Mercurial > repos > fubar > jbrowse2
diff 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 |
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--- a/jbrowse2.py Thu Apr 25 07:25:52 2024 +0000 +++ b/jbrowse2.py Sat Jun 01 05:37:13 2024 +0000 @@ -22,7 +22,7 @@ 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 @@ -41,32 +41,6 @@ } -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 = """ @@ -491,7 +465,8 @@ 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() @@ -544,7 +519,8 @@ """ 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() @@ -897,7 +873,7 @@ 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: @@ -965,7 +941,7 @@ 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] @@ -1032,7 +1008,7 @@ 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 = { @@ -1078,7 +1054,7 @@ 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", @@ -1125,7 +1101,7 @@ 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: @@ -1327,6 +1303,7 @@ 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) @@ -1365,24 +1342,17 @@ "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: - [gnome, refName, end] = first[0] - start = 0 - end = int(end) - drdict = { - "refName": refName, - "start": start, - "end": end, + drdict = { "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: @@ -1400,6 +1370,13 @@ "@@@ 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"] = [ @@ -1415,7 +1392,6 @@ 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: @@ -1429,14 +1405,7 @@ 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: @@ -1461,6 +1430,33 @@ 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)) @@ -1544,10 +1540,15 @@ "version.txt", "test_data", ]: - cmd = ["rm", "-rf", os.path.join(dest, fn)] - self.subprocess_check_call(cmd) - cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest] - self.subprocess_check_call(cmd) + try: + path = os.path.join(dest, fn) + if os.path.isdir(path): + 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): @@ -1561,7 +1562,7 @@ 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)