Mercurial > repos > fubar > jbrowse2
view jbrowse2.py @ 79:14ecbe46ae9f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
| author | fubar |
|---|---|
| date | Mon, 01 Apr 2024 09:36:07 +0000 |
| parents | 7bb6259ea52f |
| children | dff27c9f6d72 |
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#!/usr/bin/env python import argparse import binascii import datetime 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 from collections import defaultdict logging.basicConfig(level=logging.DEBUG) log = logging.getLogger("jbrowse") JB2VER = "v2.10.3" # version pinned for cloning TODAY = datetime.datetime.now().strftime("%Y-%m-%d") SELF_LOCATION = os.path.dirname(os.path.realpath(__file__)) GALAXY_INFRASTRUCTURE_URL = None mapped_chars = { ">": "__gt__", "<": "__lt__", "'": "__sq__", '"': "__dq__", "[": "__ob__", "]": "__cb__", "{": "__oc__", "}": "__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 = """ function(feature, variableName, glyphObject, track) {{ var score = {score}; {opacity} return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; }} """ COLOR_FUNCTION_TEMPLATE_QUAL = r""" function(feature, variableName, glyphObject, track) {{ var search_up = function self(sf, attr){{ if(sf.get(attr) !== undefined){{ return sf.get(attr); }} if(sf.parent() === undefined) {{ return; }}else{{ return self(sf.parent(), attr); }} }}; var search_down = function self(sf, attr){{ if(sf.get(attr) !== undefined){{ return sf.get(attr); }} if(sf.children() === undefined) {{ return; }}else{{ var kids = sf.children(); for(var child_idx in kids){{ var x = self(kids[child_idx], attr); if(x !== undefined){{ return x; }} }} return; }} }}; var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color}); var score = (search_up(feature, 'score') || search_down(feature, 'score')); {opacity} if(score === undefined){{ opacity = 1; }} var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color); var red = parseInt(result[1], 16); var green = parseInt(result[2], 16); var blue = parseInt(result[3], 16); if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; }} """ OPACITY_MATH = { "linear": """ var opacity = (score - ({min})) / (({max}) - ({min})); """, "logarithmic": """ var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min})); """, "blast": """ var opacity = 0; if(score == 0.0) {{ opacity = 1; }} else {{ opacity = (20 - Math.log10(score)) / 180; }} """, } BREWER_COLOUR_IDX = 0 BREWER_COLOUR_SCHEMES = [ (166, 206, 227), (31, 120, 180), (178, 223, 138), (51, 160, 44), (251, 154, 153), (227, 26, 28), (253, 191, 111), (255, 127, 0), (202, 178, 214), (106, 61, 154), (255, 255, 153), (177, 89, 40), (228, 26, 28), (55, 126, 184), (77, 175, 74), (152, 78, 163), (255, 127, 0), ] BREWER_DIVERGING_PALLETES = { "BrBg": ("#543005", "#003c30"), "PiYg": ("#8e0152", "#276419"), "PRGn": ("#40004b", "#00441b"), "PuOr": ("#7f3b08", "#2d004b"), "RdBu": ("#67001f", "#053061"), "RdGy": ("#67001f", "#1a1a1a"), "RdYlBu": ("#a50026", "#313695"), "RdYlGn": ("#a50026", "#006837"), "Spectral": ("#9e0142", "#5e4fa2"), } def __init__(self): self.brewer_colour_idx = 0 def rgb_from_hex(self, hexstr): # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back return struct.unpack("BBB", binascii.unhexlify(hexstr)) def min_max_gff(self, gff_file): min_val = None max_val = None with open(gff_file, "r") as handle: for line in handle: try: value = float(line.split("\t")[5]) min_val = min(value, (min_val or value)) max_val = max(value, (max_val or value)) if value < min_val: min_val = value if value > max_val: max_val = value except Exception: pass return min_val, max_val def hex_from_rgb(self, r, g, b): return "#%02x%02x%02x" % (r, g, b) def _get_colours(self): r, g, b = self.BREWER_COLOUR_SCHEMES[ self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES) ] self.brewer_colour_idx += 1 return r, g, b def parse_menus(self, track): trackConfig = {"menuTemplate": [{}, {}, {}, {}]} if "menu" in track["menus"]: menu_list = [track["menus"]["menu"]] if isinstance(track["menus"]["menu"], list): menu_list = track["menus"]["menu"] for m in menu_list: tpl = { "action": m["action"], "label": m.get("label", "{name}"), "iconClass": m.get("iconClass", "dijitIconBookmark"), } if "url" in m: tpl["url"] = m["url"] if "content" in m: tpl["content"] = m["content"] if "title" in m: tpl["title"] = m["title"] trackConfig["menuTemplate"].append(tpl) return trackConfig def