jbrowse2: jbrowse2.py comparison

comparison jbrowse2.py @ 73:3b2815efa5d9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf

author	fubar
date	Mon, 01 Apr 2024 03:41:42 +0000
parents	2bdb748df098
children	13ede71c3a4b

comparison

equal deleted inserted replaced

-:2bdb748df098
+:3b2815efa5d9
 import json
 import logging
 import os
 import re
 import shutil
+import ssl
 import struct
 import subprocess
 import tempfile
 import urllib.request
 import xml.etree.ElementTree as ET
 "}": "__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 = """
 class JbrowseConnector(object):
 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.giURL = GALAXY_INFRASTRUCTURE_URL
 self.outdir = outdir
 self.jbrowse2path = jbrowse2path
 os.makedirs(self.outdir, exist_ok=True)
 self.genome_names = []
 "displays": [
 style_data,
 ]
 }
 return wstyle
+def urllib_get_2018():
+# Using a protected member like this is not any more fragile
+# than extending the class and using it. I would use it.
+url = "https://localhost:6667/my-endpoint"
+ssl._create_default_https_context = ssl._create_unverified_context
+with urllib.request.urlopen(url=url) as f:
+print(f.read().decode("utf-8"))
+def urllib_get_2022():
+# Finally! Able to use the publice API. Happy happy!
+url = "https://localhost:6667/my-endpoint"
+scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
+scontext.verify_mode = ssl.VerifyMode.CERT_NONE
+with urllib.request.urlopen(url=url, context=scontext) as f:
+print(f.read().decode("utf-8"))
 def process_genomes(self, genomes):
 assembly = []
 assmeta = []
 useuri = False
 if genome_name not in genome_names:
 # pafs with shared references
 fapath = genome_node["path"]
 if not useuri:
 fapath = os.path.realpath(fapath)
-assem = self.make_assembly(fapath, genome_name, useuri)
+assem, first_contig = self.make_assembly(fapath, genome_name, useuri)
 assembly.append(assem)
+self.ass_first_contigs.append(first_contig)
 if len(genome_names) == 0:
 this_genome["genome_name"] = genome_name  # first one for all tracks
 genome_names.append(genome_name)
 this_genome["genome_sequence_adapter"] = assem["sequence"][
 "adapter"
 ].strip()
 else:
 this_genome["genome_firstcontig"] = fl
 else:
 try:
-fl = urllib.request.urlopen(fapath + ".fai").readline()
+scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
+scontext.verify_mode = ssl.VerifyMode.CERT_NONE
+with urllib.request.urlopen(
+url=fapath + ".fai", context=scontext
+) as f:
+fl = f.readline()
 except Exception:
 fl = None
 if fl:  # is first row of the text fai so the first contig name
 this_genome["genome_firstcontig"] = (
 fl.decode("utf8").strip().split()[0]
 self.tracksToAdd[genome_names[0]] = []
 self.genome_names += genome_names
 return this_genome["genome_name"]
 def make_assembly(self, fapath, gname, useuri):
+"""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
 adapter = {
 "type": "BgzipFastaAdapter",
 "fastaLocation": {"uri": faname, "locationType": "UriLocation"},
 "faiLocation": {"uri": faname + ".fai", "locationType": "UriLocation"},
 "gziLocation": {"uri": faname + ".gzi", "locationType": "UriLocation"},
 }
+scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
+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
 else:
 faname = gname + ".fa.gz"
 fadest = os.path.realpath(os.path.join(self.outdir, faname))
 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
 fapath,
 },
 "gziLocation": {
 "uri": faname + ".gzi",
 },
 }
+contig = open(fadest + ".fai", "r").readline().strip()
+first_contig = contig.split()[:2]
+first_contig.insert(0, gname)
 trackDict = {
 "name": gname,
 "sequence": {
 "type": "ReferenceSequenceTrack",
 "trackId": gname,
 "type": "LinearGCContentDisplay",
 "displayId": "%s-LinearGCContentDisplay" % gname,
 },
 ],
 }
-return trackDict
+return (trackDict, first_contig)
 def add_default_view(self):
 cmd = [
 "jbrowse",
 "set-default-session",
 ["cp", os.path.realpath(cram_index), dest + ".crai"]
 )
 else:
 cpath = os.path.realpath(dest) + ".crai"
 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)]
-logging.debug("executing cmd %s" % " ".join(cmd))
 self.subprocess_check_call(cmd)
 trackDict = {
 "type": "AlignmentsTrack",
 "trackId": tId,
 "name": trackData["name"],
 "https://"
 )
 if gname not in self.genome_names:
 # ignore if already there - eg for duplicates among pafs.
-asstrack = self.make_assembly(pgpaths[i], gname, useuri)
+asstrack, first_contig = self.make_assembly(pgpaths[i], gname, useuri)
 self.genome_names.append(gname)
 self.tracksToAdd[gname] = []
 self.assemblies.append(asstrack)
 trackDict = {
 "type": "SyntenyTrack",
 for gnome in self.genome_names:
 tracks_data = []
 for track_conf in self.tracksToAdd[gnome]:
 tId = track_conf["trackId"]
 track_types[tId] = track_conf["type"]
-style_data = default_data["style"].get(tId, None)
+style_data = default_data[gnome]["style"].get(tId, None)
 if not style_data:
 logging.debug(
 "### No style data in default data %s for %s"
 % (default_data, tId)
 )
 self.config_json.update(config_json)
 logging.debug("defaultSession=%s" % (pp))
 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):
