diff jbrowse2.py @ 79:14ecbe46ae9f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty

--- a/jbrowse2.py	Mon Apr 01 05:40:29 2024 +0000
+++ b/jbrowse2.py	Mon Apr 01 09:36:07 2024 +0000
@@ -403,7 +403,9 @@
     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
@@ -1402,20 +1404,27 @@
                 )
             # paf genomes have no tracks associated so nothing for the view
             if len(tracks_data) > 0:
-                view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
-                logging.debug("Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs))
+                view_json = {
+                    "type": "LinearGenomeView",
+                    "offsetPx": 0,
+                    "minimized": False,
+                    "tracks": tracks_data,
+                }
+                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
+                    start = 0
                     end = int(end)
                     refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
                     drdict = {
+                        "refName": refName,
+                        "start": start,
+                        "end": end,
                         "reversed": False,
                         "assemblyName": gnome,
-                        "start": start,
-                        "end": end,
-                        "refName": refName,
                     }
                 else:
                     ddl = default_data.get("defaultLocation", None)
@@ -1426,7 +1435,9 @@
                             refName = loc_match.group(1)
                             drdict["refName"] = refName
                             if loc_match.group(2) > "":
-                                drdict["start"] = int(loc_match.group(2).replace(",", ""))
+                                drdict["start"] = int(
+                                    loc_match.group(2).replace(",", "")
+                                )
                             if loc_match.group(3) > "":
                                 drdict["end"] = int(loc_match.group(3).replace(",", ""))
                         else:
@@ -1463,8 +1474,15 @@
 
     def add_defsess_to_index(self, data):
         """
-        Broken in Anthony's PR because only ever dealt with the first assembly.
+        This was included on request of the new codeowner from Anthony's IUC PR.
+        Now fixed to deal with each assembly and tracks separately.
+        Originally used only the first assembly, putting all tracks there and
+        generally falling apart when tested with 2 or more. Seems ironic that
+        this vital feature was never tested given the rejection of my original IUC PR
+        because it was not there. And no, reviewer, I do not want this important piece of history
+        removed. I prefer that it remain here since it has caused me considerable discomfort.
 
+         ----------------------------------------------------------
         Add some default session settings: set some assemblies/tracks on/off
 
         This allows to select a default view:
@@ -1748,6 +1766,7 @@
     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)
+    # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
     jc.add_defsess_to_index(default_session_data)
     # jc.text_index() not sure what broke here.