parse_colours(self, track, trackFormat, gff3=None): # Wiggle tracks have a bicolor pallete trackConfig = {"style": {}} if trackFormat == "wiggle": trackConfig["style"]["pos_color"] = track["wiggle"]["color_pos"] trackConfig["style"]["neg_color"] = track["wiggle"]["color_neg"] if trackConfig["style"]["pos_color"] == "__auto__": trackConfig["style"]["neg_color"] = self.hex_from_rgb( *self._get_colours() ) trackConfig["style"]["pos_color"] = self.hex_from_rgb( *self._get_colours() ) # Wiggle tracks can change colour at a specified place bc_pivot = track["wiggle"]["bicolor_pivot"] if bc_pivot not in ("mean", "zero"): # The values are either one of those two strings # or a number bc_pivot = float(bc_pivot) trackConfig["bicolor_pivot"] = bc_pivot elif "scaling" in track: if track["scaling"]["method"] == "ignore": if track["scaling"]["scheme"]["color"] != "__auto__": trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"] else: trackConfig["style"]["color"] = self.hex_from_rgb( *self._get_colours() ) else: # Scored method algo = track["scaling"]["algo"] # linear, logarithmic, blast scales = track["scaling"]["scales"] # type __auto__, manual (min, max) scheme = track["scaling"]["scheme"] # scheme -> (type (opacity), color) # ================================== # GENE CALLS OR BLAST # ================================== if trackFormat == "blast": red, green, blue = self._get_colours() color_function = self.COLOR_FUNCTION_TEMPLATE.format( **{ "score": "feature._parent.get('score')", "opacity": self.OPACITY_MATH["blast"], "red": red, "green": green, "blue": blue, } ) trackConfig["style"]["color"] = color_function.replace("\n", "") elif trackFormat == "gene_calls": # Default values, based on GFF3 spec min_val = 0 max_val = 1000 # Get min/max and build a scoring function since JBrowse doesn't if scales["type"] == "automatic" or scales["type"] == "__auto__": min_val, max_val = self.min_max_gff(gff3) else: min_val = scales.get("min", 0) max_val = scales.get("max", 1000) if scheme["color"] == "__auto__": user_color = "undefined" auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) elif scheme["color"].startswith("#"): user_color = "'%s'" % self.hex_from_rgb( *self.rgb_from_hex(scheme["color"][1:]) ) auto_color = "undefined" else: user_color = "undefined" auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format( **{ "opacity": self.OPACITY_MATH[algo].format( **{"max": max_val, "min": min_val} ), "user_spec_color": user_color, "auto_gen_color": auto_color, } ) trackConfig["style"]["color"] = color_function.replace("\n", "") return trackConfig def etree_to_dict(t): if t is None: return {} d = {t.tag: {} if t.attrib else None} children = list(t) if children: dd = defaultdict(list) for dc in map(etree_to_dict, children): for k, v in dc.items(): dd[k].append(v) d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}} if t.attrib: d[t.tag].update(("@" + k, v) for k, v in t.attrib.items()) if t.text: text = t.text.strip() if children or t.attrib: if text: d[t.tag]["#text"] = text else: d[t.tag] = text return d INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) def metadata_from_node(node): metadata = {} try: if len(node.findall("dataset")) != 1: # exit early return metadata except Exception: return {} for (key, value) in node.findall("dataset")[0].attrib.items(): metadata["dataset_%s" % key] = value if node.findall("history"): for (key, value) in node.findall("history")[0].attrib.items(): metadata["history_%s" % key] = value if node.findall("metadata"): for (key, value) in node.findall("metadata")[0].attrib.items(): metadata["metadata_%s" % key] = value # Additional Mappings applied: metadata[ "dataset_edam_format" ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format( metadata["dataset_edam_format"], metadata["dataset_file_ext"] ) metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format( metadata["history_user_email"] ) metadata["hist_name"] = metadata["history_display_name"] metadata[ "history_display_name" ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format( galaxy=GALAXY_INFRASTRUCTURE_URL, encoded_hist_id=metadata.get("history_id", "not available"), hist_name=metadata.get("history_display_name", "not available"), ) if node.findall("tool"): for (key, value) in node.findall("tool")[0].attrib.items(): metadata["tool_%s" % key] = value metadata[ "tool_tool" ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}{tool_version}</a>'.format( galaxy=GALAXY_INFRASTRUCTURE_URL, encoded_id=metadata.get("dataset_id", ""), tool_id=metadata.get("tool_tool_id", ""), tool_version=metadata.get("tool_tool_version", ""), ) return metadata 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 = [] self.trackIdlist = [] self.tracksToAdd = {} self.config_json = {} self.config_json_file = os.path.join(outdir, "config.json") self.clone_jbrowse() def get_cwd(self, cwd): if cwd: return self.outdir else: return subprocess.check_output(["pwd"]).decode("utf-8").strip() # return None def subprocess_check_call(self, command, output=None, cwd=True): if output: log.debug("cd %s && %s > %s", self.get_cwd(cwd), " ".join(command), output) subprocess.check_call(command, cwd=self.get_cwd(cwd), stdout=output) else: log.debug("cd %s && %s", self.get_cwd(cwd), " ".join(command)) subprocess.check_call(command, cwd=self.get_cwd(cwd)) def subprocess_popen(self, command, cwd=True): log.debug(command) p = subprocess.Popen( command, cwd=self.get_cwd(cwd), shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, ) output, err = p.communicate() retcode = p.returncode if retcode != 0: log.error(command) log.error(output) log.error(err) raise RuntimeError("Command failed with exit code %s" % (retcode)) def subprocess_check_output(self, command): log.debug(" ".join(command)) return subprocess.check_output(command, cwd=self.outdir) def symlink_or_copy(self, src, dest): if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool( os.environ["GALAXY_JBROWSE_SYMLINKS"] ): cmd = ["ln", "-s", src, dest] else: cmd = ["cp", src, dest] return self.subprocess_check_call(cmd) def _prepare_track_style(self, trackDict): style_data = { "type": "LinearBasicDisplay", "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"], } if trackDict.get("displays", None): # use first if multiple like bed style_data["type"] = trackDict["displays"][0]["type"] style_data["displayId"] = trackDict["displays"][0]["displayId"] wstyle = { "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 genome_names = [] for i, genome_node in enumerate(genomes): this_genome = {} if genome_node["useuri"] == "yes": useuri = True genome_name = genome_node["label"].strip() if len(genome_name.split()) > 1: genome_name = genome_name.split()[0] # spaces and cruft break scripts when substituted if genome_name not in genome_names: # pafs with shared references fapath = genome_node["path"] if not useuri: fapath = os.path.realpath(fapath) 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" ] this_genome["genome_firstcontig"] = None if not useuri: fl = open(fapath, "r").readline() fls = fl.strip().split(">") if len(fls) > 1: fl = fls[1] if len(fl.split()) > 1: this_genome["genome_firstcontig"] = fl.split()[ 0 ].strip() else: this_genome["genome_firstcontig"] = fl else: try: 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] ) assmeta.append(this_genome) self.assemblies += assembly self.assmeta[genome_names[0]] = assmeta 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, fadest, fadest, fadest, ) self.subprocess_popen(cmd) adapter = { "type": "BgzipFastaAdapter", "fastaLocation": { "uri": faname, }, "faiLocation": { "uri": faname + ".fai", }, "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, "adapter": adapter, }, "displays": [ { "type": "LinearReferenceSequenceDisplay", "displayId": "%s-LinearReferenceSequenceDisplay" % gname, }, { "type": "LinearGCContentDisplay", "displayId": "%s-LinearGCContentDisplay" % gname, }, ], } return (trackDict, first_contig) def add_default_view(self): cmd = [ "jbrowse", "set-default-session", "-s", self.config_json_file, "-t", ",".join(self.trackIdlist), "-n", "JBrowse2 in Galaxy", "--target", self.config_json_file, "-v", " LinearGenomeView", ] self.subprocess_check_call(cmd) def write_config(self): with open(self.config_json_file, "w") as fp: json.dump(self.config_json, fp, indent=2) def text_index(self): # Index tracks args = [ "jbrowse", "text-index", "--target", self.outdir, "--assemblies", self.genome_name, ] tracks = ",".join(self.trackIdlist) if tracks: args += ["--tracks", tracks] self.subprocess_check_call(args) def add_hic(self, data, trackData): """ HiC adapter. https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md for testing locally, these work: HiC data is from https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic using hg19 reference track as a 'BgzipFastaAdapter' fastaLocation: uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz', faiLocation: uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai', gziLocation: uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi', Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438 """ tId = trackData["label"] # can be served - if public. # dsId = trackData["metadata"]["dataset_id"] # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId) useuri = trackData["useuri"].lower() == "yes" if useuri: uri = data else: uri = "%s.hic" % trackData["label"] # slashes in names cause path trouble dest = os.path.join(self.outdir, uri) cmd = ["cp", data, dest] self.subprocess_check_call(cmd) categ = trackData["category"] trackDict = { "type": "HicTrack", "trackId": tId, "name": trackData["name"], "assemblyNames": [trackData["assemblyNames"]], "category": [ categ, ], "adapter": {"type": "HicAdapter", "hicLocation": {"uri": uri}}, } self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def add_maf(self, data, trackData): """ from https://github.com/cmdcolin/maf2bed Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name e.g. hg38.chr1 in the sequence identifiers. need the reference id - eg hg18, for maf2bed.pl as the first parameter """ tId = trackData["label"] mafPlugin = { "plugins": [ { "name": "MafViewer", "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js", } ] } categ = trackData["category"] fname = "%s" % tId dest = "%s/%s" % (self.outdir, fname) gname = trackData["assemblyNames"] cmd = [ "bash", os.path.join(INSTALLED_TO, "convertMAF.sh"), data, gname, INSTALLED_TO, dest, ] self.subprocess_check_call(cmd) mafs = open(data, "r").readlines() mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))] samp = [x.split()[1] for x in mafss if len(x.split()) > 0] sampu = list(dict.fromkeys(samp)) samples = [x.split(".")[0] for x in sampu] samples.sort() logging.debug( "$$$$ cmd=%s, mafss=%s samp=%s samples=%s" % (" ".join(cmd), mafss, samp, samples) ) trackDict = { "type": "MafTrack", "trackId": tId, "name": trackData["name"], "category": [ categ, ], "adapter": { "type": "MafTabixAdapter", "samples": samples, "bedGzLocation": { "uri": fname + ".sorted.bed.gz", }, "index": { "location": { "uri": fname + ".sorted.bed.gz.tbi", }, }, }, "assemblyNames": [trackData["assemblyNames"]], "displays": [ { "type": "LinearBasicDisplay", "displayId": "%s-LinearBasicDisplay" % tId, }, {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId}, ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[gname].append(trackDict) self.trackIdlist.append(tId) if self.config_json.get("plugins", None): self.config_json["plugins"].append(mafPlugin[0]) else: self.config_json.update(mafPlugin) def _blastxml_to_gff3(self, xml, min_gap=10): gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) cmd = [ "python", os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"), "--trim", "--trim_end", "--include_seq", "--min_gap", str(min_gap), xml, ] subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) gff3_unrebased.close() logging.debug("### blastxml to gff3 cmd = %s" % " ".join(cmd)) return gff3_unrebased.name def add_blastxml(self, data, trackData, blastOpts, **kwargs): gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"]) if "parent" in blastOpts and blastOpts["parent"] != "None": gff3_rebased = tempfile.NamedTemporaryFile(delete=False) cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")] if blastOpts.get("protein", "false") == "true": cmd.append("--protein2dna") cmd.extend([os.path.realpath(blastOpts["parent"]), gff3]) subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) logging.debug("### gff3rebase cmd = %s" % " ".join(cmd)) gff3_rebased.close() # Replace original gff3 file shutil.copy(gff3_rebased.name, gff3) os.unlink(gff3_rebased.name) url = "%s.gff3.gz" % trackData["label"] dest = "%s/%s" % (self.outdir, url) self._sort_gff(gff3, dest) tId = trackData["label"] categ = trackData["category"] trackDict = { "type": "FeatureTrack", "trackId": tId, "name": trackData["name"], "assemblyNames": [trackData["assemblyNames"]], "category": [ categ, ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": url, }, "index": { "location": { "uri": url + ".tbi", } }, }, "displays": [ { "type": "LinearBasicDisplay", "displayId": "%s-LinearBasicDisplay" % tId, }, { "type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId, }, ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) os.unlink(gff3) def add_bigwig(self, data, trackData): useuri = trackData["useuri"].lower() == "yes" if useuri: url = data else: url = "%s.bigwig" % trackData["label"] # slashes in names cause path trouble dest = os.path.join(self.outdir, url) cmd = ["cp", data, dest] self.subprocess_check_call(cmd) bwloc = {"uri": url} tId = trackData["label"] categ = trackData["category"] trackDict = { "type": "QuantitativeTrack", "trackId": tId, "name": trackData["name"], "category": [ categ, ], "assemblyNames": [trackData["assemblyNames"]], "adapter": { "type": "BigWigAdapter", "bigWigLocation": bwloc, }, "displays": [ { "type": "LinearWiggleDisplay", "displayId": "%s-LinearWiggleDisplay" % tId, } ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def add_bam(self, data, trackData, bam_index=None, **kwargs): tId = trackData["label"] useuri = trackData["useuri"].lower() == "yes" bindex = bam_index categ = trackData["category"] if useuri: url = data else: fname = "%s.bam" % trackData["label"] dest = "%s/%s" % (self.outdir, fname) url = fname bindex = fname + ".bai" self.subprocess_check_call(["cp", data, dest]) if bam_index is not None and os.path.exists(bam_index): if not os.path.exists(bindex): # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest self.subprocess_check_call(["cp", bam_index, bindex]) else: # Can happen in exotic condition # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam # => no index generated by galaxy, but there might be one next to the symlink target # this trick allows to skip the bam sorting made by galaxy if already done outside if os.path.exists(os.path.realpath(data) + ".bai"): self.symlink_or_copy(os.path.realpath(data) + ".bai", bindex) else: log.warn("Could not find a bam index (.bai file) for %s", data) trackDict = { "type": "AlignmentsTrack", "trackId": tId, "name": trackData["name"], "category": [ categ, ], "assemblyNames": [trackData["assemblyNames"]], "adapter": { "type": "BamAdapter", "bamLocation": {"uri": url}, "index": { "location": { "uri": bindex, } }, }, "displays": [ { "type": "LinearAlignmentsDisplay", "displayId": "%s-LinearAlignmentsDisplay" % tId, }, ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def add_cram(self, data, trackData, cram_index=None, **kwargs): tId = trackData["label"] categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" 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)) if useuri: url = data else: fname = "%s.cram" % trackData["label"] dest = "%s/%s" % (self.outdir, fname) url = fname self.subprocess_check_call(["cp", data, dest]) if cram_index is not None and os.path.exists(cram_index): if not os.path.exists(dest + ".crai"): # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest self.subprocess_check_call( ["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)] self.subprocess_check_call(cmd) trackDict = { "type": "AlignmentsTrack", "trackId": tId, "name": trackData["name"], "category": [ categ, ], "assemblyNames": [trackData["assemblyNames"]], "adapter": { "type": "CramAdapter", "cramLocation": {"uri": url}, "craiLocation": { "uri": url + ".crai", }, "sequenceAdapter": genseqad, }, "displays": [ { "type": "LinearAlignmentsDisplay", "displayId": "%s-LinearAlignmentsDisplay" % tId, }, ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def add_vcf(self, data, trackData): tId = trackData["label"] # url = "%s/api/datasets/%s/display" % ( # self.giURL, # trackData["metadata"]["dataset_id"], # ) categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" if useuri: url = data else: url = "%s.vcf.gz" % tId dest = "%s/%s" % (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 = { "type": "VariantTrack", "trackId": tId, "name": trackData["name"], "assemblyNames": [trackData["assemblyNames"]], "category": [ categ, ], "adapter": { "type": "VcfTabixAdapter", "vcfGzLocation": {"uri": url}, "index": { "location": { "uri": url + ".tbi", } }, }, "displays": [ { "type": "LinearVariantDisplay", "displayId": "%s-LinearVariantDisplay" % tId, }, { "type": "ChordVariantDisplay", "displayId": "%s-ChordVariantDisplay" % tId, }, { "type": "LinearPairedArcDisplay", "displayId": "%s-LinearPairedArcDisplay" % tId, }, ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def _sort_gff(self, data, dest): # Only index if not already done if not os.path.exists(dest): cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % ( data, dest, ) # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" self.subprocess_popen(cmd) self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest]) def _sort_bed(self, data, dest): # Only index if not already done if not os.path.exists(dest): cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest) self.subprocess_popen(cmd) cmd = ["tabix", "-f", "-p", "bed", dest] self.subprocess_check_call(cmd) def add_gff(self, data, ext, trackData): useuri = trackData["useuri"].lower() == "yes" if useuri: url = trackData["path"] else: url = "%s.