Mercurial > repos > fubar > jbrowse2
view jbrowse2.py @ 93:4c517a0041a8 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
| author | fubar |
|---|---|
| date | Wed, 24 Apr 2024 02:29:32 +0000 |
| parents | 3c4db8203fad |
| children | 74074746ccd8 |
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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 = "v2.11.0" # version pinned if cloning - but not cloning now logCommands = True # 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__", "<": "__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.trackCounter = 0 # to avoid name clashes 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: if logCommands: 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: if logCommands: 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): if logCommands: 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): if logCommands: 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"] return style_data def getNrow(self, url): useuri = url.startswith("https://") or url.startswith("http://") if not useuri: fl = open(url, "r").readlines() nrow = len(fl) else: try: scontext = ssl.SSLContext(ssl.PROTOCOL_TLS) scontext.verify_mode = ssl.VerifyMode.CERT_NONE with urllib.request.urlopen(url, context=scontext) as f: fl = f.readlines() nrow = len(fl) except Exception: nrow = 0 logging.debug("### getNrow %s returning %d" % (url, nrow)) return nrow def process_genomes(self, genomes): assembly = [] assmeta = [] useuri = False primaryGenome = None 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) == 0: genome_name = os.path.splitext(os.path.basename(genome_node["path"]))[0] if len(genome_name.split()) > 1: genome_name = genome_name.split()[0] # spaces and cruft break scripts when substituted if not primaryGenome: primaryGenome = genome_name if genome_name not in self.genome_names: self.genome_names.append(genome_name) 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 genome_name == primaryGenome: # first one this_genome["genome_name"] = genome_name # first one for all tracks this_genome["genome_sequence_adapter"] = assem["sequence"][ "adapter" ] this_genome["genome_firstcontig"] = first_contig assmeta.append(this_genome) self.assemblies += assembly self.assmeta[primaryGenome] = assmeta self.tracksToAdd[primaryGenome] = [] return primaryGenome 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 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) contig = open(fadest + ".fai", "r").readline().strip() adapter = { "type": "BgzipFastaAdapter", "fastaLocation": { "uri": faname, }, "faiLocation": { "uri": faname + ".fai", }, "gziLocation": { "uri": faname + ".gzi", }, } 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"] wasCool = trackData["wasCool"] # 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" logging.debug("wasCool=%s, data=%s, tId=%s" % (wasCool, data, tId)) if useuri: uri = data else: uri = tId + ".hic" if not wasCool: dest = os.path.join(self.outdir, uri) if not os.path.exists(dest): cmd = ["cp", data, dest] self.subprocess_check_call(cmd) else: logging.error("not wasCool but %s exists" % dest) 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 = 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() if logCommands: 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) self.add_gff(gff3, trackData, **kwargs) def add_bigwig(self, data, trackData): tId = trackData["label"] useuri = trackData["useuri"].lower() == "yes" if useuri: url = data else: url = tId # 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} 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_indexes=None, **kwargs): tId = trackData["label"] realFName = trackData["path"] useuri = trackData["useuri"].lower() == "yes" categ = trackData["category"] if useuri: url = data else: fname = tId dest = "%s/%s" % (self.outdir, fname) self.subprocess_check_call(["cp", data, dest]) url = fname bindex = fname + ".bai" bi = bam_indexes.split(",") bam_index = [ x.split(" ~ ")[1].strip() for x in bi if " ~ " in x and x.split(" ~ ")[0].strip() == realFName ] logging.debug( "===realFName=%s got %s as bam_indexes %s as bi, %s for bam_index" % (realFName, bam_indexes, bi, bam_index) ) if len(bam_index) > 0 and os.path.exists(os.path.realpath(bam_index[0])): self.subprocess_check_call(["cp", bam_index[0], bindex]) else: cmd = ["samtools", "index", "-b", "-o", bindex, data] self.subprocess_check_call(cmd) 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_indexes=None, **kwargs): tId = trackData["label"] realFName = trackData["path"] 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 = tId dest = os.path.join(self.outdir, fname) url = fname self.subprocess_check_call(["cp", data, dest]) ci = cram_indexes.split(",") cram_index = [ x.split(" ~ ")[1].strip() for x in ci if " ~ " in x and x.split(" ~ ")[0].strip() == realFName ] logging.debug( "===realFName=%s got %s as cram_indexes %s as ci, %s for cram_index" % (realFName, cram_indexes, ci, cram_index) ) if len(cram_index) > 0 and os.path.exists(cram_index[0]): 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[0]), 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 = 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, ) 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, trackData): tId = trackData["label"] useuri = trackData["useuri"].lower() == "yes" if useuri: url = trackData["path"] else: url = tId + ".gz" dest = "%s/%s" % (self.outdir, url) self._sort_gff(data, dest) 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 = tId + ".gz" 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 = 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) nrow = self.getNrow(dest) else: url = data nrow = self.getNrow(url) categ = trackData["category"] pg = pafOpts["genome"].split(",") pgc = [x.strip() for x in pg if x.strip() > ""] gnomes = [x.split(" ~ ") for x in