# HG changeset patch
# User fubar
# Date 1711621867 0
# Node ID c8190283090099a932fd61bfd005899308452fc6
# Parent  497fd2d27aa2ff0c8a80916feab03b579248034a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e

diff -r 497fd2d27aa2 -r c81902830900 autogenJB2.py
--- a/autogenJB2.py	Thu Mar 28 09:15:57 2024 +0000
+++ b/autogenJB2.py	Thu Mar 28 10:31:07 2024 +0000
@@ -200,11 +200,10 @@
             # "font_size": root.find("metadata/general/font_size").text,
             # }
             # jc.add_general_configuration(general_data)
-            trackconf = jc.config_json.get("tracks", None)
-            if trackconf:
-                jc.config_json["tracks"].update(jc.tracksToAdd)
-            else:
-                jc.config_json["tracks"] = jc.tracksToAdd
+            trackconf = jc.config_json.get("tracks", [])
+            for gnome in jc.genome_names:
+                trackconf += jc.tracksToAdd[gnome]
+            jc.config_json["tracks"] = trackconf
             jc.write_config()
             defLoc = makeDefaultLocation()
             default_session_data.update(
diff -r 497fd2d27aa2 -r c81902830900 jbrowse2.py
--- a/jbrowse2.py	Thu Mar 28 09:15:57 2024 +0000
+++ b/jbrowse2.py	Thu Mar 28 10:31:07 2024 +0000
@@ -15,7 +15,7 @@
 import xml.etree.ElementTree as ET
 from collections import defaultdict
 
-logging.basicConfig(level=logging.INFO)
+logging.basicConfig(level=logging.DEBUG)
 log = logging.getLogger("jbrowse")
 
 JB2VER = "v2.10.3"
@@ -1343,17 +1343,16 @@
                 )
             # The view for the assembly we're adding
             view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
-            refName = None
+            refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
             drdict = {
                 "reversed": False,
                 "assemblyName": gnome,
                 "start": 1,
                 "end": 100000,
-                "refName": "x",
+                "refName": refName
             }
-
-            if default_data.get("defaultLocation", ""):
-                ddl = default_data["defaultLocation"]
+            ddl = default_data.get("defaultLocation", None)
+            if ddl:
                 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
                 # allow commas like 100,000 but ignore as integer
                 if loc_match:
@@ -1368,8 +1367,6 @@
                         "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                         % ddl
                     )
-            else:
-                drdict["refName"] = gnome
             if drdict.get("refName", None):
                 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
                 view_json["displayedRegions"] = [