%s.gz" % (trackData["label"], ext) dest = "%s/%s" % (self.outdir, url) self._sort_gff(data, dest) tId = trackData["label"] categ = trackData["category"] trackDict = { "type": "FeatureTrack", "trackId": tId, "name": trackData["name"], "assemblyNames": [trackData["assemblyNames"]], "category": [ categ, ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": url, }, "index": { "location": { "uri": url + ".tbi", } }, }, "displays": [ { "type": "LinearBasicDisplay", "displayId": "%s-LinearBasicDisplay" % tId, }, { "type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId, }, ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def add_bed(self, data, ext, trackData): tId = trackData["label"] categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" if useuri: url = data else: url = "%s.%s.gz" % (trackData["label"], ext) dest = "%s/%s" % (self.outdir, url) self._sort_bed(data, dest) trackDict = { "type": "FeatureTrack", "trackId": tId, "name": trackData["name"], "assemblyNames": [trackData["assemblyNames"]], "adapter": { "category": [ categ, ], "type": "BedTabixAdapter", "bedGzLocation": { "uri": url, }, "index": { "location": { "uri": url + ".tbi", } }, }, "displays": [ { "type": "LinearBasicDisplay", "displayId": "%s-LinearBasicDisplay" % tId, }, { "type": "LinearPileupDisplay", "displayId": "%s-LinearPileupDisplay" % tId, }, { "type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId, }, ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def add_paf(self, data, trackData, pafOpts, **kwargs): tname = trackData["name"] tId = trackData["label"] url = "%s.paf" % tId useuri = data.startswith("http://") or data.startswith("https://") if not useuri: dest = "%s/%s" % (self.outdir, url) self.symlink_or_copy(os.path.realpath(data), dest) else: url = data categ = trackData["category"] pgnames = [ x.strip() for x in pafOpts["genome_label"].split(",") if len(x.strip()) > 0 ] pgpaths = [ x.strip() for x in pafOpts["genome"].split(",") if len(x.strip()) > 0 ] passnames = [trackData["assemblyNames"]] # always first logging.debug( "### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s" % (pafOpts, pgnames, pgpaths, tId) ) for i, gname in enumerate(pgnames): if len(gname.split()) > 1: gname = gname.split()[0] passnames.append(gname) # trouble from spacey names in command lines avoidance useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith( "https://" ) if gname not in self.genome_names: # ignore if already there - eg for duplicates among pafs. 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", "trackId": tId, "assemblyNames": passnames, "category": [ categ, ], "name": tname, "adapter": { "type": "PAFAdapter", "pafLocation": {"uri": url}, "assemblyNames": passnames, }, "displays": [ { "type": "LGVSyntenyDisplay", "displayId": "%s-LGVSyntenyDisplay" % tId, }, { "type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % tId, }, { "type": "LinearComparativeDisplay", "displayId": "%s-LinearComparativeDisplay" % tId, }, { "type": "LinearSyntenyDisplay", "displayId": "%s-LinearSyntenyDisplay" % tId, }, ], } style_json = { "displays": [ { "type": "LGVSyntenyDisplay", "displayId": "%s-LGVSyntenyDisplay" % tId, } ] } trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) def process_annotations(self, track): category = track["category"].replace("__pd__date__pd__", TODAY) for i, ( dataset_path, dataset_ext, useuri, track_human_label, extra_metadata, ) in enumerate(track["trackfiles"]): if not dataset_path.strip().startswith("http"): # Unsanitize labels (element_identifiers are always sanitized by Galaxy) for key, value in mapped_chars.items(): track_human_label = track_human_label.replace(value, key) track_human_label = track_human_label.replace(" ", "_") outputTrackConfig = { "category": category, "style": {}, } outputTrackConfig["assemblyNames"] = track["assemblyNames"] 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" % ( dataset_ext, i, track_human_label, ) outputTrackConfig["metadata"] = extra_metadata