comparison jbrowse2.py @ 19:bde6b1d09f7d draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty

18:2e6c48910819

#!/usr/bin/env python
# change to accumulating all configuration for config.json based on the default from the clone
import argparse
import binascii
import datetime
import hashlib
import json
import logging
import os
import re
import shutil

JB2VER = "v2.10.1"
# version pinned for cloning

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.0"
# version pinned for cloning

mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",

                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:

                            "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 {}

    for (key, value) in node.findall("dataset")[0].attrib.items():
        metadata["dataset_%s" % key] = value

    for (key, value) in node.findall("history")[0].attrib.items():
        metadata["history_%s" % key] = value

    for (key, value) in node.findall("metadata")[0].attrib.items():
        metadata["metadata_%s" % key] = value

    for (key, value) in node.findall("tool")[0].attrib.items():
        metadata["tool_%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["history_id"],
        hist_name=metadata["history_display_name"],
    )
    metadata[
        "tool_tool"
    ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
        galaxy=GALAXY_INFRASTRUCTURE_URL,
        encoded_id=metadata["dataset_id"],
        tool_id=metadata["tool_tool_id"],
        # tool_version=metadata['tool_tool_version'],
    )
    return metadata


class JbrowseConnector(object):
    def __init__(self, outdir, genomes):

        self.config_json_file = os.path.join(outdir, "config.json")
        self.clone_jbrowse()

    def subprocess_check_call(self, command, output=None):
        if output:
            log.debug("cd %s && %s >  %s", self.outdir, " ".join(command), output)
            subprocess.check_call(command, cwd=self.outdir, stdout=output)
        else:
            log.debug("cd %s && %s", self.outdir, " ".join(command))
            subprocess.check_call(command, cwd=self.outdir)

            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

    def make_assembly(self, fapath, gname):
        hashData = [
            fapath,
            gname,
        ]
        hashData = "|".join(hashData).encode("utf-8")
        ghash = hashlib.md5(hashData).hexdigest()
        faname = ghash + ".fa.gz"
        fadest = os.path.join(self.outdir, faname)
        cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
            fapath,
            fadest,
            fadest,

            },
            "gziLocation": {
                "uri": faname + ".gzi",
            },
        }
        trackDict = {
            "name": gname,
            "sequence": {
                "type": "ReferenceSequenceTrack",
                "trackId": gname,

        """
        mafPlugin = {
            "plugins": [
                {
                    "name": "MafViewer",
                    "url": "https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
                }
            ]
        }
        tId = trackData["label"]
        fname = "%s.bed" % tId

            dest,
        ]
        self.subprocess_check_call(cmd)
        # Construct samples list
        # We could get this from galaxy metadata, not sure how easily.
        ps = subprocess.Popen(["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE)
        output = subprocess.check_output(("sort", "-u"), stdin=ps.stdout)
        ps.wait()
        outp = output.decode("ascii")
        soutp = outp.split("\n")
        samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")]

        fname = "%s.bam" % trackData["label"]
        dest = "%s/%s" % (self.outdir, fname)
        url = fname
        self.subprocess_check_call(["cp", data, dest])
        bloc = {"uri": url}
        if bam_index is not None and os.path.exists(os.path.realpath(bam_index)):
            # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
            self.subprocess_check_call(
                ["cp", os.path.realpath(bam_index), dest + ".bai"]
            )
        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", dest + ".bai")
            else:
                log.warn("Could not find a bam index (.bai file) for %s", data)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.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"],
        )
        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]

            cmd = "jbrowse sort-gff %s | bgzip -c > %s.gz" % (
                data,
                dest,
            )  # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'"
            self.subprocess_popen(cmd)
            self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest + ".gz"])

    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)

