# HG changeset patch
# User fubar
# Date 1711950029 0
# Node ID 7bb6259ea52f1165bfb9987d77a81788c9f129c3
# Parent  3dcda36b97b4b3834f82f62f4da4c6e7aa07174c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty

diff -r 3dcda36b97b4 -r 7bb6259ea52f jbrowse2.py
--- a/jbrowse2.py	Mon Apr 01 04:35:23 2024 +0000
+++ b/jbrowse2.py	Mon Apr 01 05:40:29 2024 +0000
@@ -403,9 +403,7 @@
     def __init__(self, outdir, jbrowse2path):
         self.assemblies = []  # these require more than a few line diff.
         self.assmeta = {}
-        self.ass_first_contigs = (
-            []
-        )  # for default session - these are read as first line of the assembly .fai
+        self.ass_first_contigs = []  # for default session - these are read as first line of the assembly .fai
         self.giURL = GALAXY_INFRASTRUCTURE_URL
         self.outdir = outdir
         self.jbrowse2path = jbrowse2path
@@ -1372,6 +1370,7 @@
             config_json.update(self.config_json)
         if "defaultSession" in config_json:
             session_json = config_json["defaultSession"]
+            session_views = []
         else:
             session_json = {}
             session_views = []
@@ -1404,30 +1403,37 @@
             # paf genomes have no tracks associated so nothing for the view
             if len(tracks_data) > 0:
                 view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
-                refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
-                drdict = {
-                    "reversed": False,
-                    "assemblyName": gnome,
-                    "start": 0,
-                    "end": 100000,
-                    "refName": refName,
-                }
-                ddl = default_data.get("defaultLocation", None)
-                if ddl:
-                    loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
-                    # allow commas like 100,000 but ignore as integer
-                    if loc_match:
-                        refName = loc_match.group(1)
-                        drdict["refName"] = refName
-                        if loc_match.group(2) > "":
-                            drdict["start"] = int(loc_match.group(2).replace(",", ""))
-                        if loc_match.group(3) > "":
-                            drdict["end"] = int(loc_match.group(3).replace(",", ""))
-                    else:
-                        logging.info(
-                            "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
-                            % ddl
-                        )
+                logging.debug("Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs))
+                first = [x for x in self.ass_first_contigs if x[0] == gnome]
+                if len(first) > 0:
+                    [gnome, refName, end] = first[0]
+                    start = 1
+                    end = int(end)
+                    refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
+                    drdict = {
+                        "reversed": False,
+                        "assemblyName": gnome,
+                        "start": start,
+                        "end": end,
+                        "refName": refName,
+                    }
+                else:
+                    ddl = default_data.get("defaultLocation", None)
+                    if ddl:
+                        loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
+                        # allow commas like 100,000 but ignore as integer
+                        if loc_match:
+                            refName = loc_match.group(1)
+                            drdict["refName"] = refName
+                            if loc_match.group(2) > "":
+                                drdict["start"] = int(loc_match.group(2).replace(",", ""))
+                            if loc_match.group(3) > "":
+                                drdict["end"] = int(loc_match.group(3).replace(",", ""))
+                        else:
+                            logging.info(
+                                "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
+                                % ddl
+                            )
                 if drdict.get("refName", None):
                     # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
                     view_json["displayedRegions"] = [
@@ -1436,7 +1442,7 @@
                     logging.info("@@@ defaultlocation %s for default session" % drdict)
                 else:
                     logging.info(
-                        "@@@ no contig name found for default session - please add one!"
+                        "@@@ no track location for default session - please add one!"
                     )
                 session_views.append(view_json)
         session_name = default_data.get("session_name", "New session")
@@ -1490,16 +1496,6 @@
             logging.debug("first contig=%s" % self.ass_first_contigs)
             [gnome, refName, end] = first_contig
             start = 0
-            # if False or data.get("defaultLocation", ""):
-                # loc_match = re.search(
-                    # r"^([^:]+):([\d,]*)\.*([\d,]*)$", data["defaultLocation"]
-                # )
-                # # loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"])
-                # if loc_match:
-                    # refName = loc_match.group(1)
-                    # start = int(loc_match.group(2))
-                    # end = int(loc_match.group(3))
-            # else:
             aview = {
                 "assembly": gnome,
                 "loc": "{}:{}..{}".format(refName, start, end),
@@ -1752,6 +1748,6 @@
     jc.config_json["assemblies"] = assconf
     logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
     jc.write_config()
-    # jc.add_default_session(default_session_data)
+    jc.add_default_session(default_session_data)
     jc.add_defsess_to_index(default_session_data)
     # jc.text_index() not sure what broke here.