outputTrackConfig["name"] = track_human_label if dataset_ext in ("gff", "gff3"): self.add_gff( dataset_path, dataset_ext, outputTrackConfig, ) elif dataset_ext in ("hic", "juicebox_hic"): self.add_hic( dataset_path, outputTrackConfig, ) elif dataset_ext in ("cool", "mcool", "scool"): hic_url = "%s_%d.hic" % (track_human_label, i) hic_path = os.path.join(self.outdir, hic_url) self.subprocess_check_call( [ "hictk", "convert", "-f", "--output-fmt", "hic", dataset_path, hic_path, ] ) self.add_hic( hic_url, outputTrackConfig, ) elif dataset_ext in ("bed",): self.add_bed( dataset_path, dataset_ext, outputTrackConfig, ) elif dataset_ext in ("maf",): self.add_maf( dataset_path, outputTrackConfig, ) elif dataset_ext == "bigwig": self.add_bigwig( dataset_path, outputTrackConfig, ) elif dataset_ext == "bam": real_indexes = track["conf"]["options"]["bam"]["bam_index"] self.add_bam( dataset_path, outputTrackConfig, bam_index=real_indexes, ) elif dataset_ext == "cram": real_indexes = track["conf"]["options"]["cram"]["cram_index"] self.add_cram( dataset_path, outputTrackConfig, cram_index=real_indexes, ) elif dataset_ext == "blastxml": self.add_blastxml( dataset_path, outputTrackConfig, track["conf"]["options"]["blast"], ) elif dataset_ext == "vcf": self.add_vcf(dataset_path, outputTrackConfig) elif dataset_ext == "paf": self.add_paf( dataset_path, outputTrackConfig, track["conf"]["options"]["paf"], ) else: logging.warn("Do not know how to handle %s", dataset_ext) # Return non-human label for use in other fields yield outputTrackConfig["label"] def add_default_session(self, default_data): """ 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 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) if "defaultSession" in config_json: session_json = config_json["defaultSession"] session_views = [] else: session_json = {} session_views = [] 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[gnome]["style"].get(tId, None) if not style_data: logging.debug( "### No style data in default data %s for %s" % (default_data, tId) ) style_data = {"type": "LinearBasicDisplay"} if "displays" in track_conf: disp = track_conf["displays"][0]["type"] style_data["type"] = disp if track_conf.get("style_labels", None): # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work # TODO move this to per track displays? style_data["labels"] = track_conf["style_labels"] tracks_data.append( { "type": track_types[tId], "configuration": tId, "displays": [style_data], } ) # paf genomes have no tracks associated so nothing for the view if len(tracks_data) > 0: 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 = 0 end = int(end) refName = self.assmeta[gnome][0].get("genome_firstcontig", None) drdict = { "refName": refName, "start": start, "end": end, "reversed": False, "assemblyName": gnome, } 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 if loc_match: refName = loc_match.group(1) drdict["refName"] = refName if loc_match.group(2) > "": drdict["start"] = int( loc_match.group(2).replace(",", "") ) if loc_match.group(3) > "": drdict["end"] = int(loc_match.group(3).replace(",", "")) else: logging.info( "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" % ddl ) 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, ] logging.info("@@@ defaultlocation %s for default session" % drdict) else: logging.info( "@@@ no track location for default session - please add one!" ) 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) config_json["defaultSession"] = session_json 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): """ 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: - 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 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) [gnome, refName, end] = first_contig start = 0 aview = { "assembly": gnome, "loc": "{}:{}..