+"""
+Broken in Anthony's PR because only ever dealt with the first assembly.
+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
+- default tracks
+- ...
+Different methods to do that were tested/discussed:
+- using a defaultSession item in config.json: this proved to be difficult:
+forced to write a full session block, including hard-coded/hard-to-guess items,
+no good way to let Jbrowse2 display a scaffold without knowing its size
+- using JBrowse2 as an embedded React component in a tool-generated html file:
+it works but it requires generating js code to actually do what we want = chosing default view, assembly, tracks, ...
+- writing a session-spec inside the config.json file: this is not yet supported as of 2.10.2 (see PR 4148 below)
+a session-spec is a kind of simplified defaultSession where you don't need to specify every aspect of the session
+- passing a session-spec through URL params by embedding the JBrowse2 index.html inside an iframe
+we selected this option
+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
+"""
+new_index = "Nothing written"
+session_spec = {"views": []}
+logging.debug("def data=%s" % data)
+for first_contig in 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:
+if refName:
+view = {
+"assembly": gnome,
+"loc": "{}:{}-{}".format(refName, start, end),
+"type": "LinearGenomeView",
+"tracks": data[gnome]["tracks"],
+}
+session_spec["views"].append(view)
+sess = json.dumps(session_spec, sort_keys=True, indent=2)
+new_index = INDEX_TEMPLATE.replace(
+"__SESSION_SPEC__", "&session=spec-{}".format(sess)
+)
+os.rename(
+os.path.join(self.outdir, "index.html"),
+os.path.join(self.outdir, "index_noview.html"),
+)
+with open(os.path.join(self.outdir, "index.html"), "w") as nind:
+nind.write(new_index)
+logging.debug(
+"#### add_defsession gnome=%s refname=%s\nsession_spec=%s\nnew_index=%s"
+% (gnome, refName, sess, new_index)
+)
 def add_general_configuration(self, data):
 """
 Add some general configuration to the config.json file
 """
 config_json["configuration"].update(config_data)
 self.config_json.update(config_json)
 with open(config_path, "w") as config_file:
 json.dump(self.config_json, config_file, indent=2)
-def clone_jbrowse(self, realclone=True):
+def clone_jbrowse(self, realclone=False):
 """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now
 Leave as True between version updates on temporary tools - requires manual conda trigger :(
 """
 dest = self.outdir
 if realclone:
 # be GET and not POST so it should redirect OK
 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
 jc = JbrowseConnector(outdir=args.outdir, jbrowse2path=args.jbrowse2path)
-default_session_data = {
+default_session_data = {}
-"visibility": {
-"default_on": [],
-"default_off": [],
-},
-"style": {},
-"style_labels": {},
-}
 for ass in root.findall("assembly"):
 genomes = [
 {
 "path": x.attrib["path"],
 "meta": metadata_from_node(x.find("metadata")),
 }
 for x in ass.findall("metadata/genomes/genome")
 ]
 assref_name = jc.process_genomes(genomes)
+if not default_session_data.get(assref_name, None):
+default_session_data[assref_name] = {
+"tracks": [],
+"style": {},
+"style_labels": {},
+"visibility": {
+"default_on": [],
+"default_off": [],
+},
+}
 for track in ass.find("tracks"):
 track_conf = {}
 track_conf["trackfiles"] = []
 track_conf["assemblyNames"] = assref_name
 is_multi_bigwig = False
 if keys:
 for key in keys:
 vis = track.attrib.get("visibility", "default_off")
 if not vis:
 vis = "default_off"
-default_session_data["visibility"][vis].append(key)
+default_session_data[assref_name]["visibility"][vis].append(key)
 if track.find("options/style"):
-default_session_data["style"][key] = {
+default_session_data[assref_name]["style"][key] = {
 item.tag: parse_style_conf(item)
 for item in track.find("options/style")
 }
 else:
-default_session_data["style"][key] = {}
+default_session_data[assref_name]["style"][key] = {}
-logging.debug("@@@@ no options/style found for %s" % (key))
+logging.debug("no options/style found for %s" % (key))
 if track.find("options/style_labels"):
-default_session_data["style_labels"][key] = {
+default_session_data[assref_name]["style_labels"][key] = {
 item.tag: parse_style_conf(item)
 for item in track.find("options/style_labels")
 }
+default_session_data[assref_name]["tracks"].append(key)
 default_session_data["defaultLocation"] = root.find(
 "metadata/general/defaultLocation"
 ).text
 default_session_data["session_name"] = root.find(
 "metadata/general/session_name"
 trackconf += jc.tracksToAdd[gnome]
 jc.config_json["tracks"] = trackconf
 assconf = jc.config_json.get("assemblies", [])
 assconf += jc.assemblies
 jc.config_json["assemblies"] = assconf
-logging.debug("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
+logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
 jc.write_config()
 jc.add_default_session(default_session_data)
+jc.add_defsess_to_index(default_session_data)
 # jc.text_index() not sure what broke here.

Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 73:3b2815efa5d9 draft