Merge branch 'release_23.1' into release_23.2

galaxyproject · Dec 23, 2023 · 7105af4 · 7105af4
2 parents 4fa0403 + 687bcf9
commit 7105af4
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Showing 4 changed files with 24 additions and 12 deletions.
diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -41,15 +41,15 @@
         <test>
             <param name="input1" ftype="bed" value="droPer1.bed"/>
             <output name="output1" ftype="bgzip" value="droPer1.bgzip" decompress="true">
-                <expand macro="assert_size" value="131"/>
+                <expand macro="assert_size" value="120"/>
             </output>
             <assert_command>
                 <has_text text="-k1,1 -k2,2n -k3,3n"/>
             </assert_command>
         </test>
         <test>
             <param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
-            <output name="output1" ftype="bgzip">
+            <output name="output1" ftype="bgzip" decompress="true">
                 <expand macro="assert_size" value="143">
                     <has_text_matching expression="^#" negate="true"/>
                 </expand>
@@ -61,7 +61,7 @@
         <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">
-                <expand macro="assert_size" value="638"/>
+                <expand macro="assert_size" value="3824"/>
             </output>
             <assert_command>
                 <has_text text="-k1,1 -k4,4n"/>
@@ -71,7 +71,7 @@
         <test>
             <param name="input1" ftype="interval" value="2.interval"/>
             <output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
-                <expand macro="assert_size" value="208"/>
+                <expand macro="assert_size" value="501"/>
             </output>
             <assert_command>
                 <has_text text="-k1,1 -k2,2n -k3,3n"/>
@@ -80,10 +80,9 @@
         <test>
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
             <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 +91,9 @@
         </test>
         <test>
             <param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
-            <output name="output1" ftype="bgzip" >
+            <output name="output1" ftype="bgzip" decompress="true">
                 <assert_contents>
-                    <has_size value="270" delta="10" />
+                    <has_size value="887"/>
                 </assert_contents>
             </output>
             <assert_command>

diff --git 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>

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -11004,7 +11004,9 @@ def __repr__(self):
 # 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
@@ -692,6 +692,17 @@ def _non_empty_flush(self):
         session.add(lf)
         session.flush()
 
+    def test_current_session(self):
+        user = model.User(email="[email protected]", 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