# HG changeset patch
# User fubar
# Date 1709721469 0
# Node ID 460d5b6c5d9827ad95cdf0d675ee117e79ba422b
# Parent  3e53204c2419f9fc5add24e87857e03f547e689c
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty

diff -r 3e53204c2419 -r 460d5b6c5d98 autogenJB2.py
--- a/autogenJB2.py	Wed Mar 06 00:23:02 2024 +0000
+++ b/autogenJB2.py	Wed Mar 06 10:37:49 2024 +0000
@@ -90,13 +90,14 @@
                 "style": {},
                 "style_labels": {},
             }
-
+            track_conf = {}
             listtracks = trackList
             # foo.paf must have a foo_paf.fasta or fasta.gz to match
             tnames = [x[2] for x in listtracks]
             texts = [x[1] for x in listtracks]
             for i, track in enumerate(listtracks):
                 tpath, trext, trackname = track[:3]
+                track_conf["dataset_id"] = trackname
                 if trext == "paf":
                     refname = trackname + "_paf.fasta"
                     refdat = [x[2] for x in listtracks if x[2] == refname]
@@ -107,13 +108,13 @@
                         )
                         sys.exit(3)
                     else:
-                        track_conf = {
+                        track_conf.update({
                             "conf": {
                                 "options": {
                                     "paf": {"genome": refdat, "genome_label": trackname}
                                 }
                             }
-                        }
+                        })
                 elif trext == "bam":
                     ipath  = track[3]
                     if not os.path.exists(ipath):
@@ -121,7 +122,7 @@
                         cmd = ["samtools", "index", "-b", "-o", ipath, os.path.realpath(track[0])]
                         sys.stdout.write('#### calling %s' % ' '.join(cmd))
                         jc.subprocess_check_call(cmd)
-                    track_conf = {"conf": {"options": {"bam": {"bam_index": ipath}}}}
+                    track_conf.update({"conf": {"options": {"bam": {"bam_index": ipath}}}})
                 elif trext == "cram":
                     ipath  = track[3]
                     if not os.path.exists(ipath):
@@ -130,9 +131,8 @@
                         cmd = ["samtools", "index", "-c", "-o", ipath, os.path.realpath(track[0])]
                         sys.stdout.write('#### calling %s' % ' '.join(cmd))
                         jc.subprocess_check_call(cmd)
-                    track_conf = {"conf": {"options": {"cram": {"cram_index": ipath}}}}
-                else:
-                    track_conf = {}
+                    track_conf.update({"conf": {"options": {"cram": {"cram_index": ipath}}}})
+                track_conf["path"] = tpath
                 track_conf["format"] = trext
                 track_conf["name"] = trackname
                 track_conf["label"] = trackname
@@ -140,9 +140,9 @@
                 useuri = 'no'
                 if useu:
                     useuri = 'yes'
-                track_conf["trackfiles"] = [
-                    (tpath, trext, useuri, trackname, {}),
-                ]
+                    track_conf["trackfiles"] = [
+                        (tpath, trext, useuri, trackname, {}),
+                    ]
                 track_conf["category"] = "Autogenerated"
                 keys = jc.process_annotations(track_conf)
 
diff -r 3e53204c2419 -r 460d5b6c5d98 cert.pem
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cert.pem	Wed Mar 06 10:37:49 2024 +0000
@@ -0,0 +1,22 @@
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----
diff -r 3e53204c2419 -r 460d5b6c5d98 jb2_urlconf.py
--- a/jb2_urlconf.py	Wed Mar 06 00:23:02 2024 +0000
+++ b/jb2_urlconf.py	Wed Mar 06 10:37:49 2024 +0000
@@ -1,6 +1,6 @@
 inconf = open('config.json', 'r').readlines()
 with open('config.json.local', 'w') as bak:
-    bak.write('\n'.join(inconf))
+    bak.write(''.join(inconf))
 urlbase = "https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/hum/"
 utag = '"uri":'
 for i, row in enumerate(inconf):
@@ -10,7 +10,7 @@
             parth = row.split(utag)[1].strip()
             inconf[i] = '%s%s' % (urlbase, parth)
 with open('config.json', 'w') as outconf:
-    outconf.write('\n'.join(inconf))
+    outconf.write(''.join(inconf))
 