                "style": {},
            }

            outputTrackConfig["key"] = track_human_label

            # We add extra data to hash for the case of REST + SPARQL.
            if (
                "conf" in track
                and "options" in track["conf"]
                and "url" in track["conf"]["options"]
            ):
                rest_url = track["conf"]["options"]["url"]
            else:
                rest_url = ""
            outputTrackConfig["trackset"] = track.get("trackset", {})
            # I chose to use track['category'] instead of 'category' here. This
            # is intentional. This way re-running the tool on a different date
            # will not generate different hashes and make comparison of outputs
            # much simpler.
            hashData = [
                str(dataset_path),
                track_human_label,
                track["category"],
                rest_url,
            ]
            hashData = "|".join(hashData).encode("utf-8")
            outputTrackConfig["label"] = hashlib.md5(hashData).hexdigest() + "_%s" % i
            outputTrackConfig["metadata"] = extra_metadata
            outputTrackConfig["name"] = track_human_label

            if dataset_ext in ("gff", "gff3"):
                self.add_gff(

                self.add_bigwig(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext == "bam":
                real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][
                    "bam_index"
                ]
                if not isinstance(real_indexes, list):
                    # <bam_indices>
                    #  <bam_index>/path/to/a.bam.bai</bam_index>
                    # </bam_indices>
                    #
                    # The above will result in the 'bam_index' key containing a
                    # string. If there are two or more indices, the container
                    # becomes a list. Fun!
                    real_indexes = [real_indexes]

                self.add_bam(
                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["pileup"],
                    bam_index=real_indexes[i],
                )
            elif dataset_ext == "blastxml":
                self.add_blastxml(
                    dataset_path,
                    outputTrackConfig,

            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"] = {}

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--xml", help="Track Configuration")
    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")
    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

            )
        track_conf["category"] = track.attrib["cat"]
        track_conf["format"] = track.attrib["format"]
        if track.find("options/style"):
            track_conf["style"] = {
                item.tag: parse_style_conf(item) for item in track.find("options/style")
            }
        if track.find("options/style_labels"):
            track_conf["style_labels"] = {
                item.tag: parse_style_conf(item)
                for item in track.find("options/style_labels")

        track_conf["conf"] = etree_to_dict(track.find("options"))
        track_conf["category"] = track.attrib["cat"]
        track_conf["format"] = track.attrib["format"]
        try:
            # Only pertains to gff3 + blastxml. TODO?
            track_conf["style"] = {t.tag: t.text for t in track.find("options/style")}
        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        keys = jc.process_annotations(track_conf)

    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", None)
    if trackconf:

19:bde6b1d09f7d

#!/usr/bin/env python
# change to accumulating all configuration for config.json based on the default from the clone
import argparse
import binascii
import datetime
import json
import logging
import os
import re
import shutil

JB2VER = "v2.10.1"
# version pinned for cloning

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.1"
# version pinned for cloning

mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",

                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:

                            "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 {}

    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["history_id"],
                hist_name=metadata["history_display_name"],
            )
    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, genomes):

        self.config_json_file = os.path.join(outdir, "config.json")
        self.clone_jbrowse()

    def subprocess_check_call(self, command, output=None):
        if output:
            log.debug(
                "cd %s && %s >  %s", self.outdir, " ".join(command), output
            )
            subprocess.check_call(command, cwd=self.outdir, stdout=output)
        else:
            log.debug("cd %s && %s", self.outdir, " ".join(command))
            subprocess.check_call(command, cwd=self.outdir)

            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

    def make_assembly(self, fapath, gname):

        faname = gname + ".fa.gz"
        fadest = os.path.join(self.outdir, faname)
        cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
            fapath,
            fadest,
            fadest,

            },
            "gziLocation": {
                "uri": faname + ".gzi",
            },
        }
        self.genome_sequence_adapter = adapter
        trackDict = {
            "name": gname,
            "sequence": {
                "type": "ReferenceSequenceTrack",
                "trackId": gname,

