jbrowse2: jbrowse2.py comparison

comparison jbrowse2.py @ 97:74074746ccd8 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99

author	fubar
date	Sat, 01 Jun 2024 05:37:13 +0000
parents	4c517a0041a8
children	b1260bca5fdc

comparison

equal deleted inserted replaced

-:5ef1ba2031f2
+:74074746ccd8
 log = logging.getLogger("jbrowse")
 JB2VER = "v2.11.0"
 # version pinned if cloning - but not cloning now
 logCommands = True
-# useful for seeing what's being written but not for production setups
+# useful for seeing what's being written but NOT for production setups
 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
 SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))
 GALAXY_INFRASTRUCTURE_URL = None
 mapped_chars = {
 ">": "__gt__",
 "}": "__cc__",
 "@": "__at__",
 "#": "__pd__",
 "": "__cn__",
 }
-INDEX_TEMPLATE = """<!doctype html>
-<html lang="en" style="height:100%">
-<head>
-<meta charset="utf-8"/>
-<link rel="shortcut icon" href="./favicon.ico"/>
-<meta name="viewport" content="width=device-width,initial-scale=1"/>
-<meta name="theme-color" content="#000000"/>
-<meta name="description" content="A fast and flexible genome browser"/>
-<link rel="manifest" href="./manifest.json"/>
-<title>JBrowse</title>
-</script>
-</head>
-<body style="overscroll-behavior:none; height:100%; margin: 0;">
-<iframe
-id="jbframe"
-title="JBrowse2"
-frameborder="0"
-width="100%"
-height="100%"
-src='index_noview.html?config=config.json__SESSION_SPEC__'>
-</iframe>
-</body>
-</html>
-"""
 class ColorScaling(object):
 COLOR_FUNCTION_TEMPLATE = """
 if not useuri:
 fl = open(url, "r").readlines()
 nrow = len(fl)
 else:
 try:
-scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
+scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
+scontext.check_hostname = False
 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
 with urllib.request.urlopen(url, context=scontext) as f:
 fl = f.readlines()
 nrow = len(fl)
 except Exception:
 """added code to grab the first contig name and length for broken default session from Anthony and Helena's code
 that poor Bjoern is trying to figure out.
 """
 if useuri:
 faname = fapath
-scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
+scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
+scontext.check_hostname = False
 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
 with urllib.request.urlopen(url=faname + ".fai", context=scontext) as f:
 fl = f.readline()
 contig = fl.decode("utf8").strip()
 # Merlin  172788  8       60      61
 gsa = self.assmeta.get(trackData["assemblyNames"], None)
 if gsa:
 genseqad = gsa[0]["genome_sequence_adapter"]
 else:
 genseqad = "Not found"
-logging.warn("No adapter found for cram %s in gsa=%s" % (tId, gsa))
+logging.warning("No adapter found for cram %s in gsa=%s" % (tId, gsa))
 if useuri:
 url = data
 else:
 fname = tId
 dest = os.path.join(self.outdir, fname)
 useuri = trackData["useuri"].lower() == "yes"
 if useuri:
 url = data
 else:
 url = tId
-dest = "%s/%s" % (self.outdir, url)
+dest = os.path.join(self.outdir, url)
 cmd = "bgzip -c %s  > %s" % (data, dest)
 self.subprocess_popen(cmd)
 cmd = ["tabix", "-f", "-p", "vcf", dest]
 self.subprocess_check_call(cmd)
 trackDict = {
 useuri = trackData["useuri"].lower() == "yes"
 if useuri:
 url = trackData["path"]
 else:
 url = tId + ".gz"
-dest = "%s/%s" % (self.outdir, url)
+dest = os.path.join(self.outdir, url)
 self._sort_gff(data, dest)
 categ = trackData["category"]
 trackDict = {
 "type": "FeatureTrack",
 "trackId": tId,
 useuri = trackData["useuri"].lower() == "yes"
 if useuri:
 url = data
 else:
 url = tId + ".gz"
-dest = "%s/%s" % (self.outdir, url)
+dest = os.path.join(self.outdir, url)
 self._sort_bed(data, dest)
 trackDict = {
 "type": "FeatureTrack",
 "trackId": tId,
 "name": trackData["name"],
 tname = trackData["name"]
 tId = trackData["label"]
 url = tId
 useuri = data.startswith("http://") or data.startswith("https://")
 if not useuri:
-dest = "%s/%s" % (self.outdir, url)
+dest = os.path.join(self.outdir, url)
 self.symlink_or_copy(os.path.realpath(data), dest)
 nrow = self.getNrow(dest)
 else:
 url = data
 nrow = self.getNrow(url)
 default session settings are hard and fragile.
 .add_default_view() and other configuration code adapted from
 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
 """
 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
+bpPerPx = 50 # this is tricky since browser window width is unknown - this seems a compromise that sort of works....
 track_types = {}
 with open(self.config_json_file, "r") as config_file:
 config_json = json.load(config_file)
 if self.config_json:
 config_json.update(self.config_json)
 "type": track_types[tId],
 "configuration": tId,
 "displays": [style_data],
 }
 )
-view_json = {
-"type": "LinearGenomeView",
-"offsetPx": 0,
-"minimized": False,
-"tracks": tracks_data,
-}
 first = [x for x in self.ass_first_contigs if x[0] == gnome]
-if len(first) > 0:
+drdict = {
-[gnome, refName, end] = first[0]
-start = 0
-end = int(end)
-drdict = {
-"refName": refName,
-"start": start,
-"end": end,
 "reversed": False,
 "assemblyName": gnome,
 }
+if len(first) > 0:
+[gnome, refName, end] = first[0]
+drdict["refName"] = refName
+drdict["start"] = 0
+end = int(end)
+drdict["end"] = end
 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
 else:
 logging.info(
 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
 % ddl
 )
+view_json = {
+"type": "LinearGenomeView",
+"offsetPx": 0,
+"bpPerPx" : bpPerPx,
+"minimized": False,
+"tracks": tracks_data
+}
 if drdict.get("refName", None):
 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
 view_json["displayedRegions"] = [
 drdict,
 ]
 session_views.append(view_json)
 session_name = default_data.get("session_name", "New session")
 for key, value in mapped_chars.items():
 session_name = session_name.replace(value, key)
 session_json["name"] = session_name
 if "views" not in session_json:
 session_json["views"] = session_views
 else:
 session_json["views"] += session_views
 pp = json.dumps(session_views, indent=2)
 with open(self.config_json_file, "w") as config_file:
 json.dump(self.config_json, config_file, indent=2)
 def add_defsess_to_index(self, data):
 """
-PROBABLY NOW BROKEN by changes since this was deprecated temporarily as at April 18
+----------------------------------------------------------
-Included on request of the new codeowner, from Anthony's IUC PR.
-Had to be fixed to keep each assembly with the associated tracks for a default view.
-Originally used only the first assembly, putting all tracks there and so breaking some
-when tested with 2 or more.
-----------------------------------------------------------
 Add some default session settings: set some assemblies/tracks on/off
 This allows to select a default view:
 - jb type (Linear, Circular, etc)
 - default location on an assembly
 Xrefs to understand the choices:
 https://github.com/GMOD/jbrowse-components/issues/2708
 https://github.com/GMOD/jbrowse-components/discussions/3568
 https://github.com/GMOD/jbrowse-components/pull/4148
 """
+INDEX_TEMPLATE = """<!doctype html>
+<html lang="en" style="height:100%">
+<head>
+<meta charset="utf-8"/>
+<link rel="shortcut icon" href="./favicon.ico"/>
+<meta name="viewport" content="width=device-width,initial-scale=1"/>
+<meta name="theme-color" content="#000000"/>
+<meta name="description" content="A fast and flexible genome browser"/>
+<link rel="manifest" href="./manifest.json"/>
+<title>JBrowse</title>
+</script>
+</head>
+<body style="overscroll-behavior:none; height:100%; margin: 0;">
+<iframe
+id="jbframe"
+title="JBrowse2"
+frameborder="0"
+width="100%"
+height="100%"
+src='index_noview.html?config=config.json__SESSION_SPEC__'>
+</iframe>
+</body>
+</html>
+"""
 new_index = "Nothing written"
 session_spec = {"views": []}
 logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data))
 for first_contig in self.ass_first_contigs:
 logging.debug("first contig=%s" % self.ass_first_contigs)
 "robots.txt",
 "umd_plugin.js",
 "version.txt",
 "test_data",
 ]:
-cmd = ["rm", "-rf", os.path.join(dest, fn)]
+try:
-self.subprocess_check_call(cmd)
+path = os.path.join(dest, fn)
-cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest]
+if os.path.isdir(path):
-self.subprocess_check_call(cmd)
+shutil.rmtree(path)
+else:
+os.remove(path)
+except OSError as e:
+log.error("Error: %s - %s." % (e.filename, e.strerror))
+shutil.copyfile(os.path.join(INSTALLED_TO, "jb2_webserver.py"), os.path.join(dest, "jb2_webserver.py"))
 def parse_style_conf(item):
 if item.text.lower() in ["false", "true", "yes", "no"]:
 return item.text.lower in ("yes", "true")
 if __name__ == "__main__":
 parser = argparse.ArgumentParser(description="", epilog="")
 parser.add_argument("--xml", help="Track Configuration")
 parser.add_argument(
-"--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"
+"--jbrowse2path", help="Path to JBrowse2 directory in BioContainer or Conda"
 )
 parser.add_argument("--outdir", help="Output directory", default="out")
 parser.add_argument("--version", "-V", action="version", version=JB2VER)
 args = parser.parse_args()
 tree = ET.parse(args.xml)

Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 97:74074746ccd8 draft