 
 
diff -r 3e53204c2419 -r 460d5b6c5d98 jb2_webserver.py
--- a/jb2_webserver.py	Wed Mar 06 00:23:02 2024 +0000
+++ b/jb2_webserver.py	Wed Mar 06 10:37:49 2024 +0000
@@ -38,11 +38,12 @@
 import os
 import re
 import socketserver
+import ssl
 import webbrowser
 from http.server import SimpleHTTPRequestHandler
 
 
-DEFAULT_PORT = 8081
+DEFAULT_PORT = 8443
 
 
 def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024):
@@ -153,6 +154,17 @@
 class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer):
     allow_reuse_address = True
 
+    def server_bind(self):
+        ctx = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
+        ctx.load_cert_chain('cert.pem', 'key.pem')
+        socketserver.TCPServer.server_bind(self)
+        self.socket = ctx.wrap_socket(  self.socket, server_hostname = "127.0.0.1", server_side=False,)
+
+
+    def get_request(self):
+        (socket, addr) = socketserver.TCPServer.get_request(self)
+        socket.do_handshake()
+        return (socket, addr)
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
@@ -171,17 +183,17 @@
     )
     parser.add_argument(
         "--bind",
-        default="0.0.0.0",
-        help="IP address to bind to (default: 0.0.0.0)",
+        default="127.0.0.1",
+        help="IP address to bind to (default: 127.0.0.1)",
     )
     args = parser.parse_args()
 
     handler = functools.partial(RangeRequestHandler, directory=args.root)
 
-    webbrowser.open(f"http://{args.bind}:{args.port}")
+    webbrowser.open(f"https://{args.bind}:{args.port}")
 
     with ThreadedTCPServer((args.bind, args.port), handler) as httpd:
         print(
-            f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)"
+            f"Serving HTTPS on {args.bind} port {args.port} (https://{args.bind}:{args.port}/)"
         )
         httpd.serve_forever()
diff -r 3e53204c2419 -r 460d5b6c5d98 jbrowse2.py
--- a/jbrowse2.py	Wed Mar 06 00:23:02 2024 +0000
+++ b/jbrowse2.py	Wed Mar 06 10:37:49 2024 +0000
@@ -1148,6 +1148,8 @@
 
             outputTrackConfig["key"] = track_human_label
             outputTrackConfig["useuri"] = useuri
+            outputTrackConfig["path"] = dataset_path
+            outputTrackConfig["ext"] = dataset_ext
 
