comparison jbrowse2.py @ 80:dff27c9f6d72 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f

79:14ecbe46ae9f

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 = {

    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

                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

        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

        # 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"]

                    "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",

            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"],

        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):

            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

        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)

        # 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

            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"],

        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,

        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",

                {
                    "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,

                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",

                    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(

                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,

        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:

        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"],

            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"],

    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.

80:dff27c9f6d72

logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger("jbrowse")

JB2VER = "v2.10.3"
# version pinned if cloning - but not cloning now

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))
GALAXY_INFRASTRUCTURE_URL = None
mapped_chars = {

    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

                style_data,
            ]
        }
        return wstyle

    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 returning %d" % nrow)
        return nrow

    def process_genomes(self, genomes):
        assembly = []
        assmeta = []
        useuri = False

        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 genome_name not in genome_names:
                # pafs with shared references

        # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            uri = data
        else:
            uri = tId
            # 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"]

                    "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",

            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"],

        bindex = bam_index
        categ = trackData["category"]
        if useuri:
            url = data
        else:
            fname = tId
            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):

            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])
            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

        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)

        # 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

            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"],

        categ = trackData["category"]
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = tId
            dest = "%s/%s" % (self.outdir, url)
            self._sort_bed(data, dest)
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,

        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"]
        pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")]
        pgpaths = [
            x.strip() for x in pafOpts["genome"].split(",") if len(x.strip()) > 0
        ]
        passnames = [trackData["assemblyNames"]]  # always first
        for i, gp in enumerate(pgpaths):
            if len(pgnames[i].strip()) == 0:
                # user may have left it blank - cannot make non-optional if want optional tracks.
                gn = os.path.basename(gp)
                pgnames[i] = os.path.splitext(gn)[0]
        logging.debug(
            "### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s"
            % (pafOpts, pgnames, pgpaths, tId)
        )
        for i, gp in enumerate(pgpaths):
            gname = pgnames[i]
            if len(gname.split()) > 1:
                gname = gname.split()[0]
            passnames.append(gname)
            # trouble from spacey names in command lines avoidance
            useuri = gp.startswith("http://") or gp.startswith("https://")

            if gname not in self.genome_names:
                # ignore if already there - eg for duplicates among pafs.
                asstrack, first_contig = self.make_assembly(gp, gname, useuri)
                self.genome_names.append(gname)
                self.tracksToAdd[gname] = []
                self.assemblies.append(asstrack)
        trackDict = {
            "type": "SyntenyTrack",

                {
                    "type": "LinearComparativeDisplay",
                    "displayId": "%s-LinearComparativeDisplay" % tId,
                },
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearSyntenyDisplay" % tId,
                },
            ],
        }
        if nrow > 50000:
            style_json = {
                "displays": [
                    {
                        "type": "LGVSyntenyDisplay",
                        "displayId": "%s-LGVSyntenyDisplay" % tId,
                    }
                ]
            }
        else:
            style_json = {
                "displays": [
                    {
                        "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,

                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_%d.%s" % (
                track_human_label,
                self.trackCounter,
                dataset_ext,
            )
            self.trackCounter += 1
            outputTrackConfig["metadata"] = extra_metadata
            outputTrackConfig["name"] = track_human_label

            if dataset_ext in ("gff", "gff3"):
                self.add_gff(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("hic", "juicebox_hic"):
                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)
                self.subprocess_check_call(
                    [
                        "hictk",
                        "convert",

                    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(

                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,

        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):
        """
        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. Seems ironic that this vital feature could not have ever been tested
        given that my declining to add it was the basis for a reviewer's rejection of my original IUC PR.
        A simple 2 line diff apparently.

        The technical problem is that this index.html hack breaks the promise of all the form fields
        for track controls such as visibility default that were working mostly. They need to be removed from the form by whoever
        thought this method was a good solution to the JB2 bug breaking config.json style default
        view coordinates.

        And no, dear reviewer of this code, please leave this piece of history.
        It is true and I prefer that it remain here to document my considerable discomfort at this unfair treatment.

         ----------------------------------------------------------
        Add some default session settings: set some assemblies/tracks on/off

        This allows to select a default view:

        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"],

            trackfiles = track.findall("files/trackFile")
            if trackfiles:
                for x in track.findall("files/trackFile"):
                    track_conf["label"] = x.attrib["label"]
                    track_conf["useuri"] = x.attrib["useuri"]
                    if is_multi_bigwig:
                        multi_bigwig_paths.append(
                            (
                                x.attrib["label"],

    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.