                    <has_size value="1182"/>
                 </assert_contents>
             </output>
         </test>

From 1113f4c7441b49afd0acb8611b16fa91c8c41c1f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 23 Dec 2023 10:34:11 +0100
Subject: [PATCH 4/4] Fix User.current_galaxy_session

---
 lib/galaxy/model/__init__.py          |  4 +++-
 test/unit/data/test_galaxy_mapping.py | 11 +++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 722afb197ff7..c19ec9770bcf 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -10761,7 +10761,9 @@ class CleanupEventImplicitlyConvertedDatasetAssociationAssociation(Base):
 # See https://github.com/sqlalchemy/sqlalchemy/discussions/7638 for approach
 session_partition = select(
     GalaxySession,
-    func.row_number().over(order_by=GalaxySession.update_time, partition_by=GalaxySession.user_id).label("index"),
+    func.row_number()
+    .over(order_by=GalaxySession.update_time.desc(), partition_by=GalaxySession.user_id)
+    .label("index"),
 ).alias()
 partitioned_session = aliased(GalaxySession, session_partition)
 User.current_galaxy_session = relationship(
diff --git a/test/unit/data/test_galaxy_mapping.py b/test/unit/data/test_galaxy_mapping.py
index ccda99693847..1f19f0df8600 100644
--- a/test/unit/data/test_galaxy_mapping.py
+++ b/test/unit/data/test_galaxy_mapping.py
@@ -698,6 +698,17 @@ def _non_empty_flush(self):
         session.add(lf)
         session.flush()
 
+    def test_current_session(self):
+        user = model.User(email="testworkflows@bx.psu.edu", password="password")
+        galaxy_session = model.GalaxySession()
+        galaxy_session.user = user
+        self.persist(user, galaxy_session)
+        assert user.current_galaxy_session == galaxy_session
+        new_galaxy_session = model.GalaxySession()
+        new_galaxy_session.user = user
+        self.persist(user, new_galaxy_session)
+        assert user.current_galaxy_session == new_galaxy_session
+
     def test_flush_refreshes(self):
         # Normally I don't believe in unit testing library code, but the behaviors around attribute
         # states and flushing in SQL Alchemy is very subtle and it is good to have a executable