             outputTrackConfig["trackset"] = track.get("trackset", {})
             outputTrackConfig["label"] = "%s_%i_%s" % (
diff -r 3e53204c2419 -r 460d5b6c5d98 jbrowse2.xml
--- a/jbrowse2.xml	Wed Mar 06 00:23:02 2024 +0000
+++ b/jbrowse2.xml	Wed Mar 06 10:37:49 2024 +0000
@@ -138,7 +138,18 @@
     <tracks>
         #for $tg in $track_groups:
             #for $track in $tg.data_tracks:
-                #if $track.data_format.useuri.insource == "history":
+                #if $track.data_format.useuri.insource == "uri":
+                   <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
+                      <files>
+                        <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes">
+                            <metadata>
+                            <dataset id = "${track.data_format.useuri.annouri}" />
+                            </metadata>
+                         </trackFile>
+                     </files>
+                    <options/>
+                </track>
+                #else if $track.data_format.useuri.insource == "history":
                     #if $track.data_format.useuri.annotation:
                     <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
                     <files>
@@ -204,7 +215,7 @@
                             <protein>${track.data_format.is_protein}</protein>
                             <min_gap>${track.data_format.min_gap}</min_gap>
                         </blast>
-                    #else if str($track.data_format.data_format_select) == "gene_calls":
+                    #else if str($track.data_format.data_format_select) == "gff":
                         <gff>
                           #if $track.data_format.match_part.match_part_select == "true":
                             <match>${track.data_format.match_part.name}</match>
@@ -229,6 +240,9 @@
                     #else if str($track.data_format.data_format_select) == "cool":
                         <cool>
                         </cool>
+                    #else if str($track.data_format.data_format_select) == "bed":
+                        <bed>
+                        </bed>
                     #else if str($track.data_format.data_format_select) == "sparql":
                         <label>${track.data_format.label}</label>
                         <sparql>
@@ -240,17 +254,6 @@
                     </options>
                   </track>
                   #end if
-                #else if track.data_format.useuri.annouri:
-                   <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
-                      <files>
-                        <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes">
-                            <metadata>
-                            <dataset id = "${track.data_format.useuri.annouri}" />
-                            </metadata>
-                         </trackFile>
-                     </files>
-                    <options/>
-                </track>
                 #end if
             #end for
         #end for
@@ -312,11 +315,12 @@
                 <conditional name="data_format" label="Track Data Selection Options">
                     <param type="select" label="Track Type" name="data_format_select">
                         <option value="bam">BAM Pileup track</option>
+                        <option value="bed">BED track</option>
                         <option value="bigwig">BigWig track</option>
                         <option value="blastxml">Blast XML track - converted to GFF</option>
                         <option value="cool">HiC as cool/mcool/scool format files</option>
                         <option value="cram">CRAM</option>
-                        <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
+                        <option value="gff" selected="true">GFF/GFF3 feature track</option>
                         <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
                         <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
                         <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
@@ -350,8 +354,8 @@
                         <expand macro="track_styling_vcf"/>
                         <expand macro="track_visibility" />
                     </when>
-                    <when value="gene_calls">
-                        <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
+                    <when value="gff">
+                        <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3" />
                         <conditional name="match_part" label="match/match_part data">
                         <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select">
                             <option selected="True" value="false">Not match/match part data</option>
@@ -373,6 +377,10 @@
                         <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                         <expand macro="track_visibility" />
                     </when>
+                    <when value="bed">
+                        <expand macro="input_conditional" label="BED Track Data" format="bed" />
+                        <expand macro="track_visibility" />
+                    </when>
                     <when value="cram">
                         <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
                         <expand macro="track_visibility" />
@@ -497,7 +505,7 @@
                 <param name="category" value="Default" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="bed"/>
                        <conditional name="useuri">
                             <param name="insource" value="history"/>
                             <param name="annotation" value="bed/test-3.bed"/>
@@ -525,7 +533,7 @@
                 <param name="category" value="Auto Coloured" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="insource" value="history"/>
                            <param name="annotation" value="gff3/A.gff"/>
@@ -549,7 +557,7 @@
                 <param name="category" value="Ignore Scale" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="insource" value="history"/>
                         <param name="annotation" value="gff3/1.gff"/>
@@ -574,7 +582,7 @@
                 <param name="category" value="Scaled Colour" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="insource" value= "history"/>
                             <param name="annotation" value="gff3/C.gff"/>
@@ -601,7 +609,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="annotation" value="gff3/B.gff"/>
                             <param name="insource" value= "history"/>
@@ -629,7 +637,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="annotation" value="gff3/A.gff"/>
                             <param name="insource" value= "history"/>
@@ -658,7 +666,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                             <param name="annotation" value="gff3/1.gff"/>
                             <param name="insource" value= "history"/>
@@ -692,7 +700,7 @@
                 <param name="category" value="Realistic" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                             <param name="annotation" value="gff3/interpro.gff"/>
                             <param name="insource" value= "history"/>
@@ -712,7 +720,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                          <conditional name="useuri">
                             <param name="annotation" value="gff3/2.gff"/>
                             <param name="insource" value= "history"/>
@@ -755,7 +763,7 @@
                 <param name="category" value="With menu or index" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                             <param name="annotation" value="gff3/1.gff"/>
                             <param name="insource" value= "history"/>
@@ -790,7 +798,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                          <conditional name="useuri">
                             <param name="annotation" value="gff3/1.gff"/>
                             <param name="insource" value= "history"/>
@@ -815,7 +823,7 @@
             <output name="output">
                 <assert_contents>
                     <has_text text="With menu or index"/>
-                    <has_text text="gene_calls"/>
+                    <has_text text="gff"/>
                 </assert_contents>
             </output>
         </test>
diff -r 3e53204c2419 -r 460d5b6c5d98 key.pem
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/key.pem	Wed Mar 06 10:37:49 2024 +0000
@@ -0,0 +1,28 @@
+-----BEGIN PRIVATE KEY-----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+-----END PRIVATE KEY-----
diff -r 3e53204c2419 -r 460d5b6c5d98 macros.xml
--- a/macros.xml	Wed Mar 06 00:23:02 2024 +0000
+++ b/macros.xml	Wed Mar 06 10:37:49 2024 +0000
@@ -528,7 +528,7 @@
                        <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
                 </when>
                 <when value="uri">
-                       <param label="@LABEL@" name="annouri" multiple="false" type="text" />
+                       <param label="@LABEL@" name="annouri"  type="text" />
                        <param label="Short name for track display" name="annoname" type="text" >
                              <sanitizer invalid_char="_">
                                 <valid initial="string.printable" >