pgc] logging.debug("pg=%s, gnomes=%s" % (pg, gnomes)) passnames = [trackData["assemblyNames"]] # always first for i, (gpath, gname) in enumerate(gnomes): # may have been forgotten by user for uri if len(gname) == 0: gn = os.path.basename(gpath) gname = os.path.splitext(gn)[0] # trouble from spacey names in command lines avoidance if len(gname.split()) > 1: gname = gname.split()[0] if gname not in passnames: passnames.append(gname) useuri = pafOpts["useuri"] == "true" if gname not in self.genome_names: # ignore if already there - eg for duplicates among pafs. asstrack, first_contig = self.make_assembly(gpath, gname, useuri) self.genome_names.append(gname) self.tracksToAdd[gname] = [] self.assemblies.append(asstrack) self.ass_first_contigs.append(first_contig) 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": "LinearBasicDisplay", "displayId": "%s-LinearSyntenyDisplay" % tId, }, ], } if nrow > 10000: style_json = { "type": "LGVSyntenyDisplay", "displayId": "%s-LGVSyntenyDisplay" % tId, } else: style_json = { "type": "LinearBasicDisplay", "displayId": "%s-LinearBasicDisplay" % 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 trackIndex, ( 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"] = track["label"] outputTrackConfig["metadata"] = extra_metadata outputTrackConfig["name"] = track_human_label if track["label"] in self.trackIdlist: logging.error( "### not adding %s already in %s" % (track["label"], self.trackIdlist) ) yield None if dataset_ext in ("gff", "gff3"): self.add_gff( dataset_path, outputTrackConfig, ) elif dataset_ext in ("hic", "juicebox_hic"): outputTrackConfig["wasCool"] = False self.add_hic( dataset_path, outputTrackConfig, ) elif dataset_ext in ("cool", "mcool", "scool"): hic_url = outputTrackConfig["label"] hic_path = os.path.join(self.outdir, hic_url) + ".hic" outputTrackConfig["wasCool"] = True self.subprocess_check_call( [ "hictk", "convert", "-f", "--output-fmt", "hic", dataset_path, hic_path, ] ) logging.debug( "### ext=cool: wasCool=%s, hic_path=%s" % (outputTrackConfig["wasCool"], hic_path) ) self.add_hic( hic_path, 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"] logging.debug("**** add bam got %s for indexes" % real_indexes) self.add_bam( dataset_path, outputTrackConfig, bam_indexes=real_indexes, ) elif dataset_ext == "cram": real_indexes = track["conf"]["options"]["cram"]["cram_index"] logging.debug("**** add cram got %s for indexes" % real_indexes) self.add_cram( dataset_path, outputTrackConfig, cram_indexes=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.assmeta.keys(): # assemblies have their own tracks tracks_data = [] for track_conf in self.tracksToAdd[gnome]: tId = track_conf["trackId"] if tId in default_data[gnome]["visibility"]["default_on"]: track_types[tId] = track_conf["type"] style_data = default_data[gnome]["style"].get(tId, None) if not style_data: logging.debug( "### No style data for %s in available default data %s" % (tId, default_data) ) 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], } ) 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, "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): """ 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 - 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 = {} trackI = 0 for ass in root.findall("assembly"): genomes = [ { "path": x.attrib["path"], "label": x.attrib["label"].split(" ")[0].replace(",", ""), "useuri": x.attrib["useuri"], "meta": metadata_from_node(x.find("metadata")), } for x in ass.findall("metadata/genomes/genome") ] primaryGenome = jc.process_genomes(genomes) if not default_session_data.get(primaryGenome, None): default_session_data[primaryGenome] = { "tracks": [], "style": {}, "style_labels": {}, "visibility": { "default_on": [], "default_off": [], }, } for track in ass.find("tracks"): track_conf = {} track_conf["trackfiles"] = [] track_conf["assemblyNames"] = primaryGenome 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 trackfiles: track_conf["label"] = "%s_%d" % ( x.attrib["label"].replace(" ", "_").replace(",", ""), trackI, ) trackI += 1 track_conf["useuri"] = x.attrib["useuri"] if is_multi_bigwig: multi_bigwig_paths.append( ( track_conf["label"], track_conf["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"], track_conf["label"], metadata, ) else: tfa = ( os.path.realpath(x.attrib["path"]), x.attrib["ext"], x.attrib["useuri"], track_conf["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")) 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[primaryGenome]["visibility"][vis].append(key) trakdat = jc.tracksToAdd[primaryGenome] stile = {} for trak in trakdat: if trak["trackId"] == key: stile = trak.get("style", {}) if track.find("options/style"): supdate = { item.tag: parse_style_conf(item) for item in track.find("options/style") } stile.update(supdate) default_session_data[primaryGenome]["style"][key] = stile if track.find("options/style_labels"): default_session_data[primaryGenome]["style_labels"][key] = { item.tag: parse_style_conf(item) for item in track.find("options/style_labels") } default_session_data[primaryGenome]["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" % (json.dumps(default_session_data, indent=2))) 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: gtracks = jc.tracksToAdd[gnome] if len(gtracks) > 0: logging.debug( "for genome %s adding gtracks %s" % (gnome, json.dumps(gtracks, indent=2)) ) trackconf += gtracks jc.config_json["tracks"] = trackconf assconf = jc.config_json.get("assemblies", []) assconf += jc.assemblies jc.config_json["assemblies"] = assconf logging.debug( "assmeta=%s, first_contigs=%s, assemblies=%s, gnames=%s, trackidlist=%s, tracks=%s" % ( jc.assmeta, jc.ass_first_contigs, json.dumps(assconf, indent=2), jc.genome_names, jc.trackIdlist, json.dumps(trackconf, indent=2), ) ) 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.