{}".format(refName, start, end), "type": "LinearGenomeView", "tracks": data[gnome]["tracks"], } session_spec["views"].append(aview) 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_path = self.config_json_file if os.path.exists(config_path): with open(config_path, "r") as config_file: config_json = json.load(config_file) else: config_json = {} if self.config_json: config_json.update(self.config_json) config_data = {} config_data["disableAnalytics"] = data.get("analytics", "false") == "true" config_data["theme"] = { "palette": { "primary": {"main": data.get("primary_color", "#0D233F")}, "secondary": {"main": data.get("secondary_color", "#721E63")}, "tertiary": {"main": data.get("tertiary_color", "#135560")}, "quaternary": {"main": data.get("quaternary_color", "#FFB11D")}, }, "typography": {"fontSize": int(data.get("font_size", 10))}, } if not config_json.get("configuration", None): config_json["configuration"] = {} 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=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: self.subprocess_check_call( ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"] ) else: shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True) for fn in [ "asset-manifest.json", "favicon.ico", "robots.txt", "umd_plugin.js", "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) def parse_style_conf(item): if item.text.lower() in ["false", "true", "yes", "no"]: return item.text.lower in ("yes", "true") else: return item.text 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" ) 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) root = tree.getroot() # This should be done ASAP GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text # Sometimes this comes as `localhost` without a protocol if not GALAXY_INFRASTRUCTURE_URL.startswith("http"): # so we'll prepend `http://` and hope for the best. Requests *should* # 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 = {} for ass in root.findall("assembly"): genomes = [ { "path": x.attrib["path"], "label": x.attrib["label"], "useuri": x.attrib["useuri"], "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 try: if track.find("options/wiggle/multibigwig") and ( track.find("options/wiggle/multibigwig").text == "True" ): is_multi_bigwig = True multi_bigwig_paths = [] except KeyError: pass trackfiles = track.findall("files/trackFile") if trackfiles: for x in track.findall("files/trackFile"): track_conf["label"] = x.attrib["label"] trackkey = track_conf["label"] track_conf["useuri"] = x.attrib["useuri"] if is_multi_bigwig: multi_bigwig_paths.append( ( x.attrib["label"], x.attrib["useuri"], os.path.realpath(x.attrib["path"]), ) ) else: if trackfiles: metadata = metadata_from_node(x.find("metadata")) track_conf["dataset_id"] = metadata.get( "dataset_id", "None" ) if x.attrib["useuri"].lower() == "yes": tfa = ( x.attrib["path"], x.attrib["ext"], x.attrib["useuri"], x.attrib["label"], metadata, ) else: tfa = ( os.path.realpath(x.attrib["path"]), x.attrib["ext"], x.attrib["useuri"], x.attrib["label"], metadata, ) track_conf["trackfiles"].append(tfa) if is_multi_bigwig: metadata = metadata_from_node(x.find("metadata")) track_conf["trackfiles"].append( ( multi_bigwig_paths, # Passing an array of paths to represent as one track "bigwig_multiple", "MultiBigWig", # Giving an hardcoded name for now {}, # No metadata for multiple bigwig ) ) track_conf["category"] = track.attrib["cat"] track_conf["format"] = track.attrib["format"] track_conf["conf"] = etree_to_dict(track.find("options")) track_conf["category"] = track.attrib["cat"] track_conf["format"] = track.attrib["format"] keys = jc.process_annotations(track_conf) if keys: for key in keys: vis = track.attrib.get("visibility", "default_off") if not vis: vis = "default_off" default_session_data[assref_name]["visibility"][vis].append(key) if track.find("options/style"): default_session_data[assref_name]["style"][key] = { item.tag: parse_style_conf(item) for item in track.find("options/style") } else: default_session_data[assref_name]["style"][key] = {} logging.debug("no options/style found for %s" % (key)) if track.find("options/style_labels"): 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" ).text logging.debug("default_session=%s" % (default_session_data)) jc.zipOut = root.find("metadata/general/zipOut").text == "true" general_data = { "analytics": root.find("metadata/general/analytics").text, "primary_color": root.find("metadata/general/primary_color").text, "secondary_color": root.find("metadata/general/secondary_color").text, "tertiary_color": root.find("metadata/general/tertiary_color").text, "quaternary_color": root.find("metadata/general/quaternary_color").text, "font_size": root.find("metadata/general/font_size").text, } jc.add_general_configuration(general_data) trackconf = jc.config_json.get("tracks", []) for gnome in jc.genome_names: 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)) jc.write_config() # 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.