        """
        mafPlugin = {
            "plugins": [
                {
                    "name": "MafViewer",
                    "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
                }
            ]
        }
        tId = trackData["label"]
        fname = "%s.bed" % tId

            dest,
        ]
        self.subprocess_check_call(cmd)
        # Construct samples list
        # We could get this from galaxy metadata, not sure how easily.
        ps = subprocess.Popen(
            ["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE
        )
        output = subprocess.check_output(("sort", "-u"), stdin=ps.stdout)
        ps.wait()
        outp = output.decode("ascii")
        soutp = outp.split("\n")
        samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")]

        fname = "%s.bam" % trackData["label"]
        dest = "%s/%s" % (self.outdir, fname)
        url = fname
        self.subprocess_check_call(["cp", data, dest])
        bloc = {"uri": url}
        if bam_index is not None and os.path.exists(
            os.path.realpath(bam_index)
        ):
            # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
            self.subprocess_check_call(
                ["cp", os.path.realpath(bam_index), dest + ".bai"]
            )
        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", dest + ".bai"
                )
            else:
                log.warn("Could not find a bam index (.bai file) for %s", data)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_cram(self, data, trackData, cramOpts, cram_index=None, **kwargs):
        tId = trackData["label"]
        fname = "%s.cram" % trackData["label"]
        dest = "%s/%s" % (self.outdir, fname)
        url = fname
        self.subprocess_check_call(["cp", data, dest])
        bloc = {"uri": url}
        if cram_index is not None and os.path.exists(
            os.path.realpath(cram_index)
        ):
            # 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:
            # 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) + ".crai"):
                self.symlink_or_copy(
                    os.path.realpath(data) + ".crai", dest + ".crai"
                )
            else:
                log.warn(
                    "Could not find a cram index (.crai file) for %s", data
                )
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "CramAdapter",
                "cramLocation": bloc,
                "craiLocation": {"uri": fname + ".crai",},
                "sequenceAdapter": self.genome_sequence_adapter,
                },
            "displays": [
                {
                    "type": "LinearAlignmentsDisplay",
                    "displayId": "%s-LinearAlignmentsDisplay" % tId,
                },
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.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"],
        # )
        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]

            cmd = "jbrowse sort-gff %s | bgzip -c > %s.gz" % (
                data,
                dest,
            )  # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'"
            self.subprocess_popen(cmd)
            self.subprocess_check_call(
                ["tabix", "-f", "-p", "gff", dest + ".gz"]
            )

    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)

                "style": {},
            }

            outputTrackConfig["key"] = track_human_label

            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(

                self.add_bigwig(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext == "bam":
                real_indexes = track["conf"]["options"]["pileup"][
                    "bam_indices"
                ]["bam_index"]
                if not isinstance(real_indexes, list):
                    real_indexes = [real_indexes]

                self.add_bam(
                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["pileup"],
                    bam_index=real_indexes[i],
                )
            elif dataset_ext == "cram":
                real_indexes = track["conf"]["options"]["cram"][
                    "cram_indices"
                ]["cram_index"]
                if not isinstance(real_indexes, list):
                    real_indexes = [real_indexes]

                self.add_cram(
                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["cram"],
                    cram_index=real_indexes[i],
                )
            elif dataset_ext == "blastxml":
                self.add_blastxml(
                    dataset_path,
                    outputTrackConfig,

            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"] = {}

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--xml", help="Track Configuration")
    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument(
        "--version", "-V", action="version", version="%(prog)s 2.0.1"
    )
    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

            )
        track_conf["category"] = track.attrib["cat"]
        track_conf["format"] = track.attrib["format"]
        if track.find("options/style"):
            track_conf["style"] = {
                item.tag: parse_style_conf(item)
                for item in track.find("options/style")
            }
        if track.find("options/style_labels"):
            track_conf["style_labels"] = {
                item.tag: parse_style_conf(item)
                for item in track.find("options/style_labels")

        track_conf["conf"] = etree_to_dict(track.find("options"))
        track_conf["category"] = track.attrib["cat"]
        track_conf["format"] = track.attrib["format"]
        try:
            # Only pertains to gff3 + blastxml. TODO?
            track_conf["style"] = {
                t.tag: t.text for t in track.find("options/style")
            }
        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        keys = jc.process_annotations(track_conf)

    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", None)
    if trackconf: